2024-03-28T22:56:02Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/6210172019-08-30T11:34:48Zcom_10033_620968col_10033_620969
Humanized mice for modeling human infectious disease: challenges, progress, and outlook.
Legrand, Nicolas
Ploss, Alexander
Balling, Rudi
Becker, Pablo D
Borsotti, Chiara
Brezillon, Nicolas
Debarry, Jennifer
de Jong, Ype
Deng, Hongkui
Di Santo, James P
Eisenbarth, Stephanie
Eynon, Elizabeth
Flavell, Richard A
Guzman, Carlos A
Huntington, Nicholas D
Kremsdorf, Dina
Manns, Michael P
Manz, Markus G
Mention, Jean-Jacques
Ott, Michael
Rathinam, Chozhavendan
Rice, Charles M
Rongvaux, Anthony
Stevens, Sean
Spits, Hergen
Strick-Marchand, Hélène
Takizawa, Hitoshi
van Lent, Anja U
Wang, Chengyan
Weijer, Kees
Willinger, Tim
Ziegler, Patrick
Over 800 million people worldwide are infected with hepatitis viruses, human immunodeficiency virus (HIV), and malaria, resulting in more than 5 million deaths annually. Here we discuss the potential and challenges of humanized mouse models for developing effective and affordable therapies and vaccines, which are desperately needed to combat these diseases.
2017-07-25T10:31:53Z
2017-07-25T10:31:53Z
2009-07-23
Article
Humanized mice for modeling human infectious disease: challenges, progress, and outlook. 2009, 6 (1):5-9 Cell Host Microbe
1934-6069
19616761
10.1016/j.chom.2009.06.006
http://hdl.handle.net/10033/621017
Cell host & microbe
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210232019-08-30T11:25:11Zcom_10033_620968col_10033_620969
Resolving host-pathogen interactions by dual RNA-seq.
Westermann, Alexander J
Barquist, Lars
Vogel, Jörg
Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
2017-07-28T12:39:33Z
2017-07-28T12:39:33Z
2017-02
Article
Resolving host-pathogen interactions by dual RNA-seq. 2017, 13 (2):e1006033 PLoS Pathog.
1553-7374
28207848
10.1371/journal.ppat.1006033
http://hdl.handle.net/10033/621023
PLoS pathogens
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210842019-08-30T11:28:24Zcom_10033_620968col_10033_620969
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq.
Heidrich, Nadja
Bauriedl, Saskia
Barquist, Lars
Li, Lei
Schoen, Christoph
Vogel, Jörg
HIRI, Helmholtz Institut für RNA-basierte Infektionsforschung, Josef Schneider-Straß2 2, 97080 Würzburg, Germany.
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
2017-08-31T13:50:16Z
2017-08-31T13:50:16Z
2017-06-02
Article
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. 2017, 45 (10):6147-6167 Nucleic Acids Res.
1362-4962
28334889
10.1093/nar/gkx168
http://hdl.handle.net/10033/621084
Nucleic acids research
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210942019-08-30T11:33:57Zcom_10033_620968col_10033_620969
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
Chao, Yanjie
Li, Lei
Girodat, Dylan
Förstner, Konrad U
Said, Nelly
Corcoran, Colin
Śmiga, Michał
Papenfort, Kai
Reinhardt, Richard
Wieden, Hans-Joachim
Luisi, Ben F
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3' fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators.
2017-09-06T09:27:44Z
2017-09-06T09:27:44Z
2017-01-05
Article
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. 2017, 65 (1):39-51 Mol. Cell
1097-4164
28061332
10.1016/j.molcel.2016.11.002
http://hdl.handle.net/10033/621094
Molecular cell
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210972019-08-30T11:33:29Zcom_10033_620968col_10033_620969
Global snapshots of bacterial RNA networks.
Hör, Jens
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung,Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
2017-09-07T13:49:35Z
2017-09-07T13:49:35Z
2017-02-01
Article
Global snapshots of bacterial RNA networks. 2017, 36 (3):245-247 EMBO J.
1460-2075
28031253
10.15252/embj.201696072
http://hdl.handle.net/10033/621097
The EMBO journal
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211252019-08-30T11:27:16Zcom_10033_620968col_10033_620969
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins.
Tawk, Caroline
Sharan, Malvika
Eulalio, Ana
Vogel, Jörg
Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße2, 97080 Würzburg, Germany.
Many pathogenic bacteria utilize specialized secretion systems to deliver proteins called effectors into eukaryotic cells for manipulation of host pathways. The vast majority of known effector targets are host proteins, whereas a potential targeting of host nucleic acids remains little explored. There is only one family of effectors known to target DNA directly, and effectors binding host RNA are unknown. Here, we take a two-pronged approach to search for RNA-binding effectors, combining biocomputational prediction of RNA-binding domains (RBDs) in a newly assembled comprehensive dataset of bacterial secreted proteins, and experimental screening for RNA binding in mammalian cells. Only a small subset of effectors were predicted to carry an RBD, indicating that if RNA targeting was common, it would likely involve new types of RBDs. Our experimental evaluation of effectors with predicted RBDs further argues for a general paucity of RNA binding activities amongst bacterial effectors. We obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities. Our study presenting the first systematic evaluation of the RNA-targeting potential of bacterial effectors offers a basis for discussion of whether or not host RNA is a prominent target of secreted bacterial proteins.
2017-09-27T12:17:24Z
2017-09-27T12:17:24Z
2017-08-24
Article
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. 2017, 7 (1):9328 Sci Rep
2045-2322
28839189
10.1038/s41598-017-09527-0
http://hdl.handle.net/10033/621125
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211412019-08-30T11:28:12Zcom_10033_620968col_10033_620970col_10033_620969
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess
Saliba, Antoine-Emmanuel
Westermann, Alexander J.
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg. Germany.
2017-10-23T14:17:43Z
2017-10-23T14:17:43Z
2017-10-11
Article
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess 2017, 23 (5):525 BIOspektrum
0947-0867
1868-6249
10.1007/s12268-017-0836-y
http://hdl.handle.net/10033/621141
BIOspektrum
http://link.springer.com/10.1007/s12268-017-0836-y
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6213162019-08-30T11:25:11Zcom_10033_620968col_10033_620969
Bacterial RNA Biology on a Genome Scale.
Hör, Jens
Gorski, Stanislaw A
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over.
2018-03-09T09:13:39Z
2018-03-09T09:13:39Z
2018-01-16
Article
Bacterial RNA Biology on a Genome Scale. 2018 Mol. Cell
1097-4164
29358079
10.1016/j.molcel.2017.12.023
http://hdl.handle.net/10033/621316
Molecular cell
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6214042019-08-30T11:25:06Zcom_10033_620968col_10033_621182
Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.
Wheeler, Nicole E
Gardner, Paul P
Barquist, Lars
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Emerging pathogens are a major threat to public health, however understanding how pathogens adapt to new niches remains a challenge. New methods are urgently required to provide functional insights into pathogens from the massive genomic data sets now being generated from routine pathogen surveillance for epidemiological purposes. Here, we measure the burden of atypical mutations in protein coding genes across independently evolved Salmonella enterica lineages, and use these as input to train a random forest classifier to identify strains associated with extraintestinal disease. Members of the species fall along a continuum, from pathovars which cause gastrointestinal infection and low mortality, associated with a broad host-range, to those that cause invasive infection and high mortality, associated with a narrowed host range. Our random forest classifier learned to perfectly discriminate long-established gastrointestinal and invasive serovars of Salmonella. Additionally, it was able to discriminate recently emerged Salmonella Enteritidis and Typhimurium lineages associated with invasive disease in immunocompromised populations in sub-Saharan Africa, and within-host adaptation to invasive infection. We dissect the architecture of the model to identify the genes that were most informative of phenotype, revealing a common theme of degradation of metabolic pathways in extraintestinal lineages. This approach accurately identifies patterns of gene degradation and diversifying selection specific to invasive serovars that have been captured by more labour-intensive investigations, but can be readily scaled to larger analyses.
2018-06-18T13:59:04Z
2018-06-18T13:59:04Z
2018-01-01
Article
1553-7404
29738521
10.1371/journal.pgen.1007333
http://hdl.handle.net/10033/621404
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
PLoS genetics
oai:repository.helmholtz-hzi.de:10033/6214252019-08-30T11:32:37Zcom_10033_620968col_10033_620969col_10033_621236
CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level.
El Mouali, Youssef
Gaviria-Cantin, Tania
Sánchez-Romero, María Antonia
Gibert, Marta
Westermann, Alexander J
Vogel, Jörg
Balsalobre, Carlos
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3'UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3'UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3'UTR as a hub for post-transcriptional control of Salmonella invasion gene expression.
2018-07-17T11:50:09Z
2018-07-17T11:50:09Z
2018-01-01
Article
1553-7404
29879120
10.1371/journal.pgen.1007401
http://hdl.handle.net/10033/621425
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
PLoS genetics
oai:repository.helmholtz-hzi.de:10033/6214382019-08-30T11:33:54Zcom_10033_620968col_10033_621182
Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.
Cain, Amy K
Boinett, Christine J
Barquist, Lars
Dordel, Janina
Fookes, Maria
Mayho, Matthew
Ellington, Matthew J
Goulding, David
Pickard, Derek
Wick, Ryan R
Holt, Kathryn E
Parkhill, Julian
Thomson, Nicholas R
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of col
2018-08-07T09:45:02Z
2018-08-07T09:45:02Z
2018-06-29
Article
2045-2322
29959380
10.1038/s41598-018-28199-y
http://hdl.handle.net/10033/621438
en
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Scientific reports
oai:repository.helmholtz-hzi.de:10033/6214562019-08-30T11:29:14Zcom_10033_620968col_10033_620969
The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells.
Heidrich, Nadja
Hagmann, Antony
Bauriedl, Saskia
Vogel, Jörg
Schoen, Christoph
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
CRISPR/Cas
Cas9
Neisseria meningitidis
RIP-seq
RNA-seq
nasopharynx
virulence
Neisseria meningitidis, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. A recent genome-wide association study suggested an association of its type II-C CRISPR/Cas system with carriage and thus less invasive lineages. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. Transcriptome sequencing data further suggest that meningococcal Cas9 does not affect the expression of surface adhesins but rather exerts its effect on cell adhesion in an indirect manner. Consequently, we speculate that the meningococcal CRISPR/Cas system exerts novel functions beyond its established role in defence against foreign DNA.
2018-08-28T13:54:37Z
2018-08-28T13:54:37Z
2018-07-30
Article
1555-8584
30059276
10.1080/15476286.2018.1486660
http://hdl.handle.net/10033/621456
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
RNA biology
oai:repository.helmholtz-hzi.de:10033/6214712019-08-30T11:31:48Zcom_10033_620968col_10033_621187
Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting.
Matsumoto, Saki
Caliskan, Neva
Rodnina, Marina V
Murata, Asako
Nakatani, Kazuhiko
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Programmed -1 ribosomal frameshifting (-1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. -1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure element, which is often a pseudoknot. In this study we engineered the frameshifting pseudoknot from the mouse mammary tumor virus to respond to a rationally designed small molecule naphthyridine carbamate tetramer (NCTn). We demonstrate that NCTn can stabilize the pseudoknot structure in mRNA and activate -1PRF both in vitro and in human cells. The results illustrate how NCTn-inducible -1PRF may serve as an important component of the synthetic biology toolbox for the precise control of gene expression using small synthetic molecules.
2018-09-06T14:03:30Z
2018-09-06T14:03:30Z
2018-08-02
Article
1362-4962
30085309
10.1093/nar/gky689
http://hdl.handle.net/10033/621471
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/6214842019-08-30T11:33:04Zcom_10033_620968col_10033_620969
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes.
Yu, Sung-Huan
Vogel, Jörg
Förstner, Konrad U
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
2018-09-17T14:32:06Z
2018-09-17T14:32:06Z
2018-09-01
Article
2047-217X
30169674
10.1093/gigascience/giy096
http://hdl.handle.net/10033/621484
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
GigaScience
oai:repository.helmholtz-hzi.de:10033/6214902019-08-30T11:29:15Zcom_10033_620968col_10033_620969
Molecular mechanism of mRNA repression in by a ProQ-dependent small RNA.
Smirnov, Alexandre
Wang, Chuan
Drewry, Lisa L
Vogel, Jörg
HIRI, Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
HU‐α
ProQ
RaiZ
small RNA
translation inhibition
Research into post-transcriptional control of mRNAs by small
noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and
Salmonella enterica has mainly focused on sRNAs that associate
with the RNA chaperone Hfq. However, the recent discovery of the
protein ProQ as a common binding partner that stabilizes a
distinct large class of structured sRNAs suggests that additional
RNA regulons exist in these organisms. The cellular functions and
molecular mechanisms of these new ProQ-dependent sRNAs are
largely unknown. Here, we report in Salmonella Typhimurium the
mode-of-action of RaiZ, a ProQ-dependent sRNA that is made from
the 30 end of the mRNA encoding ribosome-inactivating protein
RaiA. We show that RaiZ is a base-pairing sRNA that represses in
trans the mRNA of histone-like protein HU-a. RaiZ forms an RNA
duplex with the ribosome-binding site of hupA mRNA, facilitated
by ProQ, to prevent 30S ribosome loading and protein synthesis
of HU-a. Similarities and differences between ProQ- and Hfqmediated regulation will be discussed.
2018-09-24T09:11:07Z
2018-09-24T09:11:07Z
2017-04-13
Article
1460-2075
28336682
10.15252/embj.201696127
http://hdl.handle.net/10033/621490
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
The EMBO journal
oai:repository.helmholtz-hzi.de:10033/6215062019-08-30T11:30:31Zcom_10033_620968col_10033_620969
New RNA-seq approaches for the study of bacterial pathogens.
Saliba, Antoine-Emmanuel
C Santos, Sara
Vogel, Jörg
Helmoltz-Institut für RNA-basierteInfektionsforschung, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself. Dual RNA-seq analyzing pathogen and host simultaneously has revealed roles of noncoding RNAs during infection and enabled the correlation of bacterial gene activity with specific host responses. Single-cell RNA-seq studies have addressed how heterogeneity among individual host cells may determine infection outcomes.
2018-10-02T09:59:51Z
2018-10-02T09:59:51Z
2017-01-01
Article
1879-0364
28214646
10.1016/j.mib.2017.01.001
http://hdl.handle.net/10033/621506
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Current opinion in microbiology
oai:repository.helmholtz-hzi.de:10033/6215362019-08-30T11:29:40Zcom_10033_620968col_10033_621277
RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity.
Smyth, Redmond P
Negroni, Matteo
Lever, Andrew M
Mak, Johnson
Kenyon, Julia C
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
RNA structure
immune evasion
secondary structure
viral RNA
viral evolution
The central dogma of molecular biology describes the flow of genetic information from DNA to protein via an RNA intermediate. For many years, RNA has been considered simply as a messenger relaying information between DNA and proteins. Recent advances in next generation sequencing technology, bioinformatics, and non-coding RNA biology have highlighted the many important roles of RNA in virtually every biological process. Our understanding of RNA biology has been further enriched by a number of significant advances in probing RNA structures. It is now appreciated that many cellular and viral biological processes are highly dependent on specific RNA structures and/or sequences, and such reliance will undoubtedly impact on the evolution of both hosts and viruses. As a contribution to this special issue on host immunity and virus evolution, it is timely to consider how RNA sequences and structures could directly influence the co-evolution between hosts and viruses. In this manuscript, we begin by stating some of the basic principles of RNA structures, followed by describing some of the critical RNA structures in both viruses and hosts. More importantly, we highlight a number of available new tools to predict and to evaluate novel RNA structures, pointing out some of the limitations readers should be aware of in their own analyses.
2018-11-05T14:31:57Z
2018-11-05T14:31:57Z
2018-01-01
Article
1664-3224
30283444
10.3389/fimmu.2018.02097
http://hdl.handle.net/10033/621536
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Frontiers in immunology
oai:repository.helmholtz-hzi.de:10033/6215632019-08-30T11:27:40Zcom_10033_620968col_10033_620969
HHV-6 encoded small non-coding RNAs define an intermediate and early stage in viral reactivation.
Prusty, Bhupesh K
Gulve, Nitish
Chowdhury, Suvagata Roy
Schuster, Michael
Strempel, Sebastian
Descamps, Vincent
Rudel, Thomas
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Human herpesvirus 6A and 6B frequently acquires latency. HHV-6 activation has been associated with various human diseases. Germ line inheritance of chromosomally integrated HHV-6 makes viral DNA-based analysis difficult for determination of early stages of viral activation. We characterized early stages of HHV-6 activation using high throughput transcriptomics studies and applied the results to understand virus activation under clinical conditions. Using a latent HHV-6A cell culture model in U2OS cells, we identified an early stage of viral reactivation, which we define as transactivation that is marked by transcription of several viral small non-coding RNAs (sncRNAs) in the absence of detectable increase in viral replication and proteome. Using deep sequencing approaches, we detected previously known as well as a new viral sncRNAs that characterized viral transactivation and differentiated it from latency. Here we show changes in human transcriptome upon viral transactivation that reflect multiple alterations in mitochondria-associated pathways, which was supported by observation of increased mitochondrial fragmentation in virus reactivated cells. Furthermore, we present here a unique clinical case of DIHS/DRESS associated death where HHV-6 sncRNA-U14 was abundantly detected throughout the body of the patient in the presence of low viral DNA. In this study, we have identified a unique and early stage of viral activation that is characterized by abundant transcription of viral sncRNAs, which can serve as an ideal biomarker under clinical conditions.
2018-11-14T10:28:51Z
2018-11-14T10:28:51Z
2018-01-01
Article
2056-7944
30210807
10.1038/s41525-018-0064-5
http://hdl.handle.net/10033/621563
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
NPJ genomic medicine
oai:repository.helmholtz-hzi.de:10033/6215722019-08-30T11:29:43Zcom_10033_620968col_10033_620969
Nuclear lncRNA stabilization in the host response to bacterial infection.
Munschauer, Mathias
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Long non-coding RNAs (lncRNAs) play important roles in many cellular pathways, but their contribution to the defense of eukaryotic cells against pathogens remains poorly understood. A new study from Imamura et al in The EMBO Journal reports that Salmonella infection in human cells impacts nuclear RNA decay, which in turn drives the accumulation of otherwise unstable nuclear lncRNAs, some of which may have protective effects against this common bacterial pathogen. These unexpected findings demand more efforts to fully decrypt the molecular functions of lncRNAs in innate and adaptive immunity.
2018-11-19T08:59:58Z
2018-11-19T08:59:58Z
2018-07-02
Article
1460-2075
29934294
10.15252/embj.201899875
http://hdl.handle.net/10033/621572
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
The EMBO journal
oai:repository.helmholtz-hzi.de:10033/6215732019-08-30T11:29:43Zcom_10033_620968col_10033_620969
Long Noncoding RNA SSR42 Controls Staphylococcus aureus Alpha-Toxin Transcription in Response to Environmental Stimuli.
Horn, Jessica
Klepsch, Maximilian
Manger, Michelle
Wolz, Christiane
Rudel, Thomas
Fraunholz, Martin
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Staphylococcus aureus
hemolysin gene regulation
noncoding RNA
β-lactams
Staphylococcus aureus is a human pathogen causing a variety of diseases by versatile expression of a large set of virulence factors that most prominently features the cytotoxic and hemolytic pore-forming alpha-toxin. Expression of
alpha-toxin is regulated by an intricate network of transcription factors. These include two-component systems sensing quorum and environmental signals as well as
regulators reacting to the nutritional status of the pathogen. We previously identified the repressor of surface proteins (Rsp) as a virulence regulator. Acute cytotoxicity and hemolysis are strongly decreased in rsp mutants, which are characterized by
decreased transcription of toxin genes as well as loss of transcription of a 1,232-
nucleotide (nt)-long noncoding RNA (ncRNA), SSR42. Here, we show that SSR42 is the effector of Rsp in transcription regulation of the alpha-toxin gene, hla. SSR42 transcription
is enhanced after exposure of S. aureus to subinhibitory concentrations of oxacillin
which thus leads to an SSR42-dependent increase in hemolysis. Aside from Rsp, SSR42
transcription is under the control of additional global regulators, such as CodY, AgrA,
CcpE, and B, but is positioned upstream of the two-component system SaeRS in the
regulatory cascade leading to alpha-toxin production. Thus, alpha-toxin expression depends on two long ncRNAs, SSR42 and RNAIII, which control production of the cytolytic
toxin on the transcriptional and translational levels, respectively, with SSR42 as an important regulator of SaeRS-dependent S. aureus toxin production in response to environmental and metabolic signals.
IMPORTANCE Staphylococcus aureus is a major cause of life-threatening infections.
The bacterium expresses alpha-toxin, a hemolysin and cytotoxin responsible for
many of the pathologies of S. aureus. Alpha-toxin production is enhanced by subinhibitory concentrations of antibiotics. Here, we show that this process is dependent
on the long noncoding RNA, SSR42. Further, SSR42 itself is regulated by several
global regulators, thereby integrating environmental and nutritional signals that
modulate hemolysis of the pathogen.
2018-11-20T09:17:35Z
2018-11-20T09:17:35Z
2018-11-15
Article
1098-5530
30150231
10.1128/JB.00252-18
http://hdl.handle.net/10033/621573
: PMC6199474
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Journal of bacteriology
oai:repository.helmholtz-hzi.de:10033/6215762019-08-30T11:29:42Zcom_10033_620968col_10033_620970col_10033_620969
Genome organization and DNA accessibility control antigenic variation in trypanosomes.
Müller, Laura S M
Cosentino, Raúl O
Förstner, Konrad U
Guizetti, Julien
Wedel, Carolin
Kaplan, Noam
Janzen, Christian J
Arampatzi, Panagiota
Vogel, Jörg
Steinbiss, Sascha
Otto, Thomas D
Saliba, Antoine-Emmanuel
Sebra, Robert P
Siegel, T Nicolai
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility2,3. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding4. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses—Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing—that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
2018-11-20T14:22:49Z
2018-11-20T14:22:49Z
2018-01-01
Article
1476-4687
30333624
10.1038/s41586-018-0619-8
http://hdl.handle.net/10033/621576
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Nature
oai:repository.helmholtz-hzi.de:10033/6215852019-08-30T11:28:46Zcom_10033_620968col_10033_621182
A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa.
Nolan, Laura M
Whitchurch, Cynthia B
Barquist, Lars
Katrib, Marilyn
Boinett, Christine J
Mayho, Matthew
Goulding, David
Charles, Ian G
Filloux, Alain
Parkhill, Julian
Cain, Amy K
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
2018-11-27T12:42:20Z
2018-11-27T12:42:20Z
2018-11-01
Article
2057-5858
30383525
10.1099/mgen.0.000229
http://hdl.handle.net/10033/621585
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Microbiology Society
Microbial genomics
oai:repository.helmholtz-hzi.de:10033/6215952019-08-30T11:29:12Zcom_10033_620968col_10033_620969
Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens.
Tawk, Caroline
Nigro, Giulia
Rodrigues Lopes, Ines
Aguilar, Carmen
Lisowski, Clivia
Mano, Miguel
Sansonetti, Philippe
Vogel, Jörg
Eulalio, Ana
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Salmonella
Shigella
acid sphingomyelinase
host stress response
membrane remodeling
While mucosal inflammation is a major source of stress during enteropathogen infection, it remains to be
fully elucidated how the host benefits from this environment to clear the pathogen. Here, we show that
host stress induced by different stimuli mimicking inflammatory conditions strongly reduces the binding
of Shigella flexneri to epithelial cells. Mechanistically, stress activates acid sphingomyelinase leading to
host membrane remodeling. Consequently, knockdown or pharmacological inhibition of the acid
sphingomyelinase blunts the stress-dependent inhibition of Shigella binding to host cells. Interestingly,
stress caused by intracellular Shigella replication also results in remodeling of the host cell membrane, in
vitro and in vivo, which precludes re-infection by this and other non-motile pathogens. In contrast,
Salmonella Typhimurium overcomes the shortage of permissive entry sites by gathering effectively at the
remaining platforms through its flagellar motility. Overall, our findings reveal host membrane remodeling
as a novel stress-responsive cell-autonomous defense mechanism that protects epithelial cells from
infection by non-motile bacterial pathogens.
2018-12-03T10:43:31Z
2018-12-03T10:43:31Z
2018-11-02
Article
1460-2075
30389666
10.15252/embj.201798529
http://hdl.handle.net/10033/621595
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
The EMBO journal
oai:repository.helmholtz-hzi.de:10033/6216012019-08-30T11:29:12Zcom_10033_620968col_10033_621258
The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays.
Liao, Chunyu
Slotkowski, Rebecca A
Achmedov, Tatjana
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CRISPR
Cpf1
RNA structure
TXTL
terminator
The Class 2 Type V-A CRISPR effector protein Cas12a/Cpf1 has gained widespread attention in part because of the ease in achieving multiplexed genome editing, gene regulation, and DNA detection. Multiplexing derives from the ability of Cas12a alone to generate multiple guide RNAs from a transcribed CRISPR array encoding alternating conserved repeats and targeting spacers. While array design has focused on how to optimize guide-RNA sequences, little attention has been paid to sequences outside of the CRISPR array. Here, we show that a structured hairpin located immediately downstream of the 3' repeat interferes with utilization of the adjacent encoded guide RNA by Francisella novicida (Fn)Cas12a. We first observed that a synthetic Rho-independent terminator immediately downstream of an array impaired DNA cleavage based on plasmid clearance in E. coli and DNA cleavage in a cell-free transcription-translation (TXTL) system. TXTL-based cleavage assays further revealed that inhibition was associated with incomplete processing of the transcribed CRISPR array and could be attributed to the stable hairpin formed by the terminator. We also found that the inhibitory effect partially extended to upstream spacers in a multi-spacer array. Finally, we found that removing the terminal repeat from the array increased the inhibitory effect, while replacing this repeat with an unprocessable terminal repeat from a native FnCas12a array restored cleavage activity directed by the adjacent encoded guide RNA. Our study thus revealed that sequences surrounding a CRISPR array can interfere with the function of a CRISPR nuclease, with implications for the design and evolution of CRISPR arrays.
2018-12-04T13:53:22Z
2018-12-04T13:53:22Z
2018-10-12
Article
1555-8584
30252595
10.1080/15476286.2018.1526537
http://hdl.handle.net/10033/621601
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
RNA biology
oai:repository.helmholtz-hzi.de:10033/6216202019-08-30T11:30:55Zcom_10033_620968col_10033_621182
Functional analysis of Salmonella Typhi adaptation to survival in water.
Kingsley, Robert A
Langridge, Gemma
Smith, Sarah E
Makendi, Carine
Fookes, Maria
Wileman, Tom M
El Ghany, Moataz Abd
Keith Turner, A
Dyson, Zoe A
Sridhar, Sushmita
Pickard, Derek
Kay, Sally
Feasey, Nicholas
Wong, Vanessa
Barquist, Lars
Dougan, Gordon
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Contaminated water is a major risk factor associated with the transmission of Salmonella enterica serovar Typhi (S. Typhi), the aetiological agent of human typhoid. However, little is known about how this pathogen adapts to living in the aqueous environment. We used transcriptome analysis (RNA-seq) and transposon mutagenesis (TraDIS) to characterize these adaptive changes and identify multiple genes that contribute to survival. Over half of the genes in the S. Typhi genome altered expression level within the first 24 h following transfer from broth culture to water, although relatively few did so in the first 30 min. Genes linked to central metabolism, stress associated with arrested proton motive force and respiratory chain factors changed expression levels. Additionally, motility and chemotaxis genes increased expression, consistent with a scavenging lifestyle. The viaB-associated gene tviC encoding a glcNAc epimerase that is required for Vi polysaccharide biosynthesis was, along with several other genes, shown to contribute to survival in water. Thus, we define regulatory adaptation operating in S. Typhi that facilitates survival in water.
2018-12-19T11:44:21Z
2018-12-19T11:44:21Z
2018-11-18
Article
1462-2920
30450829
10.1111/1462-2920.14458
http://hdl.handle.net/10033/621620
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
Environmental microbiology
oai:repository.helmholtz-hzi.de:10033/6216622019-08-30T11:33:27Zcom_10033_620968col_10033_620969col_10033_621236
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium.
Westermann, Alexander J
Venturini, Elisa
Sellin, Mikael E
Förstner, Konrad U
Hardt, Wolf-Dietrich
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Hfq
ProQ
RNA-seq
bacterial pathogen
noncoding RNA
posttranscriptional control
FinO domain proteins such as ProQ of the model pathogen
2019-01-18T15:15:29Z
2019-01-18T15:15:29Z
2019-01-02
Article
MBio. 2019 Jan 2;10(1). pii: mBio.02504-18. doi: 10.1128/mBio.02504-18.
2150-7511
30602583
10.1128/mBio.02504-18
http://hdl.handle.net/10033/621662
mBio
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Amercan Society of Microbiology
mBio
oai:repository.helmholtz-hzi.de:10033/6216682019-08-30T11:33:28Zcom_10033_620968col_10033_621258
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator.
Westbrook, Alexandra
Tang, Xun
Marshall, Ryan
Maxwell, Colin S
Chappell, James
Agrawal, Deepak K
Dunlop, Mary J
Noireaux, Vincent
Beisel, Chase L
Lucks, Julius
Franco, Elisa
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bayesian methods
CRISPRi
RNA-based circuits
model-guided design
sRNA
To build complex genetic networks with predictable behaviours, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely employed to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and CRISPR interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ODE-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modelling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity. This article is protected by copyright. All rights reserved.
2019-01-28T14:18:34Z
2019-01-28T14:18:34Z
2019-01-13
Article
Biotechnol Bioeng. 2019 Jan 13. doi: 10.1002/bit.26918
1097-0290
30636320
10.1002/bit.26918
http://hdl.handle.net/10033/621668
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
Biotechnology and bioengineering
oai:repository.helmholtz-hzi.de:10033/6217412019-08-30T11:31:43Zcom_10033_620968col_10033_620970col_10033_620969col_10033_621391
Salmonella persisters undermine host immune defenses during antibiotic treatment.
Stapels, Daphne A C
Hill, Peter W S
Westermann, Alexander J
Fisher, Robert A
Thurston, Teresa L
Saliba, Antoine-Emmanuel
Blommestein, Isabelle
Vogel, Jörg
Helaine, Sophie
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of antibiotic-tolerant persisters. In vitro, persister cells appear to be dormant. After uptake of Salmonella species by macrophages, nongrowing persisters also occur, but their physiological state is poorly understood. In this work, we show that Salmonella persisters arising during macrophage infection maintain a metabolically active state. Persisters reprogram macrophages by means of effectors secreted by the Salmonella pathogenicity island 2 type 3 secretion system. These effectors dampened proinflammatory innate immune responses and induced anti-inflammatory macrophage polarization. Such reprogramming allowed nongrowing Salmonella cells to survive for extended periods in their host. Persisters undermining host immune defenses might confer an advantage to the pathogen during relapse once antibiotic pressure is relieved.
2019-04-10T07:56:27Z
2019-04-10T07:56:27Z
2018-12-07
Article
Science. 2018 Dec 7;362(6419):1156-1160. doi: 10.1126/science.aat7148.
1095-9203
30523110
10.1126/science.aat7148
http://hdl.handle.net/10033/621741
Science
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Association for the Advancement of Science
Science (New York, N.Y.)
oai:repository.helmholtz-hzi.de:10033/6217432019-08-30T11:31:43Zcom_10033_620968col_10033_620969
RNA-binding proteins in bacteria.
Holmqvist, Erik
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
RNA-binding proteins (RBPs) are central to most if not all cellular processes,
dictating the fate of virtually all RNA molecules in the cell. Starting with
pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the
way for molecular studies of RNA-protein interactions. Work over the years has
identified major RBPs that act on cellular transcripts at the various stages of
bacterial gene expression and that enable their integration into
post-transcriptional networks that also comprise small non-coding RNAs. Bacterial
RBP research has now entered a new era in which RNA sequencing-based methods
permit mapping of RBP activity in a truly global manner in vivo. Moreover, the
soaring interest in understudied members of host-associated microbiota and
environmental communities is likely to unveil new RBPs and to greatly expand our
knowledge of RNA-protein interactions in bacteria.
2019-04-10T09:47:32Z
2019-04-10T09:47:32Z
2018-10-01
Article
Nat Rev Microbiol. 2018 Oct;16(10):601-615. doi: 10.1038/s41579-018-0049-5.
1740-1534
29995832
10.1038/s41579-018-0049-5
http://hdl.handle.net/10033/621743
Nature Reviews Microbiology
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer Nature
Nature reviews. Microbiology
oai:repository.helmholtz-hzi.de:10033/6217502019-08-30T11:32:10Zcom_10033_620968col_10033_621258
Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus Symbiosis.
Martino, Maria Elena
Joncour, Pauline
Leenay, Ryan
Gervais, Hugo
Shah, Malay
Hughes, Sandrine
Gillet, Benjamin
Beisel, Chase
Leulier, François
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Drosophila
experimental evolution
lactobacilli
microbiota
symbiosis
Animal-microbe facultative symbioses play a fundamental role in ecosystem and organismal health. Yet, due to the flexible nature of their association, the selection pressures that act on animals and their facultative symbionts remain elusive. Here we apply experimental evolution to Drosophila melanogaster associated with its growth-promoting symbiont Lactobacillus plantarum, representing a well-established model of facultative symbiosis. We find that the diet of the host, rather than the host itself, is a predominant driving force in the evolution of this symbiosis. Furthermore, we identify a mechanism resulting from the bacterium's adaptation to the diet, which confers growth benefits to the colonized host. Our study reveals that bacterial adaptation to the host's diet may be the foremost step in determining the evolutionary course of a facultative animal-microbe symbiosis.
2019-04-16T09:57:57Z
2019-04-16T09:57:57Z
2018-07-11
Article
Cell Host Microbe. 2018 Jul 11;24(1):109-119.e6. doi: 10.1016/j.chom.2018.06.001 Epub 2018 Jun 28
1934-6069
30008290
10.1016/j.chom.2018.06.001
http://hdl.handle.net/10033/621750
Cell Host and Microbe
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
Cell host & microbe
oai:repository.helmholtz-hzi.de:10033/6217972019-08-30T11:36:28Zcom_10033_620968col_10033_621182
Transcriptional noise and exaptation as sources for bacterial sRNAs.
Jose, Bethany R
Gardner, Paul P
Barquist, Lars
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
bacteria
exaptation
ncRNA
sRNAs
selection
transcriptional noise
Understanding how new genes originate and integrate into cellular networks is key to understanding evolution. Bacteria present unique opportunities for both the natural history and experimental study of gene origins, due to their large effective population sizes, rapid generation times, and ease of genetic manipulation. Bacterial small non-coding RNAs (sRNAs), in particular, many of which operate through a simple antisense regulatory logic, may serve as tractable models for exploring processes of gene origin and adaptation. Understanding how and on what timescales these regulatory molecules arise has important implications for understanding the evolution of bacterial regulatory networks, in particular, for the design of comparative studies of sRNA function. Here, we introduce relevant concepts from evolutionary biology and review recent work that has begun to shed light on the timescales and processes through which non-functional transcriptional noise is co-opted to provide regulatory functions. We explore possible scenarios for sRNA origin, focusing on the co-option, or exaptation, of existing genomic structures which may provide protected spaces for sRNA evolution.
2019-06-04T12:51:12Z
2019-06-04T12:51:12Z
2019-04-30
Article
Biochem Soc Trans. 2019 Apr 30;47(2):527-539. doi: 10.1042/BST20180171. Epub 2019 Mar 5.
1470-8752
30837318
10.1042/BST20180171
http://hdl.handle.net/10033/621797
Biochemical Society Transactions
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Portland Press
Biochemical Society transactions
oai:repository.helmholtz-hzi.de:10033/6218562019-08-30T11:26:09Zcom_10033_620968col_10033_621182col_10033_620969
Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends.
Holmqvist, Erik
Li, Lei
Bischler, Thorsten
Barquist, Lars
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
3′ UTR
CLIP-seq
ProQ
RNA-binding protein
exoribonuclease
post-transcriptional control
The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used in vivo UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in Salmonella enterica and Escherichia coli. Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3′ end of mRNAs. Using the cspE mRNA as a model for 3′ end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs.
2019-07-10T08:45:54Z
2019-07-10T08:45:54Z
2018-06-07
Article
Mol Cell. 2018 Jun 7;70(5):971-982.e6. doi: 10.1016/j.molcel.2018.04.017. Epub 2018 May 24.
1097-4164
29804828
10.1016/j.molcel.2018.04.017
http://hdl.handle.net/10033/621856
Molecular Cell
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
Molecular cell
oai:repository.helmholtz-hzi.de:10033/6218582019-08-30T11:27:09Zcom_10033_620968col_10033_621258
An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system.
Wandera, Katharina G
Collins, Scott P
Wimmer, Franziska
Marshall, Ryan
Noireaux, Vincent
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Anti-CRISPR proteins
Cas9
Genome editing
TXTL
sgRNA
The characterization of CRISPR-Cas immune systems in bacteria was quickly followed by the discovery of anti-CRISPR proteins (Acrs) in bacteriophages. These proteins block different steps of CRISPR-based immunity and, as some inhibit Cas nucleases, can offer tight control over CRISPR technologies. While Acrs have been identified against a few CRISPR-Cas systems, likely many more await discovery and application. Here, we report a rapid and scalable method for characterizing putative Acrs against Cas nucleases using an E. coli-derived cell-free transcription-translation system. Using known Acrs against type II Cas9 nucleases as models, we demonstrate how the method can be used to measure the inhibitory activity of individual Acrs in under two days. We also show how the method can overcome non-specific inhibition of gene expression observed for some Acrs. In total, the method should accelerate the interrogation and application of Acrs as CRISPR-Cas inhibitors.
2019-07-10T14:37:17Z
2019-07-10T14:37:17Z
2019-05-21
Article
Methods. 2019 May 21. pii: S1046-2023(19)30001-5. doi: 10.1016/j.ymeth.2019.05.014.
1095-9130
31121300
10.1016/j.ymeth.2019.05.014
http://hdl.handle.net/10033/621858
Methods
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
Methods (San Diego, Calif.)
oai:repository.helmholtz-hzi.de:10033/6218772019-08-30T11:24:28Zcom_10033_620968col_10033_621182
Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Typhimurium ST313.
Ondari, Edna M
Klemm, Elizabeth J
Msefula, Chisomo L
El Ghany, Moataz Abd
Heath, Jennifer N
Pickard, Derek J
Barquist, Lars
Dougan, Gordon
Kingsley, Robert A
MacLennan, Calman A
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Invasive salmonellosis
antibody
complement
genome
serum resistance
transcriptome
Background: Salmonella Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal Salmonellae is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in S. Typhimurium ST313. Methods: Six S. Typhimurium ST313 bloodstream isolates, three of which were antibody resistant, were studied. Genomic content (single nucleotide polymorphisms and larger chromosomal modifications) of the strains was determined by Illumina and PACBIO sequencing, and functionally characterized using RNA-seq, transposon directed insertion site sequencing (TraDIS), targeted gene deletion and transfer of selected point mutations in an attempt to identify features associated with serum resistance. Results: Sequence polymorphisms in genes from strains with atypical serum susceptibility when transferred from strains that were highly resistant or susceptible to a strain that exhibited intermediate susceptibility did not significantly alter serum killing phenotype. No large chromosomal modifications typified serum resistance or susceptibility. Genes required for resistance to serum identified by TraDIS and RNA-seq included those involved in exopolysaccharide synthesis, iron scavenging and metabolism. Most of the down-regulated genes were associated with membrane proteins. Resistant and susceptible strains had distinct transcriptional responses to serum, particularly related to genes responsible for polysaccharide biosynthesis. There was higher upregulation of wca locus genes, involved in the biosynthesis of colanic acid exopolysaccharide, in susceptible strains and increased expression of fepE, a regulator of very long-chain lipopolysaccharide in resistant strains. Conclusion: Clinical isolates of S. Typhimurium ST313 exhibit distinct antibody susceptibility phenotypes that may be associated with changes in gene expression on exposure to serum.
2019-07-16T07:55:59Z
2019-07-16T07:55:59Z
2019-01-01
Article
Wellcome Open Res. 2019 Apr 25;4:74. doi: 10.12688/wellcomeopenres.15059.1. eCollection 2019.
2398-502X
31231691
10.12688/wellcomeopenres.15059.1
http://hdl.handle.net/10033/621877
Wellcome Open Research
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
F1000Research
Wellcome open research
oai:repository.helmholtz-hzi.de:10033/6219972019-10-30T10:50:02Zcom_10033_620968col_10033_621308
Barriers to genome editing with CRISPR in bacteria.
Vento, Justin M
Crook, Nathan
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteria
CRISPR
Genome editing
Nuclease
Recombineering
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
2019-10-29T22:08:49Z
2019-10-29T22:08:49Z
2019-06-05
Article
J Ind Microbiol Biotechnol. 2019 Jun 5. pii: 10.1007/s10295-019-02195-1. doi: 10.1007/s10295-019-02195-1.
1476-5535
31165970
10.1007/s10295-019-02195-1
http://hdl.handle.net/10033/621997
Journal of Industrial Microbiology and Biotechnology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer
Journal of industrial microbiology & biotechnology
oai:repository.helmholtz-hzi.de:10033/6219982019-10-30T10:50:15Zcom_10033_620968col_10033_621308
Barriers to genome editing with CRISPR in bacteria.
Vento, Justin M
Crook, Nathan
Beisel, Chase L
Bacteria
CRISPR
Genome editing
Nuclease
Recombineering
2019-10-30T08:55:44Z
2019-10-30T08:55:44Z
2019-06-05
Article
1476-5535
31165970
10.1007/s10295-019-02195-1
http://hdl.handle.net/10033/621998
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Journal of industrial microbiology & biotechnology
oai:repository.helmholtz-hzi.de:10033/6218952019-08-30T11:26:11Zcom_10033_620968col_10033_621258
Barriers to genome editing with CRISPR in bacteria.
Vento, Justin M
Crook, Nathan
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteria
CRISPR
Genome editing
Nuclease
Recombineering
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
2019-08-12T11:33:21Z
2019-08-12T11:33:21Z
2019-06-05
Article
J Ind Microbiol Biotechnol. 2019 Jun 5. pii: 10.1007/s10295-019-02195-1. doi: 10.1007/s10295-019-02195-1.
1476-5535
31165970
10.1007/s10295-019-02195-1
http://hdl.handle.net/10033/621895
Journal of Industrial Microbiology and Biotechnology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer
Journal of industrial microbiology & biotechnology
oai:repository.helmholtz-hzi.de:10033/6219042019-08-30T11:26:11Zcom_10033_620968col_10033_621391
Induced Pluripotent Stem Cell-Derived Brain Endothelial Cells as a Cellular Model to Study Infection.
Martins Gomes, Sara F
Westermann, Alexander J
Sauerwein, Till
Hertlein, Tobias
Förstner, Konrad U
Ohlsen, Knut
Metzger, Marco
Shusta, Eric V
Kim, Brandon J
Appelt-Menzel, Antje
Schubert-Unkmeir, Alexandra
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Neisseria meningitidis
bacteria
blood-brain barrier
blood-cerebrospinal fluid barrier
brain endothelial cells
meningococcus
stem cells
Meningococcal meningitis is a severe central nervous system infection that occurs when Neisseria meningitidis (Nm) penetrates brain endothelial cells (BECs) of the meningeal blood-cerebrospinal fluid barrier. As a human-specific pathogen, in vivo models are greatly limited and pose a significant challenge. In vitro cell models have been developed, however, most lack critical BEC phenotypes limiting their usefulness. Human BECs generated from induced pluripotent stem cells (iPSCs) retain BEC properties and offer the prospect of modeling the human-specific Nm interaction with BECs. Here, we exploit iPSC-BECs as a novel cellular model to study Nm host-pathogen interactions, and provide an overview of host responses to Nm infection. Using iPSC-BECs, we first confirmed that multiple Nm strains and mutants follow similar phenotypes to previously described models. The recruitment of the recently published pilus adhesin receptor CD147 underneath meningococcal microcolonies could be verified in iPSC-BECs. Nm was also observed to significantly increase the expression of pro-inflammatory and neutrophil-specific chemokines IL6, CXCL1, CXCL2, CXCL8, and CCL20, and the secretion of IFN-γ and RANTES. For the first time, we directly observe that Nm disrupts the three tight junction proteins ZO-1, Occludin, and Claudin-5, which become frayed and/or discontinuous in BECs upon Nm challenge. In accordance with tight junction loss, a sharp loss in trans-endothelial electrical resistance, and an increase in sodium fluorescein permeability and in bacterial transmigration, was observed. Finally, we established RNA-Seq of sorted, infected iPSC-BECs, providing expression data of Nm-responsive host genes. Altogether, this model provides novel insights into Nm pathogenesis, including an impact of Nm on barrier properties and tight junction complexes, and suggests that the paracellular route may contribute to Nm traversal of BECs.
2019-08-16T08:32:24Z
2019-08-16T08:32:24Z
2019-01-01
Article
Front Microbiol. 2019 May 29;10:1181. doi: 10.3389/fmicb.2019.01181. eCollection 2019.
1664-302X
31191497
10.3389/fmicb.2019.01181
http://hdl.handle.net/10033/621904
Frontiers in Microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Frontiers
Frontiers in microbiology
oai:repository.helmholtz-hzi.de:10033/6219092019-08-30T11:26:12Zcom_10033_620968col_10033_621258
Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis.
Liao, Chunyu
Ttofali, Fani
Slotkowski, Rebecca A
Denny, Steven R
Cecil, Taylor D
Leenay, Ryan T
Keung, Albert J
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CRISPR-Cas systems inherently multiplex through CRISPR arrays—whether to defend against different invaders or mediate multi-target editing, regulation, imaging, or sensing. However, arrays remain difficult to generate due to their reoccurring repeat sequences. Here, we report a modular, one-pot scheme called CRATES to construct CRISPR arrays and array libraries. CRATES allows assembly of repeat-spacer subunits using defined assembly junctions within the trimmed portion of spacers. Using CRATES, we construct arrays for the single-effector nucleases Cas9, Cas12a, and Cas13a that mediated multiplexed DNA/RNA cleavage and gene regulation in cell-free systems, bacteria, and yeast. CRATES further allows the one-pot construction of array libraries and composite arrays utilized by multiple Cas nucleases. Finally, array characterization reveals processing of extraneous CRISPR RNAs from Cas12a terminal repeats and sequence- and context-dependent loss of RNA-directed nuclease activity via global RNA structure formation. CRATES thus can facilitate diverse multiplexing applications and help identify factors impacting crRNA biogenesis.
2019-08-19T13:12:35Z
2019-08-19T13:12:35Z
2019-07-03
Article
Nat Commun. 2019 Jul 3;10(1):2948. doi: 10.1038/s41467-019-10747-3.
2041-1723
31270316
10.1038/s41467-019-10747-3
http://hdl.handle.net/10033/621909
Nature Communications
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer-Nature
Nature communications
oai:repository.helmholtz-hzi.de:10033/6219252019-08-30T11:24:31Zcom_10033_620968col_10033_620970col_10033_620969
scSLAM-seq reveals core features of transcription dynamics in single cells.
Erhard, Florian
Baptista, Marisa A P
Krammer, Tobias
Hennig, Thomas
Lange, Marius
Arampatzi, Panagiota
Jürges, Christopher S
Theis, Fabian J
Saliba, Antoine-Emmanuel
Dölken, Lars
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease1. However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling2, biochemical nucleoside conversion3 and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.
2019-08-28T14:24:24Z
2019-08-28T14:24:24Z
2019-01-01
Article
Nature. 2019 Jul;571(7765):419-423. doi: 10.1038/s41586-019-1369-y. Epub 2019 Jul 10.
1476-4687
31292545
10.1038/s41586-019-1369-y
http://hdl.handle.net/10033/621925
Nature
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer-Nature
Nature
oai:repository.helmholtz-hzi.de:10033/6219532019-09-20T01:28:43Zcom_10033_620968col_10033_620969
RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
Michaux, Charlotte
Holmqvist, Erik
Vasicek, Erin
Sharan, Malvika
Barquist, Lars
Westermann, Alexander J
Gunn, John S
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
RNA-binding protein
Salmonella
bacterial pathogenesis
cold-shock protein
stress response
The functions of many bacterial RNA-binding proteins remain obscure because of a lack of knowledge of their cellular ligands. Although well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, others are highly expressed in infection-relevant conditions. Here, we have profiled transcripts bound in vivo by the CspA family members of Salmonella enterica serovar Typhimurium to link the constitutively expressed CspC and CspE proteins with virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, double deletion of cspC and cspE fully attenuates Salmonella in systemic mouse infection. In other words, the RNA ligand-centric approach taken here overcomes a problematic molecular redundancy of CspC and CspE that likely explains why these proteins have evaded selection in previous virulence factor screens in animals. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy. They also suggest that globally acting RNA-binding proteins are more common in bacteria than currently appreciated.
2019-09-19T14:08:50Z
2019-09-19T14:08:50Z
2017-06-27
Article
Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):6824-6829. doi: 10.1073/pnas.1620772114. Epub 2017 Jun 13.
1091-6490
28611217
10.1073/pnas.1620772114
http://hdl.handle.net/10033/621953
Proceedings of the National Academy of Sciences.
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
National Academy of Sciences
Proceedings of the National Academy of Sciences of the United States of America
oai:repository.helmholtz-hzi.de:10033/6219802019-10-17T01:33:46Zcom_10033_620968col_10033_621258
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9.
Dugar, Gaurav
Leenay, Ryan T
Eisenbart, Sara K
Bischler, Thorsten
Aul, Belinda U
Beisel, Chase L
Sharma, Cynthia M
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CRISPR
Campylobacter jejuni
Cas9
RIP-seq
RNA binding proteins
RNA cleavage
crRNA
genome editing
non-coding RNA
post-transcriptional regulation
Cas9 nucleases naturally utilize CRISPR RNAs (crRNAs) to silence foreign double-stranded DNA. While recent work has shown that some Cas9 nucleases can also target RNA, RNA recognition has required nuclease modifications or accessory factors. Here, we show that the Campylobacter jejuni Cas9 (CjCas9) can bind and cleave complementary endogenous mRNAs in a crRNA-dependent manner. Approximately 100 transcripts co-immunoprecipitated with CjCas9 and generally can be subdivided through their base-pairing potential to the four crRNAs. A subset of these RNAs was cleaved around or within the predicted binding site. Mutational analyses revealed that RNA binding was crRNA and tracrRNA dependent and that target RNA cleavage required the CjCas9 HNH domain. We further observed that RNA cleavage was PAM independent, improved with greater complementarity between the crRNA and the RNA target, and was programmable in vitro. These findings suggest that C. jejuni Cas9 is a promiscuous nuclease that can coordinately target both DNA and RNA.
2019-10-16T12:56:46Z
2019-10-16T12:56:46Z
2018-03-01
Article
Mol Cell. 2018 Mar 1;69(5):893-905.e7. doi: 10.1016/j.molcel.2018.01.032.
1097-4164
29499139
10.1016/j.molcel.2018.01.032
http://hdl.handle.net/10033/621980
Molecular Cell
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier/ Cel Press
Molecular cell
oai:repository.helmholtz-hzi.de:10033/6220052019-11-07T01:59:20Zcom_10033_620968col_10033_621187
Thermodynamic control of -1 programmed ribosomal frameshifting.
Bock, Lars V
Caliskan, Neva
Korniy, Natalia
Peske, Frank
Rodnina, Marina V
Grubmüller, Helmut
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
mRNA contexts containing a 'slippery' sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the -1 reading frame. In this study we build a thermodynamic model based on Bayesian statistics to explain how -1 programmed ribosome frameshifting can work. As training sets for the model, we measured frameshifting efficiencies on 64 dnaX mRNA sequence variants in vitro and also used 21 published in vivo efficiencies. With the obtained free-energy difference between mRNA-tRNA base pairs in the 0 and -1 frames, the frameshifting efficiency of a given sequence can be reproduced and predicted from the tRNA-mRNA base pairing in the two frames. Our results further explain how modifications in the tRNA anticodon modulate frameshifting and show how the ribosome tunes the strength of the base-pair interactions.
2019-11-06T11:31:31Z
2019-11-06T11:31:31Z
2019-10-10
Article
Nat Commun. 2019 Oct 10;10(1):4598. doi: 10.1038/s41467-019-12648-x.
2041-1723
31601802
10.1038/s41467-019-12648-x
http://hdl.handle.net/10033/622005
Nature Communications
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature Research
Nature communications
oai:repository.helmholtz-hzi.de:10033/6220492019-12-12T01:59:56Zcom_10033_620968col_10033_621236
MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data
Simon, L. M.
Karg, S.
Westermann, A. J.
Engel, M.
Elbehery, A. H.A.
Hense, B.
Heinig, M.
Deng, L.
Theis, F. J.
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Big data
High-performance computing
Human disease
Infection
Metatranscriptomics
Microbiome
RNA-seq
Sequence read archive
Virome
Background:
With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.
Findings:
We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.
Conclusions:
Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.
2019-12-11T16:04:40Z
2019-12-11T16:04:40Z
2018-06-01
Article
Gigascience. 2018 Jun 1;7(6). pii: 5036539. doi: 10.1093/gigascience/giy070.
29901703
10.1093/gigascience/giy070
https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85050892432&origin=inward
http://hdl.handle.net/10033/622049
Gigascience
2-s2.0-85050892432
SCOPUS_ID:85050892432
en
GigaScience
6
7
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford University Press
oai:repository.helmholtz-hzi.de:10033/6220832020-01-15T02:19:04Zcom_10033_620968col_10033_620969
The conserved 3' UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration.
Wang, Chuan
Chao, Yanjie
Matera, Gianluca
Gao, Qian
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Small noncoding RNAs (sRNAs) from mRNA 3' UTRs seem to present a previously unrecognized layer of bacterial post-transcriptional control whereby mRNAs influence each other's expression, independently of transcriptional control. Studies in Escherichia coli and Salmonella enterica showed that such sRNAs are natural products of RNase E-mediated mRNA decay and associate with major RNA-binding proteins (RBPs) such as Hfq and ProQ. If so, there must be additional sRNAs from mRNAs that accumulate only under specific physiological conditions. We test this prediction by characterizing candidate NarS that represents the 3' UTR of nitrate transporter NarK whose gene is silent during standard aerobic growth. We find that NarS acts by Hfq-dependent base pairing to repress the synthesis of the nitrite transporter, NirC, resulting in mRNA cross-regulation of nitrate and nitrite transporter genes. Interestingly, the NarS-mediated repression selectively targets the nirC cistron of the long nirBDC-cysG operon, an observation that we rationalize as a mechanism to protect the bacterial cytoplasm from excessive nitrite toxicity during anaerobic respiration with abundant nitrate. Our successful functional assignment of a 3' UTR sRNA from a non-standard growth condition supports the notion that mRNA crossregulation is more pervasive than currently appreciated.
2020-01-14T14:58:36Z
2020-01-14T14:58:36Z
2019-12-21
Article
Nucleic Acids Res. 2019 Dec 21. pii: 5682904. doi: 10.1093/nar/gkz1168.
1362-4962
31863581
10.1093/nar/gkz1168
http://hdl.handle.net/10033/622083
Nucleic Acids Research
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford Academic
Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/6220872020-09-28T12:40:26Zcom_10033_620968col_10033_620969
An RNA Surprise in Bacterial Effector Mechanisms
Gerovac, Milan
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Microbiology
Parasitology
Virology
acterial pathogens secrete effector proteins to manipulate host signaling proteins and cellular structures. In this issue of Cell Host & Microbe, Pagliuso et al. (2019) propose an effector mechanism in Listeria monocytogenes whereby an RNA-binding protein associates with bacterial RNA that stimulates RIG-I (retinoic acid inducible gene I)-based innate immunity in the host cytosol.
2020-01-16T14:51:11Z
2020-01-16T14:51:11Z
2019-12
Article
Gerovac und Vogel,An RNA Surprise in Bacterial Effector Mechanisms, (2019)Cell Host & Microbe.26(6)pp.709-11.
1931-3128
31951583
10.1016/j.chom.2019.11.005
http://hdl.handle.net/10033/622087
Cell Host and Microbe
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier BV
26
6
709-711
oai:repository.helmholtz-hzi.de:10033/6221342020-02-15T02:01:00Zcom_10033_620968col_10033_621258
An educational module to explore CRISPR technologies with a cell-free transcription-translation system
Collias, Daphne
Marshall, Ryan
Collins, Scott P.
Beisel, Chase L.
Noireaux, Vincent
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Cas9
CRISPR
education modules
synthetic biology
TXTL
Within the last 6 years, CRISPR-Cas systems have transitioned from adaptive defense systems in bacteria and archaea to revolutionary genome-editing tools. The resulting CRISPR technologies have driven innovations for treating genetic diseases and eradicating human pests while raising societal questions about gene editing in human germline cells as well as crop plants. Bringing CRISPR into the classroom therefore offers a means to expose students to cutting edge technologies and to promote discussions about ethical questions at the intersection of science and society. However, working with these technologies in a classroom setting has been difficult because typical experiments rely on cellular systems such as bacteria or mammalian cells. We recently reported the use of an E. coli cell-free transcription-translation (TXTL) system that simplifies the demonstration and testing of CRISPR technologies with shorter experiments and limited equipment. Here, we describe three educational modules intended to expose undergraduate students to CRISPR technologies using TXTL. The three sequential modules comprise (i) designing the RNAs that guide DNA targeting, (ii) measuring DNA cleavage activity in TXTL and (iii) testing how mutations to the targeting sequence or RNA backbone impact DNA binding and cleavage. The modules include detailed protocols, questions for group discussions or individual evaluation, and lecture slides to introduce CRISPR and TXTL. We expect these modules to allow students to experience the power and promise of CRISPR technologies in the classroom and to engage with their instructor and peers about the opportunities and potential risks for society.
2020-02-14T11:44:55Z
2020-02-14T11:44:55Z
2019-05-21
Article
19397267
10.1093/synbio/ysz005
https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85065856447&origin=inward
http://hdl.handle.net/10033/622134
Synthetic Biology
2-s2.0-85065856447
SCOPUS_ID:85065856447
en
Synthetic Biology
1
4
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford Academic
oai:repository.helmholtz-hzi.de:10033/6221352020-02-15T02:01:08Zcom_10033_620968col_10033_620969
Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27.
Wang, Xiuye
Hennig, Thomas
Whisnant, Adam W
Erhard, Florian
Prusty, Bhupesh K
Friedel, Caroline C
Forouzmand, Elmira
Hu, William
Erber, Luke
Chen, Yue
Sandri-Goldin, Rozanne M
Dölken, Lars
Shi, Yongsheng
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Infection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses causewidespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) inhost genes. However, the underlying mechanisms remain unclear. Here, we demonstrate thatthe HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essentialmRNA 3’processing factor CPSF. It thereby induces the assembly of a dead-end 3’processing complex, blocking mRNA 3’cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3’processing for viral and a subset of host transcripts.Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced hostshutoff and identify CPSF as an important factor that mediates regulation of transcriptiontermination. Thesefindings have broad implications for understanding the regulation oftranscription termination by other viruses, cellular stress and cancer.
2020-02-14T14:18:58Z
2020-02-14T14:18:58Z
2020-01-15
Article
Nat Commun. 2020 Jan 15;11(1):293. doi: 10.1038/s41467-019-14109-x.
2041-1723
31941886
10.1038/s41467-019-14109-x
http://hdl.handle.net/10033/622135
Nature communications
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature publishing group
Nature communications
oai:repository.helmholtz-hzi.de:10033/6221462020-02-19T02:01:17Zcom_10033_620968col_10033_621258
Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products.
Siedler, Solvej
Rau, Martin Holm
Bidstrup, Susanne
Vento, Justin M
Aunsbjerg, Stina Dissing
Bosma, Elleke F
McNair, Laura M
Beisel, Chase L
Neves, Ana Rute
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
A prominent feature of lactic acid bacteria (LAB) is their ability to inhibit growth of spoilage organisms in food, but hitherto research efforts to establish the mechanisms underlying bioactivity focused on the production of antimicrobial compounds by LAB. We show in this study, that competitive exclusion, i.e, competition for a limited resource by different organisms, is a major mechanism of fungal growth inhibition by lactobacilli in fermented dairy products. The depletion of the essential trace element manganese by two Lactobacillus species was uncovered as the main mechanism for growth inhibition of dairy spoilage yeast and molds. A manganese transporter (MntH1), representing one of the highest expressed gene products in both lactobacilli, facilitates the exhaustive manganese scavenging. Expression of the mntH1 gene was found to be strain-dependent, affected by species co-culturing and growth phase. Further, deletion of the mntH1 gene in one of the strains resulted in loss of bioactivity, proving this gene to be important for manganese depletion. The presence of a mntH gene displayed a distinct phylogenetic pattern within the Lactobacillus genus. Moreover, assaying the bioprotective ability in fermented milk of selected lactobacilli from ten major phylogenetic groups identified a correlation between the presence of mntH and bioprotective activity. Thus, manganese scavenging emerges as a common trait within the Lactobacillus genus, but differences in expression result in some strains showing more bioprotective effect than others.In summary, competitive exclusion through ion depletion is herein reported a novel mechanism in LAB to delay growth of spoilage contaminants in dairy products.IMPORTANCE In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of "good bacteria" to protect food against spoilage organisms has a long successful history, even though the molecular mechanisms are not fully understood. In this study, we show that depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provides a link to the distinct non-enzymatic manganese catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative Lactobacillus species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.
2020-02-18T12:54:54Z
2020-02-18T12:54:54Z
2020-01-31
Article
1098-5336
32005739
10.1128/AEM.02312-19
http://hdl.handle.net/10033/622146
Applied and environmental microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Society of Microbiology
Applied and environmental microbiology
oai:repository.helmholtz-hzi.de:10033/6221502020-02-21T02:03:49Zcom_10033_620968col_10033_620969
The chlamydial deubiquitinase Cdu1 supports recruitment of Golgi vesicles to the inclusion.
Auer, Daniela
Hügelschäffer, Sophie D
Fischer, Annette B
Rudel, Thomas
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Chlamydia trachomatis
Cdu1
ChlaDUB1
DUB
Golgi
autophagy
xenophagy
Chlamydia trachomatis is the main cause of sexually transmitted diseases worldwide. As obligate intracellular bacteria Chlamydia replicate in a membrane bound vacuole called inclusion and acquire nutrients for growth and replication from their host cells. However, like all intracellular bacteria, Chlamydia have to prevent eradication by the host's cell autonomous system. The chlamydial deubiquitinase Cdu1 is secreted into the inclusion membrane, facing the host cell cytosol where it deubiquitinates cellular proteins. Here we show that inactivation of Cdu1 causes a growth defect of C. trachomatis in primary cells. Moreover, ubiquitin and several autophagy receptors are recruited to the inclusion membrane of Cdu1-deficient Chlamydia. Interestingly, the growth defect of cdu1 mutants is not rescued when autophagy is prevented. We find reduced recruitment of Golgi vesicles to the inclusion of Cdu1 mutants indicating that vesicular trafficking is altered in bacteria without active deubiquitinase (DUB). Our work elucidates an important role of Cdu1 in the functional preservation of the chlamydial inclusion surface.
2020-02-20T09:58:27Z
2020-02-20T09:58:27Z
2019-11-01
Article
Cell Microbiol. 2019 Nov 1:e13136. doi: 10.1111/cmi.13136.
1462-5822
31677225
10.1111/cmi.13136
http://hdl.handle.net/10033/622150
Cellular Microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley
Cellular microbiology
oai:repository.helmholtz-hzi.de:10033/6221722020-03-12T03:28:38Zcom_10033_620968col_10033_621258
CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers.
Wimmer, Franziska
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CRISPR-Cas
anti-CRISPR proteins
autoimmunity
gene regulation
spacer acquisition
CRISPR-Cas immune systems in bacteria and archaea record prior infections as spacers within each system's CRISPR arrays. Spacers are normally derived from invasive genetic material and direct the immune system to complementary targets as part of future infections. However, not all spacers appear to be derived from foreign genetic material and instead can originate from the host genome. Their presence poses a paradox, as self-targeting spacers would be expected to induce an autoimmune response and cell death. In this review, we discuss the known frequency of self-targeting spacers in natural CRISPR-Cas systems, how these spacers can be incorporated into CRISPR arrays, and how the host can evade lethal attack. We also discuss how self-targeting spacers can become the basis for alternative functions performed by CRISPR-Cas systems that extend beyond adaptive immunity. Overall, the acquisition of genome-targeting spacers poses a substantial risk but can aid in the host's evolution and potentially lead to or support new functionalities.
2020-02-26T09:14:18Z
2020-02-26T09:14:18Z
2019-01-01
Article
Front Microbiol. 2020 Jan 22;10:3078. doi: 10.3389/fmicb.2019.03078. eCollection 2019.
1664-302X
32038537
10.3389/fmicb.2019.03078
http://hdl.handle.net/10033/622172
Frontiers in microbiology
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Frontiers
Frontiers in microbiology
oai:repository.helmholtz-hzi.de:10033/6221752020-03-12T03:28:58Zcom_10033_620968com_10033_620597col_10033_620970col_10033_620598
Eleven grand challenges in single-cell data science.
Lähnemann, David
Köster, Johannes
Szczurek, Ewa
McCarthy, Davis J
Hicks, Stephanie C
Robinson, Mark D
Vallejos, Catalina A
Campbell, Kieran R
Beerenwinkel, Niko
Mahfouz, Ahmed
Pinello, Luca
Skums, Pavel
Stamatakis, Alexandros
Attolini, Camille Stephan-Otto
Aparicio, Samuel
Baaijens, Jasmijn
Balvert, Marleen
Barbanson, Buys de
Cappuccio, Antonio
Corleone, Giacomo
Dutilh, Bas E
Florescu, Maria
Guryev, Victor
Holmer, Rens
Jahn, Katharina
Lobo, Thamar Jessurun
Keizer, Emma M
Khatri, Indu
Kielbasa, Szymon M
Korbel, Jan O
Kozlov, Alexey M
Kuo, Tzu-Hao
Lelieveldt, Boudewijn P F
Mandoiu, Ion I
Marioni, John C
Marschall, Tobias
Mölder, Felix
Niknejad, Amir
Raczkowski, Lukasz
Reinders, Marcel
Ridder, Jeroen de
Saliba, Antoine-Emmanuel
Somarakis, Antonios
Stegle, Oliver
Theis, Fabian J
Yang, Huan
Zelikovsky, Alex
McHardy, Alice C
Raphael, Benjamin J
Shah, Sohrab P
Schönhuth, Alexander
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.;HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
2020-02-26T10:38:33Z
2020-02-26T10:38:33Z
2020-02-07
Article
Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6.
1474-760X
32033589
10.1186/s13059-020-1926-6
http://hdl.handle.net/10033/622175
Genome Biology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
BMC
Genome biology
oai:repository.helmholtz-hzi.de:10033/6221842020-03-11T02:09:08Zcom_10033_620968col_10033_621258
Methods for characterizing, applying, and teaching CRISPR-Cas systems.
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effec-tively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltrans-ferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associ-ated antibiotic effects, especially the lack of resistance development, probably stem from the compound’s polypharmacology.
2020-03-02T13:12:53Z
2020-03-02T13:12:53Z
2020-01-16
Article
Methods. 2020 Jan 16. pii: S1046-2023(20)30020-7. doi: 10.1016/j.ymeth.2020.01.004.
1095-9130
31954772
10.1016/j.ymeth.2020.01.004
http://hdl.handle.net/10033/622184
Methods
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
Methods (San Diego, Calif.)
oai:repository.helmholtz-hzi.de:10033/6221972020-03-12T03:26:10Zcom_10033_620968col_10033_620969col_10033_621236
An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Infection.
Schulte, Leon N
Schweinlin, Matthias
Westermann, Alexander J
Janga, Harshavardhan
Santos, Sara C
Appenzeller, Silke
Walles, Heike
Vogel, Jörg
Metzger, Marco
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Salmonella
gene expression
infectious disease
A major obstacle in infection biology is the limited ability to recapitulate human disease trajectories in traditional cell culture and animal models, which impedes the translation of basic research into clinics. Here, we introduce a three-dimensional (3D) intestinal tissue model to study human enteric infections at a level of detail that is not achieved by conventional two-dimensional monocultures. Our model comprises epithelial and endothelial layers, a primary intestinal collagen scaffold, and immune cells. Upon Salmonella infection, the model mimics human gastroenteritis, in that it restricts the pathogen to the epithelial compartment, an advantage over existing mouse models. Application of dual transcriptome sequencing to the Salmonella-infected model revealed the communication of epithelial, endothelial, monocytic, and natural killer cells among each other and with the pathogen. Our results suggest that Salmonella uses its type III secretion systems to manipulate STAT3-dependent inflammatory responses locally in the epithelium without accompanying alterations in the endothelial compartment. Our approach promises to reveal further human-specific infection strategies employed by Salmonella and other pathogens.IMPORTANCE Infection research routinely employs in vitro cell cultures or in vivo mouse models as surrogates of human hosts. Differences between murine and human immunity and the low level of complexity of traditional cell cultures, however, highlight the demand for alternative models that combine the in vivo-like properties of the human system with straightforward experimental perturbation. Here, we introduce a 3D tissue model comprising multiple cell types of the human intestinal barrier, a primary site of pathogen attack. During infection with the foodborne pathogen Salmonella enterica serovar Typhimurium, our model recapitulates human disease aspects, including pathogen restriction to the epithelial compartment, thereby deviating from the systemic infection in mice. Combination of our model with state-of-the-art genetics revealed Salmonella-mediated local manipulations of human immune responses, likely contributing to the establishment of the pathogen's infection niche. We propose the adoption of similar 3D tissue models to infection biology, to advance our understanding of molecular infection strategies employed by bacterial pathogens in their human host.
2020-03-11T12:51:05Z
2020-03-11T12:51:05Z
2020-02-18
Article
mBio. 2020 Feb 18;11(1). pii: mBio.03348-19. doi: 10.1128/mBio.03348-19.
2150-7511
32071273
10.1128/mBio.03348-19
http://hdl.handle.net/10033/622197
mBio
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Society for Microbiology (ASM)
mBio
oai:repository.helmholtz-hzi.de:10033/6222372020-04-22T04:54:07Zcom_10033_620968col_10033_620969
Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control.
Hör, Jens
Garriss, Geneviève
Di Giorgio, Silvia
Hack, Lisa-Marie
Vanselow, Jens T
Förstner, Konrad U
Schlosser, Andreas
Henriques-Normark, Birgitta
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Streptococcus pneumoniae
Cbf1
Grad-seq
RNA-protein complex
competence
RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram-positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA-based regulation of virulence-relevant pathways.
2020-04-21T11:55:13Z
2020-04-21T11:55:13Z
2020-03-30
Article
EMBO J. 2020 Mar 30:e103852. doi: 10.15252/embj.2019103852.
32227509
10.15252/embj.2019103852
http://hdl.handle.net/10033/622237
1460-2075
The EMBO journal
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
EMBO Press
e103852
The EMBO journal
England
oai:repository.helmholtz-hzi.de:10033/6222492020-05-15T11:46:19Zcom_10033_620968col_10033_620970
Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry.
Winkels, Holger
Ehinger, Erik
Vassallo, Melanie
Buscher, Konrad
Dinh, Huy Q
Kobiyama, Kouji
Hamers, Anouk A J
Cochain, Clément
Vafadarnejad, Ehsan
Saliba, Antoine-Emmanuel
Zernecke, Alma
Pramod, Akula Bala
Ghosh, Amlan K
Anto Michel, Nathaly
Hoppe, Natalie
Hilgendorf, Ingo
Zirlik, Andreas
Hedrick, Catherine C
Ley, Klaus
Wolf, Dennis
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
atherosclerosis
flow cytometry
immune system
leukocytes
lymphocytes
macrophages
mass cytometry
single-cell RNA-sequencing
Using single-cell RNA-sequencing of aortic leukocytes from chow diet- and Western diet-fed Apoe-/- and Ldlr-/- mice, we detected 11 principal leukocyte clusters with distinct phenotypic and spatial characteristics while the cellular repertoire in healthy aortas was less diverse. Gene set enrichment analysis on the single-cell level established that multiple pathways, such as for lipid metabolism, proliferation, and cytokine secretion, were confined to particular leukocyte clusters. Leukocyte populations were differentially regulated in atherosclerotic Apoe-/- and Ldlr-/- mice. We confirmed the phenotypic diversity of these clusters with a novel mass cytometry 35-marker panel with metal-labeled antibodies and conventional flow cytometry. Cell populations retrieved by these protein-based approaches were highly correlated to transcriptionally defined clusters. In an integrated screening strategy of single-cell RNA-sequencing, mass cytometry, and fluorescence-activated cell sorting, we detected 3 principal B-cell subsets with alterations in surface markers, functional pathways, and in vitro cytokine secretion. Leukocyte cluster gene signatures revealed leukocyte frequencies in 126 human plaques by a genetic deconvolution strategy. This approach revealed that human carotid plaques and microdissected mouse plaques were mostly populated by macrophages, T-cells, and monocytes. In addition, the frequency of genetically defined leukocyte populations in carotid plaques predicted cardiovascular events in patients.
2020-05-07T15:18:46Z
2020-05-07T15:18:46Z
2018-03-15
Article
Other
Circ Res. 2018 Jun 8;122(12):1675-1688. doi: 10.1161/CIRCRESAHA.117.312513. Epub 2018 Mar 15.
29545366
10.1161/CIRCRESAHA.117.312513
http://hdl.handle.net/10033/622249
1524-4571
Circulation research
MC5993603
en
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993603/
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Amercan Heart Association
122
12
1675
1688
Circulation research
United States
United States
United States
United States
United States
United States
United States
oai:repository.helmholtz-hzi.de:10033/6222752020-05-27T11:12:11Zcom_10033_620968col_10033_620969
An RNA biology perspective on species-specific programmable RNA antibiotics.
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
RNA-seq
antibiotic
microbiome
small RNA
Our body is colonized by a vast array of bacteria the sum of which forms our microbiota. The gut alone harbors >1,000 bacterial species. An understanding of their individual or synergistic contributions to human health and disease demands means to interfere with their functions on the species level. Most of the currently available antibiotics are broad-spectrum, thus too unspecific for a selective depletion of a single species of interest from the microbiota. Programmable RNA antibiotics in the form of short antisense oligonucleotides (ASOs) promise to achieve precision manipulation of bacterial communities. These ASOs are coupled to small peptides that carry them inside the bacteria to silence mRNAs of essential genes, for example, to target antibiotic-resistant pathogens as an alternative to standard antibiotics. There is already proof-of-principle with diverse bacteria, but many open questions remain with respect to true species specificity, potential off-targeting, choice of peptides for delivery, bacterial resistance mechanisms and the host response. While there is unlikely a one-fits-all solution for all microbiome species, I will discuss how recent progress in bacterial RNA biology may help to accelerate the development of programmable RNA antibiotics for microbiome editing and other applications.
2020-05-27T10:05:35Z
2020-05-27T10:05:35Z
2020-03-17
Review
Other
Mol Microbiol. 2020;113(3):550‐559. doi:10.1111/mmi.14476.
32185839
10.1111/mmi.14476
http://hdl.handle.net/10033/622275
1365-2958
Molecular microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley
113
3
550
559
Molecular microbiology
England
oai:repository.helmholtz-hzi.de:10033/6222792020-06-04T02:28:57Zcom_10033_620968col_10033_621258
Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems.
Jacobsen, Thomas
Yi, Gloria
Al Asafen, Hadel
Jermusyk, Ashley A
Beisel, Chase L
Reeves, Gregory T
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5' vs. 3' untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.
2020-06-03T09:56:11Z
2020-06-03T09:56:11Z
2020-04-30
Article
PLoS One. 2020;15(4):e0232046. Published 2020 Apr 30. doi:10.1371/journal.pone.0232046
32352996
10.1371/journal.pone.0232046
http://hdl.handle.net/10033/622279
1932-6203
PloS one
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
PLOS
15
4
e0232046
PloS one
United States
United States
oai:repository.helmholtz-hzi.de:10033/6223162020-06-27T01:30:32Zcom_10033_620968col_10033_620969
Increasing storage stability of freeze-dried plasma using trehalose.
Brogna, Raffaele
Oldenhof, Harriëtte
Sieme, Harald
Figueiredo, Constança
Kerrinnes, Tobias
Wolkers, Willem F
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Preservation of blood plasma in the dried state would facilitate long-term storage and transport at ambient temperatures, without the need of to use liquid nitrogen tanks or freezers. The aim of this study was to investigate the feasibility of dry preservation of human plasma, using sugars as lyoprotectants, and evaluate macromolecular stability of plasma components during storage. Blood plasma from healthy donors was freeze dried using 0-10% glucose, sucrose, or trehalose, and stored at various temperatures. Differential scanning calorimetry was used to measure the glass transition temperatures of freeze-dried samples. Protein aggregation, the overall protein secondary structure, and oxidative damage were studied under different storage conditions. Differential scanning calorimetry measurements showed that plasma freeze-dried with glucose, sucrose and trehalose have glass transition temperatures of respectively 72±3.4°C, 46±11°C, 15±2.4°C. It was found that sugars diminish freeze-drying induced protein aggregation in a dose-dependent manner, and that a 10% (w/v) sugar concentration almost entirely prevents protein aggregation. Protein aggregation after rehydration coincided with relatively high contents of β-sheet structures in the dried state. Trehalose reduced the rate of protein aggregation during storage at elevated temperatures, and plasma that is freeze- dried plasma with trehalose showed a reduced accumulation of reactive oxygen species and protein oxidation products during storage. In conclusion, freeze-drying plasma with trehalose provides an attractive alternative to traditional cryogenic preservation
2020-06-26T14:16:22Z
2020-06-26T14:16:22Z
2020-06-11
Article
PLoS One. 2020 Jun 11;15(6):e0234502. doi: 10.1371/journal.pone.0234502 eCollection 2020.
32525915
10.1371/journal.pone.0234502
http://hdl.handle.net/10033/622316
1932-6203
PloS one
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
PLOS
15
6
e0234502
PloS one
United States
oai:repository.helmholtz-hzi.de:10033/6223452020-07-10T01:32:28Zcom_10033_620968col_10033_621258
A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs.
Maxwell, Colin S
Jacobsen, Thomas
Marshall, Ryan
Noireaux, Vincent
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Cas12a
Cas9
PAM
TXTL
crRNA
sgRNA
The RNA-guided nucleases derived from the CRISPR-Cas systems in bacteria and archaea have found numerous applications in biotechnology, including genome editing, imaging, and gene regulation. However, the discovery of novel Cas nucleases has outpaced their characterization and subsequent exploitation. A key step in characterizing Cas nucleases is determining which protospacer-adjacent motif (PAM) sequences they recognize. Here, we report advances to an in vitro method based on an E. coli cell-free transcription-translation system (TXTL) to rapidly elucidate PAMs recognized by Cas nucleases. The method obviates the need for cloning Cas nucleases or gRNAs, does not require the purification of protein or RNA, and can be performed in less than a day. To advance our previously published method, we incorporated an internal GFP cleavage control to assess the extent of library cleavage as well as Sanger sequencing of the cleaved library to assess PAM depletion prior to next-generation sequencing. We also detail the methods needed to construct all relevant DNA constructs, and how to troubleshoot the assay. We finally demonstrate the technique by determining PAM sequences recognized by the Neisseria meningitidis Cas9, revealing subtle sequence requirements of this highly specific PAM. The overall method offers a rapid means to identify PAMs recognized by diverse CRISPR nucleases, with the potential to greatly accelerate our ability to characterize and harness novel CRISPR nucleases across their many uses.
2020-07-09T11:02:40Z
2020-07-09T11:02:40Z
2018-02-24
Article
Other
Methods. 2018;143:48-57. doi:10.1016/j.ymeth.2018.02.016.
29486239
10.1016/j.ymeth.2018.02.016
http://hdl.handle.net/10033/622345
1095-9130
Methods (San Diego, Calif.)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
143
48
57
Methods (San Diego, Calif.)
United States
United States
United States
oai:repository.helmholtz-hzi.de:10033/6223552020-07-23T01:24:36Zcom_10033_620968col_10033_621182col_10033_620969col_10033_621391
Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen.
Mika-Gospodorz, Bozena
Giengkam, Suparat
Westermann, Alexander J
Wongsantichon, Jantana
Kion-Crosby, Willow
Chuenklin, Suthida
Wang, Loo Chien
Sunyakumthorn, Piyanate
Sobota, Radoslaw M
Subbian, Selvakumar
Vogel, Jörg
Barquist, Lars
Salje, Jeanne
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium that causes the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning to study the transcriptional architecture of Ot, we find evidence for wide-spread post-transcriptional antisense regulation. Comparing the host response to two clinical isolates, we identify distinct immune response networks for each strain, leading to predictions of relative virulence that are validated in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
2020-07-22T11:25:56Z
2020-07-22T11:25:56Z
2020-07-03
Article
Nat Commun. 2020;11(1):3363. Published 2020 Jul 3. doi:10.1038/s41467-020-17094-8.
32620750
10.1038/s41467-020-17094-8
http://hdl.handle.net/10033/622355
2041-1723
Nature communications
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature Publishing Group
11
1
3363
Nature communications
England
oai:repository.helmholtz-hzi.de:10033/6223632020-07-25T01:29:41Zcom_10033_211390com_10033_620652com_10033_620968col_10033_620666col_10033_620969col_10033_620673col_10033_211409
Seropositivity for pathogens associated with chronic infections is a risk factor for all-cause mortality in the elderly: findings from the Memory and Morbidity in Augsburg Elderly (MEMO) Study.
Zeeb, Marius
Kerrinnes, Tobias
Cicin-Sain, Luka
Guzman, Carlos A
Puppe, Wolfram
Schulz, Thomas F
Peters, Annette
Berger, Klaus
Castell, Stefanie
Karch, André
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
All-cause mortality
Borrelia burgdorferi sensu lato
CMV
Elderly
Helicobacter pylori
Immunostimulation by chronic infection has been linked to an increased risk for different non-communicable diseases, which in turn are leading causes of death in high- and middle-income countries. Thus, we investigated if a positive serostatus for pathogens responsible for common chronic infections is individually or synergistically related to reduced overall survival in community dwelling elderly. We used data of 365 individuals from the German MEMO (Memory and Morbidity in Augsburg Elderly) cohort study with a median age of 73 years at baseline and a median follow-up of 14 years. We examined the effect of a positive serostatus at baseline for selected pathogens associated with chronic infections (Helicobacter pylori, Borrelia burgdorferi sensu lato, Toxoplasma gondii, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1/2, and human herpesvirus 6) on all-cause mortality with multivariable parametric survival models. We found a reduced survival time in individuals with a positive serostatus for Helicobacter pylori (accelerated failure time (AFT) - 15.92, 95% CI - 29.96; - 1.88), cytomegalovirus (AFT - 22.81, 95% CI - 36.41; - 9.22) and Borrelia burgdorferi sensu lato (AFT - 25.25, 95% CI - 43.40; - 7.10), after adjusting for potential confounders. The number of infectious agents an individual was seropositive for had a linear effect on all-cause mortality (AFT per additional infection - 12.42 95% CI - 18.55; - 6.30). Our results suggest an effect of seropositivity for Helicobacter pylori, cytomegalovirus, and Borrelia burgdorferi sensu lato on all-cause mortality in older community dwelling individuals. Further research with larger cohorts and additional biomarkers is required, to assess mediators and molecular pathways of this effect.
2020-07-24T13:30:06Z
2020-07-24T13:30:06Z
2020-07-09
Article
Geroscience. 2020;10.1007/s11357-020-00216-x. doi:10.1007/s11357-020-00216-x.
32648237
10.1007/s11357-020-00216-x
http://hdl.handle.net/10033/622363
2509-2723
GeroScience
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer
GeroScience
Switzerland
oai:repository.helmholtz-hzi.de:10033/6223682020-07-30T02:31:26Zcom_10033_620968col_10033_621182
Plugging Small RNAs into the Network.
Barquist, Lars
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
ncRNA
network inference
sRNA
Small RNAs (sRNAs) have been discovered in every bacterium examined and have been shown to play important roles in the regulation of a diverse range of behaviors, from metabolism to infection. However, despite a wide range of available techniques for discovering and validating sRNA regulatory interactions, only a minority of these molecules have been well characterized. In part, this is due to the nature of posttranscriptional regulation: the activity of an sRNA depends on the state of the transcriptome as a whole, so characterization is best carried out under the conditions in which it is naturally active. In this issue of mSystems, Arrieta-Ortiz and colleagues (M. L. Arrieta-Ortiz, C. Hafemeister, B. Shuster, N. S. Baliga, et al., mSystems 5:e00057-20, 2020, https://doi.org/10.1128/mSystems.00057-20) present a network inference approach based on estimating sRNA activity across transcriptomic compendia. This shows promise not only for identifying new sRNA regulatory interactions but also for pinpointing the conditions in which these interactions occur, providing a new avenue toward functional characterization of sRNAs.
2020-07-29T08:59:21Z
2020-07-29T08:59:21Z
2020-06-02
Article
mSystems. 2020;5(3):e00422-20. Published 2020 Jun 2. doi:10.1128/mSystems.00422-20.
2379-5077
32487744
10.1128/mSystems.00422-20
http://hdl.handle.net/10033/622368
mSystems
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
ASM
5
3
mSystems
United States
oai:repository.helmholtz-hzi.de:10033/6223742020-07-31T01:24:42Zcom_10033_620968col_10033_621182
A decade of advances in transposon-insertion sequencing.
Cain, Amy K
Barquist, Lars
Goodman, Andrew L
Paulsen, Ian T
Parkhill, Julian
van Opijnen, Tim
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications.
2020-07-30T09:41:24Z
2020-07-30T09:41:24Z
2020-06-12
Review
Other
Nat Rev Genet. 2020;1-15. doi:10.1038/s41576-020-0244-x.
32533119
10.1038/s41576-020-0244-x
http://hdl.handle.net/10033/622374
1471-0064
Nature reviews. Genetics
PMC7291929
en
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291929/
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer Nature
Nature reviews. Genetics
United States
England
oai:repository.helmholtz-hzi.de:10033/6223902020-08-06T02:29:41Zcom_10033_620968col_10033_620969
Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression.
Parhi, Lishay
Alon-Maimon, Tamar
Sol, Asaf
Nejman, Deborah
Shhadeh, Amjad
Fainsod-Levi, Tanya
Yajuk, Olga
Isaacson, Batya
Abed, Jawad
Maalouf, Naseem
Nissan, Aviram
Sandbank, Judith
Yehuda-Shnaidman, Einav
Ponath, Falk
Vogel, Jörg
Mandelboim, Ofer
Granot, Zvi
Straussman, Ravid
Bachrach, Gilad
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Fusobacterium nucleatum is an oral anaerobe recently found to be prevalent in human colorectal cancer (CRC) where it is associated with poor treatment outcome. In mice, hematogenous F. nucleatum can colonize CRC tissue using its lectin Fap2, which attaches to tumor-displayed Gal-GalNAc. Here, we show that Gal-GalNAc levels increase as human breast cancer progresses, and that occurrence of F. nucleatum gDNA in breast cancer samples correlates with high Gal-GalNAc levels. We demonstrate Fap2-dependent binding of the bacterium to breast cancer samples, which is inhibited by GalNAc. Intravascularly inoculated Fap2-expressing F. nucleatum ATCC 23726 specifically colonize mice mammary tumors, whereas Fap2-deficient bacteria are impaired in tumor colonization. Inoculation with F. nucleatum suppresses accumulation of tumor infiltrating T cells and promotes tumor growth and metastatic progression, the latter two of which can be counteracted by antibiotic treatment. Thus, targeting F. nucleatum or Fap2 might be beneficial during treatment of breast cancer.
2020-08-05T14:38:43Z
2020-08-05T14:38:43Z
2020-06-26
Article
Nat Commun. 2020;11(1):3259. Published 2020 Jun 26. doi:10.1038/s41467-020-16967-2.
32591509
10.1038/s41467-020-16967-2
http://hdl.handle.net/10033/622390
2041-1723
Nature communications
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature Research
11
1
3259
Nature communications
England
oai:repository.helmholtz-hzi.de:10033/6223922020-08-07T01:36:05Zcom_10033_620968col_10033_620969col_10033_621391
Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads.
Prezza, Gianluca
Heckel, Tobias
Dietrich, Sascha
Homberger, Christina
Westermann, Alexander J
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteroides
CRISPR
Cas9
DASH
Salmonella
bacterial RNA-seq
ribosomal RNA
A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative nonribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. To overcome this, we adopted DASH (depletion of abundant sequences by hybridization), initially developed for eukaryotic cells, to improve both the sensitivity and depth of bacterial RNA-seq. DASH uses the Cas9 nuclease to remove unwanted cDNA sequences prior to library amplification. We report the design, evaluation, and optimization of DASH experiments for standard bacterial short-read sequencing approaches, including software for automated guide RNA (gRNA) design for Cas9-mediated cleavage in bacterial rDNA sequences. Using these gRNA pools, we effectively removed rRNA reads (56%-86%) in RNA-seq libraries from two different model bacteria, the Gram-negative pathogen Salmonella enterica and the anaerobic gut commensal Bacteroides thetaiotaomicron DASH works robustly, even with subnanogram amounts of input RNA. Its efficiency, high sensitivity, ease of implementation, and low cost (∼$5 per sample) render DASH an attractive alternative to rRNA removal protocols, in particular for material-constrained studies where conventional ribodepletion techniques fail.
2020-08-06T14:07:16Z
2020-08-06T14:07:16Z
2020-04-28
Article
RNA. 2020;26(8):1069-1078. doi:10.1261/rna.075945.120.
32345633
10.1261/rna.075945.120
http://hdl.handle.net/10033/622392
1469-9001
RNA (New York, N.Y.)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Cold Spring Harbor Laboratory Press
26
8
1069
1078
RNA (New York, N.Y.)
United States
oai:repository.helmholtz-hzi.de:10033/6224312020-09-10T01:49:53Zcom_10033_620968col_10033_620970
Letter by Cochain et al Regarding Article, "Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models".
Cochain, Clément
Saliba, Antoine-Emmanuel
Zernecke, Alma
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
2020-09-09T12:05:25Z
2020-09-09T12:05:25Z
Article
Other
Circ Res. 2018;123(11):e48-e49. doi:10.1161/CIRCRESAHA.118.314120.
30571470
10.1161/CIRCRESAHA.118.314120
http://hdl.handle.net/10033/622431
1524-4571
Circulation research
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Lippincott, Williams & Wilkins
123
11
e48
e49
Circulation research
United States
oai:repository.helmholtz-hzi.de:10033/6224352020-09-11T04:23:37Zcom_10033_620618com_10033_620968col_10033_620969col_10033_620621
Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection.
Groma, Michaela
Horst, Sarah A
Das, Sudip
Huettel, Bruno
Klepsch, Maximilian
Rudel, Thomas
Medina, Eva
Fraunholz, Martin
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Staphylococcus aureus
metabolic adaptation
secondary site infection
transcriptional regulation
Staphylococcus aureus is a common cause of bacteremia that can lead to severe complications once the bacteria exit the bloodstream and establish infection in secondary organs. Despite its clinical relevance, little is known about the bacterial factors facilitating the development of these metastatic infections. Here, we used an S. aureus transposon mutant library coupled to transposon insertion sequencing (Tn-Seq) to identify genes that are critical for efficient bacterial colonization of secondary organs in a murine model of metastatic bloodstream infection. Our transposon screen identified a LysR-type transcriptional regulator (LTTR), which was required for efficient colonization of secondary organs such as the kidneys in infected mice. The critical role of LTTR in secondary organ colonization was confirmed using an isogenic mutant deficient in the expression of LTTR. To identify the set of genes controlled by LTTR, we used an S. aureus strain carrying the LTTR gene in an inducible expression plasmid. Gene expression analysis upon induction of LTTR showed increased transcription of genes involved in branched-chain amino acid biosynthesis, a methionine sulfoxide reductase, and a copper transporter as well as decreased transcription of genes coding for urease and components of pyrimidine nucleotides. Furthermore, we show that transcription of LTTR is repressed by glucose, is induced under microaerobic conditions, and required trace amounts of copper ions. Our data thus pinpoints LTTR as an important element that enables a rapid adaptation of S. aureus to the changing host microenvironment.IMPORTANCEStaphylococcus aureus is an important pathogen that can disseminate via the bloodstream and establish metastatic infections in distant organs. To achieve a better understanding of the bacterial factors facilitating the development of these metastatic infections, we used in this study a Staphylococcus aureus transposon mutant library in a murine model of intravenous infection, where bacteria first colonize the liver as the primary infection site and subsequently progress to secondary sites such as the kidney and bones. We identified a novel LysR-type transcriptional regulator (LTTR), which was specifically required by S. aureus for efficient colonization of secondary organs. We also determined the transcriptional activation as well as the regulon of LTTR, which suggests that this regulator is involved in the metabolic adaptation of S. aureus to the host microenvironment found in secondary infection sites.
2020-09-10T08:38:13Z
2020-09-10T08:38:13Z
2020-08-25
Article
mBio. 2020;11(4):e01646-20. Published 2020 Aug 25.
32843554
10.1128/mBio.01646-20
http://hdl.handle.net/10033/622435
2150-7511
mBio
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
ASM
11
4
mBio
United States
oai:repository.helmholtz-hzi.de:10033/6224572020-09-25T03:25:00Zcom_10033_620968col_10033_620970col_10033_620969
LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, Nikolaus
Almouzni, Geneviève
Gorski, Stanislaw A
Aerts, Stein
Amit, Ido
Bertero, Michela G
Bock, Christoph
Bredenoord, Annelien L
Cavalli, Giacomo
Chiocca, Susanna
Clevers, Hans
De Strooper, Bart
Eggert, Angelika
Ellenberg, Jan
Fernández, Xosé M
Figlerowicz, Marek
Gasser, Susan M
Hubner, Norbert
Kjems, Jørgen
Knoblich, Jürgen A
Krabbe, Grietje
Lichter, Peter
Linnarsson, Sten
Marine, Jean-Christophe
Marioni, John
Marti-Renom, Marc A
Netea, Mihai G
Nickel, Dörthe
Nollmann, Marcelo
Novak, Halina R
Parkinson, Helen
Piccolo, Stefano
Pinheiro, Inês
Pombo, Ana
Popp, Christian
Reik, Wolf
Roman-Roman, Sergio
Rosenstiel, Philip
Schultze, Joachim L
Stegle, Oliver
Tanay, Amos
Testa, Giuseppe
Thanos, Dimitris
Theis, Fabian J
Torres-Padilla, Maria-Elena
Valencia, Alfonso
Vallot, Céline
van Oudenaarden, Alexander
Vidal, Marie
Voet, Thierry
TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany.
LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
2020-09-24T13:10:04Z
2020-09-24T13:10:04Z
2020-09-07
Article
Other
Nature. 2020 Sep 7. doi: 10.1038/s41586-020-2715-9. Epub ahead of print.
32894860
10.1038/s41586-020-2715-9
http://hdl.handle.net/10033/622457
1476-4687
Nature
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature publishing group(NPG)
Nature
England
oai:repository.helmholtz-hzi.de:10033/6224592021-07-29T12:44:12Zcom_10033_620968col_10033_621258
A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9.
Collias, D
Leenay, R T
Slotkowski, R A
Zuo, Z
Collins, S P
McGirr, B A
Liu, J
Beisel, C L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CRISPR technologies have overwhelmingly relied on the Streptococcus pyogenes Cas9 (SpyCas9), with its consensus NGG and less preferred NAG and NGA protospacer-adjacent motifs (PAMs). Here, we report that SpyCas9 also recognizes sequences within an N(A/C/T)GG motif. These sequences were identified on the basis of preferential enrichment in a growth-based screen in Escherichia coli. DNA binding, cleavage, and editing assays in bacteria and human cells validated recognition, with activities paralleling those for NAG(A/C/T) PAMs and dependent on the first two PAM positions. Molecular-dynamics simulations and plasmid-clearance assays with mismatch-intolerant variants supported induced-fit recognition of an extended PAM by SpyCas9 rather than recognition of NGG with a bulged R-loop. Last, the editing location for SpyCas9-derived base editors could be shifted by one nucleotide by selecting between (C/T)GG and adjacent N(C/T)GG PAMs. SpyCas9 and its enhanced variants thus recognize a larger repertoire of PAMs, with implications for precise editing, off-target predictions, and CRISPR-based immunity.
2020-09-25T09:55:08Z
2020-09-25T09:55:08Z
2020-07-15
Article
Sci Adv. 2020 Jul 15;6(29):eabb4054. doi: 10.1126/sciadv.abb4054.
32832642
10.1126/sciadv.abb4054
http://hdl.handle.net/10033/622459
2375-2548
Science advances
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
AAAS
6
29
eabb4054
Science advances
United States
oai:repository.helmholtz-hzi.de:10033/6224882020-09-29T03:08:56Zcom_10033_620968col_10033_620970col_10033_620969
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria.
Imdahl, Fabian
Vafadarnejad, Ehsan
Homberger, Christina
Saliba, Antoine-Emmanuel
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed1. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes1, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions2. Fluorescent reporter constructs have played a pivotal role in deciphering heterogeneous gene expression within bacterial populations3 but have been limited to recording the activity of single genes in a few genetically tractable model species, whereas the vast majority of bacteria remain difficult to engineer and/or even to cultivate. Single-cell transcriptomics is revolutionizing the analysis of phenotypic cell-to-cell variation in eukaryotes, but technical hurdles have prevented its robust application to prokaryotes. Here, using an improved poly(A)-independent single-cell RNA-sequencing protocol, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria across all RNA classes and genomic regions. These transcriptomes provide important reference points for single-cell RNA-sequencing of other bacterial species, mixed microbial communities and host-pathogen interactions.
2020-09-28T13:29:01Z
2020-09-28T13:29:01Z
2020-08-17
Article
Nat Microbiol. 2020 Oct;5(10):1202-1206. doi: 10.1038/s41564-020-0774-1. Epub 2020 Aug 17. PMID: 32807892.
32807892
10.1038/s41564-020-0774-1
http://hdl.handle.net/10033/622488
2058-5276
Nature microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature research
5
10
1202
1206
Nature microbiology
England
oai:repository.helmholtz-hzi.de:10033/6224922021-07-29T12:44:12Zcom_10033_620968col_10033_621258
Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination.
Collins, Scott P
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Jin et al. (2020) engineered new variants of CRISPR base editors that make precise genomic edits in rice protoplasts while minimizing untargeted mutagenesis.
2020-10-01T09:39:08Z
2020-10-01T09:39:08Z
2020-09-03
Article
Other
Mol Cell. 2020 Sep 3;79(5):703-704. doi: 10.1016/j.molcel.2020.07.030.
32888434
10.1016/j.molcel.2020.07.030
http://hdl.handle.net/10033/622492
1097-4164
Molecular cell
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier
79
5
703
704
Molecular cell
United States
oai:repository.helmholtz-hzi.de:10033/6225002020-10-09T01:33:48Zcom_10033_620968col_10033_621236
An RNA-centric view on gut Bacteroidetes.
Ryan, Daniel
Prezza, Gianluca
Westermann, Alexander J
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteroides
CRISPR-Cas
GibS
microbiota
noncoding RNA
small RNA
Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.
2020-10-08T12:35:36Z
2020-10-08T12:35:36Z
2020-09-24
Article
Other
Biol Chem. 2020 Sep 24:/j/bchm.ahead-of-print/hsz-2020-0230/hsz-2020-0230.xml. doi: 10.1515/hsz-2020-0230. Epub ahead of print.
32881707
10.1515/hsz-2020-0230
http://hdl.handle.net/10033/622500
1437-4315
Biological chemistry
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Walter de Gruyter
Biological chemistry
Germany
oai:repository.helmholtz-hzi.de:10033/6225032020-10-09T01:34:23Zcom_10033_620597com_10033_621852com_10033_620968com_10033_620636col_10033_621853col_10033_620970col_10033_620969col_10033_620598col_10033_620638
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping, Jonas
Reusch, Nico
Paclik, Daniela
Baßler, Kevin
Schlickeiser, Stephan
Zhang, Bowen
Krämer, Benjamin
Krammer, Tobias
Brumhard, Sophia
Bonaguro, Lorenzo
De Domenico, Elena
Wendisch, Daniel
Grasshoff, Martin
Kapellos, Theodore S
Beckstette, Michael
Pecht, Tal
Saglam, Adem
Dietrich, Oliver
Mei, Henrik E
Schulz, Axel R
Conrad, Claudia
Kunkel, Désirée
Vafadarnejad, Ehsan
Xu, Cheng-Jian
Horne, Arik
Herbert, Miriam
Drews, Anna
Thibeault, Charlotte
Pfeiffer, Moritz
Hippenstiel, Stefan
Hocke, Andreas
Müller-Redetzky, Holger
Heim, Katrin-Moira
Machleidt, Felix
Uhrig, Alexander
Bosquillon de Jarcy, Laure
Jürgens, Linda
Stegemann, Miriam
Glösenkamp, Christoph R
Volk, Hans-Dieter
Goffinet, Christine
Landthaler, Markus
Wyler, Emanuel
Georg, Philipp
Schneider, Maria
Dang-Heine, Chantip
Neuwinger, Nick
Kappert, Kai
Tauber, Rudolf
Corman, Victor
Raabe, Jan
Kaiser, Kim Melanie
Vinh, Michael To
Rieke, Gereon
Meisel, Christian
Ulas, Thomas
Becker, Matthias
Geffers, Robert
Witzenrath, Martin
Drosten, Christian
Suttorp, Norbert
von Kalle, Christof
Kurth, Florian
Händler, Kristian
Schultze, Joachim L
Aschenbrenner, Anna C
Li, Yang
Nattermann, Jacob
Sawitzki, Birgit
Saliba, Antoine-Emmanuel
Sander, Leif Erik
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.; HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.; CiiM, Zentrum für individualisierte Infektionsmedizin, Feodor-Lynen-Str.7, 30625 Hannover.; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
COVID-19
SARS-CoV-2
dysfunctional neutrophils
emergency myelopoiesis
immune profiling
mass cytometry
monocytes
neutrophils
scRNA-seq
Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
2020-10-08T14:17:42Z
2020-10-08T14:17:42Z
2020-08-05
Article
Other
Cell. 2020 Sep 17;182(6):1419-1440.e23. doi: 10.1016/j.cell.2020.08.001.
32810438
10.1016/j.cell.2020.08.001
http://hdl.handle.net/10033/622503
1097-4172
Cell
en
info:eu-repo/grantAgreement/EC/H2020/733100
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier /Cell Press)
182
6
1419
1440.e23
Cell
United States
oai:repository.helmholtz-hzi.de:10033/6225092020-10-14T01:39:04Zcom_10033_620968col_10033_621182col_10033_620969
Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing.
Chihara, Kotaro
Bischler, Thorsten
Barquist, Lars
Monzon, Vivian A
Noda, Naohiro
Vogel, Jörg
Tsuneda, Satoshi
CLIP-seq
Hfq
Pseudomonas aeruginosa
biofilms
noncoding RNA
Bacterial small noncoding RNAs (sRNAs) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the Pseudomonas aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5' untranslated regions (UTRs) and sRNAs and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that the association of sRNAs with Hfq is primarily a function of their expression levels, strongly supporting the notion that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of posttranscriptional regulation in P. aeruginosaIMPORTANCE The Gram-negative bacterium P. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. Although the presence of a large number of putative sRNAs and widely conserved RNA chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of RNA chaperones such as Hfq in the P. aeruginosa transcriptome, especially under different environmental conditions. Here, we characterize Hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. A combinatorial comparative CLIP-seq and total RNA-seq approach uncovered condition-dependent association of RNAs with Hfq in vivo and expands the potential direct regulatory targets of Hfq in the P. aeruginosa transcriptome.
2020-10-12T15:14:17Z
2020-10-12T15:14:17Z
2019-12-03
Article
2379-5077
31796567
10.1128/mSystems.00590-19
http://hdl.handle.net/10033/622509
mSystems
en
4
6
mSystems
United States
oai:repository.helmholtz-hzi.de:10033/6225172020-10-17T01:32:29Zcom_10033_620968col_10033_620969
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.
Hör, Jens
Di Giorgio, Silvia
Gerovac, Milan
Venturini, Elisa
Förstner, Konrad U
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ∼85% of all E. coli transcripts and ∼49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacterium E. coli through providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.
2020-10-16T11:10:17Z
2020-10-16T11:10:17Z
2020-08-19
Article
Nucleic Acids Res. 2020 Sep 18;48(16):9301-9319. doi: 10.1093/nar/gkaa676.
32813020
10.1093/nar/gkaa676
http://hdl.handle.net/10033/622517
1362-4962
Nucleic acids research
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford University Press
48
16
9301
9319
Nucleic acids research
England
oai:repository.helmholtz-hzi.de:10033/6225152020-10-17T01:32:11Zcom_10033_620857com_10033_620618com_10033_620968col_10033_620969col_10033_621236col_10033_620858col_10033_620619
Amidochelocardin Overcomes Resistance Mechanisms Exerted on Tetracyclines and Natural Chelocardin.
Hennessen, Fabienne
Miethke, Marcus
Zaburannyi, Nestor
Loose, Maria
Lukežič, Tadeja
Bernecker, Steffen
Hüttel, Stephan
Jansen, Rolf
Schmiedel, Judith
Fritzenwanker, Moritz
Imirzalioglu, Can
Vogel, Jörg
Westermann, Alexander J
Hesterkamp, Thomas
Stadler, Marc
Wagenlehner, Florian
Petković, Hrvoje
Herrmann, Jennifer
Müller, Rolf
HIPS, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Universitätscampus E8.1 66123 Saarbrücken, Germany.; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.; HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
AcrAB-TolC efflux pump
atypical tetracyclines
broad-spectrum antibiotics
chelocardins
clinical isolates
mechanism of resistance
resistance-breaking properties
urinary tract infection (UTI)
uropathogens
The reassessment of known but neglected natural compounds is a vital strategy for providing novel lead structures urgently needed to overcome antimicrobial resistance. Scaffolds with resistance-breaking properties represent the most promising candidates for a successful translation into future therapeutics. Our study focuses on chelocardin, a member of the atypical tetracyclines, and its bioengineered derivative amidochelocardin, both showing broad-spectrum antibacterial activity within the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) panel. Further lead development of chelocardins requires extensive biological and chemical profiling to achieve favorable pharmaceutical properties and efficacy. This study shows that both molecules possess resistance-breaking properties enabling the escape from most common tetracycline resistance mechanisms. Further, we show that these compounds are potent candidates for treatment of urinary tract infections due to their in vitro activity against a large panel of multidrug-resistant uropathogenic clinical isolates. In addition, the mechanism of resistance to natural chelocardin was identified as relying on efflux processes, both in the chelocardin producer Amycolatopsis sulphurea and in the pathogen Klebsiella pneumoniae. Resistance development in Klebsiella led primarily to mutations in ramR, causing increased expression of the acrAB-tolC efflux pump. Most importantly, amidochelocardin overcomes this resistance mechanism, revealing not only the improved activity profile but also superior resistance-breaking properties of this novel antibacterial compound.
2020-10-16T09:20:01Z
2020-10-16T09:20:01Z
2020-09-18
Article
Antibiotics (Basel). 2020 Sep 18;9(9):E619. doi: 10.3390/antibiotics9090619.
2079-6382
32962088
10.3390/antibiotics9090619
http://hdl.handle.net/10033/622515
Antibiotics (Basel, Switzerland)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
MDPI
9
9
Antibiotics (Basel, Switzerland)
Switzerland
oai:repository.helmholtz-hzi.de:10033/6225302020-10-31T02:02:47Zcom_10033_620968col_10033_620969
Reprogramming of host glutamine metabolism during Chlamydia trachomatis infection and its key role in peptidoglycan synthesis.
Rajeeve, Karthika
Vollmuth, Nadine
Janaki-Raman, Sudha
Wulff, Thomas F
Baluapuri, Apoorva
Dejure, Francesca R
Huber, Claudia
Fink, Julian
Schmalhofer, Maximilian
Schmitz, Werner
Sivadasan, Rajeeve
Wolf, Elmar
Eisenreich, Wolfgang
Schulze, Almut
Seibel, Jürgen
Rudel, Thomas
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Obligate intracellular bacteria such as Chlamydia trachomatis undergo a complex developmental cycle between infectious, non-replicative elementary-body and non-infectious, replicative reticulate-body forms. Elementary bodies transform to reticulate bodies shortly after entering a host cell, a crucial process in infection, initiating chlamydial replication. As Chlamydia fail to replicate outside the host cell, it is unknown how the replicative part of the developmental cycle is initiated. Here we show, using a cell-free approach in axenic media, that the uptake of glutamine by the bacteria is crucial for peptidoglycan synthesis, which has a role in Chlamydia replication. The increased requirement for glutamine in infected cells is satisfied by reprogramming the glutamine metabolism in a c-Myc-dependent manner. Glutamine is effectively taken up by the glutamine transporter SLC1A5 and metabolized via glutaminase. Interference with this metabolic reprogramming limits the growth of Chlamydia. Intriguingly, Chlamydia failed to produce progeny in SLC1A5-knockout organoids and mice. Thus, we report on the central role of glutamine for the development of an obligate intracellular pathogenic bacterium and the reprogramming of host glutamine metabolism, which may provide a basis for innovative anti-infection strategies.
2020-10-23T09:50:31Z
2020-10-23T09:50:31Z
2020-08-03
Article
Nat Microbiol. 2020 Nov;5(11):1390-1402. doi: 10.1038/s41564-020-0762-5.
32747796
10.1038/s41564-020-0762-5
http://hdl.handle.net/10033/622530
2058-5276
Nature microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature publishing group (NPG)
5
11
1390
1402
Nature microbiology
England
oai:repository.helmholtz-hzi.de:10033/6225352020-11-04T04:37:17Zcom_10033_620968col_10033_620969
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein.
Gerovac, Milan
El Mouali, Youssef
Kuper, Jochen
Kisker, Caroline
Barquist, Lars
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CsrA
FinO/ProQ protein
FopA
Hfq
RNA-binding protein
RNase
RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq, and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalog of microbial RBPs.
2020-10-26T10:55:18Z
2020-10-26T10:55:18Z
2020-07-09
Article
RNA. 2020 Oct;26(10):1448-1463. doi: 10.1261/rna.076992.120.
32646969
10.1261/rna.076992.120
http://hdl.handle.net/10033/622535
1469-9001
RNA (New York, N.Y.)
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Cold Spring Habor Laboratory Press and RNA Society
26
10
1448
1463
RNA (New York, N.Y.)
United States
oai:repository.helmholtz-hzi.de:10033/6225362020-11-04T04:37:32Zcom_10033_620968col_10033_620969
Murine cytomegaloviruses m139 targets DDX3 to curtail interferon production and promote viral replication.
Puhach, Olha
Ostermann, Eleonore
Krisp, Christoph
Frascaroli, Giada
Schlüter, Hartmut
Brinkmann, Melanie M
Brune, Wolfram
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Cytomegaloviruses (CMV) infect many different cell types and tissues in their respective hosts. Monocytes and macrophages play an important role in CMV dissemination from the site of infection to target organs. Moreover, macrophages are specialized in pathogen sensing and respond to infection by secreting cytokines and interferons. In murine cytomegalovirus (MCMV), a model for human cytomegalovirus, several genes required for efficient replication in macrophages have been identified, but their specific functions remain poorly understood. Here we show that MCMV m139, a gene of the conserved US22 gene family, encodes a protein that interacts with the DEAD box helicase DDX3, a protein involved in pathogen sensing and interferon (IFN) induction, and the E3 ubiquitin ligase UBR5. DDX3 and UBR5 also participate in the transcription, processing, and translation of a subset of cellular mRNAs. We show that m139 inhibits DDX3-mediated IFN-α and IFN-β induction and is necessary for efficient viral replication in bone-marrow derived macrophages. In vivo, m139 is crucial for viral dissemination to local lymph nodes and to the salivary glands. An m139-deficient MCMV also replicated to lower titers in SVEC4-10 endothelial cells. This replication defect was not accompanied by increased IFN-β transcription, but was rescued by knockout of either DDX3 or UBR5. Moreover, m139 co-localized with DDX3 and UBR5 in viral replication compartments in the cell nucleus. These results suggest that m139 inhibits DDX3-mediated IFN production in macrophages and antagonizes DDX3 and UBR5-dependent functions related to RNA metabolism in endothelial cells.
2020-10-26T12:41:10Z
2020-10-26T12:41:10Z
2020-10-08
Article
PLoS Pathog. 2020 Oct 8;16(10):e1008546. doi: 10.1371/journal.ppat.1008546.
33031466
10.1371/journal.ppat.1008546
http://hdl.handle.net/10033/622536
1553-7374
PLoS pathogens
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
PLOS
16
10
e1008546
PLoS pathogens
United States
oai:repository.helmholtz-hzi.de:10033/6225642021-07-29T12:44:12Zcom_10033_620968col_10033_621258
Rapid Testing of CRISPR Nucleases and Guide RNAs in an Cell-Free Transcription-Translation System.
Marshall, Ryan
Beisel, Chase L
Noireaux, Vincent
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
We present a protocol to rapidly test DNA binding and cleavage activity by CRISPR nucleases using cell-free transcription-translation (TXTL). Nuclease activity is assessed by adding DNA encoding a nuclease, a guide RNA, and a targeted reporter to a TXTL reaction and by measuring the fluorescence for several h. The reactions, performed in a few microliters, allow for parallel testing of many nucleases and guide RNAs. The protocol includes representative results for (d)Cas9 from Streptococcus pyogenes targeting a GFP reporter gene. For complete information on the generation and use of this protocol, please refer to the paper by Marshall et al. (2018).
2020-11-09T14:19:21Z
2020-11-09T14:19:21Z
2020-06-03
Article
STAR Protoc. 2020 Jun 3;1(1):100003. doi: 10.1016/j.xpro.2019.100003.
33111065
10.1016/j.xpro.2019.100003
http://hdl.handle.net/10033/622564
2666-1667
STAR protocols
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Elsevier (CellPress)
1
1
100003
STAR protocols
United States
oai:repository.helmholtz-hzi.de:10033/6225652020-11-10T01:37:39Zcom_10033_620968col_10033_620969
Introducing differential RNA-seq mapping to track the early infection phase for phage ɸKZ.
Wicke, Laura
Ponath, Falk
Coppens, Lucas
Gerovac, Milan
Lavigne, Rob
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Pseudomonas aeruginosa
Bacteriophage ɸKZ
dRNA-seq
differential expression
phage-host interaction
transcription start site
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage - alone or together with its infected host - is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage-host interactions.
2020-11-09T14:37:23Z
2020-11-09T14:37:23Z
2020-10-25
Article
RNA Biol. 2020 Oct 25:1-12. doi: 10.1080/15476286.2020.1827785.
33103565
10.1080/15476286.2020.1827785
http://hdl.handle.net/10033/622565
1555-8584
RNA biology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Taylor & Francis
1
12
RNA biology
United States
oai:repository.helmholtz-hzi.de:10033/6226062020-12-02T01:41:21Zcom_10033_620968col_10033_620969
Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level.
Friedel, Caroline C
Whisnant, Adam W
Djakovic, Lara
Rutkowski, Andrzej J
Friedl, Marie-Sophie
Kluge, Michael
Williamson, James C
Sai, Somesh
Vidal, Ramon Oliveira
Sauer, Sascha
Hennig, Thomas
Grothey, Arnhild
Milić, Andrea
Prusty, Bhupesh K
Lehner, Paul J
Matheson, Nicholas J
Erhard, Florian
Dölken, Lars
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Herpes simplex virus 1 (HSV-1) induces a profound host shut-off during lytic infection. The virion host shut-off (vhs) protein plays a key role in this process by efficiently cleaving host and viral mRNAs. Furthermore, the onset of viral DNA replication is accompanied by a rapid decline in host transcriptional activity. To dissect relative contributions of both mechanisms and elucidate gene-specific host transcriptional responses throughout the first 8h of lytic HSV-1 infection, we employed RNA-seq of total, newly transcribed (4sU-labelled) and chromatin-associated RNA in wild-type (WT) and Δvhs infection of primary human fibroblasts. Following virus entry, vhs activity rapidly plateaued at an elimination rate of around 30% of cellular mRNAs per hour until 8h p.i. In parallel, host transcriptional activity dropped to 10-20%. While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA and was surprisingly concordant between WT and Δvhs infection. Both induced strong transcriptional up-regulation of a small subset of genes that were poorly expressed prior to infection but already primed by H3K4me3 histone marks at their promoters. Most interestingly, analysis of chromatin-associated RNA revealed vhs-nuclease-activity-dependent transcriptional down-regulation of at least 150 cellular genes, in particular of many integrin adhesome and extracellular matrix components. This was accompanied by a vhs-dependent reduction in protein levels by 8h p.i. for many of these genes. In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8h of lytic HSV-1 infection.IMPORTANCE The HSV-1 virion host shut-off (vhs) protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. In this study, we model and quantify changes in vhs activity as well as virus-induced global loss of host transcriptional activity during productive HSV-1 infection. In general, HSV-1-induced alterations in total RNA levels were dominated by these two global effects. In contrast, chromatin-associated RNA depicted gene-specific transcriptional changes. This revealed highly concordant transcriptional changes in WT and Δvhs infection, confirmed DUX4 as a key transcriptional regulator in HSV-1 infection and depicted vhs-dependent, transcriptional down-regulation of the integrin adhesome and extracellular matrix components. The latter explained seemingly gene-specific effects previously attributed to vhs-mediated mRNA degradation and resulted in a concordant loss in protein levels by 8h p.i. for many of the respective genes.
2020-11-24T12:15:46Z
2020-11-24T12:15:46Z
2020-11-04
Article
J Virol. 2020 Nov 4:JVI.01399-20. doi: 10.1128/JVI.01399-20.
33148793
10.1128/JVI.01399-20
http://hdl.handle.net/10033/622606
1098-5514
Journal of virology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Society for Microbilogy (ASM)
Journal of virology
United States
oai:repository.helmholtz-hzi.de:10033/6226172021-07-29T12:44:12Zcom_10033_620968col_10033_621258
Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides.
Orsi, Enrico
Mougiakos, Ioannis
Post, Wilbert
Beekwilder, Jules
Dompè, Marco
Eggink, Gerrit
van der Oost, John
Kengen, Servé W M
Weusthuis, Ruud A
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Growth-independent production
Isoprenoid biosynthesis
MEP
MVA
PHB
Rhodobacter sphaeroides
Microbial cell factories are usually engineered and employed for cultivations that combine product synthesis with growth. Such a strategy inevitably invests part of the substrate pool towards the generation of biomass and cellular maintenance. Hence, engineering strains for the formation of a specific product under non-growth conditions would allow to reach higher product yields. In this respect, isoprenoid biosynthesis represents an extensively studied example of growth-coupled synthesis with rather unexplored potential for growth-independent production. Rhodobacter sphaeroides is a model bacterium for isoprenoid biosynthesis, either via the native 2-methyl-d-erythritol 4-phosphate (MEP) pathway or the heterologous mevalonate (MVA) pathway, and for poly-β-hydroxybutyrate (PHB) biosynthesis.
2020-11-26T15:09:52Z
2020-11-26T15:09:52Z
2020-07-13
Article
Biotechnol Biofuels. 2020 Jul 13;13:123. doi: 10.1186/s13068-020-01765-1.
1754-6834
32684976
10.1186/s13068-020-01765-1
http://hdl.handle.net/10033/622617
Biotechnology for biofuels
en
info:eu-repo/grantAgreement/EC/H2020/834279
http://creativecommons.org/licenses/by/4.0/
openAccess
Attribution 4.0 International
BMC
13
123
Biotechnology for biofuels
England
oai:repository.helmholtz-hzi.de:10033/6226302020-12-03T01:45:07Zcom_10033_620968col_10033_620969
Trans-Acting Small RNAs and Their Effects on Gene Expression in and Escherichia coli and Salmonella.
Hör, Jens
Matera, Gianluca
Vogel, Jörg
Gottesman, Susan
Storz, Gisela
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.
2020-12-02T15:55:36Z
2020-12-02T15:55:36Z
2020-03-20
Article
EcoSal Plus. 2020 Mar;9(1):10.1128/ecosalplus.ESP-0030-2019. doi: 10.1128/ecosalplus.ESP-0030-2019.
32213244
10.1128/ecosalplus.ESP-0030-2019
http://hdl.handle.net/10033/622630
2324-6200
EcoSal Plus
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
ASM
9
1
EcoSal Plus
United States
United States
oai:repository.helmholtz-hzi.de:10033/6226362020-12-09T01:38:51Zcom_10033_620652com_10033_620968com_10033_620601col_10033_620969col_10033_620673col_10033_620602
Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model.
Seelbinder, Bastian
Wallstabe, Julia
Marischen, Lothar
Weiss, Esther
Wurster, Sebastian
Page, Lukas
Löffler, Claudia
Bussemer, Lydia
Schmitt, Anna-Lena
Wolf, Thomas
Linde, Jörg
Cicin-Sain, Luka
Becker, Jennifer
Kalinke, Ulrich
Vogel, Jörg
Panagiotou, Gianni
Einsele, Hermann
Westermann, Alexander J
Schäuble, Sascha
Loeffler, Juergen
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Aspergillus
cross-species interaction
cytomegalovirus
dendritic cells
host response
pulmonary infections
synergy
transcriptional networks
triple RNA-seq
High-throughput RNA sequencing (RNA-seq) is routinely applied to study diverse biological processes; however, when performed separately on interacting organisms, systemic noise intrinsic to RNA extraction, library preparation, and sequencing hampers the identification of cross-species interaction nodes. Here, we develop triple RNA-seq to simultaneously detect transcriptomes of monocyte-derived dendritic cells (moDCs) infected with the frequently co-occurring pulmonary pathogens Aspergillus fumigatus and human cytomegalovirus (CMV). Comparing expression patterns after co-infection with those after single infections, our data reveal synergistic effects and mutual interferences between host responses to the two pathogens. For example, CMV attenuates the fungus-mediated activation of pro-inflammatory cytokines through NF-κB (nuclear factor κB) and NFAT (nuclear factor of activated T cells) cascades, while A. fumigatus impairs viral clearance by counteracting viral nucleic acid-induced activation of type I interferon signaling. Together, the analytical power of triple RNA-seq proposes molecular hubs in the differential moDC response to fungal/viral single infection or co-infection that contribute to our understanding of the etiology and, potentially, clearance of post-transplant infections.
2020-12-08T14:54:28Z
2020-12-08T14:54:28Z
2020-11-17
Article
Cell Rep. 2020 Nov 17;33(7):108389. doi: 10.1016/j.celrep.2020.108389.
33207195
10.1016/j.celrep.2020.108389
http://hdl.handle.net/10033/622636
2211-1247
Cell reports
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Elsevier (Cell Press)
33
7
108389
Cell reports
United States
oai:repository.helmholtz-hzi.de:10033/6226712021-02-02T14:30:01Zcom_10033_620968col_10033_621182col_10033_620969
Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
Michaux, Charlotte
Hansen, Elisabeth E
Jenniches, Laura
Gerovac, Milan
Barquist, Lars
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Gram-positive bacteria
RNA-seq
post-transcriptional regulation
sRNA atlas
transcription start sites
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5' and 3' UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
2021-01-11T14:34:31Z
2021-01-11T14:34:31Z
2020-11-25
Article
33324581
10.3389/fcimb.2020.600325
http://hdl.handle.net/10033/622671
2235-2988
Frontiers in cellular and infection microbiology
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Frontiers
10
600325
Frontiers in cellular and infection microbiology
Switzerland
oai:repository.helmholtz-hzi.de:10033/6226732021-01-13T01:38:04Zcom_10033_620968col_10033_621822col_10033_620969col_10033_621187
The SARS-CoV-2 RNA-protein interactome in infected human cells.
Schmidt, Nora
Lareau, Caleb A
Keshishian, Hasmik
Ganskih, Sabina
Schneider, Cornelius
Hennig, Thomas
Melanson, Randy
Werner, Simone
Wei, Yuanjie
Zimmer, Matthias
Ade, Jens
Kirschner, Luisa
Zielinski, Sebastian
Dölken, Lars
Lander, Eric S
Caliskan, Neva
Fischer, Utz
Vogel, Jörg
Carr, Steven A
Bodem, Jochen
Munschauer, Mathias
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
2021-01-12T15:24:43Z
2021-01-12T15:24:43Z
2020-12-21
Article
Nat Microbiol. 2020 Dec 21. doi: 10.1038/s41564-020-00846-z. Epub ahead of print.
33349665
10.1038/s41564-020-00846-z
http://hdl.handle.net/10033/622673
2058-5276
Nature microbiology
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Nature research
Nature microbiology
England
oai:repository.helmholtz-hzi.de:10033/6226912021-01-22T01:29:46Zcom_10033_620968col_10033_620969col_10033_621236
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Venturini, Elisa
Svensson, Sarah L
Maaß, Sandra
Gelhausen, Rick
Eggenhofer, Florian
Li, Lei
Cain, Amy K
Parkhill, Julian
Becher, Dörte
Backofen, Rolf
Barquist, Lars
Sharma, Cynthia M
Westermann, Alexander J
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (Transposon-directed insertion sequencing), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available ‘omics’ datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
2021-01-21T13:41:16Z
2021-01-21T13:41:16Z
2020-10-17
Article
MicroLife(2020) .advance publication; DOI: 10.1093/femsml/uqaa002 .
10.1093/femsml/uqaa002
http://hdl.handle.net/10033/622691
2633-6693
MicroLife
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Oxford University Press (OUP)
1
1
microLife
oai:repository.helmholtz-hzi.de:10033/6226952021-02-02T11:45:23Zcom_10033_620968col_10033_620969
Intracellular Staphylococcus aureus Perturbs the Host Cell Ca+ Homeostasis To Promote Cell Death.
Stelzner, Kathrin
Winkler, Ann-Cathrin
Liang, Chunguang
Boyny, Aziza
Ade, Carsten P
Dandekar, Thomas
Fraunholz, Martin J
Rudel, Thomas
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Staphylococcus aureus
calcium signaling pathway
cell death
facultatively intracellular pathogens
The opportunistic human pathogen Staphylococcus aureus causes serious infectious diseases that range from superficial skin and soft tissue infections to necrotizing pneumonia and sepsis. While classically regarded as an extracellular pathogen, S. aureus is able to invade and survive within human cells. Host cell exit is associated with cell death, tissue destruction, and the spread of infection. The exact molecular mechanism employed by S. aureus to escape the host cell is still unclear. In this study, we performed a genome-wide small hairpin RNA (shRNA) screen and identified the calcium signaling pathway as being involved in intracellular infection. S. aureus induced a massive cytosolic Ca2+ increase in epithelial host cells after invasion and intracellular replication of the pathogen. This was paralleled by a decrease in endoplasmic reticulum Ca2+ concentration. Additionally, calcium ions from the extracellular space contributed to the cytosolic Ca2+ increase. As a consequence, we observed that the cytoplasmic Ca2+ rise led to an increase in mitochondrial Ca2+ concentration, the activation of calpains and caspases, and eventually to cell lysis of S. aureus-infected cells. Our study therefore suggests that intracellular S. aureus disturbs the host cell Ca2+ homeostasis and induces cytoplasmic Ca2+ overload, which results in both apoptotic and necrotic cell death in parallel or succession.IMPORTANCE Despite being regarded as an extracellular bacterium, the pathogen Staphylococcus aureus can invade and survive within human cells. The intracellular niche is considered a hideout from the host immune system and antibiotic treatment and allows bacterial proliferation. Subsequently, the intracellular bacterium induces host cell death, which may facilitate the spread of infection and tissue destruction. So far, host cell factors exploited by intracellular S. aureus to promote cell death are only poorly characterized. We performed a genome-wide screen and found the calcium signaling pathway to play a role in S. aureus invasion and cytotoxicity. The intracellular bacterium induces a cytoplasmic and mitochondrial Ca2+ overload, which results in host cell death. Thus, this study first showed how an intracellular bacterium perturbs the host cell Ca2+ homeostasis.
2021-01-22T14:48:28Z
2021-01-22T14:48:28Z
2020-12-15
Article
mBio. 2020 Dec 15;11(6):e02250-20. doi: 10.1128/mBio.02250-20.
33323513
10.1128/mBio.02250-20
http://hdl.handle.net/10033/622695
2150-7511
mBio
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
ASM
11
6
mBio
United States
oai:repository.helmholtz-hzi.de:10033/6227032021-01-27T01:36:12Zcom_10033_620968col_10033_620969
Leveraging bile solubilization of poorly water-soluble drugs by rational polymer selection.
Schlauersbach, Jonas
Hanio, Simon
Lenz, Bettina
Vemulapalli, Sahithya P B
Griesinger, Christian
Pöppler, Ann-Christin
Harlacher, Cornelius
Galli, Bruno
Meinel, Lorenz
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bile salt
Colloid
Flux
Polymer drug interaction
Simulated intestinal fluid
Poorly water-soluble drugs frequently solubilize into bile colloids and this natural mechanism is key for efficient bioavailability. We tested the impact of pharmaceutical polymers on this solubilization interplay using proton nuclear magnetic resonance spectroscopy, dynamic light scattering, and by assessing the flux across model membranes. Eudragit E, Soluplus, and a therapeutically used model polymer, Colesevelam, impacted the bile-colloidal geometry and molecular interaction. These polymer-induced changes reduced the flux of poorly water-soluble and bile interacting drugs (Perphenazine, Imatinib) but did not impact the flux of bile non-interacting Metoprolol. Non-bile interacting polymers (Kollidon VA 64, HPMC-AS) neither impacted the flux of colloid-interacting nor colloid-non-interacting drugs. These insights into the drug substance/polymer/bile colloid interplay potentially point towards a practical optimization parameter steering formulations to efficient bile-solubilization by rational polymer selection.
2021-01-26T16:52:45Z
2021-01-26T16:52:45Z
2020-12-15
Article
J Control Release. 2020 Dec 15;330:36-48. doi: 10.1016/j.jconrel.2020.12.016. Epub ahead of print.
33333120
10.1016/j.jconrel.2020.12.016
http://hdl.handle.net/10033/622703
1873-4995
Journal of controlled release : official journal of the Controlled Release Society
en
http://creativecommons.org/licenses/by-nc-nd/4.0/
Attribution-NonCommercial-NoDerivatives 4.0 International
Elsevier
330
36
48
Journal of controlled release : official journal of the Controlled Release Society
Netherlands
oai:repository.helmholtz-hzi.de:10033/6227172021-02-05T01:43:45Zcom_10033_620968col_10033_620969
Frugal Innovation for Point-of-Care Diagnostics Controlling Outbreaks and Epidemics.
Miesler, Tobias
Wimschneider, Christine
Brem, Alexander
Meinel, Lorenz
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Emerging Markets
Epidemics
Frugal Innovation
Point-of-Care-Tests
Today epidemics of infectious diseases occur more often and spread both faster and further due to globalization and changes in our lifestyle. One way to meet these biological threats are so-called "Frugal Innovations", which focus on the development of affordable, rapid, and easy-to-use diagnostics with widespread use. In this context, point-of-care-tests (POCTs), performed at the patient's bedside, reduce extensive waiting times and unnecessary treatments and enable effective containment measures. This Perspective covers advances in POCT diagnostics on the basis of frugal innovation characteristics that will enable a faster, less expensive, and more convenient reaction to upcoming epidemics. Established POCT systems on the health care market, as well as currently evolving technological advancements in that sector are discussed. Progress in POCT technology and insights on how to most effectively use them allows the handling of more patients in a shorter time frame and consequently improves clinical outcomes at lower cost.
2021-02-04T16:05:02Z
2021-02-04T16:05:02Z
2020-04-13
Article
ACS Biomater Sci Eng. 2020 May 11;6(5):2709-2725. doi: 10.1021/acsbiomaterials.9b01712. Epub 2020 Apr 13.
33463254
10.1021/acsbiomaterials.9b01712
http://hdl.handle.net/10033/622717
2373-9878
ACS biomaterials science & engineering
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
American Chemical Society (ACS)
6
5
2709
2725
ACS biomaterials science & engineering
United States
oai:repository.helmholtz-hzi.de:10033/6227212021-07-29T12:44:12Zcom_10033_620968col_10033_621258
CRISPR technologies and the search for the PAM-free nuclease.
Collias, Daphne
Beisel, Chase L
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The ever-expanding set of CRISPR technologies and their programmable RNA-guided nucleases exhibit remarkable flexibility in DNA targeting. However, this flexibility comes with an ever-present constraint: the requirement for a protospacer adjacent motif (PAM) flanking each target. While PAMs play an essential role in self/nonself discrimination by CRISPR-Cas immune systems, this constraint has launched a far-reaching expedition for nucleases with relaxed PAM requirements. Here, we review ongoing efforts toward realizing PAM-free nucleases through natural ortholog mining and protein engineering. We also address potential consequences of fully eliminating PAM recognition and instead propose an alternative nuclease repertoire covering all possible PAM sequences.
2021-02-08T13:22:46Z
2021-02-08T13:22:46Z
2021-01-22
Review
Nat Commun. 2021 Jan 22;12(1):555. doi: 10.1038/s41467-020-20633-y.
33483498
10.1038/s41467-020-20633-y
http://hdl.handle.net/10033/622721
2041-1723
Nature communications
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Nature Pulishing Group
12
1
555
Nature communications
United States
England
oai:repository.helmholtz-hzi.de:10033/6227232021-02-09T04:33:31Zcom_10033_620968col_10033_620970col_10033_620969
A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity.
Bernhardt, Laura
Dittrich, Marcus
El-Merahbi, Rabih
Saliba, Antoine-Emmanuel
Müller, Tobias
Sumara, Grzegorz
Vogel, Jörg
Nichols-Burns, Stefanie
Mitchell, Megan
Haaf, Thomas
El Hajj, Nady
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Paternal obesity is known to have a negative impact on the male's reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.
2021-02-08T14:19:16Z
2021-02-08T14:19:16Z
2021-01-21
Article
Sci Rep. 2021 Jan 21;11(1):1979. doi: 10.1038/s41598-021-81226-3.
33479343
10.1038/s41598-021-81226-3
http://hdl.handle.net/10033/622723
2045-2322
Scientific reports
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Nature Pulishing Group
11
1
1979
Scientific reports
England
oai:repository.helmholtz-hzi.de:10033/6227462021-02-17T04:32:35Zcom_10033_620968col_10033_620970col_10033_620969
Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia.
Chumduri, Cindrilla
Gurumurthy, Rajendra Kumar
Berger, Hilmar
Dietrich, Oliver
Kumar, Naveen
Koster, Stefanie
Brinkmann, Volker
Hoffmann, Kirstin
Drabkina, Marina
Arampatzi, Panagiota
Son, Dajung
Klemm, Uwe
Mollenkopf, Hans-Joachim
Herbst, Hermann
Mangler, Mandy
Vogel, Jörg
Saliba, Antoine-Emmanuel
Meyer, Thomas F
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The transition zones of the squamous and columnar epithelia constitute hotspots for the emergence of cancer, often preceded by metaplasia, in which one epithelial type is replaced by another. It remains unclear how the epithelial spatial organization is maintained and how the transition zone niche is remodelled during metaplasia. Here we used single-cell RNA sequencing to characterize epithelial subpopulations and the underlying stromal compartment of endo- and ectocervix, encompassing the transition zone. Mouse lineage tracing, organoid culture and single-molecule RNA in situ hybridizations revealed that the two epithelia derive from separate cervix-resident lineage-specific stem cell populations regulated by opposing Wnt signals from the stroma. Using a mouse model of cervical metaplasia, we further show that the endocervical stroma undergoes remodelling and increases expression of the Wnt inhibitor Dickkopf-2 (DKK2), promoting the outgrowth of ectocervical stem cells. Our data indicate that homeostasis at the transition zone results from divergent stromal signals, driving the differential proliferation of resident epithelial lineages.
2021-02-16T13:51:59Z
2021-02-16T13:51:59Z
2021-01-18
Article
Nat Cell Biol. 2021 Feb;23(2):184-197. doi: 10.1038/s41556-020-00619-0. Epub 2021 Jan 18.
33462395
10.1038/s41556-020-00619-0
http://hdl.handle.net/10033/622746
1476-4679
Nature cell biology
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Nature research
23
2
184
197
Nature cell biology
England
oai:repository.helmholtz-hzi.de:10033/6227522021-02-24T01:37:33Zcom_10033_620968col_10033_620969
Transcriptome profiling and protease inhibition experiments identify proteases that activate H3N2 influenza A and influenza B viruses in murine airways.
Harbig, Anne
Mernberger, Marco
Bittel, Linda
Pleschka, Stephan
Schughart, Klaus
Steinmetzer, Torsten
Stiewe, Thorsten
Nist, Andrea
Böttcher-Friebertshäuser, Eva
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
TMPRSS2
TMPRSS4
airway proteases
cleavage
hemagglutinin
hepsin
host-pathogen interactions
infectious disease
influenza virus
mouse
mouse lung proteases
prostasin
protease gene expression
serine protease
trypsin
trypsin-like protease
virus
Cleavage of influenza virus hemagglutinin (HA) by host proteases is essential for virus infectivity. HA of most influenza A and B (IAV/IBV) viruses is cleaved at a monobasic motif by trypsin-like proteases. Previous studies have reported that transmembrane serine protease 2 (TMPRSS2) is essential for activation of H7N9 and H1N1pdm IAV in mice but that H3N2 IAV and IBV activation is independent of TMPRSS2 and carried out by as-yet-undetermined protease(s). Here, to identify additional H3 IAV- and IBV-activating proteases, we used RNA-Seq to investigate the protease repertoire of murine lower airway tissues, primary type II alveolar epithelial cells (AECIIs), and the mouse lung cell line MLE-15. Among 13 candidates identified, TMPRSS4, TMPRSS13, hepsin, and prostasin activated H3 and IBV HA in vitro IBV activation and replication was reduced in AECIIs from Tmprss2/Tmprss4-deficient mice compared with WT or Tmprss2-deficient mice, indicating that murine TMPRSS4 is involved in IBV activation. Multicycle replication of H3N2 IAV and IBV in AECIIs of Tmprss2/Tmprss4-deficient mice varied in sensitivity to protease inhibitors, indicating that different, but overlapping, sets of murine proteases facilitate H3 and IBV HA cleavages. Interestingly, human hepsin and prostasin orthologs did not activate H3, but they did activate IBV HA in vitro Our results indicate that TMPRSS4 is an IBV-activating protease in murine AECIIs and suggest that TMPRSS13, hepsin, and prostasin cleave H3 and IBV HA in mice. They further show that hepsin and prostasin orthologs might contribute to the differences observed in TMPRSS2-independent activation of H3 in murine and human airways.
2021-02-23T15:44:38Z
2021-02-23T15:44:38Z
2020-04-17
Article
J Biol Chem. 2020 Aug 14;295(33):11388-11407. doi: 10.1074/jbc.RA120.012635. Epub 2020 Apr 17.
32303635
10.1074/jbc.RA120.012635
http://hdl.handle.net/10033/622752
1083-351X
The Journal of biological chemistry
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Elsevier
295
33
11388
11407
The Journal of biological chemistry
United States
oai:repository.helmholtz-hzi.de:10033/6227572021-02-27T01:33:19Zcom_10033_620968col_10033_620969
A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions.
Gerovac, Milan
Wicke, Laura
Chihara, Kotaro
Schneider, Cornelius
Lavigne, Rob
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Grad-seq
Pseudomonas
Pseudomonas aeruginosa
RNA-binding proteins
bacteriophage
infection
noncoding RNA
phage
ΦKZ
The Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.IMPORTANCE Stable complexes by cellular proteins and RNA molecules lie at the heart of gene regulation and physiology in any bacterium of interest. It is therefore crucial to globally determine these complexes in order to identify and characterize new molecular players and regulation mechanisms. Pseudomonads harbor some of the largest genomes known in bacteria, encoding ∼5,500 different proteins. Here, we provide a first glimpse on which proteins and cellular transcripts form stable complexes in the human pathogen Pseudomonas aeruginosa We additionally performed this analysis with bacteria subjected to the important and frequently encountered biological stress of a bacteriophage infection. We identified several molecules with established roles in a variety of cellular pathways, which were affected by the phage and can now be explored for their role during phage infection. Most importantly, we observed strong colocalization of phage transcripts and host ribosomes, indicating the existence of specialized translation mechanisms during phage infection. All data are publicly available in an interactive and easy to use browser.
2021-02-26T15:54:05Z
2021-02-26T15:54:05Z
2021-02-09
Article
mBio. 2021 Feb 9;12(1):e03454-20. doi: 10.1128/mBio.03454-20.
33563827
10.1128/mBio.03454-20
http://hdl.handle.net/10033/622757
2150-7511
mBio
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
American Society for Microbiology (ASM)
12
1
mBio
United States
oai:repository.helmholtz-hzi.de:10033/6227642021-03-03T01:35:08Zcom_10033_620968col_10033_620969col_10033_621391
How Insertion of a Single Tryptophan in the N-Terminus of a Cecropin A-Melittin Hybrid Peptide Changes Its Antimicrobial and Biophysical Profile.
Ferreira, Ana Rita
Teixeira, Cátia
Sousa, Carla F
Bessa, Lucinda J
Gomes, Paula
Gameiro, Paula
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
CAMP
antibiotic resistance
cation-π interactions
cecropin-melittin peptides
large unilamellar vesicles
membrane-targeting activity
tryptophan
n the era of antibiotic resistance, there is an urgent need for efficient antibiotic therapies to fight bacterial infections. Cationic antimicrobial peptides (CAMP) are promising lead compounds given their membrane-targeted mechanism of action, and high affinity towards the anionic composition of bacterial membranes. We present a new CAMP, W-BP100, derived from the highly active BP100, holding an additional tryptophan at the N-terminus. W-BP100 showed a broader antibacterial activity, demonstrating a potent activity against Gram-positive strains. Revealing a high partition constant towards anionic over zwitterionic large unilamellar vesicles and inducing membrane saturation at a high peptide/lipid ratio, W-BP100 has a preferential location for hydrophobic environments. Contrary to BP100, almost no aggregation of anionic vesicles is observed around saturation conditions and at higher concentrations no aggregation is observed. With these results, it is possible to state that with the incorporation of a single tryptophan to the N-terminus, a highly active peptide was obtained due to the π-electron system of tryptophan, resulting in negatively charged clouds, that participate in cation-π interactions with lysine residues. Furthermore, we propose that W-BP100 action can be achieved by electrostatic interactions followed by peptide translocation.
2021-03-02T15:13:58Z
2021-03-02T15:13:58Z
2021-01-12
Article
Membranes (Basel). 2021 Jan 12;11(1):48. doi: 10.3390/membranes11010048.
2077-0375
33445476
10.3390/membranes11010048
http://hdl.handle.net/10033/622764
Membranes
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
MDPI
11
1
Membranes
Switzerland
oai:repository.helmholtz-hzi.de:10033/6227692021-03-05T02:33:22Zcom_10033_620968col_10033_620969col_10033_621391
MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT.
Correia Santos, Sara
Bischler, Thorsten
Westermann, Alexander J
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
MS2 affinity purification and RNA-seq
PinT
host-pathogen interaction
infection
noncoding RNA
post-transcriptional control
A full understanding of the contribution of small RNAs (sRNAs) to bacterial virulence demands knowledge of their target suites under infection-relevant conditions. Here, we take an integrative approach to capturing targets of the Hfq-associated sRNA PinT, a known post-transcriptional timer of the two major virulence programs of Salmonella enterica. Using MS2 affinity purification and RNA sequencing (MAPS), we identify PinT ligands in bacteria under in vitro conditions mimicking specific stages of the infection cycle and in bacteria growing inside macrophages. This reveals PinT-mediated translational inhibition of the secreted effector kinase SteC, which had gone unnoticed in previous target searches. Using genetic, biochemical, and microscopic assays, we provide evidence for PinT-mediated repression of steC mRNA, eventually delaying actin rearrangements in infected host cells. Our findings support the role of PinT as a central post-transcriptional regulator in Salmonella virulence and illustrate the need for complementary methods to reveal the full target suites of sRNAs.
2021-03-04T12:25:27Z
2021-03-04T12:25:27Z
2021-02-02
Article
Cell Rep. 2021 Feb 2;34(5):108722. doi: 10.1016/j.celrep.2021.108722.
33535041
10.1016/j.celrep.2021.108722
http://hdl.handle.net/10033/622769
2211-1247
Cell reports
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Elsevier (Cell Press)
34
5
108722
Cell reports
United States
oai:repository.helmholtz-hzi.de:10033/6227752021-03-10T01:35:40Zcom_10033_620968col_10033_620969
Drug-Induced Dynamics of Bile Colloids.
Hanio, Simon
Schlauersbach, Jonas
Lenz, Bettina
Spiegel, Franziska
Böckmann, Rainer A
Schweins, Ralf
Nischang, Ivo
Schubert, Ulrich S
Endres, Sebastian
Pöppler, Ann-Christin
Brandl, Ferdinand P
Smit, Theo M
Kolter, Karl
Meinel, Lorenz
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bile colloids containing taurocholate and lecithin are essential for the solubilization of hydrophobic molecules including poorly water-soluble drugs such as Perphenazine. We detail the impact of Perphenazine concentrations on taurocholate/lecithin colloids using analytical ultracentrifugation, dynamic light scattering, small-angle neutron scattering, nuclear magnetic resonance spectroscopy, coarse-grained molecular dynamics simulations, and isothermal titration calorimetry. Perphenazine impacted colloidal molecular arrangement, structure, and binding thermodynamics in a concentration-dependent manner. At low concentration, Perphenazine was integrated into stable and large taurocholate/lecithin colloids and close to lecithin. Integration of Perphenazine into these colloids was exothermic. At higher Perphenazine concentration, the taurocholate/lecithin colloids had an approximately 5-fold reduction in apparent hydrodynamic size, heat release was less exothermic upon drug integration into the colloids, and Perphenazine interacted with both lecithin and taurocholate. In addition, Perphenazine induced a morphological transition from vesicles to wormlike micelles as indicated by neutron scattering. Despite these surprising colloidal dynamics, these natural colloids successfully ensured stable relative amounts of free Perphenazine throughout the entire drug concentration range tested here. Future studies are required to further detail these findings both on a molecular structural basis and in terms of in vivo relevance.
2021-03-09T12:36:07Z
2021-03-09T12:36:07Z
2021-02-15
Article
Langmuir. 2021 Mar 2;37(8):2543-2551. doi: 10.1021/acs.langmuir.0c02282. Epub 2021 Feb 15.
33587852
10.1021/acs.langmuir.0c02282
http://hdl.handle.net/10033/622775
1520-5827
Langmuir : the ACS journal of surfaces and colloids
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Society for Chemistry (ACS)
37
8
2543
2551
Langmuir : the ACS journal of surfaces and colloids
United States
rdf///com_10033_620968/100