2024-03-29T05:45:49Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/2813532019-08-30T11:30:32Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Hasenberg, Mike
author
Stegemann-Koniszewski, Sabine
author
Gunzer, Matthias
author
2013-01
The lung constantly interacts with the environment through thousands of liters of air that are inhaled daily. This continually transports toxic chemicals and particles or pathogenic microorganisms deep into the respiratory system, posing a challenge to physicochemical barriers and the local immune system. Thus, complex structures and mechanisms have evolved to recognize and fend off environmental dangers while at the same time allowing efficient gas exchange. Here we review our current knowledge regarding cellular mechanisms of the immune system in context with the highly specialized anatomical features of the airways and especially the alveolar compartment. The focus is on fungal and viral infections, merging anatomical aspects well known to pulmonologists with fundamental immunological concepts. We discuss the specialized morphological constraints of immune cells compressed under a continuous layer of the surfactant lining within alveoli as well as the importance of functional polarization of respiratory tract epithelia. Furthermore, we summarize the different types of innate and adaptive immune cells and their relative contribution to lung homeostasis with respect to localization. Finally, we provide a list of currently unresolved questions with high relevance for the field that might serve as food for thought regarding future research directions.
Cellular immune reactions in the lung. 2013, 251 (1):189-214 Immunol. Rev.
1600-065X
23278750
10.1111/imr.12020
http://hdl.handle.net/10033/281353
Immunological reviews
Cellular immune reactions in the lung.
oai:repository.helmholtz-hzi.de:10033/3019042019-08-30T11:36:33Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Chylinski, Krzysztof
author
Le Rhun, Anaïs
author
Charpentier, Emmanuelle
author
2013-05
CRISPR-Cas is a rapidly evolving RNA-mediated adaptive immune system that protects bacteria and archaea against mobile genetic elements. The system relies on the activity of short mature CRISPR RNAs (crRNAs) that guide Cas protein(s) to silence invading nucleic acids. A set of CRISPR-Cas, type II, requires a trans-activating small RNA, tracrRNA, for maturation of precursor crRNA (pre-crRNA) and interference with invading sequences. Following co-processing of tracrRNA and pre-crRNA by RNase III, dual-tracrRNA:crRNA guides the CRISPR-associated endonuclease Cas9 (Csn1) to cleave site-specifically cognate target DNA. Here, we screened available genomes for type II CRISPR-Cas loci by searching for Cas9 orthologs. We analyzed 75 representative loci, and for 56 of them we predicted novel tracrRNA orthologs. Our analysis demonstrates a high diversity in cas operon architecture and position of the tracrRNA gene within CRISPR-Cas loci. We observed a correlation between locus heterogeneity and Cas9 sequence diversity, resulting in the identification of various type II CRISPR-Cas subgroups. We validated the expression and co-processing of predicted tracrRNAs and pre-crRNAs by RNA sequencing in five bacterial species. This study reveals tracrRNA family as an atypical, small RNA family with no obvious conservation of structure, sequence or localization within type II CRISPR-Cas loci. The tracrRNA family is however characterized by the conserved feature to base-pair to cognate pre-crRNA repeats, an essential function for crRNA maturation and DNA silencing by dual-RNA:Cas9. The large panel of tracrRNA and Cas9 ortholog sequences should constitute a useful database to improve the design of RNA-programmable Cas9 as genome editing tool.
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. 2013, 10 (5):726-37 RNA Biol
1555-8584
23563642
10.4161/rna.24321
http://hdl.handle.net/10033/301904
RNA biology
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems.
oai:repository.helmholtz-hzi.de:10033/3064232019-08-30T11:24:31Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Fonfara, Ines
author
Le Rhun, Anaïs
author
Chylinski, Krzysztof
author
Makarova, Kira S
author
Lécrivain, Anne-Laure
author
Bzdrenga, Janek
author
Koonin, Eugene V
author
Charpentier, Emmanuelle
author
2013-11-22
The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool.
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. 2013: Nucleic Acids Res.
1362-4962
24270795
10.1093/nar/gkt1074
http://hdl.handle.net/10033/306423
Nucleic acids research
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems.
oai:repository.helmholtz-hzi.de:10033/3443832019-08-30T11:37:00Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Thevenard, Jessica
author
Verzeaux, Laurie
author
Devy, Jerôme
author
Etique, Nicolas
author
Jeanne, Albin
author
Schneider, Christophe
author
Hachet, Cathy
author
Ferracci, Géraldine
author
David, Marion
author
Martiny, Laurent
author
Charpentier, Emmanuelle
author
Khrestchatisky, Michel
author
Rivera, Santiago
author
Dedieu, Stéphane
author
Emonard, Hervé
author
2014
Tissue inhibitor of metalloproteinases-1 (TIMP-1) regulates the extracellular matrix turnover by inhibiting the proteolytic activity of matrix metalloproteinases (MMPs). TIMP-1 also displays MMP-independent activities that influence the behavior of various cell types including neuronal plasticity, but the underlying molecular mechanisms remain mostly unknown. The trans-membrane receptor low-density lipoprotein receptor-related protein-1 (LRP-1) consists of a large extracellular chain with distinct ligand-binding domains that interact with numerous ligands including TIMP-2 and TIMP-3 and a short transmembrane chain with intracellular motifs that allow endocytosis and confer signaling properties to LRP-1. We addressed TIMP-1 interaction with recombinant ligand-binding domains of LRP-1 expressed by CHO cells for endocytosis study, or linked onto sensor chips for surface plasmon resonance analysis. Primary cortical neurons bound and internalized endogenous TIMP-1 through a mechanism mediated by LRP-1. This resulted in inhibition of neurite outgrowth and increased growth cone volume. Using a mutated inactive TIMP-1 variant we showed that TIMP-1 effect on neurone morphology was independent of its MMP inhibitory activity. We conclude that TIMP-1 is a new ligand of LRP-1 and we highlight a new example of its MMP-independent, cytokine-like functions.
Low-density lipoprotein receptor-related protein-1 mediates endocytic clearance of tissue inhibitor of metalloproteinases-1 and promotes its cytokine-like activities. 2014, 9 (7):e103839 PLoS ONE
1932-6203
25075518
10.1371/journal.pone.0103839
http://hdl.handle.net/10033/344383
PloS one
Low-density lipoprotein receptor-related protein-1 mediates endocytic clearance of tissue inhibitor of metalloproteinases-1 and promotes its cytokine-like activities.
oai:repository.helmholtz-hzi.de:10033/5584162019-08-30T11:26:42Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Charpentier, Emmanuelle
author
Richter, Hagen
author
van der Oost, John
author
White, Malcolm F
author
2015-05
CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences acquired from invading mobile genomes is transcribed as a precursor crRNA (pre-crRNA) molecule. This pre-crRNA undergoes one or two maturation steps to generate the mature crRNAs that guide CRISPR-associated (Cas) protein(s) to cognate invading genomes for their destruction. Different types of CRISPR-Cas systems have evolved distinct crRNA biogenesis pathways that implicate highly sophisticated processing mechanisms. In Types I and III CRISPR-Cas systems, a specific endoribonuclease of the Cas6 family, either standalone or in a complex with other Cas proteins, cleaves the pre-crRNA within the repeat regions. In Type II systems, the trans-acting small RNA (tracrRNA) base pairs with each repeat of the pre-crRNA to form a dual-RNA that is cleaved by the housekeeping RNase III in the presence of the protein Cas9. In this review, we present a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the three CRISPR-Cas types.
Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. 2015, 39 (3):428-441 FEMS Microbiol. Rev.
1574-6976
25994611
10.1093/femsre/fuv023
http://hdl.handle.net/10033/558416
FEMS microbiology reviews
Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity.
oai:repository.helmholtz-hzi.de:10033/6060262019-08-30T11:32:16Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Le Rhun, Anaïs
author
Beer, Yan Yan
author
Reimegård, Johan
author
Chylinski, Krzysztof
author
Charpentier, Emmanuelle
author
2016-02
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. 2016, 13 (2):177-95 RNA Biol
1555-8584
26580233
10.1080/15476286.2015.1110674
http://hdl.handle.net/10033/606026
RNA biology
RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
oai:repository.helmholtz-hzi.de:10033/6157802019-08-30T11:33:26Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Charpentier, Emmanuelle
author
2015-04
CRISPR-Cas9: how research on a bacterial RNA-guided mechanism opened new perspectives in biotechnology and biomedicine. 2015, 7 (4):363-5 EMBO Mol Med
1757-4684
25796552
10.15252/emmm.201504847
http://hdl.handle.net/10033/615780
EMBO molecular medicine
CRISPR-Cas9: how research on a bacterial RNA-guided mechanism opened new perspectives in biotechnology and biomedicine.
oai:repository.helmholtz-hzi.de:10033/6201342019-08-30T11:33:30Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Sternberg, Samuel H
author
Richter, Hagen
author
Charpentier, Emmanuelle
author
Qimron, Udi
author
2016-03-17
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptation. During the past 3 years, significant progress has been made on the genetic requirements and molecular mechanisms of adaptation. Here we review these recent advances, with a focus on the experimental approaches that have been developed, the insights they generated, and a proposed mechanism for self- versus non-self-discrimination during the process of spacer selection. We further describe the regulation of adaptation and the protein players involved in this fascinating process that allows bacteria and archaea to harbor adaptive immunity.
Adaptation in CRISPR-Cas Systems. 2016, 61 (6):797-808 Mol. Cell
1097-4164
26949040
10.1016/j.molcel.2016.01.030
http://hdl.handle.net/10033/620134
Molecular cell
Adaptation in CRISPR-Cas Systems.
oai:repository.helmholtz-hzi.de:10033/6205572019-08-30T11:25:43Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Heckl, Dirk
author
Charpentier, Emmanuelle
author
2015-05-21
Targeted regulation of gene expression holds huge promise for biomedical research. In a series of recent publications (Gilbert et al., 2014; Konermann et al., 2015; Zalatan et al., 2015), sophisticated, multiplex-compatible transcriptional activator systems based on the CRISPR-Cas9 technology and genome-scale libraries advance the field toward whole-transcriptome control.
Toward Whole-Transcriptome Editing with CRISPR-Cas9. 2015, 58 (4):560-2 Mol. Cell
1097-4164
26000839
10.1016/j.molcel.2015.05.016
http://hdl.handle.net/10033/620557
Molecular cell
Toward Whole-Transcriptome Editing with CRISPR-Cas9.
oai:repository.helmholtz-hzi.de:10033/6210602019-08-30T11:36:05Zcom_10033_264694com_10033_6815com_10033_6814com_10033_620644com_10033_621723col_10033_621724col_10033_264695col_10033_620650
00925njm 22002777a 4500
dc
Fabiani, Florian D
author
Renault, Thibaud T
author
Peters, Britta
author
Dietsche, Tobias
author
Gálvez, Eric J C
author
Guse, Alina
author
Freier, Karen
author
Charpentier, Emmanuelle
author
Strowig, Till
author
Franz-Wachtel, Mirita
author
Macek, Boris
author
Wagner, Samuel
author
Hensel, Michael
author
Erhardt, Marc
author
2017-08
Many bacteria move using a complex, self-assembling nanomachine, the bacterial flagellum. Biosynthesis of the flagellum depends on a flagellar-specific type III secretion system (T3SS), a protein export machine homologous to the export machinery of the virulence-associated injectisome. Six cytoplasmic (FliH/I/J/G/M/N) and seven integral-membrane proteins (FlhA/B FliF/O/P/Q/R) form the flagellar basal body and are involved in the transport of flagellar building blocks across the inner membrane in a proton motive force-dependent manner. However, how the large, multi-component transmembrane export gate complex assembles in a coordinated manner remains enigmatic. Specific for most flagellar T3SSs is the presence of FliO, a small bitopic membrane protein with a large cytoplasmic domain. The function of FliO is unknown, but homologs of FliO are found in >80% of all flagellated bacteria. Here, we demonstrate that FliO protects FliP from proteolytic degradation and promotes the formation of a stable FliP-FliR complex required for the assembly of a functional core export apparatus. We further reveal the subcellular localization of FliO by super-resolution microscopy and show that FliO is not part of the assembled flagellar basal body. In summary, our results suggest that FliO functions as a novel, flagellar T3SS-specific chaperone, which facilitates quality control and productive assembly of the core T3SS export machinery.
A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum. 2017, 15 (8):e2002267 PLoS Biol.
1545-7885
28771474
10.1371/journal.pbio.2002267
http://hdl.handle.net/10033/621060
PLoS biology
A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum.
oai:repository.helmholtz-hzi.de:10033/6210912019-08-30T11:32:41Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Le Rhun, Anaïs
author
Lécrivain, Anne-Laure
author
Reimegård, Johan
author
Proux-Wéra, Estelle
author
Broglia, Laura
author
Della Beffa, Cristina
author
Charpentier, Emmanuelle
author
2017-03-17
A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. 2017, 45 (5):2329-2340 Nucleic Acids Res.
1362-4962
28082390
10.1093/nar/gkw1316
http://hdl.handle.net/10033/621091
Nucleic acids research
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes.
oai:repository.helmholtz-hzi.de:10033/6213172019-08-30T11:28:51Zcom_10033_264694com_10033_6815com_10033_6814col_10033_264695
00925njm 22002777a 4500
dc
Resch, Ulrike
author
Tsatsaronis, James Anthony
author
Le Rhun, Anaïs
author
Stübiger, Gerald
author
Rohde, M
author
Kasvandik, Sergo
author
Holzmeister, Susanne
author
Tinnefeld, Philip
author
Wai, Sun Nyunt
author
Charpentier, Emmanuelle
author
2016
Export of macromolecules via extracellular membrane-derived vesicles (MVs) plays an important role in the biology of Gram-negative bacteria. Gram-positive bacteria have also recently been reported to produce MVs; however, the composition and mechanisms governing vesiculogenesis in Gram-positive bacteria remain undefined. Here, we describe MV production in the Gram-positive human pathogen group A streptococcus (GAS), the etiological agent of necrotizing fasciitis and streptococcal toxic shock syndrome. M1 serotype GAS isolates in culture exhibit MV structures both on the cell wall surface and in the near vicinity of bacterial cells. A comprehensive analysis of MV proteins identified both virulence-associated protein substrates of the general secretory pathway in addition to "anchorless surface proteins." Characteristic differences in the contents, distributions, and fatty acid compositions of specific lipids between MVs and GAS cell membrane were also observed. Furthermore, deep RNA sequencing of vesicular RNAs revealed that GAS MVs contained differentially abundant RNA species relative to bacterial cellular RNA. MV production by GAS strains varied in a manner dependent on an intact two-component system, CovRS, with MV production negatively regulated by the system. Modulation of MV production through CovRS was found to be independent of both GAS cysteine protease SpeB and capsule biosynthesis. Our data provide an explanation for GAS secretion of macromolecules, including RNAs, lipids, and proteins, and illustrate a regulatory mechanism coordinating this secretory response.
A Two-Component Regulatory System Impacts Extracellular Membrane-Derived Vesicle Production in Group A Streptococcus. 2016, 7 (6) MBio
2150-7511
27803183
10.1128/mBio.00207-16
http://hdl.handle.net/10033/621317
mBio
A Two-Component Regulatory System Impacts Extracellular Membrane-Derived Vesicle Production in Group A Streptococcus.