2024-03-29T09:59:41Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/2295732019-08-30T11:25:43Zcom_10033_620636col_10033_620637
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
Gabdoulline, R
Eckweiler, D
Kel, A
Stegmaier, P
Heinrich-Heine University of Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38234 Braunschweig, GeneXplain GmbH, Am Exer 10 b, 38302 Wolfenbüttel, BIOBASE GmbH, Halchtersche Str. 33, 38304 Wolfenbüttel, Germany and Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Science, 10 Lavrentyev Ave, 630090 Novosibirsk, Russia.
We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.
2012-06-19T09:08:55Z
2012-06-19T09:08:55Z
2012-06-19T09:08:55Z
2012-06-11
Article
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. 2012:notNucleic Acids Res
1362-4962
22693215
10.1093/nar/gks551
http://hdl.handle.net/10033/229573
Nucleic acids research
Archived with thanks to Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/2446912019-08-30T11:33:05Zcom_10033_620636col_10033_620637
A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa.
Düvel, Juliane
Bertinetti, Daniela
Möller, Stefan
Schwede, Frank
Morr, Michael
Wissing, Josef
Radamm, Lena
Zimmermann, Bastian
Genieser, Hans-Gottfried
Jänsch, Lothar
Herberg, Friedrich W
Häussler, Susanne
Department of Cell Biology, Helmholtz Center for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
In many bacteria, high levels of the ubiquitous second messenger c-di-GMP have been demonstrated to suppress motility and to promote the establishment of surface-adherent biofilm communities. While molecular mechanisms underlying the synthesis and degradation of c-di-GMP have been comprehensively characterized, little is known about how c-di-GMP mediates its regulatory effects. In this study, we have established a chemical proteomics approach to identify c-di-GMP interacting proteins in the opportunistic pathogen Pseudomonas aeruginosa. A functionalized c-di-GMP analog, 2'-aminohexylcarbamoyl-c-di-GMP (2'-AHC-c-di-GMP), was chemically synthesized and following its immobilization used to perform affinity pull down experiments. Enriched proteins were subsequently identified by high-resolution mass spectrometry. 2'-AHC-c-di-GMP was also employed in surface plasmon resonance studies to evaluate and quantify the interaction of c-di-GMP with its potential target molecules in vitro. The biochemical tools presented here may serve the identification of novel classes of c-di-GMP effectors and thus contribute to a better characterization and understanding of the complex c-di-GMP signaling network.
2012-09-18T14:16:26Z
2012-09-18T14:16:26Z
2012-09-18T14:16:26Z
2012-02
Article
A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa. 2012, 88 (2):229-36 J. Microbiol. Methods
1872-8359
22178430
10.1016/j.mimet.2011.11.015
http://hdl.handle.net/10033/244691
Journal of microbiological methods
en
Archived with thanks to Journal of microbiological methods
oai:repository.helmholtz-hzi.de:10033/2471392019-08-30T11:24:31Zcom_10033_620636col_10033_620637
The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways.
Malone, Jacob G
Jaeger, Tina
Manfredi, Pablo
Dötsch, Andreas
Blanka, Andrea
Bos, Raphael
Cornelis, Guy R
Häussler, Susanne
Jenal, Urs
Biozentrum of the University of Basel, Basel, Switzerland.
The genetic adaptation of pathogens in host tissue plays a key role in the establishment of chronic infections. While whole genome sequencing has opened up the analysis of genetic changes occurring during long-term infections, the identification and characterization of adaptive traits is often obscured by a lack of knowledge of the underlying molecular processes. Our research addresses the role of Pseudomonas aeruginosa small colony variant (SCV) morphotypes in long-term infections. In the lungs of cystic fibrosis patients, the appearance of SCVs correlates with a prolonged persistence of infection and poor lung function. Formation of P. aeruginosa SCVs is linked to increased levels of the second messenger c-di-GMP. Our previous work identified the YfiBNR system as a key regulator of the SCV phenotype. The effector of this tripartite signaling module is the membrane bound diguanylate cyclase YfiN. Through a combination of genetic and biochemical analyses we first outline the mechanistic principles of YfiN regulation in detail. In particular, we identify a number of activating mutations in all three components of the Yfi regulatory system. YfiBNR is shown to function via tightly controlled competition between allosteric binding sites on the three Yfi proteins; a novel regulatory mechanism that is apparently widespread among periplasmic signaling systems in bacteria. We then show that during long-term lung infections of CF patients, activating mutations invade the population, driving SCV formation in vivo. The identification of mutational "scars" in the yfi genes of clinical isolates suggests that Yfi activity is both under positive and negative selection in vivo and that continuous adaptation of the c-di-GMP network contributes to the in vivo fitness of P. aeruginosa during chronic lung infections. These experiments uncover an important new principle of in vivo persistence, and identify the c-di-GMP network as a valid target for novel anti-infectives directed against chronic infections.
2012-10-05T09:35:11Z
2012-10-05T09:35:11Z
2012-10-05T09:35:11Z
2012-06
Article
The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways. 2012, 8 (6):e1002760 PLoS Pathog.
1553-7374
22719254
10.1371/journal.ppat.1002760
http://hdl.handle.net/10033/247139
PLoS pathogens
en
Archived with thanks to PLoS pathogens
oai:repository.helmholtz-hzi.de:10033/2756122019-08-30T11:32:41Zcom_10033_306379com_10033_620636col_10033_306382col_10033_620637
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance.
Bruchmann, Sebastian
Dötsch, Andreas
Nouri, Bianka
Chaberny, Iris F
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Quinolone antibiotics constitute a clinically successful and widely used class of broad-spectrum antibiotics; however, the emergence and spread of resistance increasingly limits the use of fluoroquinolones in the treatment and management of microbial disease. In this study, we evaluated the quantitative contributions of quinolone target alteration and efflux pump expression to fluoroquinolone resistance in Pseudomonas aeruginosa. We generated isogenic mutations in hot spots of the quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, and parC and inactivated the efflux regulator genes so as to overexpress the corresponding multidrug resistance (MDR) efflux pumps. We then introduced the respective mutations into the reference strain PA14 singly and in various combinations. Whereas the combined inactivation of two efflux regulator-encoding genes did not lead to resistance levels higher than those obtained by inactivation of only one efflux regulator-encoding gene, the combination of mutations leading to increased efflux and target alteration clearly exhibited an additive effect. This combination of target alteration and overexpression of efflux pumps was commonly observed in clinical P. aeruginosa isolates; however, these two mechanisms were frequently found not to be sufficient to explain the level of fluoroquinolone resistance. Our results suggest that there are additional mechanisms, independent of the expression of the MexAB-OprM, MexCD-OprJ, MexEF-OprN, and/or MexXY-OprM efflux pump, that increase ciprofloxacin resistance in isolates with mutations in the QRDRs.
2013-03-21T15:17:19Z
2013-03-21T15:17:19Z
2013-03-21T15:17:19Z
2013-03
Article
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance. 2013, 57 (3):1361-8 Antimicrob. Agents Chemother.
1098-6596
23274661
10.1128/AAC.01581-12
http://hdl.handle.net/10033/275612
Antimicrobial agents and chemotherapy
en
info:eu-repo/grantAgreement/EC/FP7/260276/
Archived with thanks to Antimicrobial agents and chemotherapy
openAccess
oai:repository.helmholtz-hzi.de:10033/2795122019-08-30T11:27:16Zcom_10033_620636col_10033_620637
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites.
Bielecki, Piotr
Komor, Uliana
Bielecka, Agata
Müsken, Mathias
Puchałka, Jacek
Pletz, Mathias W
Ballmann, Manfred
Martins dos Santos, Vítor A P
Weiss, Siegfried
Häussler, Susanne
Bielecki, Piotr
Komor, Uliana
Bielecka, Agata
Müsken, Mathias
Puchałka, Jacek
Pletz, Mathias W
Ballmann, Manfred
Martins dos Santos, Vítor A P
Weiss, Siegfried
Häussler, Susanne
Institute for Molecular Bacteriology, Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research and the Hannover Medical School, Hannover, 30625, Germany.
Institute for Molecular Bacteriology, Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research and the Hannover Medical School, Hannover, 30625, Germany.
The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P. aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases.
The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P. aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases.
2013-04-09T13:17:22Z
2013-04-09T13:17:22Z
2013-04-09T13:17:22Z
2013-02
Article
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites. 2013, 15 (2):570-87 Environ. Microbiol.
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites. 2013, 15 (2):570-87 Environ. Microbiol.
1462-2920
23145907
10.1111/1462-2920.12024
http://hdl.handle.net/10033/279512
Environmental microbiology
Environmental microbiology
en
eu-repo/grantAgreement/EC/FP7/260276
Archived with thanks to Environmental microbiology
openAccess
oai:repository.helmholtz-hzi.de:10033/2798712019-08-30T11:25:11Zcom_10033_620636col_10033_620637
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa.
Gödeke, Julia
Pustelny, Christian
Häussler, Susanne
Gödeke, Julia
Pustelny, Christian
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.
Acute and chronic infections caused by the opportunistic pathogen Pseudomonas aeruginosa pose a serious threat to human health worldwide, and its increasing resistance to antibiotics requires alternative treatments that are more effective than available strategies. Clinical studies have clearly demonstrated that cystic fibrosis (CF) patients with chronic P. aeruginosa infections benefit from long-term low-dose azithromycin (AZM) treatment. Immunomodulating activity, the impact of AZM on the expression of quorum-sensing-dependent virulence factors, type three secretion, and motility in P. aeruginosa seem to contribute to the therapeutic response. However, to date, the molecular mechanisms underlying these AZM effects have remained elusive. Our data indicate that the AZM-mediated phenotype is caused by a depletion of the intracellular pools of tRNAs available for protein synthesis. Overexpression of the P. aeruginosa peptidyl-tRNA hydrolase, which recycles the tRNA from peptidyl-tRNA drop-off during translation, counteracted the effects of AZM on stationary-phase cell killing, cytotoxicity, and the production of rhamnolipids and partially restored swarming motility. Intriguingly, the exchange of a rare for a frequent codon in rhlR also explicitly diminished the AZM-mediated decreased production of rhamnolipids. These results indicate that depletion of the tRNA pools by AZM seems to affect the translation of genes that use rare aminoacyl-tRNA isoacceptors to a great extent and might explain the selective activity of AZM on the P. aeruginosa proteome and possibly also on the protein expression profiles of other bacterial pathogens.
Acute and chronic infections caused by the opportunistic pathogen Pseudomonas aeruginosa pose a serious threat to human health worldwide, and its increasing resistance to antibiotics requires alternative treatments that are more effective than available strategies. Clinical studies have clearly demonstrated that cystic fibrosis (CF) patients with chronic P. aeruginosa infections benefit from long-term low-dose azithromycin (AZM) treatment. Immunomodulating activity, the impact of AZM on the expression of quorum-sensing-dependent virulence factors, type three secretion, and motility in P. aeruginosa seem to contribute to the therapeutic response. However, to date, the molecular mechanisms underlying these AZM effects have remained elusive. Our data indicate that the AZM-mediated phenotype is caused by a depletion of the intracellular pools of tRNAs available for protein synthesis. Overexpression of the P. aeruginosa peptidyl-tRNA hydrolase, which recycles the tRNA from peptidyl-tRNA drop-off during translation, counteracted the effects of AZM on stationary-phase cell killing, cytotoxicity, and the production of rhamnolipids and partially restored swarming motility. Intriguingly, the exchange of a rare for a frequent codon in rhlR also explicitly diminished the AZM-mediated decreased production of rhamnolipids. These results indicate that depletion of the tRNA pools by AZM seems to affect the translation of genes that use rare aminoacyl-tRNA isoacceptors to a great extent and might explain the selective activity of AZM on the P. aeruginosa proteome and possibly also on the protein expression profiles of other bacterial pathogens.
2013-04-11T08:36:52Z
2013-04-11T08:36:52Z
2013-04-11T08:36:52Z
2013-04
Article
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa. 2013, 57 (4):1617-24 Antimicrob. Agents Chemother.
Recycling of Peptidyl-tRNAs by Peptidyl-tRNA Hydrolase Counteracts Azithromycin-Mediated Effects on Pseudomonas aeruginosa. 2013, 57 (4):1617-24 Antimicrob. Agents Chemother.
1098-6596
23318806
10.1128/AAC.02582-12
http://hdl.handle.net/10033/279871
Antimicrobial agents and chemotherapy
Antimicrobial agents and chemotherapy
en
eu-repo/grantAgreement/EC/FP7/260276
Archived with thanks to Antimicrobial agents and chemotherapy
openAccess
oai:repository.helmholtz-hzi.de:10033/2931492019-08-30T11:25:11Zcom_10033_620636col_10033_620637
The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosa PA14.
Pustelny, Christian
Brouwer, Stephan
Müsken, Mathias
Bielecka, Agata
Dötsch, Andreas
Nimtz, Manfred
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany. Christian.pustelny@helmholtz-hzi.de
Pseudomonas aeruginosa pathogenicity and its capability to adapt to multiple environments are dependent on the production of diverse virulence factors, controlled by the sophisticated quorum sensing (QS) network of P. aeruginosa. To better understand the molecular mechanisms that underlie this adaptation we searched for novel key regulators of virulence factor production by screening a PA14 transposon mutant library for potential candidates acting downstream of the unique 2-alkyl-4-quinolone (AQ) QS system of P. aeruginosa. We focused the work on a protein named HemK with high homology to PrmC of Escherichia coli displaying a similar enzymatic activity (therefore also referred to as PrmC). In this study, we demonstrate that PrmC is an S-adenosyl-l-methionine (AdoMet)-dependent methyltransferase of peptide chain release factors (RFs) essential for the expression of several virulence factors, such as pyocyanin, rhamnolipids and the type III-secreted toxin ExoT. Furthermore, the PA14_prmC mutant strain is unable to grow under anoxic conditions and has a significantly reduced pathogenicity in the infection model Galleria mellonella. Along with transcriptomic and proteomic analyses, the presented data indicate that the methylation of RFs in P. aeruginosa seems to have a global effect on cellular processes related to the virulence of this nosocomial pathogen.
2013-05-31T11:03:57Z
2013-05-31T11:03:57Z
2013-05-31T11:03:57Z
2013-02
Article
The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosa PA14. 2013, 15 (2):597-609 Environ. Microbiol.
1462-2920
23278968
10.1111/1462-2920.12040
http://hdl.handle.net/10033/293149
Environmental microbiology
en
info:eu-repo/grantAgreement/EC/FP7/260276/
Archived with thanks to Environmental microbiology
openAccess
oai:repository.helmholtz-hzi.de:10033/2980862019-08-30T11:25:43Zcom_10033_620636col_10033_620637
Biofilms 2012: new discoveries and significant wrinkles in a dynamic field.
Haussler, Susanne
Fuqua, Clay
Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research, Braunschweig, and the Hannover Medical School, Hannover, Germany.
The ASM 6th Conference on Biofilms was held in Miami, Florida, 29 September to 4 October, 2012. The conference provided an opportunity for the exchange of new findings and ideas with regard to biofilm research. A wide range of findings, spanning applied biology, evolution, ecology, physiology, and molecular biology, were presented at the conference. This review summarizes the presentations with regard to emerging biofilm-related themes.
2013-08-13T13:36:35Z
2013-08-13T13:36:35Z
2013-08-13T13:36:35Z
2013-07
Article
Biofilms 2012: new discoveries and significant wrinkles in a dynamic field. 2013, 195 (13):2947-58 J. Bacteriol.
1098-5530
23625847
10.1128/JB.00239-13
http://hdl.handle.net/10033/298086
Journal of bacteriology
en
Archived with thanks to Journal of bacteriology
oai:repository.helmholtz-hzi.de:10033/3119392019-08-30T11:25:11Zcom_10033_620636col_10033_620637
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265.
Eckweiler, Denitsa
Bunk, Boyke
Spröer, Cathrin
Overmann, Jörg
Häussler, Susanne
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
The evolution of small-colony variants within Pseudomonas aeruginosa populations chronically infecting the cystic fibrosis lung is one example of the emergence of adapted subpopulations. Here, we present the complete genome sequence of the autoaggregative and hyperpiliated P. aeruginosa small-colony variant SCV20265, which was isolated from a cystic fibrosis (CF) patient.
2014-01-28T10:18:46Z
2014-01-28T10:18:46Z
2014-01-28T10:18:46Z
2014
Article
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265. 2014, 2 (1): Genome Announc
2169-8287
24459283
10.1128/genomeA.01232-13
http://hdl.handle.net/10033/311939
Genome announcements
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3173872019-08-30T11:36:05Zcom_10033_620636col_10033_620637
Effects of green tea compound epigallocatechin-3-gallate against Stenotrophomonas maltophilia infection and biofilm.
Vidigal, Pedrina G
Müsken, Mathias
Becker, Katrin A
Häussler, Susanne
Wingender, Jost
Steinmann, Eike
Kehrmann, Jan
Gulbins, Erich
Buer, Jan
Rath, Peter Michael
Steinmann, Jörg
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
We investigated the in vitro and in vivo activities of epigallocatechin-3-gallate (EGCg), a green tea component, against Stenotrophomonas maltophilia (Sm) isolates from cystic fibrosis (CF) patients. In vitro effects of EGCg and the antibiotic colistin (COL) on growth inhibition, survival, and also against young and mature biofilms of S. maltophilia were determined. Qualitative and quantitative changes on the biofilms were assessed by confocal laser scanning microscopy (CLSM). Further, in vivo effects of nebulized EGCg in C57BL/6 and Cftr mutant mice during acute Sm lung infection were evaluated. Subinhibitory concentrations of EGCg significantly reduced not only biofilm formation, but also the quantity of viable cells in young and mature biofilms. CLSM showed that EGCg-exposed biofilms exhibited either a change in total biofilm biovolume or an increase of the fraction of dead cells contained within the biofilm in a dose depended manner. Sm infected wild-type and Cftr mutant mice treated with 1,024 mg/L EGCg by inhalation exhibited significantly lower bacterial counts than those undergoing no treatment or treated with COL. EGCg displayed promising inhibitory and anti-biofilm properties against CF Sm isolates in vitro and significantly reduced Sm bacterial counts in an acute infection model with wild type and CF mice. This natural compound may represent a novel therapeutic agent against Sm infection in CF.
2014-05-23T13:53:16Z
2014-05-23T13:53:16Z
2014-05-23T13:53:16Z
2014
Article
Effects of green tea compound epigallocatechin-3-gallate against Stenotrophomonas maltophilia infection and biofilm. 2014, 9 (4):e92876 PLoS ONE
1932-6203
24690894
10.1371/journal.pone.0092876
http://hdl.handle.net/10033/317387
PloS one
en
Archived with thanks to PloS one
oai:repository.helmholtz-hzi.de:10033/3380202019-08-30T11:25:11Zcom_10033_620636col_10033_620637
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles.
Bielecki, Piotr
Muthukumarasamy, Uthayakumar
Eckweiler, Denitsa
Bielecka, Agata
Pohl, Sarah
Schanz, Ansgar
Niemeyer, Ute
Oumeraci, Tonio
von Neuhoff, Nils
Ghigo, Jean-Marc
Häussler, Susanne
Helmholtz Centre for infection research; Inhoffenstr. 7; D-38124 Braunschweig; Germany.
mRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease. Importance: Urinary tract infections (UTI) are very common; at least half of all women experience UTI, most of which are caused by pathogenic Escherichia coli strains. In this study, we applied massive parallel cDNA sequencing (RNA-seq) to provide unbiased, deep, and accurate insight into the nature and the dimension of the uropathogenic E. coli gene expression profile during an acute UTI within the human host. This work was undertaken to identify key players in physiological adaptation processes and, hence, potential targets for new infection prevention and therapy interventions specifically aimed at sabotaging bacterial adaptation to the human host.
2015-01-12T13:13:10Z
2015-01-12T13:13:10Z
2015-01-12T13:13:10Z
2014
Article
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles. 2014, 5 (4):e01075-14 MBio
2150-7511
25096872
10.1128/mBio.01075-14
http://hdl.handle.net/10033/338020
mBio
en
eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3381972019-08-30T11:26:13Zcom_10033_620636col_10033_620637
The extensive set of accessory Pseudomonas aeruginosa genomic components.
Pohl, Sarah
Klockgether, Jens
Eckweiler, Denitsa
Khaledi, Ariane
Schniederjans, Monika
Chouvarine, Philippe
Tümmler, Burkhard
Häussler, Susanne
Up to 20% of the chromosomal Pseudomonas aeruginosa DNA belong to the so-called accessory genome. Its elements are specific for subgroups or even single strains and are likely acquired by horizontal gene transfer (HGT). Similarities of the accessory genomic elements to DNA from other bacterial species, mainly the DNA of γ- and β-proteobacteria, indicate a role of interspecies HGT. In this study, we analysed the expression of the accessory genome in 150 clinical P. aeruginosa isolates as uncovered by transcriptome sequencing and the presence of accessory genes in eleven additional isolates. Remarkably, despite the large number of P. aeruginosa strains that have been sequenced to date, we found new strain-specific compositions of accessory genomic elements and a high portion (10-20%) of genes without P. aeruginosa homologues. Although some genes were detected to be expressed/present in several isolates, individual patterns regarding the genes, their functions and the possible origin of the DNA were widespread among the tested strains. Our results demonstrate the unaltered potential to discover new traits within the P. aeruginosa population and underline that the P. aeruginosa pangenome is likely to increase with increasing sequence information.
2015-01-13T15:52:31Z
2015-01-13T15:52:31Z
2015-01-13T15:52:31Z
2014-07
Article
The extensive set of accessory Pseudomonas aeruginosa genomic components. 2014, 356 (2):235-41 FEMS Microbiol. Lett.
1574-6968
24766399
10.1111/1574-6968.12445
http://hdl.handle.net/10033/338197
FEMS microbiology letters
en
eu-repo/grantAgreement/EC/FP7/260276
embargoedAccess
oai:repository.helmholtz-hzi.de:10033/3382112019-08-30T11:35:39Zcom_10033_620636col_10033_620637
The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.
Dötsch, Andreas
Eckweiler, Denitsa
Schniederjans, Monika
Zimmermann, Ariane
Jensen, Vanessa
Scharfe, Maren
Geffers, Robert
Häussler, Susanne
Helmholtz Centre of infection research; Inhoffenstr. 7; D-38124 Braunschweig; Germany.
In this study, we evaluated how gene expression differs in mature Pseudomonas aeruginosa biofilms as opposed to planktonic cells by the use of RNA sequencing technology that gives rise to both quantitative and qualitative information on the transcriptome. Although a large proportion of genes were consistently regulated in both the stationary phase and biofilm cultures as opposed to the late exponential growth phase cultures, the global biofilm gene expression pattern was clearly distinct indicating that biofilms are not just surface attached cells in stationary phase. A large amount of the genes found to be biofilm specific were involved in adaptation to microaerophilic growth conditions, repression of type three secretion and production of extracellular matrix components. Additionally, we found many small RNAs to be differentially regulated most of them similarly in stationary phase cultures and biofilms. A qualitative analysis of the RNA-seq data revealed more than 3000 putative transcriptional start sites (TSS). By the use of rapid amplification of cDNA ends (5'-RACE) we confirmed the presence of three different TSS associated with the pqsABCDE operon, two in the promoter of pqsA and one upstream of the second gene, pqsB. Taken together, this study reports the first transcriptome study on P. aeruginosa that employs RNA sequencing technology and provides insights into the quantitative and qualitative transcriptome including the expression of small RNAs in P. aeruginosa biofilms.
2015-01-13T14:55:28Z
2015-01-13T14:55:28Z
2015-01-13T14:55:28Z
2012
Article
The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. 2012, 7 (2):e31092 PLoS ONE
1932-6203
22319605
10.1371/journal.pone.0031092
http://hdl.handle.net/10033/338211
PloS one
en
eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3384912019-08-30T11:26:42Zcom_10033_306379com_10033_620636col_10033_306382col_10033_620637
Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity.
Blanka, Andrea
Schulz, Sebastian
Eckweiler, Denitsa
Franke, Raimo
Bielecka, Agata
Nicolai, Tanja
Casilag, Fiordiligie
Düvel, Juliane
Abraham, Wolf-Rainer
Kaever, Volkhard
Häussler, Susanne
Helmholtz Centre of infection research; Inhoffenstr. 7; D38124 Braunschweig; Germany.
Pseudomonas aeruginosa is distinguished by its broad metabolic diversity and its remarkable capability for adaptation, which relies on a large collection of transcriptional regulators and alternative sigma (σ) factors. The largest group of alternative σ factors is that of the extracytoplasmic function (ECF) σ factors, which control key transduction pathways for maintenance of envelope homeostasis in response to external stress and cell growth. In addition, there are specific roles of alternative σ factors in regulating the expression of virulence and virulence-associated genes. Here, we analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX-dependent regulon in P. aeruginosa in response to low-osmolarity-medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and cyclic di-GMP (c-di-GMP) signaling. In accordance, a sigX deletion mutant exhibited altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels, and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative σ factor SigX, revealing its role in complex virulence-associated phenotypes in P. aeruginosa.
2015-01-16T15:07:52Z
2015-01-16T15:07:52Z
2015-01-16T15:07:52Z
2014-01
Article
Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity. 2014, 196 (2):345-56 J. Bacteriol.
1098-5530
24187091
10.1128/JB.01034-13
http://hdl.handle.net/10033/338491
Journal of bacteriology
en
info:eu-repo/grantAgreement/EC/FP7/260276/
openAccess
oai:repository.helmholtz-hzi.de:10033/3442322019-08-30T11:25:43Zcom_10033_620636col_10033_620637
The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms.
Brouwer, Stephan
Pustelny, Christian
Ritter, Christiane
Klinkert, Birgit
Narberhaus, Franz
Häussler, Susanne
Regulation of gene expression plays a key role in bacterial adaptability to changes in the environment. An integral part of this gene regulatory network is achieved via quorum sensing (QS) systems that coordinate bacterial responses under high cellular densities. In the nosocomial pathogen Pseudomonas aeruginosa, the 2-alkyl-4-quinolone (pqs) signaling pathway is crucial for bacterial survival under stressful conditions. Biosynthesis of the Pseudomonas quinolone signal (PQS) is dependent on the pqsABCDE operon, which is positively regulated by the LysR family regulator PqsR and repressed by the transcriptional regulator protein RhlR. However, the molecular mechanisms underlying this inhibition have remained elusive. Here, we demonstrate that not only PqsR but also RhlR activates transcription of pqsA. The latter uses an alternative transcriptional start site and induces expression of a longer transcript that forms a secondary structure in the 5' untranslated leader region. As a consequence, access of the ribosome to the Shine-Dalgarno sequence is restricted and translation efficiency reduced. We propose a model of a novel posttranscriptional regulation mechanism that fine-tunes PQS biosynthesis, thus highlighting the complexity of quorum sensing in P. aeruginosa.
2015-02-06T10:26:06Z
2015-02-06T10:26:06Z
2015-02-06T10:26:06Z
2014-12
Article
The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms. 2014, 196 (23):4163-71 J. Bacteriol.
1098-5530
25225275
10.1128/JB.02000-14
http://hdl.handle.net/10033/344232
Journal of bacteriology
en
oai:repository.helmholtz-hzi.de:10033/3451682019-08-30T11:29:47Zcom_10033_620636col_10033_620637
Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system.
Pustelny, Christian
Komor, Uliana
Pawar, Vinay
Lorenz, Anne
Bielecka, Agata
Moter, Annette
Gocht, Benjamin
Eckweiler, Denitsa
Müsken, Mathias
Grothe, Claudia
Lünsdorf, Heinrich
Weiss, Siegfried
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The recent finding that high numbers of strict anaerobes are present in the respiratory tract of cystic fibrosis (CF) patients has drawn attention to the pathogenic contribution of the CF microbiome to airway disease. In this study, we investigated the specific interactions of the most dominant bacterial CF pathogen, Pseudomonas aeruginosa, with the anaerobic bacterium Veillonella parvula, which has been recovered at comparable cell numbers from the respiratory tract of CF patients. In addition to growth competition experiments, transcriptional profiling, and analyses of biofilm formation by in vitro studies, we used our recently established in vivo murine tumor model to investigate mutual influences of the two pathogens during a biofilm-associated infection process. We found that P. aeruginosa and V. parvula colonized distinct niches within the tumor. Interestingly, significantly higher cell numbers of P. aeruginosa could be recovered from the tumor tissue when mice were coinfected with both bacterial species than when mice were monoinfected with P. aeruginosa. Concordantly, the results of in vivo transcriptional profiling implied that the presence of V. parvula supports P. aeruginosa growth at the site of infection in the host, and the higher P. aeruginosa load correlated with clinical deterioration of the host. Although many challenges must be overcome to dissect the specific interactions of coinfecting bacteria during an infection process, our findings exemplarily demonstrate that the complex interrelations between coinfecting microorganisms and the immune responses determine clinical outcome to a much greater extent than previously anticipated.
2015-02-24T15:27:08Z
2015-02-24T15:27:08Z
2015-02-24T15:27:08Z
2015-01
Article
Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system. 2015, 83 (1):417-29 Infect. Immun.
1098-5522
25385800
10.1128/IAI.02234-14
http://hdl.handle.net/10033/345168
Infection and immunity
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3465532019-08-30T11:26:42Zcom_10033_620636col_10033_620637
Comprehensive MALDI-TOF Biotyping of the Non-Redundant Harvard Pseudomonas aeruginosa PA14 Transposon Insertion Mutant Library.
Oumeraci, Tonio
Jensen, Vanessa
Talbot, Steven R
Hofmann, Winfried
Kostrzewa, Markus
Schlegelberger, Brigitte
von Neuhoff, Nils
Häussler, Susanne
Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments.
2015-03-12T11:05:27Z
2015-03-12T11:05:27Z
2015-03-12T11:05:27Z
2015
Article
Comprehensive MALDI-TOF Biotyping of the Non-Redundant Harvard Pseudomonas aeruginosa PA14 Transposon Insertion Mutant Library. 2015, 10 (2):e0117144 PLoS ONE
1932-6203
25665154
10.1371/journal.pone.0117144
http://hdl.handle.net/10033/346553
PloS one
en
oai:repository.helmholtz-hzi.de:10033/3467122019-08-30T11:26:42Zcom_10033_620636col_10033_620637
Pseudomonas aeruginosa ceftolozane-tazobactam resistance development requires multiple mutations leading to overexpression and structural modification of AmpC.
Cabot, Gabriel
Bruchmann, Sebastian
Mulet, Xavier
Zamorano, Laura
Moyà, Bartolomé
Juan, Carlos
Haussler, Susanne
Oliver, Antonio
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
We compared the dynamics and mechanisms of resistance development to ceftazidime, meropenem, ciprofloxacin, and ceftolozane-tazobactam in wild-type (PAO1) and mutator (PAOMS, ΔmutS) P. aeruginosa. The strains were incubated for 24 h with 0.5 to 64× MICs of each antibiotic in triplicate experiments. The tubes from the highest antibiotic concentration showing growth were reinoculated in fresh medium containing concentrations up to 64× MIC for 7 consecutive days. The susceptibility profiles and resistance mechanisms were assessed in two isolated colonies from each step, antibiotic, and strain. Ceftolozane-tazobactam-resistant mutants were further characterized by whole-genome analysis through RNA sequencing (RNA-seq). The development of high-level resistance was fastest for ceftazidime, followed by meropenem and ciprofloxacin. None of the mutants selected with these antibiotics showed cross-resistance to ceftolozane-tazobactam. On the other hand, ceftolozane-tazobactam resistance development was much slower, and high-level resistance was observed for the mutator strain only. PAO1 derivatives that were moderately resistant (MICs, 4 to 8 μg/ml) to ceftolozane-tazobactam showed only 2 to 4 mutations, which determined global pleiotropic effects associated with a severe fitness cost. High-level-resistant (MICs, 32 to 128 μg/ml) PAOMS derivatives showed 45 to 53 mutations. Major changes in the global gene expression profiles were detected in all mutants, but only PAOMS mutants showed ampC overexpression, which was caused by dacB or ampR mutations. Moreover, all PAOMS mutants contained 1 to 4 mutations in the conserved residues of AmpC (F147L, Q157R, G183D, E247K, or V356I). Complementation studies revealed that these mutations greatly increased ceftolozane-tazobactam and ceftazidime MICs but reduced those of piperacillin-tazobactam and imipenem, compared to those in wild-type ampC. Therefore, the development of high-level resistance to ceftolozane-tazobactam appears to occur efficiently only in a P. aeruginosa mutator background, in which multiple mutations lead to overexpression and structural modifications of AmpC.
2015-03-16T15:20:35Z
2015-03-16T15:20:35Z
2015-03-16T15:20:35Z
2014-06
Article
Pseudomonas aeruginosa ceftolozane-tazobactam resistance development requires multiple mutations leading to overexpression and structural modification of AmpC. 2014, 58 (6):3091-9 Antimicrob. Agents Chemother.
1098-6596
24637685
10.1128/AAC.02462-13
http://hdl.handle.net/10033/346712
Antimicrobial agents and chemotherapy
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/3468462019-08-30T11:27:16Zcom_10033_620636col_10033_620637
Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk.
Schulz, Sebastian
Eckweiler, Denitsa
Bielecka, Agata
Nicolai, Tanja
Franke, Raimo
Dötsch, Andreas
Hornischer, Klaus
Bruchmann, Sebastian
Düvel, Juliane
Häussler, Susanne
Institute for Molecular Bacteriology, TWINCORE GmbH.
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.
2015-03-18T14:57:33Z
2015-03-18T14:57:33Z
2015-03-18T14:57:33Z
2015-03
Article
Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk. 2015, 11 (3):e1004744 PLoS Pathog.
1553-7374
25780925
10.1371/journal.ppat.1004744
http://hdl.handle.net/10033/346846
PLoS pathogens
oai:repository.helmholtz-hzi.de:10033/5582862019-08-30T11:28:23Zcom_10033_620636col_10033_620637
Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition.
Blanka, Andrea
Düvel, Juliane
Dötsch, Andreas
Klinkert, Birgit
Abraham, Wolf-Rainer
Kaever, Volkhard
Ritter, Christiane
Narberhaus, Franz
Häussler, Susanne
Institute for Molecular Bacteriology, TWINCORE,30625 Hannover, Germany.
Most bacteria can form multicellular communities called biofilms on biotic and abiotic surfaces. This multicellular response to surface contact correlates with an increased resistance to various adverse environmental conditions, including those encountered during infections of the human host and exposure to antimicrobial compounds. Biofilm formation occurs when freely swimming (planktonic) cells encounter a surface, which stimulates the chemosensory-like, surface-sensing system Wsp and leads to generation of the intracellular second messenger 3',5'-cyclic-di-guanosine monophosphate (c-di-GMP). We identified adaptive mutations in a clinical small colony variant (SCV) of Pseudomonas aeruginosa and correlated their presence with self-aggregating growth behavior and an enhanced capacity to form biofilms. We present evidence that a point mutation in the 5' untranslated region of the accBC gene cluster, which encodes components of an enzyme responsible for fatty acid biosynthesis, was responsible for a stabilized mRNA structure that resulted in reduced translational efficiency and an increase in the proportion of short-chain fatty acids in the plasma membrane. We propose a model in which these changes in P. aeruginosa serve as a signal for the Wsp system to constitutively produce increased amounts of c-di-GMP and thus play a role in the regulation of adhesion-stimulated bacterial responses.
2015-06-19T13:28:02Z
2015-06-19T13:28:02Z
2015-06-19T13:28:02Z
2015
Article
Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition. 2015, 8 (372):ra36 Sci Signal
1937-9145
25872871
10.1126/scisignal.2005943
http://hdl.handle.net/10033/558286
Science signaling
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/5607452019-08-30T11:36:32Zcom_10033_620636col_10033_620637
In Vivo Efficacy of Antimicrobials against Biofilm-Producing Pseudomonas aeruginosa.
Pawar, Vinay
Komor, Uliana
Kasnitz, Nadine
Bielecki, Piotr
Pils, Marina C
Gocht, Benjamin
Moter, Annette
Rohde, Manfred
Weiss, Siegfried
Häussler, Susanne
Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, Hannover, Germany.
Patients suffering from cystic fibrosis (CF) are commonly affected by chronic Pseudomonas aeruginosa biofilm infections. This is the main cause for the high disease severity. In this study, we demonstrate that P. aeruginosa is able to efficiently colonize murine solid tumors after intravenous injection and to form biofilms in this tissue. Biofilm formation was evident by electron microscopy. Such structures could not be observed with transposon mutants, which were defective in biofilm formation. Comparative transcriptional profiling of P. aeruginosa indicated physiological similarity of the bacteria in the murine tumor model and the CF lung. The efficacy of currently available antibiotics for treatment of P. aeruginosa-infected CF lungs, such as ciprofloxacin, colistin, and tobramycin, could be tested in the tumor model. We found that clinically recommended doses of these antibiotics were unable to eliminate wild-type P. aeruginosa PA14 while being effective against biofilm-defective mutants. However, colistin-tobramycin combination therapy significantly reduced the number of P. aeruginosa PA14 cells in tumors at lower concentrations. Hence, we present a versatile experimental system that is providing a platform to test approved and newly developed antibiofilm compounds.
2015-07-20T13:07:42Z
2015-07-20T13:07:42Z
2015-07-20T13:07:42Z
2015-08
Article
In Vivo Efficacy of Antimicrobials against Biofilm-Producing Pseudomonas aeruginosa. 2015, 59 (8):4974-81 Antimicrob. Agents Chemother.
1098-6596
26055372
10.1128/AAC.00194-15
http://hdl.handle.net/10033/560745
Antimicrobial agents and chemotherapy
en
oai:repository.helmholtz-hzi.de:10033/6207012019-08-30T11:36:32Zcom_10033_620636col_10033_620637
Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome
Dötsch, Andreas
Pommerenke, Claudia
Bredenbruch, Florian
Geffers, Robert
Häussler, Susanne
Abstract Background Whole genome sequencing techniques have added a new dimension to studies on bacterial adaptation, evolution and diversity in chronic infections. By using this powerful approach it was demonstrated that Pseudomonas aeruginosa undergoes intense genetic adaptation processes, crucial in the development of persistent disease. The challenge ahead is to identify universal infection relevant adaptive bacterial traits as potential targets for the development of alternative treatment strategies. Results We developed a microarray-based method applicable for discovery of single nucleotide polymorphisms (SNPs) in P. aeruginosa as an easy and economical alternative to whole genome sequencing. About 50% of all SNPs theoretically covered by the array could be detected in a comparative hybridization of PAO1 and PA14 genomes at high specificity (> 0.996). Variations larger than SNPs were detected at much higher sensitivities, reaching nearly 100% for genetic differences affecting multiple consecutive probe oligonucleotides. The detailed comparison of the in silico alignment with experimental hybridization data lead to the identification of various factors influencing sensitivity and specificity in SNP detection and to the identification of strain specific features such as a large deletion within the PA4684 and PA4685 genes in the Washington Genome Center PAO1. Conclusion The application of the genome array as a tool to identify adaptive mutations, to depict genome organizations, and to identify global regulons by the "ChIP-on-chip" technique will expand our knowledge on P. aeruginosa adaptation, evolution and regulatory mechanisms of persistence on a global scale and thus advance the development of effective therapies to overcome persistent disease.
2017-01-16T09:19:13Z
2017-01-16T09:19:13Z
2017-01-16T09:19:13Z
2009-01-19
Journal Article
BMC Genomics. 2009 Jan 19;10(1):29
http://dx.doi.org/10.1186/1471-2164-10-29
http://hdl.handle.net/10033/620701
en
Dötsch et al.
oai:repository.helmholtz-hzi.de:10033/5814172019-08-30T11:27:46Zcom_10033_620636col_10033_620637
Cross talk between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa.
Bielecki, Piotr
Jensen, Vanessa
Schulze, Wiebke
Gödeke, Julia
Strehmel, Janine
Eckweiler, Denitsa
Nicolai, Tanja
Bielecka, Agata
Wille, Thorsten
Gerlach, Roman G
Häussler, Susanne
HZI-Helmholzzentrum für Infektionsforschung
Two-component systems (TCS) serve as stimulus-response coupling mechanisms to allow organisms to adapt to a variety of environmental conditions. The opportunistic pathogen Pseudomonas aeruginosa encodes for more than 100 TCS components. To avoid unwanted cross-talk, signaling cascades are very specific, with one sensor talking to its cognate response regulator (RR). However, cross-regulation may provide means to integrate different environmental stimuli into a harmonized output response. By applying a split luciferase complementation assay, we identified a functional interaction of two RRs of the OmpR/PhoB subfamily, namely PhoB and TctD in P. aeruginosa. Transcriptional profiling, ChIP-seq analysis and a global motif scan uncovered the regulons of the two RRs as well as a quadripartite binding motif in six promoter regions. Phosphate limitation resulted in PhoB-dependent expression of the downstream genes, whereas the presence of TctD counteracted this activation. Thus, the integration of two important environmental signals e.g. phosphate availability and the carbon source are achieved by a titration of the relative amounts of two phosphorylated RRs that inversely regulate a common subset of genes. In conclusion, our results on the PhoB and TctD mediated two-component signal transduction pathways exemplify how P. aeruginosa may exploit cross-regulation to adapt bacterial behavior to complex environments.
2015-10-29T11:59:02Z
2015-10-29T11:59:02Z
2015-10-29T11:59:02Z
2015-07-27
Article
Cross talk between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa. 2015, 43 (13):6413-25 Nucleic Acids Res.
1362-4962
26082498
10.1093/nar/gkv599
http://hdl.handle.net/10033/581417
Nucleic acids research
en
oai:repository.helmholtz-hzi.de:10033/5822942019-08-30T11:27:46Zcom_10033_620636col_10033_620637
The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation.
Dötsch, Andreas
Schniederjans, Monika
Khaledi, Ariane
Hornischer, Klaus
Schulz, Sebastian
Bielecka, Agata
Eckweiler, Denitsa
Pohl, Sarah
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Phenotypic variability among bacteria depends on gene expression in response to different environments, and it also reflects differences in genomic structure. In this study, we analyzed transcriptome sequencing (RNA-seq) profiles of 151 Pseudomonas aeruginosa clinical isolates under standard laboratory conditions and of one P. aeruginosa type strain under 14 different environmental conditions. Our approach allowed dissection of the impact of the genetic background versus environmental cues on P. aeruginosa gene expression profiles and revealed that phenotypic variation was larger in response to changing environments than between genomically different isolates. We demonstrate that mutations within the global regulator LasR affect more than one trait (pleiotropy) and that the interaction between mutations (epistasis) shapes the P. aeruginosa phenotypic plasticity landscape. Because of pleiotropic and epistatic effects, average genotype and phenotype measures appeared to be uncorrelated in P. aeruginosa.
2015-11-17T14:55:00Z
2015-11-17T14:55:00Z
2015-11-17T14:55:00Z
2015
Article
The Pseudomonas aeruginosa Transcriptional Landscape Is Shaped by Environmental Heterogeneity and Genetic Variation. 2015, 6 (4):e00749 MBio
2150-7511
26126853
10.1128/mBio.00749-15
http://hdl.handle.net/10033/582294
mBio
en
info:eu-repo/grantAgreement/EC/FP7/260276
openAccess
oai:repository.helmholtz-hzi.de:10033/5839882019-08-30T11:30:58Zcom_10033_620636col_10033_620637
Application of Synthetic Peptide Arrays To Uncover Cyclic Di-GMP Binding Motifs
Düvel, Juliane
Bense, Sarina
Möller, Stefan
Bertinetti, Daniela
Schwede, Frank
Morr, Michael
Eckweiler, Denitsa
Genieser, Hans-Gottfried
Jänsch, Lothar
Herberg, Friedrich W.
Frank, Ronald
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
ABSTRACT High levels of the universal bacterial second messenger cyclic di-GMP (c-di-GMP) promote the establishment of surface-attached growth in many bacteria. Not only can c-di-GMP bind to nucleic acids and directly control gene expression, but it also binds to a diverse array of proteins of specialized functions and orchestrates their activity. Since its development in the early 1990s, the synthetic peptide array technique has become a powerful tool for high-throughput approaches and was successfully applied to investigate the binding specificity of protein-ligand interactions. In this study, we used peptide arrays to uncover the c-di-GMP binding site of a Pseudomonas aeruginosa protein (PA3740) that was isolated in a chemical proteomics approach. PA3740 was shown to bind c-di-GMP with a high affinity, and peptide arrays uncovered LKKALKKQTNLR to be a putative c-di-GMP binding motif. Most interestingly, different from the previously identified c-di-GMP binding motif of the PilZ domain (RXXXR) or the I site of diguanylate cyclases (RXXD), two leucine residues and a glutamine residue and not the charged amino acids provided the key residues of the binding sequence. Those three amino acids are highly conserved across PA3740 homologs, and their singular exchange to alanine reduced c-di-GMP binding within the full-length protein. IMPORTANCE In many bacterial pathogens the universal bacterial second messenger c-di-GMP governs the switch from the planktonic, motile mode of growth to the sessile, biofilm mode of growth. Bacteria adapt their intracellular c-di-GMP levels to a variety of environmental challenges. Several classes of c-di-GMP binding proteins have been structurally characterized, and diverse c-di-GMP binding domains have been identified. Nevertheless, for several c-di-GMP receptors, the binding motif remains to be determined. Here we show that the use of a synthetic peptide array allowed the identification of a c-di-GMP binding motif of a putative c-di-GMP receptor protein in the opportunistic pathogen P. aeruginosa . The application of synthetic peptide arrays will facilitate the search for additional c-di-GMP receptor proteins and aid in the characterization of c-di-GMP binding motifs.
2015-12-16T15:00:18Z
2015-12-16T15:00:18Z
2015-12-16T15:00:18Z
2016-01-01
Article
Application of Synthetic Peptide Arrays To Uncover Cyclic Di-GMP Binding Motifs 2016, 198 (1):138 Journal of Bacteriology
1098-5530
26324453[
10.1128/JB.00377-15
http://hdl.handle.net/10033/583988
Journal of Bacteriology
http://jb.asm.org/lookup/doi/10.1128/JB.00377-15
oai:repository.helmholtz-hzi.de:10033/5933092019-08-30T11:33:29Zcom_10033_620636col_10033_620637
Very high-density lipoprotein and vitellin as carriers of novel biliverdins IXα with a farnesyl side-chain presumably derived from heme A in Spodoptera littoralis.
Kayser, Hartmut
Nimtz, Manfred
Ringler, Philippe
Müller, Shirley A
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
Bilins in complex with specific proteins play key roles in many forms of life. Biliproteins have also been isolated from insects; however, structural details are rare and possible functions largely unknown. Recently, we identified a high-molecular weight biliprotein from a moth, Cerura vinula, as an arylphorin-type hexameric storage protein linked to a novel farnesyl biliverdin IXα; its unusual structure suggests formation by cleavage of mitochondrial heme A. In the present study of another moth, Spodoptera littoralis, we isolated two different biliproteins. These proteins were identified as a very high-density lipoprotein (VHDL) and as vitellin, respectively, by mass spectrometric sequencing. Both proteins are associated with three different farnesyl biliverdins IXα: the one bilin isolated from C. vinula and two new structurally closely related bilins, supposed to be intermediates of heme A degradation. The different bilin composition of the two biliproteins suggests that the presumed oxidations at the farnesyl side-chain take place mainly during egg development. The egg bilins are supposedly transferred from hemolymph VHDL to vitellin in the female. Both biliproteins show strong induced circular dichroism activity compatible with a predominance of the M-conformation of the bilins. This conformation is opposite to that of the arylphorin-type biliprotein from C. vinula. Electron microscopy of the VHDL-type biliprotein from S. littoralis provided a preliminary view of its structure as a homodimer and confirmed the biochemically determined molecular mass of ∼350 kDa. Further, images of S. littoralis hexamerins revealed a 2 × 3 construction identical to that known from the hexamerin from C. vinula.
2016-01-12T14:18:53Z
2016-01-12T14:18:53Z
2016-01-12T14:18:53Z
2016-01
Article
Very high-density lipoprotein and vitellin as carriers of novel biliverdins IXα with a farnesyl side-chain presumably derived from heme A in Spodoptera littoralis. 2016, 68:41-51 Insect Biochem. Mol. Biol.
1879-0240
26546815
10.1016/j.ibmb.2015.10.017
http://hdl.handle.net/10033/593309
Insect biochemistry and molecular biology
en
oai:repository.helmholtz-hzi.de:10033/5944162019-08-30T11:37:44Zcom_10033_620636col_10033_620637col_10033_620637
Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa.
Dötsch, Andreas
Klawonn, Frank
Jarek, Michael
Scharfe, Maren
Blöcker, Helmut
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus.
2016-01-20T14:08:00Z
2016-01-20T14:08:00Z
2016-01-20T14:08:00Z
2010
Article
Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa. 2010, 11:234 BMC Genomics
1471-2164
20380691
10.1186/1471-2164-11-234
http://hdl.handle.net/10033/594416
BMC genomics
en
oai:repository.helmholtz-hzi.de:10033/6010402019-08-30T11:30:58Zcom_10033_620636col_10033_620637
RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.
Tata, Muralidhar
Wolfinger, Michael T
Amman, Fabian
Roschanski, Nicole
Dötsch, Andreas
Sonnleitner, Elisabeth
Häussler, Susanne
Bläsi, Udo
Helmholtz Centre for infection research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.
The opportunistic human pathogen Pseudomonas aeruginosa can thrive under microaerophilic to anaerobic conditions in the lungs of cystic fibrosis patients. RNASeq based comparative RNA profiling of the clinical isolate PA14 cultured in synthetic cystic fibrosis medium was performed after planktonic growth (OD600 = 2.0; P), 30 min after shift to anaerobiosis (A-30) and after anaerobic biofilm growth for 96h (B-96) with the aim to reveal differentially regulated functions impacting on sustained anoxic biofilm formation as well as on tolerance towards different antibiotics. Most notably, functions involved in sulfur metabolism were found to be up-regulated in B-96 cells when compared to A-30 cells. Based on the transcriptome studies a set of transposon mutants were screened, which revealed novel functions involved in anoxic biofilm growth.In addition, these studies revealed a decreased and an increased abundance of the oprD and the mexCD-oprJ operon transcripts, respectively, in B-96 cells, which may explain their increased tolerance towards meropenem and to antibiotics that are expelled by the MexCD-OprD efflux pump. The OprI protein has been implicated as a target for cationic antimicrobial peptides, such as SMAP-29. The transcriptome and subsequent Northern-blot analyses showed that the abundance of the oprI transcript encoding the OprI protein is strongly decreased in B-96 cells. However, follow up studies revealed that the susceptibility of a constructed PA14ΔoprI mutant towards SMAP-29 was indistinguishable from the parental wild-type strain, which questions OprI as a target for this antimicrobial peptide in strain PA14.
2016-03-09T15:26:12Z
2016-03-09T15:26:12Z
2016-03-09T15:26:12Z
2016
Article
RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium. 2016, 11 (1):e0147811 PLoS ONE
1932-6203
26821182
10.1371/journal.pone.0147811
http://hdl.handle.net/10033/601040
PloS one
en
oai:repository.helmholtz-hzi.de:10033/6182422019-08-30T11:30:58Zcom_10033_620636col_10033_620637
Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation.
Bruchmann, Sebastian
Muthukumarasamy, Uthayakumar
Pohl, Sarah
Preusse, Matthias
Bielecka, Agata
Nicolai, Tanja
Hamann, Isabell
Hillert, Roger
Kola, Axel
Gastmeier, Petra
Eckweiler, Denitsa
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Health-care-associated infections by multi-drug-resistant bacteria constitute one of the greatest challenges to modern medicine. Bacterial pathogens devise various mechanisms to withstand the activity of a wide range of antimicrobial compounds, among which the acquisition of carbapenemases is one of the most concerning. In Klebsiella pneumoniae, the dissemination of the K. pneumoniae carbapenemase is tightly connected to the global spread of certain clonal lineages. Although antibiotic resistance is a key driver for the global distribution of epidemic high-risk clones, there seem to be other adaptive traits that may explain their success. Here, we exploited the power of deep transcriptome profiling (RNA-seq) to shed light on the transcriptomic landscape of 37 clinical K. pneumoniae isolates of diverse phylogenetic origins. We identified a large set of 3346 genes which was expressed in all isolates. While the core-transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence. This allowed for the identification of a diminished expression of biofilm-specific genes within the low biofilm producing ST258 isolates as a sequence type-specific trait.
2016-08-11T10:59:08Z
2016-08-11T10:59:08Z
2016-08-11T10:59:08Z
2015-11
Article
Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation. 2015, 17 (11):4690-710 Environ. Microbiol.
1462-2920
26261087
10.1111/1462-2920.13016
http://hdl.handle.net/10033/618242
Environmental microbiology
en
nfo:eu-repo/grantAgreement/EC/FP7/260276
http://creativecommons.org/licenses/by-nc-sa/4.0/
embargoedAccess
oai:repository.helmholtz-hzi.de:10033/6208712019-08-30T11:36:32Zcom_10033_620636col_10033_620637
Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.
Doberenz, Sebastian
Eckweiler, Denitsa
Reichert, Olga
Jensen, Vanessa
Bunk, Boyke
Spröer, Cathrin
Kordes, Adrian
Frangipani, Emanuela
Luong, Khai
Korlach, Jonas
Heeb, Stephan
Overmann, Jörg
Kaever, Volkhard
Häussler, Susanne
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved sequence motif targeted by an adenine methyltransferase of a type I R-M system and quantified the presence of N(6)-methyladenine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1 methylation status were dependent on growth conditions and affected P. aeruginosa pathogenicity in a Galleria mellonella infection model. Furthermore, we found that methylated motifs in promoter regions led to shifts in sense and antisense gene expression, emphasizing the role of enzymatic DNA methylation as an epigenetic control of phenotypic traits in P. aeruginosa Since the DNA methylation enzymes are not encoded in the core genome, our findings illustrate how the acquisition of accessory genes can shape the global P. aeruginosa transcriptome and thus may facilitate adaptation to new and challenging habitats.IMPORTANCE With the introduction of advanced technologies, epigenetic regulation by DNA methyltransferases in bacteria has become a subject of intense studies. Here we identified an adenosine DNA methyltransferase in the opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA methylation of a conserved sequence motif. The methylation level of all target sequences throughout the PAO1 genome was approximated to be in the range of 65 to 85% and was dependent on growth conditions. Inactivation of the methyltransferase revealed an attenuated-virulence phenotype in the Galleria mellonella infection model. Furthermore, differential expression of more than 90 genes was detected, including the small regulatory RNA prrF1, which contributes to a global iron-sparing response via the repression of a set of gene targets. Our finding of a methylation-dependent repression of the antisense transcript of the prrF1 small regulatory RNA significantly expands our understanding of the regulatory mechanisms underlying active DNA methylation in bacteria.
2017-03-24T11:43:46Z
2017-03-24T11:43:46Z
2017-03-24T11:43:46Z
2017-02-21
Article
Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles. 2017, 8 (1) MBio
2150-7511
28223461
10.1128/mBio.02312-16
http://hdl.handle.net/10033/620871
mBio
en
info:eu-repo/grantAgreement/EC/FP7/260276
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
oai:repository.helmholtz-hzi.de:10033/6209062019-08-30T11:29:47Zcom_10033_620636col_10033_620637
Unravelling post-transcriptional PrmC-dependent regulatory mechanisms in Pseudomonas aeruginosa.
Krueger, Jonas
Pohl, Sarah
Preusse, Matthias
Kordes, Adrian
Rugen, Nils
Schniederjans, Monika
Pich, Andreas
Häussler, Susanne
Twincore, Zentrum für experimentelle und klinische Infektionsforschung GmbH, Feodor-Lynen Str. 7, 30625 Hannover, Germany.
Transcriptional regulation has a central role in cellular adaptation processes and is well investigated. In contrast, the importance of the post-transcriptional regulation on these processes is less well defined. The technological advancements have been critical to precisely quantify protein and mRNA level changes and hold promise to provide more insights into how post-transcriptional regulation determines phenotypes. In Pseudomonas aeruginosa the methyltransferase PrmC methylates peptide chain release factors to facilitate translation termination. Loss of PrmC activity abolishes anaerobic growth and leads to reduced production of quorum sensing-associated virulence factors. Here, by applying SILAC technology in combination with mRNA-sequencing, they provide evidence that the P. aeruginosa phenotype can be attributed to a change in protein to mRNA ratios of selected protein groups. The UAG-dependent translation termination was more dependent on PrmC activity than the UAA- and UGA-dependent translation termination. Additionally, a bias toward UAG stop codons in global transcriptional regulators was found. The finding that this bias in stop codon usage determines the P. aeruginosa phenotype is unexpected and adds complexity to regulatory circuits. Via modulation of PrmC activity the bacterial cell can cross-regulate targets independently of transcriptional signals, a process with an underestimated impact on the bacterial phenotype.
2017-05-03T14:44:40Z
2017-05-03T14:44:40Z
2017-05-03T14:44:40Z
2016-10
Article
Unravelling post-transcriptional PrmC-dependent regulatory mechanisms in Pseudomonas aeruginosa. 2016, 18 (10):3583-3592 Environ. Microbiol.
1462-2920
27376486
10.1111/1462-2920.13435
http://hdl.handle.net/10033/620906
Environmental microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6209592019-08-30T11:27:16Zcom_10033_620636col_10033_620637
An oral multispecies biofilm model for high content screening applications.
Kommerein, Nadine
Stumpp, Sascha N
Müsken, Mathias
Ehlert, Nina
Winkel, Andreas
Häussler, Susanne
Behrens, Peter
Buettner, Falk F R
Stiesch, Meike
Helmholtz Centre for infection research, Inhoffenstr.7, 38124 Braunschweig, Germany.
Peri-implantitis caused by multispecies biofilms is a major complication in dental implant treatment. The bacterial infection surrounding dental implants can lead to bone loss and, in turn, to implant failure. A promising strategy to prevent these common complications is the development of implant surfaces that inhibit biofilm development. A reproducible and easy-to-use biofilm model as a test system for large scale screening of new implant surfaces with putative antibacterial potency is therefore of major importance. In the present study, we developed a highly reproducible in vitro four-species biofilm model consisting of the highly relevant oral bacterial species Streptococcus oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. The application of live/dead staining, quantitative real time PCR (qRT-PCR), scanning electron microscopy (SEM) and urea-NaCl fluorescence in situ hybridization (urea-NaCl-FISH) revealed that the four-species biofilm community is robust in terms of biovolume, live/dead distribution and individual species distribution over time. The biofilm community is dominated by S. oralis, followed by V. dispar, A. naeslundii and P. gingivalis. The percentage distribution in this model closely reflects the situation in early native plaques and is therefore well suited as an in vitro model test system. Furthermore, despite its nearly native composition, the multispecies model does not depend on nutrient additives, such as native human saliva or serum, and is an inexpensive, easy to handle and highly reproducible alternative to the available model systems. The 96-well plate format enables high content screening for optimized implant surfaces impeding biofilm formation or the testing of multiple antimicrobial treatment strategies to fight multispecies biofilm infections, both exemplary proven in the manuscript.
2017-06-19T13:17:48Z
2017-06-19T13:17:48Z
2017-06-19T13:17:48Z
2017
Article
An oral multispecies biofilm model for high content screening applications. 2017, 12 (3):e0173973 PLoS ONE
1932-6203
28296966
10.1371/journal.pone.0173973
http://hdl.handle.net/10033/620959
PloS one
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210032019-08-30T11:30:32Zcom_10033_620636col_10033_620637
Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa.
Pusic, Petra
Tata, Muralidhar
Wolfinger, Michael T
Sonnleitner, Elisabeth
Häussler, Susanne
Bläsi, Udo
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Pseudomonas aeruginosa (PA) can thrive in anaerobic biofilms in the lungs of cystic fibrosis (CF) patients. Here, we show that CrcZ is the most abundant PA14 RNA bound to the global regulator Hfq in anoxic biofilms grown in cystic fibrosis sputum medium. Hfq was crucial for anoxic biofilm formation. This observation complied with an RNAseq based transcriptome analysis and follow up studies that implicated Hfq in regulation of a central step preceding denitrification. CrcZ is known to act as a decoy that sequesters Hfq during relief of carbon catabolite repression, which in turn alleviates Hfq-mediated translational repression of catabolic genes. We therefore inferred that CrcZ indirectly impacts on biofilm formation by competing for Hfq. This hypothesis was supported by the findings that over-production of CrcZ mirrored the biofilm phenotype of the hfq deletion mutant, and that deletion of the crcZ gene augmented biofilm formation. To our knowledge, this is the first example where competition for Hfq by CrcZ cross-regulates an Hfq-dependent physiological process unrelated to carbon metabolism.
2017-07-11T09:45:47Z
2017-07-11T09:45:47Z
2017-07-11T09:45:47Z
2016-12-21
Article
Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa. 2016, 6:39621 Sci Rep
2045-2322
28000785
10.1038/srep39621
http://hdl.handle.net/10033/621003
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6210392019-08-30T11:37:44Zcom_10033_620533com_10033_620636com_10033_620644col_10033_620534col_10033_620637col_10033_620647
Use of Single-Frequency Impedance Spectroscopy to Characterize the Growth Dynamics of Biofilm Formation in Pseudomonas aeruginosa.
van Duuren, Jozef B J H
Müsken, Mathias
Karge, Bianka
Tomasch, Jürgen
Wittmann, Christoph
Häussler, Susanne
Brönstrup, Mark
Impedance spectroscopy has been applied in prokaryotic and eukaryotic cytometry as a label-free method for the investigation of adherent cells. In this paper, its use for characterizing the growth dynamics of P. aeruginosa biofilms is described and compared to crystal violet staining and confocal microscopy. The method allows monitoring the growth of biofilm-forming P. aeruginosa in a continuous and label-free manner over a period of 72 h in a 96 well plate format. Impedance curves obtained for P. aeruginosa PA14 wild type and mutant strains with a transposon insertion in pqsA and pelA genes exhibited distinct phases. We propose that the slope of the declining curve following a maximum at ca. 35-40 h is a measure of biofilm formation. Transplant experiments with P. aeruginosa biofilms and paraffin suggest that the impedance also reflects pellicle formation at the liquid-air interface, a barely considered contributor to impedance. Finally, the impairment of biofilm formation upon treatment of cultures with L-arginine and with ciprofloxacin, tobramycin and meropenem was studied by single frequency impedance spectroscopy. We suggest that these findings qualify impedance spectroscopy as an additional technique to characterize biofilm formation and its modulation by small molecule drugs.
2017-08-03T14:11:48Z
2017-08-03T14:11:48Z
2017-08-03T14:11:48Z
2017-07-12
Article
Use of Single-Frequency Impedance Spectroscopy to Characterize the Growth Dynamics of Biofilm Formation in Pseudomonas aeruginosa. 2017, 7 (1):5223 Sci Rep
2045-2322
28701712
10.1038/s41598-017-05273-5
http://hdl.handle.net/10033/621039
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6211692019-08-30T11:33:29Zcom_10033_620636col_10033_620637
Towards individualized diagnostics of biofilm-associated infections: a case study.
Müsken, Mathias
Klimmek, Kathi
Sauer-Heilborn, Annette
Donnert, Monique
Sedlacek, Ludwig
Suerbaum, Sebastian
Häussler, Susanne
H-Zentrum für Infektionsforschung GmbH, Inhoffenstr.7, 38124 Braunschweig, Germany.
Organized within biofilm communities, bacteria exhibit resistance towards a broad spectrum of antibiotics. Thus, one might argue that bacteria isolated from biofilm-associated chronic infections should be subjected to resistance profiling under biofilm growth conditions. Various test systems have been developed to determine the biofilm-associated resistance; however, it is not clear to what extent the in vitro results reflect the situation in vivo, and whether the biofilm-resistance profile should guide clinicians in their treatment choice. To address this issue, we used confocal microscopy in combination with live/dead staining, and profiled biofilm-associated resistance of a large number (>130) of clinical Pseudomonas aeruginosa isolates from overall 15 cystic fibrosis patients. Our results demonstrate that in addition to a general non-responsiveness of bacteria when grown under biofilm conditions, there is an isolate-specific and antibiotic-specific biofilm-resistance profile. This individual resistance profile is independent on the structural properties of the biofilms. Furthermore, biofilm resistance is not linked to the resistance profile under planktonic growth conditions, or a mucoid, or small colony morphology of the tested isolates. Instead, it seems that individual biofilm structures evolve during biofilm-associated growth and are shaped by environment-specific cues. In conclusion, our results demonstrate that biofilm resistance profiles are isolate specific and cannot be deduced from commonly studied phenotypes. Further clinical studies will have to show the added value of biofilm-resistance profiling. Individualized diagnosis of biofilm resistance might lead to more rational recommendations for antimicrobial therapy and, thus, increased effectiveness of the treatment of chronically infected patients.
2017-11-08T09:06:27Z
2017-11-08T09:06:27Z
2017-11-08T09:06:27Z
2017
Article
Towards individualized diagnostics of biofilm-associated infections: a case study. 2017, 3:22 NPJ Biofilms Microbiomes
2055-5008
PMC5620081
10.1038/s41522-017-0030-5
http://hdl.handle.net/10033/621169
NPJ biofilms and microbiomes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620081/pdf/41522_2017_Article_30.pdf
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6212512019-08-30T11:25:11Zcom_10033_620636col_10033_620665col_10033_620637
The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14.
Tata, Muralidhar
Amman, Fabian
Pawar, Vinay
Wolfinger, Michael T
Weiss, Siegfried
Häussler, Susanne
Bläsi, Udo
Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Pseudomonas aeruginosa is an opportunistic pathogen that can thrive by anaerobic respiration in the lungs of cystic fibrosis patients using nitrate as terminal electron acceptor. Here, we report the identification and characterization of the small RNA PaiI in the P. aeruginosa strain 14 (PA14). PaiI is anaerobically induced in the presence of nitrate and depends on the two-component system NarXL. Our studies revealed that PaiI is required for efficient denitrification affecting the conversion of nitrite to nitric oxide. In the absence of PaiI anaerobic growth was impaired on glucose, which can be reconciled with a decreased uptake of the carbon source under these conditions. The importance of PaiI for anaerobic growth is further underlined by the observation that a paiI deletion mutant was impaired in growth in murine tumors.
2018-01-23T14:51:07Z
2018-01-23T14:51:07Z
2018-01-23T14:51:07Z
2017
Article
The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14. 2017, 8:2312 Front Microbiol
1664-302X
29218039
10.3389/fmicb.2017.02312
http://hdl.handle.net/10033/621251
Frontiers in microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6213012019-08-30T11:25:43Zcom_10033_620659com_10033_620636col_10033_620660col_10033_620637
Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms.
Ghanbari, Azadeh
Dehghany, Jaber
Schwebs, Timo
Müsken, Mathias
Häussler, Susanne
Meyer-Hermann, Michael
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany.
Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors.
2018-03-02T14:24:49Z
2018-03-02T14:24:49Z
2018-03-02T14:24:49Z
2016-09-09
Article
Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms. 2016, 6:32097 Sci Rep
2045-2322
27611778
10.1038/srep32097
http://hdl.handle.net/10033/621301
Scientific reports
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6213832019-08-30T11:28:45Zcom_10033_620636com_10033_620644com_10033_338554col_10033_621787col_10033_620665col_10033_620650col_10033_620637
Regulation of Flagellum Biosynthesis in Response to Cell Envelope Stress in Serovar Typhimurium.
Spöring, Imke
Felgner, Sebastian
Preuße, Matthias
Eckweiler, Denitsa
Rohde, M
Häussler, Susanne
Weiss, Siegfried
Erhardt, Marc
Flagellum-driven motility of serovar Typhimurium facilitates host colonization. However, the large extracellular flagellum is also a prime target for the immune system. As consequence, expression of flagella is bistable within a population of , resulting in flagellated and nonflagellated subpopulations. This allows the bacteria to maximize fitness in hostile environments. The degenerate EAL domain protein RflP (formerly YdiV) is responsible for the bistable expression of flagella by directing the flagellar master regulatory complex FlhDC with respect to proteolytic degradation. Information concerning the environmental cues controlling expression of and thus about the bistable flagellar biosynthesis remains ambiguous. Here, we demonstrated that RflP responds to cell envelope stress and alterations of outer membrane integrity. Lipopolysaccharide (LPS) truncation mutants of Typhimurium exhibited increasing motility defects due to downregulation of flagellar gene expression. Transposon mutagenesis and genetic profiling revealed that σ (RpoE) and Rcs phosphorelay-dependent cell envelope stress response systems sense modifications of the lipopolysaccaride, low pH, and activity of the complement system. This subsequently results in activation of RflP expression and degradation of FlhDC via ClpXP. We speculate that the presence of diverse hostile environments inside the host might result in cell envelope damage and would thus trigger the repression of resource-costly and immunogenic flagellum biosynthesis via activation of the cell envelope stress response. Pathogenic bacteria such as Typhimurium sense and adapt to a multitude of changing and stressful environments during host infection. At the initial stage of gastrointestinal colonization, uses flagellum-mediated motility to reach preferred sites of infection. However, the flagellum also constitutes a prime target for the host's immune response. Accordingly, the pathogen needs to determine the spatiotemporal stage of infection and control flagellar biosynthesis in a robust manner. We found that uses signals from cell envelope stress-sensing systems to turn off production of flagella. We speculate that downregulation of flagellum synthesis after cell envelope damage in hostile environments aids survival of during late stages of infection and provides a means to escape recognition by the immune system.
2018-05-30T13:47:07Z
2018-05-30T13:47:07Z
2018-05-30T13:47:07Z
2018-05-01
Article
29717015
http://hdl.handle.net/10033/621383
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
oai:repository.helmholtz-hzi.de:10033/6215192019-08-30T11:29:45Zcom_10033_311624com_10033_6839com_10033_620636col_10033_311625col_10033_620637
Breaking the vicious cycle of antibiotic killing and regrowth of biofilm-residing .
Müsken, Mathias
Pawar, Vinay
Schwebs, Timo
Bähre, Heike
Felgner, Sebastian
Weiss, Siegfried
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Biofilm-residing bacteria embedded in an extracellular matrix are protected from diverse
physico-chemical insults. In addition to the general recalcitrance of biofilm-bacteria, high
bacterial loads in biofilm-associated infections significantly diminishes the efficacy of
antimicrobials due to a low per-cell antibiotic concentration. Accordingly, present antimicrobial
treatment protocols, that have been established to serve the eradication of acute infections, fail
to clear biofilm-associated chronic infections. In the present study, we applied automated
confocal microscopy on Pseudomonas aeruginosa to monitor dynamic killing of biofilm-grown
bacteria by tobramycin and colistin in real-time. We revealed that the time required for
surviving bacteria to repopulate the biofilm could be taken as measure for effectiveness of the
antimicrobial treatment. It depends on the: i) nature and concentration of the antibiotic, ii)
duration of antibiotic treatment; iii) application as mono or combination therapy and iv) time
intervals of drug administration. The vicious cycle of killing and repopulation of biofilm
bacteria could also be broken in an in vivo model system by applying successive antibiotic
dosages with time intervals that do not allow full reconstitution of the biofilm communities.
Treatment regimens that consider the important aspects of antimicrobial killing kinetics bear
the potential to improve control of biofilm regrowth. This is an important and underestimated
factor that is bound to ensure sustainable treatment success of chronic infections.
2018-10-19T13:48:16Z
2018-10-19T13:48:16Z
2018-10-19T13:48:16Z
2018-10-08
Article
1098-6596
30297365
10.1128/AAC.01635-18
http://hdl.handle.net/10033/621519
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
Antimicrobial agents and chemotherapy
oai:repository.helmholtz-hzi.de:10033/6215352019-08-30T11:29:11Zcom_10033_620636col_10033_620637
BACTOME-a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates.
Hornischer, Klaus
Khaledi, Ariane
Pohl, Sarah
Schniederjans, Monika
Pezoldt, Lorena
Casilag, Fiordiligie
Muthukumarasamy, Uthayakumar
Bruchmann, Sebastian
Thöming, Janne
Kordes, Adrian
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Extensive use of next-generation sequencing (NGS) for pathogen profiling has the potential to transform our understanding of how genomic plasticity contributes to phenotypic versatility. However, the storage of large amounts of NGS data and visualization tools need to evolve to offer the scientific community fast and convenient access to these data. We introduce BACTOME as a database system that links aligned DNA- and RNA-sequencing reads of clinical Pseudomonas aeruginosa isolates with clinically relevant pathogen phenotypes. The database allows data extraction for any single isolate, gene or phenotype as well as data filtering and phenotypic grouping for specific research questions. With the integration of statistical tools we illustrate the usefulness of a relational database structure for the identification of phenotype-genotype correlations as an essential part of the discovery pipeline in genomic research. Furthermore, the database provides a compilation of DNA sequences and gene expression values of a plethora of clinical isolates to give a consensus DNA sequence and consensus gene expression signature. Deviations from the consensus thereby describe the genomic landscape and the transcriptional plasticity of the species P. aeruginosa. The database is available at https://bactome.helmholtz-hzi.de.
2018-11-05T13:54:29Z
2018-11-05T13:54:29Z
2018-11-05T13:54:29Z
2018-10-01
Article
1362-4962
30272193
10.1093/nar/gky895
http://hdl.handle.net/10033/621535
info:eu-repo/grantAgreement/ERC/H2020/ 724290
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
openAccess
Attribution-NonCommercial-ShareAlike 3.0 United States
Nucleic acids research
oai:repository.helmholtz-hzi.de:10033/6215822019-08-30T11:29:44Zcom_10033_620636com_10033_620533col_10033_621891col_10033_620637
Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS).
Piwosz, Kasia
Shabarova, Tanja
Tomasch, Jürgen
Šimek, Karel
Kopejtka, Karel
Kahl, Silke
Pieper, Dietmar H
Koblížek, Michal
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.
2018-11-26T11:43:31Z
2018-11-26T11:43:31Z
2018-11-26T11:43:31Z
2018-11-01
Article
1751-7370
29980795
10.1038/s41396-018-0213-y
http://hdl.handle.net/10033/621582
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Attribution-NonCommercial-ShareAlike 3.0 United States
The ISME journal
oai:repository.helmholtz-hzi.de:10033/6216152020-08-12T13:54:07Zcom_10033_311624com_10033_6839com_10033_620626com_10033_620636col_10033_311625col_10033_620629col_10033_620637
Importance of flagella in acute and chronic Pseudomonas aeruginosa infections.
Lorenz, Anne
Preuße, Matthias
Bruchmann, Sebastian
Pawar, Vinay
Grahl, Nora
Pils, Marina C
Nolan, Laura M
Filloux, Alain
Weiss, Siegfried
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Pseudomonas aeruginosa is an environmental microorganism and a causative agent of diverse acute and chronic, biofilm-associated infections. Advancing research-based knowledge on its adaptation to conditions within the human host is bound to reveal novel strategies and targets for therapeutic intervention. Here, we investigated the traits that P. aeruginosa PA14 as well as a virulence attenuated ΔlasR mutant need to survive in selected murine infection models. Experimentally, the genetic programs that the bacteria use to adapt to biofilm-associated versus acute infections were dissected by passaging transposon mutant libraries through mouse lungs (acute) or mouse tumours (biofilm-infection). Adaptive metabolic changes of P. aeruginosa were generally required during both infection processes. Counter-selection against flagella expression was observed during acute lung infections. Obviously, avoidance of flagella-mediated activation of host immunity is advantageous for the wildtype bacteria. For the ΔlasR mutant, loss of flagella did not confer a selective advantage. Apparently, other pathogenesis mechanisms are active in this virulence attenuated strain. In contrast, the infective process of P. aeruginosa in the chronic biofilm model apparently required expression of flagellin. Together, our findings imply that the host immune reactions against the infectious agent are very decisive for acuteness and duration of the infectious disease. They direct disease outcome.
2018-12-13T09:50:30Z
2018-12-13T09:50:30Z
2018-12-13T09:50:30Z
2018-11-08
Article
1462-2920
30411474
10.1111/1462-2920.14468
http://hdl.handle.net/10033/621615
info:eu-repo/grantAgreement/ERC/H2020/ 724290
http://creativecommons.org/licenses/by-nc-sa/4.0/
embargoedAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
Environmental microbiology
oai:repository.helmholtz-hzi.de:10033/6216702020-12-01T09:40:31Zcom_10033_620533com_10033_620636col_10033_621891col_10033_620637
Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica
Arce-Rodríguez, Alejandro
Puente-Sánchez, Fernando
Avendaño, Roberto
Martínez-Cruz, María
de Moor, J Maarten
Pieper, Dietmar H
Chavarría, Max
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Archaea
Borbollones
CO2-rich thermal
Sulfur-oxidizing bacteria
Tenorio Volcano National Park
Wet mofette
Here we report the chemical and microbial characterization of the surface water of a CO2-rich hydrothermal vent known in Costa Rica as Borbollones, located at Tenorio Volcano National Park. The Borbollones showed a temperature surrounding 60 °C, a pH of 2.4 and the gas released has a composition of ~ 97% CO2, ~ 0.07% H2S, ~ 2.3% N2 and ~ 0.12% CH4. Other chemical species such as sulfate and iron were found at high levels with respect to typical fresh water bodies. Analysis by 16S rRNA gene metabarcoding revealed that in Borbollones predominates an archaeon from the order Thermoplasmatales and one bacterium from the genus Sulfurimonas. Other sulfur- (genera Thiomonas, Acidithiobacillus, Sulfuriferula, and Sulfuricurvum) and iron-oxidizing bacteria (genera Sideroxydans, Gallionella, and Ferrovum) were identified. Our results show that CO2-influenced surface water of Borbollones contains microorganisms that are usually found in acid rock drainage environments or sulfur-rich hydrothermal vents. To our knowledge, this is the first microbiological characterization of a CO2-dominated hydrothermal spring from Central America and expands our understanding of those extreme ecosystems.
2019-01-29T12:00:12Z
2019-01-29T12:00:12Z
2019-01-29T12:00:12Z
2019-01-01
Article
1433-4909
30600357
10.1007/s00792-018-01072-6
http://hdl.handle.net/10033/621670
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Extremophiles : life under extreme conditions
oai:repository.helmholtz-hzi.de:10033/6216842019-08-30T11:33:04Zcom_10033_620533com_10033_620636col_10033_620534col_10033_620637
Identification and quantification of (t)RNA modifications in Pseudomonas aeruginosa by liquid chromatography-tandem mass spectrometry.
Grobe, Svenja
Doberenz, Sebastian
Ferreira, Kevin
Krueger, Jonas
Brönstrup, Mark
Kaever, Volkhard
Häußler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Mass spectrometry
Pseudomonas aeruginosa
tRNA
tRNA modifications
Transfer RNA (tRNA) modifications impact the structure and function of tRNAs thus affecting the efficiency and fidelity of translation. In the opportunistic pathogen Pseudomonas aeruginosa translational regulation plays an important but less defined role in the adaptation to changing environments. In this study, we explored tRNA modifications in P. aeruginosa using LC-MS/MS based approaches. Neutral Loss Scan (NLS) demonstrated the potential to identify previously unknown modifications, while Multiple Reaction Monitoring (MRM) can detect modifications with high specificity and sensitivity. In this study, the MRM-based external calibration method allowed for quantification of the 4 canonical and 32 modified ribonucleosides, of which 21 tRNA modifications were quantified in the total tRNA pool of P. aeruginosa PA14. We also purified the single tRNA isoacceptors tRNA-ArgUCU, tRNA-LeuCAA and tRNA-TrpCCA and determined, both qualitatively and quantitatively, their specific modification pattern. Deeper insights into the nature and dynamics of tRNA modifications in P. aeruginosa will pave the way for further studies on posttranscriptional gene regulation as a relatively unexplored molecular mechanism of controlling bacterial pathogenicity and life style.
2019-02-12T09:29:19Z
2019-02-12T09:29:19Z
2019-02-12T09:29:19Z
2019-01-15
Article
Chembiochem. 2019 Jan 15. doi: 10.1002/cbic.201800741
1439-7633
30644616
10.1002/cbic.201800741
http://hdl.handle.net/10033/621684
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
Chembiochem : a European journal of chemical biology
oai:repository.helmholtz-hzi.de:10033/6217632019-08-30T11:35:08Zcom_10033_620636com_10033_338554col_10033_620637col_10033_338544
Spatiotemporal control of FlgZ activity impacts Pseudomonas aeruginosa flagellar motility.
Bense, Sarina
Bruchmann, Sebastian
Steffen, Anika
Stradal, Theresia E B
Häussler, Susanne
Düvel, Juliane
HZI, Helmholtz Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig Germany.
The c-di-GMP-binding effector protein FlgZ has been demonstrated to control motility in the opportunistic pathogen Pseudomonas aeruginosa and it was suggested that c-di-GMP-bound FlgZ impedes motility via its interaction with the MotCD stator. To further understand how motility is downregulated in P. aeruginosa and to elucidate the general control mechanisms operating during bacterial growth, we examined the spatiotemporal activity of FlgZ. We re-annotated the P. aeruginosaflgZ open reading frame and demonstrated that FlgZ-mediated downregulation of motility is fine-tuned via three independent mechanisms. First, we found that flgZ gene is transcribed independently from flgMN in stationary growth phase to increase FlgZ protein levels in the cell. Second, FlgZ localizes to the cell pole upon c-di-GMP binding and third, we describe that FimV, a cell pole anchor protein, is involved in increasing the polar localized c-di-GMP bound FlgZ to inhibit both, swimming and swarming motility. Our results shed light on the complex dynamics and spatiotemporal control of c-di-GMP-dependent bacterial motility phenotypes and on how the polar anchor protein FimV, the motor brake FlgZ and the stator proteins function to repress flagella-driven swimming and swarming motility.
2019-05-07T14:03:56Z
2019-05-07T14:03:56Z
2019-05-07T14:03:56Z
2019-03-12
Article
Mol Microbiol. 2019 Mar 12. doi: 10.1111/mmi.14236.
1365-2958
30864240
10.1111/mmi.14236
http://hdl.handle.net/10033/621763
Molecular microbiology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
Molecular microbiology
oai:repository.helmholtz-hzi.de:10033/6218332019-08-30T11:25:40Zcom_10033_620636col_10033_620637
Non-invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator.
Arce-Rodríguez, Alejandro
Volke, Daniel C
Bense, Sarina
Häussler, Susanne
Nikel, Pablo I
HZI, Helmholtz -Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
The ability of Pseudomonas species to thrive in all major natural environments (i.e. terrestrial, freshwater and marine) is based on its exceptional capability to adapt to physicochemical changes. Thus, environmental bacteria have to tightly control the maintenance of numerous physiological traits across different conditions. The intracellular pH (pHi ) homoeostasis is a particularly important feature, since the pHi influences a large portion of the biochemical processes in the cell. Despite its importance, relatively few reliable, easy-to-implement tools have been designed for quantifying in vivo pHi changes in Gram-negative bacteria with minimal manipulations. Here we describe a convenient, non-invasive protocol for the quantification of the pHi in bacteria, which is based on the ratiometric fluorescent indicator protein PHP (pH indicator for Pseudomonas). The DNA sequence encoding PHP was thoroughly adapted to guarantee optimal transcription and translation of the indicator in Pseudomonas species. Our PHP-based quantification method demonstrated that pHi is tightly regulated over a narrow range of pH values not only in Pseudomonas, but also in other Gram-negative bacterial species such as Escherichia coli. The maintenance of the cytoplasmic pH homoeostasis in vivo could also be observed upon internal (e.g. redirection of glucose consumption pathways in P. putida) and external (e.g. antibiotic exposure in P. aeruginosa) perturbations, and the PHP indicator was also used to follow dynamic changes in the pHi upon external pH shifts. In summary, our work describes a reliable method for measuring pHi in Pseudomonas, allowing for the detailed investigation of bacterial pHi homoeostasis and its regulation.
2019-07-01T11:21:32Z
2019-07-01T11:21:32Z
2019-07-01T11:21:32Z
2019-07-01
Article
Microb Biotechnol. 2019 Jul;12(4):799-813. doi: 10.1111/1751-7915.13439. Epub. 2019 Jun 4.
1751-7915
31162835
10.1111/1751-7915.13439
http://hdl.handle.net/10033/621833
Microbial Biotechnology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley Open
Microbial biotechnology
oai:repository.helmholtz-hzi.de:10033/6218802019-09-23T14:35:12Zcom_10033_620636col_10033_620637
Clustered core- and pan-genome content on Rhodobacteraceae chromosomes.
Kopejtka, Karel
Lin, Yan
Jakubovičová, Markéta
Koblížek, Michal
Tomasch, Jürgen
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Rhodobacteraceae
genome architecture
genome evolution
origin of replication
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully-sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
2019-07-17T07:10:15Z
2019-07-17T07:10:15Z
2019-07-17T07:10:15Z
2019-07-03
Article
Genome Biol Evol. 2019 Jul 3. pii: 5527758. doi: 10.1093/gbe/evz138.
1759-6653
31273387
10.1093/gbe/evz138
http://hdl.handle.net/10033/621880
Genome biology and evolution
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford University Press
Genome biology and evolution
oai:repository.helmholtz-hzi.de:10033/6218962019-08-30T11:26:41Zcom_10033_620636com_10033_620652col_10033_620675col_10033_620637
Establishment of an induced memory response in Pseudomonas aeruginosa during infection of a eukaryotic host.
Kordes, Adrian
Grahl, Nora
Koska, Michal
Preusse, Matthias
Arce-Rodriguez, Alejandro
Abraham, Wolf-Rainer
Kaever, Volkhard
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
In a given habitat, bacterial cells often experience recurrent exposures to the same environmental stimulus. The ability to memorize the past event and to adjust current behaviors can lead to efficient adaptation to the recurring stimulus. Here we demonstrate that the versatile bacterium Pseudomonas aeruginosa adopts a virulence phenotype after serial passage in the invertebrate model host Galleria mellonella. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under rich medium conditions in vitro. Transcriptional reprogramming seemed to be induced by a host-specific food source, as reprogramming was also observed upon cultivation of P. aeruginosa in rich medium supplemented with polyunsaturated long-chain fatty acids. The establishment of induced memory responses adds a time dimension and seems to fill the gap between long-term evolutionary genotypic adaptation and short-term induced individual responses. Efforts to unravel the fundamental mechanisms that underlie the carry-over effect to induce such memory responses will continue to be of importance as hysteretic behavior can serve survival of bacterial populations in changing and challenging habitats.
2019-08-13T08:38:38Z
2019-08-13T08:38:38Z
2019-08-13T08:38:38Z
2019-08-01
Article
ISME J. 2019 Aug;13(8):2018-2030. doi: 10.1038/s41396-019-0412-1. Epub 2019 Apr 5.
1751-7370
30952997
10.1038/s41396-019-0412-1
http://hdl.handle.net/10033/621896
ISME
en
info:eu-repo/grantAgreement/EC/H2020/724290
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Springer-Nature
The ISME journal
oai:repository.helmholtz-hzi.de:10033/6218982019-08-30T11:24:29Zcom_10033_620636col_10033_620637
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung.
Kordes, Adrian
Preusse, Matthias
Willger, Sven D
Braubach, Peter
Jonigk, Danny
Haverich, Axel
Warnecke, Gregor
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Previous studies have demonstrated substantial genetic diversification of Pseudomonas aeruginosa across sub-compartments in cystic fibrosis (CF) lungs. Here, we isolate P. aeruginosa from five different sampling areas in the upper and lower airways of an explanted CF lung, analyze ex vivo transcriptional profiles by RNA-seq, and use colony re-sequencing and deep population sequencing to determine the genetic diversity within and across the various sub-compartments. We find that, despite genetic variation, the ex vivo transcriptional profiles of P. aeruginosa populations inhabiting different regions of the CF lung are similar. Although we cannot estimate the extent to which the transcriptional response recorded here actually reflects the in vivo transcriptomes, our results indicate that there may be a common in vivo transcriptional profile in the CF lung environment.
2019-08-13T10:54:54Z
2019-08-13T10:54:54Z
2019-08-13T10:54:54Z
2019-07-30
Article
Nat Commun. 2019 Jul 30;10(1):3397. doi: 10.1038/s41467-019-11414-3.
2041-1723
31363089
10.1038/s41467-019-11414-3
http://hdl.handle.net/10033/621898
Nature Communications
en
'info:eu-repo/grantAgreement/EC/H2020/724290
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Springer-Nature
Nature communications
oai:repository.helmholtz-hzi.de:10033/6218992019-08-30T11:25:42Zcom_10033_620636col_10033_620637
Production of norspermidine contributes to aminoglycoside resistance in pmrAB mutants of Pseudomonas aeruginosa.
Bolard, Arnaud
Schniederjans, Monika
Haussler, Susanne
Triponney, Pauline
Valot, Benoît
Plesiat, Patrick
Jeannot, Katy
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Emergence of resistance to polymyxins in Pseudomonas aeruginosa is mainly due to mutations in two-components systems, that promote addition of 4-amino-4-deoxy-L-arabinose to the lipopolysaccharide (LPS) through upregulation of operon arnBCADTEF-ugd (arn) expression. Here, we demonstrate that mutations occurring in different domains of histidine kinase PmrB or in response regulator PmrA result in coresistance to aminoglycosides and colistin. All seventeen clinical strains tested exhibiting such a cross-resistance phenotype were found to be pmrAB mutants. As shown by gene deletion experiments, the decreased susceptibility of the mutants to aminoglycosides was independent from operon arn but required the efflux system MexXY(OprM) and the products of three genes, PA4773-PA4774-PA4775, that are cotranscribed and activated with genes pmrAB Gene PA4773 (annotated as speD2 in PAO1 genome) and PA4774 (speE2) are predicted to encode enzymes involved in biosynthesis of polyamines. Comparative analysis of cell surface extracts of an in vitro selected pmrAB mutant, called AB16.2, and derivatives lacking PA4773, PA4774 and PA4775, respectively revealed that these genes were needed for norspermidine production via a pathway that likely uses 1,3-diaminoprane, a precursor of polyamines. Altogether, our results suggest that norspermidine decreases the self-promoted uptake pathway of aminoglycosides across the outer membrane and thereby potentiates the activity of efflux pump MexXY(OprM).
2019-08-13T11:59:00Z
2019-08-13T11:59:00Z
2019-08-13T11:59:00Z
2019-08-05
Article
Antimicrob Agents Chemother. 2019 Aug 5. pii: AAC.01044-19. doi: 10.1128/AAC.01044-19.
1098-6596
31383668
10.1128/AAC.01044-19
http://hdl.handle.net/10033/621899
Antimicrobial agents and chemotherapy
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
American Society of microbiology
Antimicrobial agents and chemotherapy
oai:repository.helmholtz-hzi.de:10033/6219832019-10-18T02:44:10Zcom_10033_620636col_10033_620637
The Core Proteome of Biofilm-Grown Clinical Isolates.
Erdmann, Jelena
Thöming, Janne G
Pohl, Sarah
Pich, Andreas
Lenz, Christof
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
DIA
SWATH
bacteria
mass spectrometry
microbiology
Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.
2019-10-17T12:38:12Z
2019-10-17T12:38:12Z
2019-10-17T12:38:12Z
2019-09-23
Article
Cells. 2019 Sep 23;8(10). pii: cells8101129. doi: 10.3390/cells8101129
2073-4409
31547513
10.3390/cells8101129
http://hdl.handle.net/10033/621983
Cells
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
MPDI
Cells
oai:repository.helmholtz-hzi.de:10033/6219852019-10-19T01:32:12Zcom_10033_620636col_10033_620637
Detrimental Effect of Type I IFNs During Acute Lung Infection With Is Mediated Through the Stimulation of Neutrophil NETosis.
Pylaeva, Ekaterina
Bordbari, Sharareh
Spyra, Ilona
Decker, Anna Sophie
Häussler, Susanne
Vybornov, Vadim
Lang, Stephan
Jablonska, Jadwiga
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
IFN-β
IFNAR
NETs
Pseudomonas aeruginosa
bacterial infection
biofilms
innate immunity
neutrophils
Pseudomonas aeruginosa is an opportunistic multidrug-resistant pathogen, able to grow in biofilms. It causes life-threatening complications in diseases characterized by the up-regulation of type I interferon (IFN) signaling, such as cancer or viral infections. Since type I IFNs regulate multiple functions of neutrophils, which constitute the first line of anti-bacterial host defense, in this work we aimed to study how interferon-activated neutrophils influence the course of P. aeruginosa infection of the lung. In lungs of infected IFN-sufficient WT mice, significantly elevated bacteria load was observed, accompanied by the prominent lung tissue damage. At the same time IFN-deficient animals seem to be partly resistant to the infection. Lung neutrophils from such IFN-deficient animals release significantly lower amounts of neutrophil extracellular traps (NETs) and reactive oxygen species (ROS), as compared to WT neutrophils. Of note, such IFN-deficient neutrophils show significantly decreased capacity to stimulate biofilm formation by P. aeruginosa. Reduced biofilm production impairs in turn the survival of bacteria in a lung tissue. In line with that, treatment of neutrophils with recombinant IFN-β enhances their NETosis and stimulates biofilm formation by Pseudomonas after co-incubation with such neutrophils. Possibly, bacteria utilizes neutrophil-derived NETs as a scaffold for released biofilms. In agreement with this, in vivo treatment with ROS-scavengers, NETs disruption or usage of the bacterial strains unable to bind DNA, suppress neutrophil-mediated biofilm formation in the lungs. Together, our findings indicate that the excessive activation of neutrophils by type I IFNs leads to their boosted NETosis that in turn triggers biofilm formation by P. aeruginosa and supports its persistence in the infected lung. Targeting these mechanisms could offer a new therapeutic approach to prevent persistent bacterial infections in patients with diseases associated with the up-regulation of type I IFNs.
2019-10-18T14:09:19Z
2019-10-18T14:09:19Z
2019-10-18T14:09:19Z
2019-01-01
Article
Front Immunol. 2019 Sep 11;10:2190. doi: 10.3389/fimmu.2019.02190. eCollection 2019.
1664-3224
31572395
10.3389/fimmu.2019.02190
http://hdl.handle.net/10033/621985
Frontiers in Immunology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Frontiers
Frontiers in immunology
oai:repository.helmholtz-hzi.de:10033/6220642020-01-07T02:01:54Zcom_10033_620636com_10033_338554col_10033_621787col_10033_621787col_10033_620637
The immunogenic potential of bacterial flagella for Salmonella-mediated tumor therapy.
Felgner, Sebastian
Spöring, Imke
Pawar, Vinay
Kocijancic, Dino
Preusse, Matthias
Falk, Christine
Rohde, Manfred
Häussler, Susanne
Weiss, Siegfried
Erhardt, Marc
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Salmonella Typhimurium
bacteria-mediated tumor therapy
flagella
host-pathogen interaction
luminex
Genetically engineered Salmonella Typhimurium are potent vectors for prophylactic and therapeutic measures against pathogens as well as cancer. This is based on the potent adjuvanticity that supports strong immune responses. The physiology of Salmonella is well understood. It simplifies engineering of both enhanced immune‐stimulatory properties as well as safety features, thus, resulting in an appropriate balance between attenuation and efficacy for clinical applications. A major virulence factor of Salmonella is the flagellum. It is also a strong pathogen‐associated molecular pattern recognized by extra‐ and intracellular receptors of immune cells of the host. At the same time, it represents a serious metabolic burden. Accordingly, the bacteria evolved tight regulatory mechanisms that control flagella synthesis in vivo. Here, we systematically investigated the immunogenicity and adjuvant properties of various flagella mutants of Salmonella in vitro and in a mouse cancer model in vivo. We found that mutants lacking the flagellum‐specific ATPase FliHIJ or the inner membrane ring FliF displayed the greatest stimulatory capacity and strongest anti‐tumor effects, while remaining safe in vivo. Scanning electron microscopy revealed the presence of outer membrane vesicles in the ΔfliF and ΔfliHIJ mutants. Finally, the combination of the ΔfliF and ΔfliHIJ mutations with our previously described attenuated and immunogenic background strain SF102 displayed strong efficacy against the highly resistant cancer cell line RenCa. We thus conclude that manipulating flagella biosynthesis has great potential for the construction of highly efficacious and versatile Salmonella vector strains.
2020-01-06T14:38:24Z
2020-01-06T14:38:24Z
2020-01-06T14:38:24Z
2019-11-21
Article
Int J Cancer. 2019 Nov 21. doi: 10.1002/ijc.32807.
1097-0215
31755108
10.1002/ijc.32807
http://hdl.handle.net/10033/622064
International Journal of Cancer
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley-Blackwell
International journal of cancer
oai:repository.helmholtz-hzi.de:10033/6220962020-01-22T02:26:55Zcom_10033_620636col_10033_620637
Parallel evolutionary paths to produce more than one biofilm phenotype.
Thöming, Janne G
Tomasch, Jürgen
Preusse, Matthias
Koska, Michal
Grahl, Nora
Pohl, Sarah
Willger, Sven D
Kaever, Volkhard
Müsken, Mathias
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Biofilms
Next-generation sequencing
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
2020-01-21T09:21:26Z
2020-01-21T09:21:26Z
2020-01-21T09:21:26Z
2020-01-01
Article
NPJ Biofilms Microbiomes. 2020 Jan 10;6:2. doi: 10.1038/s41522-019-0113-6. eCollection 2020.
2055-5008
31934344
10.1038/s41522-019-0113-6
http://hdl.handle.net/10033/622096
NPJ Biofilms and Microbiomes.
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Nature publishing group
NPJ biofilms and microbiomes
oai:repository.helmholtz-hzi.de:10033/6222432020-04-28T02:44:59Zcom_10033_620636col_10033_620637
Single-nucleotide polymorphism-based genetic diversity analysis of clinical Pseudomonas aeruginosa isolates.
Muthukumarasamy, Uthayakumar
Preusse, Matthias
Kordes, Adrian
Koska, Michal
Schniederjans, Monika
Khaledi, Ariane
Häussler, Susanne
TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany.
Core genome
Pan-genome
SNPs
convergent and divergent evolution
Extensive use of next-generation sequencing has the potential to transform our knowledge on how genomic variation within bacterial species impacts phenotypic versatility. Since different environments have unique selection pressures, they drive divergent evolution. However, there is also parallel or convergent evolution of traits in independent bacterial isolates inhabiting similar environments. The application of tools to describe population-wide genomic diversity provides an opportunity to measure the predictability of genetic changes underlying adaptation. Here we describe patterns of sequence variations in the core genome among 99 individual Pseudomonas aeruginosa clinical isolates and identified single nucleotide polymorphisms (SNPs) that are the basis for branching of the phylogenetic tree. We also identified SNPs that were acquired independently, in separate lineages, and not through inheritance from a common ancestor. While our results demonstrate that the P. aeruginosa core genome is highly conserved and in general, not subject to adaptive evolution, instances of parallel evolution will provide an opportunity to uncover genetic changes that underlie phenotypic diversity.
2020-04-27T16:07:39Z
2020-04-27T16:07:39Z
2020-04-27T16:07:39Z
2020-03-20
Article
Genome Biol Evol. 2020 Mar 20. pii: 5810496. doi: 10.1093/gbe/evaa059.
32196089
10.1093/gbe/evaa059
http://hdl.handle.net/10033/622243
1759-6653
Genome biology and evolution
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford Academic
Genome biology and evolution
England
oai:repository.helmholtz-hzi.de:10033/6222962020-06-13T01:32:48Zcom_10033_620636col_10033_620637
Antisense transcription in Pseudomonas aeruginosa.
Eckweiler, Denitsa
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
antisense RNA regulation by alternative sigma factors
antisense transcription
A large number of antisense transcripts have been detected in diverse microbial genomes and considerable effort has been devoted to elucidating the functional role of antisense transcription. In this study, we reanalysed extensive RNA sequencing data from the opportunistic pathogen Pseudomonas aeruginosa and found that the majority of genes have a propensity for antisense transcription. Although antisense transcripts were found in more than 80 % of the genes of the P. aeruginosa genome, the majority of sequencing reads were mapping sense and only a minority (<2 %) were mapping antisense to genes. Similarly to the sense expression levels, the antisense expression levels varied under different environmental conditions, with the sense and antisense expression levels often being inversely regulated and modulated by the activity of alternative sigma factors. Environment-modulated antisense transcription showed a bias towards being antisense to genes within regions of genomic plasticity and to those encoding small regulatory RNAs. In the future, the validation and functional characterization of antisense transcripts, and novel transcripts that are antisense to small regulatory RNAs in particular, have the potential to contribute to our understanding of the various levels of transcriptional regulation and its dynamics in the bacterial pathogen P. aeruginosa.
2020-06-12T08:21:27Z
2020-06-12T08:21:27Z
2020-06-12T08:21:27Z
2018-05-08
Article
Other
Microbiology. 2018;164(6):889‐895. doi:10.1099/mic.0.000664.
29738307
10.1099/mic.0.000664
http://hdl.handle.net/10033/622296
1465-2080
Microbiology (Reading, England)
en
info:eu-repo/grantAgreement/EC/FP7/260276
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Microbiology Society
164
6
889
895
Microbiology (Reading, England)
England
oai:repository.helmholtz-hzi.de:10033/6223482020-07-15T02:28:26Zcom_10033_620533com_10033_620636col_10033_621891col_10033_620637
Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.
Arce-Rodríguez, Alejandro
Puente-Sánchez, Fernando
Avendaño, Roberto
Libby, Eduardo
Mora-Amador, Raúl
Rojas-Jimenez, Keilor
Martínez, María
Pieper, Dietmar H
Chavarría, Max
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Acid rock drainage
Costa Rica
Microbial communities
Oxygen gradient
San Cayetano
We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L-1, iron ~ 35-61 mg L-1 (waters), and ~ 8-293 g kg-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.
2020-07-14T10:56:20Z
2020-07-14T10:56:20Z
2020-07-14T10:56:20Z
2020-06-22
Article
Microb Ecol. 2020;10.1007/s00248-020-01530-9. doi:10.1007/s00248-020-01530-9.
32572534
10.1007/s00248-020-01530-9
http://hdl.handle.net/10033/622348
1432-184X
Microbial ecology
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Springer Nature
Microbial ecology
United States
oai:repository.helmholtz-hzi.de:10033/6224202020-10-20T06:58:36Zcom_10033_620533com_10033_620636col_10033_620534col_10033_620637
Untargeted LC-MS Metabolomics Differentiates Between Virulent and Avirulent Clinical Strains of Pseudomonas aeruginosa
Depke, Tobias
Thöming, Janne Gesine
Kordes, Adrian
Häussler, Susanne
Brönstrup, Mark
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
LC-MS
Pseudomonas aeruginosa
biomarker
phenotyping
random forest classification
untargeted metabolomics
virulence
Pseudomonas aeruginosa is a facultative pathogen that can cause, inter alia, acute or chronic pneumonia in predisposed individuals. The gram-negative bacterium displays considerable genomic and phenotypic diversity that is also shaped by small molecule secondary metabolites. The discrimination of virulence phenotypes is highly relevant to the diagnosis and prognosis of P. aeruginosa infections. In order to discover small molecule metabolites that distinguish different virulence phenotypes of P. aeruginosa, 35 clinical strains were cultivated under standard conditions, characterized in terms of virulence and biofilm phenotype, and their metabolomes were investigated by untargeted liquid chromatography-mass spectrometry. The data was both mined for individual candidate markers as well as used to construct statistical models to infer the virulence phenotype from metabolomics data. We found that clinical strains that differed in their virulence and biofilm phenotype also had pronounced divergence in their metabolomes, as underlined by 332 features that were significantly differentially abundant with fold changes greater than 1.5 in both directions. Important virulence-associated secondary metabolites like rhamnolipids, alkyl quinolones or phenazines were found to be strongly upregulated in virulent strains. In contrast, we observed little change in primary metabolism. A hitherto novel cationic metabolite with a sum formula of C12H15N2 could be identified as a candidate biomarker. A random forest model was able to classify strains according to their virulence and biofilm phenotype with an area under the Receiver Operation Characteristics curve of 0.84. These findings demonstrate that untargeted metabolomics is a valuable tool to characterize P. aeruginosa virulence, and to explore interrelations between clinically important phenotypic traits and the bacterial metabolome.
2020-08-31T13:00:52Z
2020-08-31T13:00:52Z
2020-08-31T13:00:52Z
2020-07-13
Article
Biomolecules. 2020;10(7):1041. Published 2020 Jul 13. doi:10.3390/biom10071041.
32668735
10.3390/biom10071041
http://hdl.handle.net/10033/622420
2218-273X
Biomolecules
en
nfo:eu-repo/grantAgreement/EC/H2020/ 654008
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
MDPI
10
7
Biomolecules
Switzerland
oai:repository.helmholtz-hzi.de:10033/6224302020-09-10T01:49:47Zcom_10033_620613com_10033_620636col_10033_620614col_10033_620637
Human airway mucus alters susceptibility of Pseudomonas aeruginosa biofilms to tobramycin, but not colistin.
Müller, Laura
Murgia, Xabier
Siebenbürger, Lorenz
Börger, Carsten
Schwarzkopf, Konrad
Sewald, Katherina
Häussler, Susanne
Braun, Armin
Lehr, Claus-Michael
Hittinger, Marius
Wronski, Sabine
HIPS, Helmholtz-Institut für Pharmazeutische Forschung Saarland, Universitätscampus E8.1 66123 Saarbrücken, Germany.
Objectives: In the context of cystic fibrosis, Pseudomonas aeruginosa biofilms often develop in the vicinity of airway mucus, which acts as a protective physical barrier to inhaled matter. However, mucus can also adsorb small drug molecules administered as aerosols, including antibiotics, thereby reducing their bioavailability. The efficacy of antibiotics is typically assessed by determining the MIC using in vitro assays. This widespread technique, however, does not consider either bacterial biofilm formation or the influence of mucus, both of which may act as diffusion barriers, potentially limiting antibiotic efficacy.
Methods: We grew P. aeruginosa biofilms in the presence or absence of human tracheal mucus and tested their susceptibility to tobramycin and colistin.
Results: A significant reduction of tobramycin efficacy was observed when P. aeruginosa biofilms were grown in the presence of mucus compared with those grown in the absence of mucus. Diffusion of tobramycin through mucus was reduced; however, this reduction was more pronounced in biofilm/mucus mixtures, suggesting that biofilms in the presence of mucus respond differently to antibiotic treatment. In contrast, the influence of mucus on colistin efficacy was almost negligible and no differences in mucus permeability were observed.
Conclusions: These findings underline the important role of mucus in the efficacy of anti-infective drugs.
2020-09-09T09:12:03Z
2020-09-09T09:12:03Z
2020-09-09T09:12:03Z
Article
Other
J Antimicrob Chemother. 2018;73(10):2762-2769. doi:10.1093/jac/dky241.
29982453
10.1093/jac/dky241
http://hdl.handle.net/10033/622430
1460-2091
The Journal of antimicrobial chemotherapy
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
Oxford Academic
73
10
2762
2769
The Journal of antimicrobial chemotherapy
England
oai:repository.helmholtz-hzi.de:10033/6225322020-10-31T02:03:01Zcom_10033_620644com_10033_620636col_10033_620650col_10033_620637
Expression of the MexXY aminoglycoside efflux pump and presence of an aminoglycoside modifying enzyme in clinical isolates are highly correlated.
Seupt, Alexander
Schniederjans, Monika
Tomasch, Jürgen
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
The impact of MexXY efflux pump expression on aminoglycoside resistance in clinical Pseudomonas aeruginosa isolates has been debated. In this study, we found that in general, elevated mexXY gene expression levels in clinical P. aeruginosa isolates confer to slight increases in aminoglycoside MIC levels, however those levels rarely lead to clinically relevant resistance phenotypes. The main driver of resistance in the clinical isolates studied here was the acquisition of aminoglycoside modifying enzymes (AMEs). Nevertheless, acquisition of an AME was strongly associated with mexY overexpression. In line with this observation, we demonstrate that the introduction of a gentamicin acetyl-transferase confers to full gentamicin resistance levels in a P. aeruginosa type strain only if the MexXY efflux pump was active. We discuss that increased mexXY activity in clinical AME harboring P. aeruginosa isolates might affect ion fluxes at the bacterial cell membrane and thus might play a role in the establishment of enhanced fitness that extends beyond aminoglycoside resistance.
2020-10-23T13:21:54Z
2020-10-23T13:21:54Z
2020-10-23T13:21:54Z
2020-10-12
Article
Antimicrob Agents Chemother. 2020 Oct 12:AAC.01166-20. doi: 10.1128/AAC.01166-20.
33046496
10.1128/AAC.01166-20
http://hdl.handle.net/10033/622532
1098-6596
Antimicrobial agents and chemotherapy
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
ASM
Antimicrobial agents and chemotherapy
United States
oai:repository.helmholtz-hzi.de:10033/6225502020-11-03T01:31:23Zcom_10033_620533com_10033_338554com_10033_620636col_10033_620534col_10033_620637col_10033_338544
Host-induced spermidine production in motile triggers phagocytic uptake.
Felgner, Sebastian
Preusse, Matthias
Beutling, Ulrike
Stahnke, Stephanie
Pawar, Vinay
Rohde, Manfred
Brönstrup, Mark
Stradal, Theresia
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Pseudomonas aeruginosa
dual-sequencing
flagella
host-pathogen interaction
infectious disease
microbiology
motility
spermidine
Exploring the complexity of host-pathogen communication is vital to understand why microbes persist within a host, while others are cleared. Here, we employed a dual-sequencing approach to unravel conversational turn-taking of dynamic host-pathogen communications. We demonstrate that upon hitting a host cell, motile Pseudomonas aeruginosa induce a specific gene expression program. This results in the expression of spermidine on the surface, which specifically activates the PIP3-pathway to induce phagocytic uptake into primary or immortalized murine cells. Non-motile bacteria are more immunogenic due to a lower expression of arnT upon host-cell contact, but do not produce spermidine and are phagocytosed less. We demonstrate that not only the presence of pathogen inherent molecular patterns induces immune responses, but that bacterial motility is linked to a host-cell-induced expression of additional immune modulators. Our results emphasize on the value of integrating microbiological and immunological findings to unravel complex and dynamic host-pathogen interactions.
2020-11-02T11:14:23Z
2020-11-02T11:14:23Z
2020-11-02T11:14:23Z
2020-09-22
Article
Elife. 2020 Sep 22;9:e55744. doi: 10.7554/eLife.55744.
32960172
10.7554/eLife.55744
http://hdl.handle.net/10033/622550
2050-084X
eLife
en
info:eu-repo/grantAgreement/EC//H2020724290
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
elifeSciences
9
eLife
International
International
International
International
England
oai:repository.helmholtz-hzi.de:10033/6225722020-11-11T03:33:41Zcom_10033_620636col_10033_620637
Analysis of the organization and expression patterns of the convergent pseudomonas aeruginosa lasr/rsal gene pair uncovers mutual influence.
Schinner, Silvia
Preusse, Matthias
Kesthely, Christopher
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Pseudomonas aeruginosa
lasR
rsaL
transcriptional interference
The two adjacent genes encoding the major Pseudomonas aeruginosa quorum sensing regulator, LasR, and its opponent, RsaL, overlap in their coding 3´ends and produce mRNA transcripts with long untranslated 3´ends that overlap with the sense transcripts of the gene on the opposing DNA strand. In this study, we evaluated whether the overlapping genes are involved in mutual regulatory events and studied interference by natural antisense transcripts. We introduced various gene expression constructs into a P. aeruginosa PA14 lasR/rsaL double deletion mutant, and found that although complementary RNA is produced, this does not interfere with the sense gene expression levels of lasR and rsaL and does not have functional consequences on down-stream gene regulation. Nevertheless, expression of lasR, but not of rsaL, was shown to be enhanced if transcription was terminated at the end of the respective gene so that no overlapping transcription was allowed. Our data indicate that the natural organization with a partial overlap at the 3´ends of the lasR/rsaL genes gives rise to a system of checks and balances to prevent dominant and unilateral control by LasR over the RsaL transcriptional regulator of opposing function.
2020-11-10T15:12:36Z
2020-11-10T15:12:36Z
2020-11-10T15:12:36Z
2020-10-19
Article
Mol Microbiol. 2020 Oct 19. doi: 10.1111/mmi.14628. Epub ahead of print.
33073409
10.1111/mmi.14628
http://hdl.handle.net/10033/622572
1365-2958
Molecular microbiology
en
info:eu-repo/grantAgreement/EC/H2020/ 724290
http://creativecommons.org/licenses/by-nc-sa/4.0/
embargoedAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Wiley
Molecular microbiology
England
oai:repository.helmholtz-hzi.de:10033/6225832020-12-01T11:41:59Zcom_10033_620533com_10033_620636col_10033_620534col_10033_620637
The Peptide Chain Release Factor Methyltransferase PrmC Influences the Pseudomonas aeruginosa PA14 Endo- and Exometabolome.
Depke, Tobias
Häussler, Susanne
Brönstrup, Mark
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
PrmC
Pseudomonas aeruginosa
metabolomics
virulence
Pseudomonas aeruginosa is one of the most important nosocomial pathogens and understanding its virulence is the key to effective control of P. aeruginosa infections. The regulatory network governing virulence factor production in P. aeruginosa is exceptionally complex. Previous studies have shown that the peptide chain release factor methyltransferase PrmC plays an important role in bacterial pathogenicity. Yet, the underlying molecular mechanism is incompletely understood. In this study, we used untargeted liquid and gas chromatography coupled to mass spectrometry to characterise the metabolome of a prmC defective P. aeruginosa PA14 strain in comparison with the corresponding strain complemented with prmC in trans. The comprehensive metabolomics data provided new insight into the influence of prmC on virulence and metabolism. prmC deficiency had broad effects on the endo- and exometabolome of P. aeruginosa PA14, with a marked decrease of the levels of aromatic compounds accompanied by reduced precursor supply from the shikimate pathway. Furthermore, a pronounced decrease of phenazine production was observed as well as lower abundance of alkylquinolones. Unexpectedly, the metabolomics data showed no prmC-dependent effect on rhamnolipid production and an increase in pyochelin levels. A putative virulence biomarker identified in a previous study was significantly less abundant in the prmC deficient strain.
2020-11-13T15:10:03Z
2020-11-13T15:10:03Z
2020-11-13T15:10:03Z
2020-10-18
Article
Metabolites. 2020 Oct 18;10(10):417. doi: 10.3390/metabo10100417.
2218-1989
33080992
10.3390/metabo10100417
http://hdl.handle.net/10033/622583
Metabolites
en
http://creativecommons.org/licenses/by-nc-sa/4.0/
Attribution-NonCommercial-ShareAlike 4.0 International
MDPI
10
10
Metabolites
Switzerland
oai:repository.helmholtz-hzi.de:10033/6225852020-11-17T01:36:26Zcom_10033_620636col_10033_620637
Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection.
Stressmann, Franziska A
Bernal-Bayard, Joaquín
Perez-Pascual, David
Audrain, Bianca
Rendueles, Olaya
Briolat, Valérie
Bruchmann, Sebastian
Volant, Stevenn
Ghozlane, Amine
Häussler, Susanne
Duchaud, Eric
Levraud, Jean-Pierre
Ghigo, Jean-Marc
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and reconventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.
2020-11-16T13:34:09Z
2020-11-16T13:34:09Z
2020-11-16T13:34:09Z
2020-10-19
Article
ISME J. 2020 Oct 19. doi: 10.1038/s41396-020-00807-8. Epub ahead of print.
33077888
10.1038/s41396-020-00807-8
http://hdl.handle.net/10033/622585
1751-7370
The ISME journal
en
info:eu-repo/grantAgreement/EC/H2020/ 842629
http://creativecommons.org/licenses/by-nc-sa/4.0/
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
Springer Nature
The ISME journal
England
oai:repository.helmholtz-hzi.de:10033/6226522020-12-16T01:38:36Zcom_10033_620636col_10033_620637
Organism-specific depletion of highly abundant RNA species from bacterial total RNA.
Engelhardt, Florian
Tomasch, Jürgen
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Pseudomonas aeruginosa
RNA-seq
RNase H
mRNA enrichment
rRNA depletion
tmRNA
High-throughput sequencing has become a standard tool for transcriptome analysis. The depletion of overrepresented RNA species from sequencing libraries plays a key role in establishing potent and cost-efficient RNA-seq routines. Commercially available kits are known to obtain good results for the reduction of ribosomal RNA (rRNA). However, we found that the transfer-messenger RNA (tmRNA) was frequently highly abundant in rRNA-depleted samples of Pseudomonas aeruginosa , consuming up to 25 % of the obtained reads. The tmRNA fraction was particularly high in samples taken from stationary cultures. This suggests that overrepresentation of this RNA species reduces the mRNA fraction when cells are grown under challenging conditions. Here, we present an RNase-H-based depletion protocol that targets the tmRNA in addition to ribosomal RNAs. We were able to increase the mRNA fraction to 93-99% and therefore outperform not only the commercially Ribo-off kit (Vazyme) operating by the same principle but also the formerly widely used Ribo-Zero kit (Illumina). Maximizing the read share of scientifically interesting RNA species enhances the discriminatory potential of next-generation RNA-seq experiments and, therefore, can contribute to a better understanding of the transcriptomic landscape of bacterial pathogens and their used mechanisms in host infection.
2020-12-15T12:43:09Z
2020-12-15T12:43:09Z
2020-12-15T12:43:09Z
2020-09-09
Article
Access Microbiol. 2020 Sep 9;2(10):acmi000159. doi: 10.1099/acmi.0.000159.
33195973
10.1099/acmi.0.000159
http://hdl.handle.net/10033/622652
2516-8290
Access microbiology
en
info:eu-repo/grantAgreement/EC/H2020/ 724290
http://creativecommons.org/licenses/by/4.0/
openAccess
Attribution 4.0 International
Microbiology Society
2
10
acmi000159
Access microbiology
England
oai:repository.helmholtz-hzi.de:10033/6226982021-01-26T03:39:43Zcom_10033_620636col_10033_620637
Quantitative image analysis of microbial communities with BiofilmQ.
Hartmann, Raimo
Jeckel, Hannah
Jelli, Eric
Singh, Praveen K
Vaidya, Sanika
Bayer, Miriam
Rode, Daniel K H
Vidakovic, Lucia
Díaz-Pascual, Francisco
Fong, Jiunn C N
Dragoš, Anna
Lamprecht, Olga
Thöming, Janne G
Netter, Niklas
Häussler, Susanne
Nadell, Carey D
Sourjik, Victor
Kovács, Ákos T
Yildiz, Fitnat H
Drescher, Knut
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ-a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.
2021-01-25T15:17:59Z
2021-01-25T15:17:59Z
2021-01-25T15:17:59Z
2021-01-04
Article
Nat Microbiol. 2021 Jan 4. doi: 10.1038/s41564-020-00817-4. Epub ahead of print.
33398098
10.1038/s41564-020-00817-4
http://hdl.handle.net/10033/622698
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:10033/6227192021-02-09T12:07:51Zcom_10033_620636col_10033_620637
Genetic determinants of Pseudomonas aeruginosa fitness during biofilm growth.
Schinner, Silvia
Engelhardt, Florian
Preusse, Matthias
Thöming, Janne Gesine
Tomasch, Jürgen
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Biofilm
Fitness determinants
Pseudomonas aeruginosa
Tn-seq
Pseudomonas aeruginosa is an environmental bacterium and an opportunistic human pathogen. It is also a well-established model organism to study bacterial adaptation to stressful conditions, such as those encountered during an infection process in the human host. Advancing knowledge on P. aeruginosa adaptation to biofilm growth conditions is bound to reveal novel strategies and targets for the treatment of chronic biofilm-associated infections. Here, we generated transposon insertion libraries in three P. aeruginosa strain backgrounds and determined the relative frequency of each insertion following biofilm growth using transposon sequencing. We demonstrate that in general the SOS response, several tRNA modifying enzymes as well as adaptation to microaerophilic growth conditions play a key role in bacterial survival under biofilm growth conditions. On the other hand, presence of genes involved in motility and PQS signaling were less important during biofilm growth. Several mutants exhibiting transposon insertions in genes detected in our screen were validated for their biofilm growth capabilities and biofilm specific transcriptional responses using independently generated transposon mutants. Our results provide new insights into P. aeruginosa adaptation to biofilm growth conditions. The detection of previously unknown determinants of biofilm survival supports the use of transposon insertion sequencing as a global genomic technology for understanding the establishment of difficult to treat biofilm-associated infections.
2021-02-05T14:21:24Z
2021-02-05T14:21:24Z
2021-02-05T14:21:24Z
2020-04-02
Article
Biofilm. 2020 Apr 2;2:100023. doi: 10.1016/j.bioflm.2020.100023.
33447809
10.1016/j.bioflm.2020.100023
http://hdl.handle.net/10033/622719
2590-2075
Biofilm
en
info:eu-repo/grantAgreement/EC/H2020/724290
http://creativecommons.org/licenses/by-nc-nd/4.0/
openAccess
Attribution-NonCommercial-NoDerivatives 4.0 International
Elsevier
2
100023
Biofilm
Netherlands
oai:repository.helmholtz-hzi.de:10033/6227302021-02-10T02:33:00Zcom_10033_620636col_10033_620637
Complete Genome Sequences of Streptococcus suis Pig-Pathogenic Strains 10, 13-00283-02, and 16085/3b.
Bunk, Boyke
Jakóbczak, Beata
Florian, Volker
Dittmar, Denise
Mäder, Ulrike
Jarek, Michael
Häußler, Susanne
Baums, Christoph Georg
Völker, Uwe
Michalik, Stephan
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Streptococcus suis is an important pathogen of pigs that, as a zoonotic agent, can also cause severe disease in humans, including meningitis, endocarditis, and septicemia. We report complete and annotated genomes of S. suis strains 10, 13-00283-02, and 16085/3b, which represent the highly prevalent serotypes cps2, cps7, and cps9, respectively.
2021-02-09T14:40:22Z
2021-02-09T14:40:22Z
2021-02-09T14:40:22Z
2021-01-14
Article
Microbiol Resour Announc. 2021 Jan 14;10(2):e01137-20. doi: 10.1128/MRA.01137-20.
33446586
10.1128/MRA.01137-20
http://hdl.handle.net/10033/622730
2576-098X
Microbiology resource announcements
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
American Society for Microbiology
10
2
Microbiology resource announcements
United States
oai:repository.helmholtz-hzi.de:10033/6228192021-04-07T01:29:27Zcom_10033_338554com_10033_620636col_10033_621787col_10033_620637
Targeting bioenergetics is key to counteracting the drug-tolerant state of biofilm-grown bacteria.
Donnert, Monique
Elsheikh, Sarah
Arce-Rodriguez, Alejandro
Pawar, Vinay
Braubach, Peter
Jonigk, Danny
Haverich, Axel
Weiss, Siegfried
Müsken, Mathias
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Embedded in an extracellular matrix, biofilm-residing bacteria are protected from diverse physicochemical insults. In accordance, in the human host the general recalcitrance of biofilm-grown bacteria hinders successful eradication of chronic, biofilm-associated infections. In this study, we demonstrate that upon addition of promethazine, an FDA approved drug, antibiotic tolerance of in vitro biofilm-grown bacteria can be abolished. We show that following the addition of promethazine, diverse antibiotics are capable of efficiently killing biofilm-residing cells at minimal inhibitory concentrations. Synergistic effects could also be observed in a murine in vivo model system. PMZ was shown to increase membrane potential and interfere with bacterial respiration. Of note, antibiotic killing activity was elevated when PMZ was added to cells grown under environmental conditions that induce low intracellular proton levels. Our results imply that biofilm-grown bacteria avoid antibiotic killing and become tolerant by counteracting intracellular alkalization through the adaptation of metabolic and transport functions. Abrogation of antibiotic tolerance by interfering with the cell's bioenergetics promises to pave the way for successful eradication of biofilm-associated infections. Repurposing promethazine as a biofilm-sensitizing drug has the potential to accelerate the introduction of new treatments for recalcitrant, biofilm-associated infections into the clinic.
2021-04-06T09:09:49Z
2021-04-06T09:09:49Z
2021-04-06T09:09:49Z
2020-12-22
Article
PLoS Pathog. 2020 Dec 22;16(12):e1009126. doi: 10.1371/journal.ppat.1009126.
33351859
10.1371/journal.ppat.1009126
http://hdl.handle.net/10033/622819
1553-7374
PLoS pathogens
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
PLOS
16
12
e1009126
PLoS pathogens
United States
oai:repository.helmholtz-hzi.de:10033/6228242021-04-08T01:41:06Zcom_10033_338554com_10033_620636col_10033_621787col_10033_620637
The Two-Component System 09 Regulates Pneumococcal Carbohydrate Metabolism and Capsule Expression.
Hirschmann, Stephanie
Gómez-Mejia, Alejandro
Mäder, Ulrike
Karsunke, Julia
Driesch, Dominik
Rohde, Manfred
Häussler, Susanne
Burchhardt, Gerhard
Hammerschmidt, Sven
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Streptococcus pneumoniae
capsule
carbohydrate metabolism
two-component system 09
Streptococcus pneumoniae two-component regulatory systems (TCSs) are important systems that perceive and respond to various host environmental stimuli. In this study, we have explored the role of TCS09 on gene expression and phenotypic alterations in S. pneumoniae D39. Our comparative transcriptomic analyses identified 67 differently expressed genes in total. Among those, agaR and the aga operon involved in galactose metabolism showed the highest changes. Intriguingly, the encapsulated and nonencapsulated hk09-mutants showed significant growth defects under nutrient-defined conditions, in particular with galactose as a carbon source. Phenotypic analyses revealed alterations in the morphology of the nonencapsulated hk09- and tcs09-mutants, whereas the encapsulated hk09- and tcs09-mutants produced higher amounts of capsule. Interestingly, the encapsulated D39∆hk09 showed only the opaque colony morphology, while the D39∆rr09- and D39∆tcs09-mutants had a higher proportion of transparent variants. The phenotypic variations of D39ΔcpsΔhk09 and D39ΔcpsΔtcs09 are in accordance with their higher numbers of outer membrane vesicles, higher sensitivity against Triton X-100 induced autolysis, and lower resistance against oxidative stress. In conclusion, these results indicate the importance of TCS09 for pneumococcal metabolic fitness and resistance against oxidative stress by regulating the carbohydrate metabolism and thereby, most likely indirectly, the cell wall integrity and amount of capsular polysaccharide.
2021-04-07T14:38:46Z
2021-04-07T14:38:46Z
2021-04-07T14:38:46Z
2021-02-24
Article
Microorganisms. 2021 Feb 24;9(3):468. doi: 10.3390/microorganisms9030468.
2076-2607
33668344
10.3390/microorganisms9030468
http://hdl.handle.net/10033/622824
Microorganisms
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
MDPI
9
3
Microorganisms
Switzerland
oai:repository.helmholtz-hzi.de:10033/6228792021-10-18T13:04:41Zcom_10033_620636col_10033_620637
Removable denture is a risk indicator for peri-implantitis and facilitates expansion of specific periodontopathogens: a cross-sectional study.
Grischke, Jasmin
Szafrański, Szymon P
Muthukumarasamy, Uthayakumar
Häussler, Susanne
Stiesch, Meike
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Biofilm
Dysbiosis
Fixed dentures
Fusobacterium nucleatum
Microbiome
Peri-implant mucositis
Peri-implantitis
Prevalence
Prevotella intermedia
RNAseq
Removable dentures
Risk indicator
Background: The prevalence of peri-implantitis ranges between 7 and 38.4% depending on risk indicators such as smoking, diabetes mellitus, lack of periodontal maintenance program, and history or presence of periodontitis. Currently, the possible effect of the type of superstructure on peri-implant health is unclear. This cross-sectional study aims to investigate the influence of the superstructure on the prevalence of peri-implant mucositis, peri-implantitis and peri-implant dysbiosis.
Methods: During a 32-month recruitment period dental implants were assessed to diagnose healthy peri-implant tissues, mucositis or peri-implantitis. The study included 1097 implants in 196 patients. Out of all peri-implantitis cases 20 randomly chosen submucosal biofilms from implants with fixed denture (FD) originating from 13 patients and 11 biofilms from implants with removable dentures (RD) originating from 3 patients were studied for microbiome analysis. Composition of transcriptionally active biofilms was revealed by RNAseq. Metatranscriptomic profiles were created for thirty-one peri-implant biofilms suffering from peri-implantitis and microbiome changes associated with superstructure types were identified.
Results: 16.41% of the implants were diagnosed with peri-implantitis, 25.00% of implants with RD and 12.68% of implants with FD, respectively. Multivariate analysis showed a significant positive association on patient (p = < 0.001) and implant level (p = 0.03) between the prevalence of peri-implantitis and RD. Eight bacterial species were associated either with FD or RD by linear discriminant analysis effect size method. However, significant intergroup confounders (e.g. smoking) were present.
Conclusions: Within the limitations of the present work, RDs appear to be a risk indicator for peri-implantitis and seem to facilitate expansion of specific periodontopathogens. Potential ecological and pathological consequences of shift in microbiome from RDs towards higher activity of Fusobacterium nucleatum subspecies animalis and Prevotella intermedia require further investigation.
2021-05-19T09:48:27Z
2021-05-19T09:48:27Z
2021-05-19T09:48:27Z
2021-04-01
Article
BMC Oral Health. 2021 Apr 1;21(1):173. doi: 10.1186/s12903-021-01529-9.
33794847
10.1186/s12903-021-01529-9
http://hdl.handle.net/10033/622879
1472-6831
BMC oral health
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
BMC
21
1
173
BMC oral health
England
oai:repository.helmholtz-hzi.de:10033/6229812021-08-06T01:53:44Zcom_10033_620533com_10033_620636col_10033_620534col_10033_620637
Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa.
Franke, Raimo
Overwin, Heike
Häussler, Susanne
Brönstrup, Mark
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
DNA gyrase
Pseudomonas aeruginosa
RNA sequencing
antibiotics
gyrase
metabolomics
mode of action
The design of novel antibiotics relies on a profound understanding of their mechanism of action. While it has been shown that cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins, and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at subinhibitory concentrations could be distinguished clearly by RNA sequencing as well as metabolomics. We observed a strong (2.8- to 212-fold) induction of autolysis-triggering pyocins in all gyrase inhibitors, which correlated with extracellular DNA (eDNA) release. Gyrase B-binding aminocoumarins induced the most pronounced changes, including a strong downregulation of phenazine and rhamnolipid virulence factors. Cystobactamids led to a downregulation of a glucose catabolism pathway. The study implies that clustering cellular mechanisms of action according to the primary target needs to take class-dependent variances into account. IMPORTANCE Novel antibiotics are urgently needed to tackle the growing worldwide problem of antimicrobial resistance. Bacterial pathogens possess few privileged targets for a successful therapy: the majority of existing antibiotics as well as current candidates in development target the complex bacterial machinery for cell wall synthesis, protein synthesis, or DNA replication. An important mechanistic question addressed by this study is whether inhibiting such a complex target at different sites with different compounds has similar or differentiated cellular consequences. Using transcriptomics and metabolomics, we demonstrate that three different classes of gyrase inhibitors can be distinguished by their molecular signatures in P. aeruginosa. We describe the cellular effects of a promising, recently identified gyrase inhibitor class, the cystobactamids, in comparison to those of the established gyrase A-binding fluoroquinolones and the gyrase B-binding aminocoumarins. The study results have implications for mode-of-action discovery approaches based on target-specific reference compounds, as they highlight the intraclass variability of cellular compound effects.
2021-08-05T13:17:15Z
2021-08-05T13:17:15Z
2021-08-05T13:17:15Z
2021-07-13
Article
mSystems. 2021 Jul 13:e0061021. doi: 10.1128/mSystems.00610-21. Epub ahead of print.
2379-5077
34254824
10.1128/mSystems.00610-21
http://hdl.handle.net/10033/622981
mSystems
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
ASM
e0061021
mSystems
United States
oai:repository.helmholtz-hzi.de:10033/6230162021-09-08T01:52:46Zcom_10033_620636col_10033_620637
Quo vadis clinical diagnostic microbiology?
Haag, Sara
Häussler, Susanne
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Antimicrobial resistance
Deep diagnosing
Molecular diagnostics
Next-generation sequencing
Pan-genomics
No abstract available
2021-09-07T14:17:14Z
2021-09-07T14:17:14Z
2021-09-07T14:17:14Z
2021-07-26
Article
Clin Microbiol Infect. 2021 Jul 26:S1198-743X(21)00404-3. doi: 10.1016/j.cmi.2021.07.013. Epub ahead of print. PMID: 34325069.
34325069
10.1016/j.cmi.2021.07.013
http://hdl.handle.net/10033/623016
1469-0691
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
en
http://creativecommons.org/licenses/by-nc-nd/4.0/
Attribution-NonCommercial-NoDerivatives 4.0 International
Elsevier
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
England
oai:repository.helmholtz-hzi.de:10033/6230492021-09-29T01:52:43Zcom_10033_620636col_10033_620637
Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria.
Tomasch, Jürgen
Koppenhöfer, Sonja
Lang, Andrew S
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
CtrA phosphorelay
gene expression
genome evolution
genome organization
replication
Most bacterial chromosomes are circular, with replication starting at one origin (ori) and proceeding on both replichores toward the terminus (ter). Several studies have shown that the location of genes relative to ori and ter can have profound effects on regulatory networks and physiological processes. The CtrA phosphorelay is a gene regulatory system conserved in most alphaproteobacteria. It was first discovered in Caulobacter crescentus where it controls replication and division into a stalked and a motile cell in coordination with other factors. The locations of the ctrA gene and targets of this response regulator on the chromosome affect their expression through replication-induced DNA hemi-methylation and specific positioning along a CtrA activity gradient in the dividing cell, respectively. Here we asked to what extent the location of CtrA regulatory network genes might be conserved in the alphaproteobacteria. We determined the locations of the CtrA phosphorelay and associated genes in closed genomes with unambiguously identifiable ori from members of five alphaproteobacterial orders. The location of the phosphorelay genes was the least conserved in the Rhodospirillales followed by the Sphingomonadales. In the Rhizobiales a trend toward certain chromosomal positions could be observed. Compared to the other orders, the CtrA phosphorelay genes were conserved closer to ori in the Caulobacterales. In contrast, the genes were highly conserved closer to ter in the Rhodobacterales. Our data suggest selection pressure results in differential positioning of CtrA phosphorelay and associated genes in alphaproteobacteria, particularly in the orders Rhodobacterales, Caulobacterales and Rhizobiales that is worth deeper investigation.
2021-09-28T14:03:17Z
2021-09-28T14:03:17Z
2021-09-28T14:03:17Z
2021-04-29
Article
Front Microbiol. 2021 Apr 29;12:662907. doi: 10.3389/fmicb.2021.662907.
1664-302X
33995326
10.3389/fmicb.2021.662907
http://hdl.handle.net/10033/623049
Frontiers in microbiology
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
Frontiers
12
662907
Frontiers in microbiology
Switzerland
oai:repository.helmholtz-hzi.de:10033/6231412022-01-27T13:32:00Zcom_10033_620636col_10033_620637
Orthodontic Forced Eruption of Permanent Anterior Teeth with Subgingival Fractures: A Systematic Review.
Reichardt, Elisabeth
Krug, Ralf
Bornstein, Michael M
Tomasch, Jürgen
Verna, Carlalberta
Krastl, Gabriel
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
crown-root fracture
dental hard tissue defects
dental trauma
orthodontic forced eruption
root resorption
subgingival defects
(1) Background: To assess orthodontic forced eruption (OFE) as a pre-restorative procedure for non-restorable permanent teeth with subgingival dental hard tissue defects after dental trauma. (2) Methods: A systematic electronic search of three databases, namely, MEDLINE, Cochrane Library, and EMBASE, revealed a total of 2757 eligible publications. Randomized controlled clinical trials (RCT), retro- and prospective clinical studies, or case series (with a minimum of three patients) were reviewed. (3) Results: Thirteen full-text papers were included: one RCT, one prospective clinical trial, two retrospective cohort studies, and nine case series. Within case series, statistical significance between age and cause of fracture (p < 0.03) was determined. The mean extrusion rate of OFE was 1.5 mm a week within a four to six weeks treatment period followed by retention. Three OFE protocols for maxillary single teeth are available: 1. OFE without migration of gingiva and alveolar bone, 2. OFE with gingival migration and slight alveolar bone migration, and 3. OFE with migration of both gingiva and alveolar bone. (4) Conclusions: The current state of the evidence suggests that OFE is a feasible pre-treatment option for non-restorable permanent teeth. OFE can promote the migration of tooth surrounding hard and soft tissues in the esthetic zone. Root resorption does not seem to be a relevant side effect of OFE.
2022-01-13T09:29:57Z
2022-01-13T09:29:57Z
2022-01-13T09:29:57Z
2021-11-29
Article
J Environ Res Public Health. 2021 Nov 29;18(23):12580. doi: 10.3390/ijerph182312580.
34886307
10.3390/ijerph182312580
http://hdl.handle.net/10033/623141
1660-4601
International journal of environmental research and public health
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
MDPI
18
23
International journal of environmental research and public health
Switzerland
oai:repository.helmholtz-hzi.de:10033/6231642022-02-16T02:00:10Zcom_10033_620626com_10033_620652com_10033_620601com_10033_620636col_10033_620666col_10033_620627col_10033_620629col_10033_620603col_10033_620638col_10033_620637
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
Sohail, Aaqib
Iqbal, Azeem A
Sahini, Nishika
Chen, Fangfang
Tantawy, Mohamed
Waqas, Fakhar
Winterhoff, Moritz
Ebensen, Thomas
Schultz, Kristin
Geffers, Robert
Schughart, Klaus
Preusse, Matthias
Shehata, Mahmoud
Bähre, Heike
Pils, Marina C
Guzman, Carlos A
Mostafa, Ahmed
Pleschka, Stephan
Falk, Christine
Michelucci, Alessandro
Pessler, Frank
TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany.; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Excessive inflammation is a major cause of morbidity and mortality in many viral infections including influenza. Therefore, there is a need for therapeutic interventions that dampen and redirect inflammatory responses and, ideally, exert antiviral effects. Itaconate is an immunomodulatory metabolite which also reprograms cell metabolism and inflammatory responses when applied exogenously. We evaluated effects of endogenous itaconate and exogenous application of itaconate and its variants dimethyl- and 4-octyl-itaconate (DI, 4OI) on host responses to influenza A virus (IAV). Infection induced expression of ACOD1, the enzyme catalyzing itaconate synthesis, in monocytes and macrophages, which correlated with viral replication and was abrogated by DI and 4OI treatment. In IAV-infected mice, pulmonary inflammation and weight loss were greater in Acod1-/- than in wild-type mice, and DI treatment reduced pulmonary inflammation and mortality. The compounds reversed infection-triggered interferon responses and modulated inflammation in human cells supporting non-productive and productive infection, in peripheral blood mononuclear cells, and in human lung tissue. Itaconates reduced ROS levels and STAT1 phosphorylation, whereas AKT phosphorylation was reduced by 4OI and DI but increased by itaconate. Single-cell RNA sequencing identified monocytes as the main target of infection and the exclusive source of ACOD1 mRNA in peripheral blood. DI treatment silenced IFN-responses predominantly in monocytes, but also in lymphocytes and natural killer cells. Ectopic synthesis of itaconate in A549 cells, which do not physiologically express ACOD1, reduced infection-driven inflammation, and DI reduced IAV- and IFNγ-induced CXCL10 expression in murine macrophages independent of the presence of endogenous ACOD1. The compounds differed greatly in their effects on cellular gene homeostasis and released cytokines/chemokines, but all three markedly reduced release of the pro-inflammatory chemokines CXCL10 (IP-10) and CCL2 (MCP-1). Viral replication did not increase under treatment despite the dramatically repressed IFN responses. In fact, 4OI strongly inhibited viral transcription in peripheral blood mononuclear cells, and the compounds reduced viral titers (4OI>Ita>DI) in A549 cells whereas viral transcription was unaffected. Taken together, these results reveal itaconates as immunomodulatory and antiviral interventions for influenza virus infection.
2022-02-15T09:24:24Z
2022-02-15T09:24:24Z
2022-02-15T09:24:24Z
2022-01-13
Article
PLoS Pathog. 2022 Jan 13;18(1):e1010219. doi: 10.1371/journal.ppat.1010219. Epub ahead of print.
35025971
10.1371/journal.ppat.1010219
http://hdl.handle.net/10033/623164
1553-7374
PLoS pathogens
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
PLOS
18
1
e1010219
PLoS pathogens
United States
oai:repository.helmholtz-hzi.de:10033/6232112022-06-14T01:55:51Zcom_10033_620636col_10033_620637
Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics
Khaledi, Ariane
Weimann, Aaron
Schniederjans, Monika
Asgari, Ehsaneddin
Kuo, Tzu‐Hao
Oliver, Antonio
Cabot, Gabriel
Kola, Axel
Gastmeier, Petra
Hogardt, Michael
Jonas, Daniel
Mofrad, Mohammad RK
Bremges, Andreas
McHardy, Alice C
Häussler, Susanne
Molecular Medicine
Limited therapy options due to antibiotic resistance underscore
the need for optimization of current diagnostics. In some bacterial
species, antimicrobial resistance can be unambiguously predicted
based on their genome sequence. In this study, we sequenced the
genomes and transcriptomes of 414 drug-resistant clinical Pseudomonas
aeruginosa isolates. By training machine learning classifiers
on information about the presence or absence of genes, their
sequence variation, and expression profiles, we generated predictive
models and identified biomarkers of resistance to four
commonly administered antimicrobial drugs. Using these data
types alone or in combination resulted in high (0.8–0.9) or very
high (> 0.9) sensitivity and predictive values. For all drugs except
for ciprofloxacin, gene expression information improved diagnostic
performance. Our results pave the way for the development of a
molecular resistance profiling tool that reliably predicts antimicrobial
susceptibility based on genomic and transcriptomic markers.
The implementation of a molecular susceptibility test system in
routine microbiology diagnostics holds promise to provide earlier
and more detailed information on antibiotic resistance profiles of
bacterial pathogens and thus could change how physicians treat
bacterial infections.
2022-06-13T09:55:49Z
2022-06-13T09:55:49Z
2022-06-13T09:55:49Z
2020-02-12
Article
1757-4676
10.15252/emmm.201910264
http://hdl.handle.net/10033/623211
1757-4684
EMBO Molecular Medicine
10.15252/emmm.201910264
en
http://creativecommons.org/licenses/by/4.0/
Attribution 4.0 International
EMBO
12
3
EMBO Molecular Medicine