1
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Potapova A, Garvey W, Dahl P, Guo S, Chang Y, Schwechheimer C, Trebino MA, Floyd KA, Phinney BS, Liu J, Malvankar NS, Yildiz FH. Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly. mBio 2024; 15:e0330423. [PMID: 38206049 PMCID: PMC10865864 DOI: 10.1128/mbio.03304-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide Vibrio polysaccharide (VPS), matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Single-cell force spectroscopy revealed that proteins critical for biofilm formation, OmpU, the matrix proteins RbmA, RbmC, Bap1, and VPS contribute to cell-surface adhesion forces at differing efficiency, with VPS showing the highest efficiency whereas Bap1 showing the lowest efficiency. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may provide new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of V. cholerae.IMPORTANCECholera remains a major public health concern. Vibrio cholerae, the causative agent of cholera, forms biofilms, which are critical for its transmission, infectivity, and environmental persistence. While we know that the V. cholerae biofilm matrix contains exopolysaccharide, matrix proteins, and extracellular DNA, we do not have a comprehensive understanding of the majority of biofilm matrix components. Here, we discover outer membrane vesicles (OMVs) within the biofilm matrix of V. cholerae. Proteomic analysis of the matrix and matrix-associated OMVs showed that OMVs carry key matrix proteins and Vibrio polysaccharide (VPS) to help build biofilms. We also characterize the role of the highly abundant outer membrane protein OmpU in biofilm formation and show that it impacts biofilm architecture in a VPS-dependent manner. Understanding V. cholerae biofilm formation is important for developing a better prevention and treatment strategy framework.
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Affiliation(s)
- Anna Potapova
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
| | - William Garvey
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
| | - Peter Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
| | - Shuaiqi Guo
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Yunjie Chang
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Carmen Schwechheimer
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
| | - Michael A. Trebino
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
| | - Kyle A. Floyd
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
| | - Brett S. Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California-Davis, Davis, California, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, USA
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2
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McCaughey CS, Trebino MA, McAtamney A, Isenberg R, Mandel MJ, Yildiz FH, Sanchez LM. A label-free approach for relative spatial quantitation of c-di-GMP in microbial biofilms. bioRxiv 2023:2023.10.10.561783. [PMID: 37873360 PMCID: PMC10592747 DOI: 10.1101/2023.10.10.561783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Microbial biofilms represent an important lifestyle for bacteria and are dynamic three dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable towards understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest in a single experiment.
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Affiliation(s)
- Catherine S McCaughey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Michael A Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Ruth Isenberg
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Current Address: Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Mark J Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064
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3
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Kitts G, Rogers A, Teschler JK, Park JH, Trebino MA, Chaudry I, Erill I, Yildiz FH. The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae. PLoS Pathog 2023; 19:e1011415. [PMID: 37216386 PMCID: PMC10237652 DOI: 10.1371/journal.ppat.1011415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/02/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
The facultative human pathogen, Vibrio cholerae, employs two-component signal transduction systems (TCS) to sense and respond to environmental signals encountered during its infection cycle. TCSs consist of a sensor histidine kinase (HK) and a response regulator (RR); the V. cholerae genome encodes 43 HKs and 49 RRs, of which 25 are predicted to be cognate pairs. Using deletion mutants of each HK gene, we analyzed the transcription of vpsL, a biofilm gene required for Vibrio polysaccharide and biofilm formation. We found that a V. cholerae TCS that had not been studied before, now termed Rvv, controls biofilm gene transcription. The Rvv TCS is part of a three-gene operon that is present in 30% of Vibrionales species. The rvv operon encodes RvvA, the HK; RvvB, the cognate RR; and RvvC, a protein of unknown function. Deletion of rvvA increased transcription of biofilm genes and altered biofilm formation, while deletion of rvvB or rvvC lead to no changes in biofilm gene transcription. The phenotypes observed in ΔrvvA depend on RvvB. Mutating RvvB to mimic constitutively active and inactive versions of the RR only impacted phenotypes in the ΔrvvA genetic background. Mutating the conserved residue required for kinase activity in RvvA did not affect phenotypes, whereas mutation of the conserved residue required for phosphatase activity mimicked the phenotype of the rvvA mutant. Furthermore, ΔrvvA displayed a significant colonization defect which was dependent on RvvB and RvvB phosphorylation state, but not on VPS production. We found that RvvA's phosphatase activity regulates biofilm gene transcription, biofilm formation, and colonization phenotypes. This is the first systematic analysis of the role of V. cholerae HKs in biofilm gene transcription and resulted in the identification of a new regulator of biofilm formation and virulence, advancing our understanding of the role TCSs play in regulating these critical cellular processes in V. cholerae.
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Affiliation(s)
- Giordan Kitts
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew Rogers
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer K. Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Michael A. Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Issac Chaudry
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
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4
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Abstract
Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jennifer K Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA;
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA;
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5
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McCaughey C, Trebino M, Yildiz FH, Sanchez LM. Utilizing imaging mass spectrometry to analyze microbial biofilm chemical responses to exogenous compounds. Methods Enzymol 2022; 665:281-304. [PMID: 35379438 PMCID: PMC9022628 DOI: 10.1016/bs.mie.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is an appealing label-free method for imaging biological samples which focuses on the spatial distribution of chemical signals. This approach has been used to study the chemical ecology of microbes and can be applied to study the chemical responses of microbes to treatment with exogenous compounds. Specific conjugated cholic acids such as taurocholic acid (TCA), have been shown to inhibit biofilm formation in the enteric pathogen Vibrio cholerae and MALDI-IMS can be used to directly observe the chemical responses of V. cholerae biofilm colonies to treatment with TCA. A major challenge of MALDI-IMS is optimizing the sample preparation and drying for a particular growth condition and microbial strain. Here we demonstrate how V. cholerae is cultured and prepared for MALDI-IMS analysis and highlight critical steps to ensure proper sample adherence to a MALDI target plate and maintain spatial distributions when applying this technique to any microbial strain. We additionally show how to use both manual interrogation and statistical analyses of MALDI-IMS data to establish the adequacy of the sample preparation protocol. This protocol can serve as a guideline for the development of sample preparation techniques and the acquisition of high quality MALDI-IMS data.
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Affiliation(s)
- Catherine McCaughey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064
| | - Michael Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064,Corresponding author, , phone: 831-459-4676
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6
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Trebino MA, Shingare RD, MacMillan JB, Yildiz FH. Strategies and Approaches for Discovery of Small Molecule Disruptors of Biofilm Physiology. Molecules 2021; 26:molecules26154582. [PMID: 34361735 PMCID: PMC8348372 DOI: 10.3390/molecules26154582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Biofilms, the predominant growth mode of microorganisms, pose a significant risk to human health. The protective biofilm matrix, typically composed of exopolysaccharides, proteins, nucleic acids, and lipids, combined with biofilm-grown bacteria’s heterogenous physiology, leads to enhanced fitness and tolerance to traditional methods for treatment. There is a need to identify biofilm inhibitors using diverse approaches and targeting different stages of biofilm formation. This review discusses discovery strategies that successfully identified a wide range of inhibitors and the processes used to characterize their inhibition mechanism and further improvement. Additionally, we examine the structure–activity relationship (SAR) for some of these inhibitors to optimize inhibitor activity.
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Affiliation(s)
- Michael A. Trebino
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA;
| | - Rahul D. Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA;
| | - John B. MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA;
- Correspondence: (J.B.M.); (F.H.Y.)
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA;
- Correspondence: (J.B.M.); (F.H.Y.)
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7
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Wong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, V Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O'Toole GA, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Phys Biol 2021; 18. [PMID: 33462162 PMCID: PMC8506656 DOI: 10.1088/1478-3975/abdc0e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022]
Abstract
Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.
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Affiliation(s)
- Gerard C L Wong
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, United States of America
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, Texas, TX 77845, United States of America
| | - Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Louis Bru
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America
| | | | - Albert Siryaporn
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Physics & Astronomy, University of California-Irvine, California, CA 92697, United States of America
| | - Jacinta C Conrad
- William A Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, TX 77204, United States of America
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yutaka Yawata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves V Brun
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Gregory B Whitfield
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Calvin K Lee
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jaime de Anda
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - William C Schmidt
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen, Germany.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States of America
| | - Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Shuai Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Biological Sciences, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Mauricio D Rojas-Andrade
- Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America
| | - Allon I Hochbaum
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America.,Department of Chemistry, University of California-Irvine, Irvine, California, CA 92697, United States of America.,Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, California, CA 92697, United States of America
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, CT 06511, United States of America
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,The Howard Hughes Medical Institute, Chevy Chase, Maryland MD 20815, United States of America
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139-4307, United States of America
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8
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Hartmann R, Jeckel H, Jelli E, Singh PK, Vaidya S, Bayer M, Rode DKH, Vidakovic L, Díaz-Pascual F, Fong JCN, Dragoš A, Lamprecht O, Thöming JG, Netter N, Häussler S, Nadell CD, Sourjik V, Kovács ÁT, Yildiz FH, Drescher K. Publisher Correction: Quantitative image analysis of microbial communities with BiofilmQ. Nat Microbiol 2021; 6:270. [PMID: 33420476 PMCID: PMC7840498 DOI: 10.1038/s41564-021-00863-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Eric Jelli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sanika Vaidya
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Miriam Bayer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel K H Rode
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Jiunn C N Fong
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, Switzerland
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niklas Netter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. .,Department of Physics, Philipps-Universität Marburg, Marburg, Germany. .,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany.
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9
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Schwechheimer C, Hebert K, Tripathi S, Singh PK, Floyd KA, Brown ER, Porcella ME, Osorio J, Kiblen JTM, Pagliai FA, Drescher K, Rubin SM, Yildiz FH. A tyrosine phosphoregulatory system controls exopolysaccharide biosynthesis and biofilm formation in Vibrio cholerae. PLoS Pathog 2020; 16:e1008745. [PMID: 32841296 PMCID: PMC7485978 DOI: 10.1371/journal.ppat.1008745] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 09/11/2020] [Accepted: 06/25/2020] [Indexed: 11/19/2022] Open
Abstract
Production of an extracellular matrix is essential for biofilm formation, as this matrix both secures and protects the cells it encases. Mechanisms underlying production and assembly of matrices are poorly understood. Vibrio cholerae, relies heavily on biofilm formation for survival, infectivity, and transmission. Biofilm formation requires Vibrio polysaccharide (VPS), which is produced by vps gene-products, yet the function of these products remains unknown. Here, we demonstrate that the vps gene-products vpsO and vpsU encode respectively for a tyrosine kinase and a cognate tyrosine phosphatase. Collectively, VpsO and VpsU act as a tyrosine phosphoregulatory system to modulate VPS production. We present structures of VpsU and the kinase domain of VpsO, and we report observed autocatalytic tyrosine phosphorylation of the VpsO C-terminal tail. The position and amount of tyrosine phosphorylation in the VpsO C-terminal tail represses VPS production and biofilm formation through a mechanism involving the modulation of VpsO oligomerization. We found that tyrosine phosphorylation enhances stability of VpsO. Regulation of VpsO phosphorylation by the phosphatase VpsU is vital for maintaining native VPS levels. This study provides new insights into the mechanism and regulation of VPS production and establishes general principles of biofilm matrix production and its inhibition. The biofilm life style protects microbes from a plethora of harm, to increase their survival and pathogenicity. Exopolysaccharides are the essential glue of the microbial biofilm matrix, and loss of this glue negates biofilm formation and renders cells more sensitive to antimicrobial agents. Here, we show that a tyrosine phosphoregulatory system controls the biosynthesis and abundance of Vibrio exopolysaccharide (VPS), an essential biofilm component of the pathogen Vibrio cholerae. The phosphorylation state of the tyrosine autokinase VpsO, mediated by the tyrosine phosphatase VpsU, directly modulates VPS production and also affects the kinase’s own degradation, to regulate VPS production. This study provides new insights into the mechanisms of V. cholerae biofilm formation and consequently ways to combat pathogens more broadly, due to conservation of tyrosine phosphoregulatory systems among exopolysaccharide producing bacteria.
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Affiliation(s)
- Carmen Schwechheimer
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Kassidy Hebert
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Praveen K. Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kyle A. Floyd
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Elise R. Brown
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Monique E. Porcella
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Jacqueline Osorio
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Joseph T. M. Kiblen
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Fernando A. Pagliai
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Seth M. Rubin
- Department of Chemistry and Biochemistry, University of California—Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SMR), (FHY)
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California—Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SMR), (FHY)
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10
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Joshi A, Mahmoud SA, Kim SK, Ogdahl JL, Lee VT, Chien P, Yildiz FH. c-di-GMP inhibits LonA-dependent proteolysis of TfoY in Vibrio cholerae. PLoS Genet 2020; 16:e1008897. [PMID: 32589664 PMCID: PMC7371385 DOI: 10.1371/journal.pgen.1008897] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/20/2020] [Accepted: 05/30/2020] [Indexed: 02/06/2023] Open
Abstract
The LonA (or Lon) protease is a central post-translational regulator in diverse bacterial species. In Vibrio cholerae, LonA regulates a broad range of behaviors including cell division, biofilm formation, flagellar motility, c-di-GMP levels, the type VI secretion system (T6SS), virulence gene expression, and host colonization. Despite LonA’s role in cellular processes critical for V. cholerae’s aquatic and infectious life cycles, relatively few LonA substrates have been identified. LonA protease substrates were therefore identified through comparison of the proteomes of wild-type and ΔlonA strains following translational inhibition. The most significantly enriched LonA-dependent protein was TfoY, a known regulator of motility and the T6SS in V. cholerae. Experiments showed that TfoY was required for LonA-mediated repression of motility and T6SS-dependent killing. In addition, TfoY was stabilized under high c-di-GMP conditions and biochemical analysis determined direct binding of c-di-GMP to LonA results in inhibition of its protease activity. The work presented here adds to the list of LonA substrates, identifies LonA as a c-di-GMP receptor, demonstrates that c-di-GMP regulates LonA activity and TfoY protein stability, and helps elucidate the mechanisms by which LonA controls important V. cholerae behaviors. This study provides insights into the mechanisms and consequences of LonA-mediated regulated proteolysis in Vibrio cholerae, the causal organism of the acute diarrheal disease cholera that is endemic in more than 47 countries across the globe. Lon is broadly conserved in bacterial systems; uncovering the molecular connection between c-di-GMP signaling and LonA-mediated proteolysis of V. cholerae will provide conceptual frameworks for the development of intervention strategies to combat virulence by bacterial pathogens.
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Affiliation(s)
- Avatar Joshi
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Samar A. Mahmoud
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Soo-Kyoung Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Justyne L. Ogdahl
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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11
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Gallego-Hernandez AL, DePas WH, Park JH, Teschler JK, Hartmann R, Jeckel H, Drescher K, Beyhan S, Newman DK, Yildiz FH. Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity. Proc Natl Acad Sci U S A 2020; 117:11010-11017. [PMID: 32355001 PMCID: PMC7245069 DOI: 10.1073/pnas.1916571117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Vibrio cholerae remains a major global health threat, disproportionately impacting parts of the world without adequate infrastructure and sanitation resources. In aquatic environments, V. cholerae exists both as planktonic cells and as biofilms, which are held together by an extracellular matrix. V. cholerae biofilms have been shown to be hyperinfective, but the mechanism of hyperinfectivity is unclear. Here we show that biofilm-grown cells, irrespective of the surfaces on which they are formed, are able to markedly outcompete planktonic-grown cells in the infant mouse. Using an imaging technique designed to render intestinal tissue optically transparent and preserve the spatial integrity of infected intestines, we reveal and compare three-dimensional V. cholerae colonization patterns of planktonic-grown and biofilm-grown cells. Quantitative image analyses show that V. cholerae colonizes mainly the medial portion of the small intestine and that both the abundance and localization patterns of biofilm-grown cells differ from that of planktonic-grown cells. In vitro biofilm-grown cells activate expression of the virulence cascade, including the toxin coregulated pilus (TCP), and are able to acquire the cholera toxin-carrying CTXФ phage. Overall, virulence factor gene expression is also higher in vivo when infected with biofilm-grown cells, and modulation of their regulation is sufficient to cause the biofilm hyperinfectivity phenotype. Together, these results indicate that the altered biogeography of biofilm-grown cells and their enhanced production of virulence factors in the intestine underpin the biofilm hyperinfectivity phenotype.
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Affiliation(s)
- A L Gallego-Hernandez
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064
| | - W H DePas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - J H Park
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064
| | - J K Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064
| | - R Hartmann
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Department of Physics, Philipps University Marburg, D-35032 Marburg, Germany
| | - H Jeckel
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Department of Physics, Philipps University Marburg, D-35032 Marburg, Germany
| | - K Drescher
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Department of Physics, Philipps University Marburg, D-35032 Marburg, Germany
| | - S Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037
| | - D K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.;
| | - F H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064;
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12
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Dippel AB, Anderson WA, Park JH, Yildiz FH, Hammond MC. Development of Ratiometric Bioluminescent Sensors for in Vivo Detection of Bacterial Signaling. ACS Chem Biol 2020; 15:904-914. [PMID: 32186367 DOI: 10.1021/acschembio.9b00800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Second messenger signaling networks allow cells to sense and adapt to changing environmental conditions. In bacteria, the nearly ubiquitous second messenger molecule cyclic di-GMP coordinates diverse processes such as motility, biofilm formation, and virulence. In bacterial pathogens, these signaling networks allow the bacteria to survive changing environmental conditions that are experienced during infection of a mammalian host. While studies have examined the effects of cyclic di-GMP levels on virulence in these pathogens, it has not been possible to visualize cyclic di-GMP levels in real time during the stages of host infection. Toward this goal, we generate the first ratiometric, chemiluminescent biosensor scaffold that selectively responds to c-di-GMP. By engineering the biosensor scaffold, a suite of Venus-YcgR-NLuc (VYN) biosensors is generated that provide extremely high sensitivity (KD < 300 pM) and large changes in the bioluminescence resonance energy transfer (BRET) signal (up to 109%). As a proof-of-concept that VYN biosensors can image cyclic di-GMP in tissues, we show that the VYN biosensors function in the context of a tissue phantom model, with only ∼103-104 biosensor-expressing E. coli cells required for the measurement. Furthermore, we utilize the biosensor in vitro to assess changes in cyclic di-GMP in V. cholerae grown with different inputs found in the host environment. The VYN sensors developed here can serve as robust in vitro diagnostic tools for high throughput screening, as well as genetically encodable tools for monitoring the dynamics of c-di-GMP in live cells, and lay the groundwork for live cell imaging of c-di-GMP dynamics in bacteria within tissues and other complex environments.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Wyatt A. Anderson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Ming C. Hammond
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
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13
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Floyd KA, Lee CK, Xian W, Nametalla M, Valentine A, Crair B, Zhu S, Hughes HQ, Chlebek JL, Wu DC, Hwan Park J, Farhat AM, Lomba CJ, Ellison CK, Brun YV, Campos-Gomez J, Dalia AB, Liu J, Biais N, Wong GCL, Yildiz FH. c-di-GMP modulates type IV MSHA pilus retraction and surface attachment in Vibrio cholerae. Nat Commun 2020; 11:1549. [PMID: 32214098 PMCID: PMC7096442 DOI: 10.1038/s41467-020-15331-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/02/2020] [Indexed: 11/21/2022] Open
Abstract
Biofilm formation by Vibrio cholerae facilitates environmental persistence, and hyperinfectivity within the host. Biofilm formation is regulated by 3',5'-cyclic diguanylate (c-di-GMP) and requires production of the type IV mannose-sensitive hemagglutinin (MSHA) pilus. Here, we show that the MSHA pilus is a dynamic extendable and retractable system, and its activity is directly controlled by c-di-GMP. The interaction between c-di-GMP and the ATPase MshE promotes pilus extension, whereas low levels of c-di-GMP correlate with enhanced retraction. Loss of retraction facilitated by the ATPase PilT increases near-surface roaming motility, and impairs initial surface attachment. However, prolonged retraction upon surface attachment results in reduced MSHA-mediated surface anchoring and increased levels of detachment. Our results indicate that c-di-GMP directly controls MshE activity, thus regulating MSHA pilus extension and retraction dynamics, and modulating V. cholerae surface attachment and colonization.
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Affiliation(s)
- Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Calvin K Lee
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Wujing Xian
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Mahmoud Nametalla
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Aneesa Valentine
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Benjamin Crair
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Shiwei Zhu
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Hannah Q Hughes
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Jennifer L Chlebek
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Daniel C Wu
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA
| | - Ali M Farhat
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Charles J Lomba
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA
| | - Courtney K Ellison
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, 355 Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - Yves V Brun
- Department of Microbiology, Infectious Diseases, and Immunology, Faculty of Medicine, University of Montreal, Pavillon Roger-Gaudry, 2900, boulevard Édouard-Montpetit, C.P. 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Javier Campos-Gomez
- Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1918 University Blvd., MCLM 702, Birmingham, AL, 35233, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University - Bloomington, 1001 East Third St., Jordan Hall 469A, Bloomington, IN, 47405, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, 840 West Campus Drive, Advanced Biosciences Center 211, West Haven, CT, 06516, USA
| | - Nicolas Biais
- Department of Biology, Brooklyn College, Room 307NE, 2900 Bedford Ave., Brooklyn, NY, 11210, USA
- CUNY Graduate Center, 365 5th Ave., New York, NY, 10016, USA
| | - Gerard C L Wong
- Departments of Bioengineering, Chemistry and Biochemistry, California Nano Systems Institute, University of California - Los Angeles, 420 Westwood Plaza, Room 5121 Engineering V, Los Angeles, CA, 90095, USA.
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California - Santa Cruz, 1156 High St., BioMed 245, Santa Cruz, CA, 95064, USA.
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14
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Díaz-Pascual F, Hartmann R, Lempp M, Vidakovic L, Song B, Jeckel H, Thormann KM, Yildiz FH, Dunkel J, Link H, Nadell CD, Drescher K. Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function. Nat Microbiol 2019; 4:2136-2145. [PMID: 31659297 PMCID: PMC6881181 DOI: 10.1038/s41564-019-0579-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/06/2019] [Indexed: 01/01/2023]
Abstract
Bacterial cells in nature are frequently exposed to changes in their chemical environment1,2. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure3-7, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms. Here, by monitoring all individual cells in Vibrio cholerae biofilms during exposure to antibiotics that are commonly administered for cholera infections, we found that translational inhibitors cause strong effects on cell size and shape, as well as biofilm architectural properties. We identified that single-cell-level responses result from the metabolic consequences of inhibition of protein synthesis and that the community-level responses result from an interplay of matrix composition, matrix dissociation and mechanical interactions between cells. We further observed that the antibiotic-induced changes in biofilm architecture have substantial effects on biofilm population dynamics and community assembly by enabling invasion of biofilms by bacteriophages and intruder cells of different species. These mechanistic causes and ecological consequences of biofilm exposure to antibiotics are an important step towards understanding collective bacterial responses to environmental changes, with implications for the effects of antimicrobial therapy on the ecological succession of biofilm communities.
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Affiliation(s)
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Carey D Nadell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany.
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany.
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15
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Meza-Villezcas A, Gallego-Hernández AL, Yildiz FH, Jaime-Acuña OE, Raymond-Herrera O, Huerta-Saquero A. Effect of antimicrobial nanocomposites on Vibrio cholerae lifestyles: Pellicle biofilm, planktonic and surface-attached biofilm. PLoS One 2019; 14:e0217869. [PMID: 31188854 PMCID: PMC6561565 DOI: 10.1371/journal.pone.0217869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
Vibrio cholerae is an important human pathogen causing intestinal disease with a high incidence in developing countries. V. cholerae can switch between planktonic and biofilm lifestyles. Biofilm formation is determinant for transmission, virulence and antibiotic resistance. Due to the enhanced antibiotic resistance observed by bacterial pathogens, antimicrobial nanomaterials have been used to combat infections by stopping bacterial growth and preventing biofilm formation. In this study, the effect of the nanocomposites zeolite-embedded silver (Ag), copper (Cu), or zinc (Zn) nanoparticles (NPs) was evaluated in V. cholerae planktonic cells, and in two biofilm states: pellicle biofilm (PB), formed between air-liquid interphase, and surface-attached biofilm (SB), formed at solid-liquid interfaces. Each nanocomposite type had a distinctive antimicrobial effect altering each V. cholerae lifestyles differently. The ZEO-AgNPs nanocomposite inhibited PB formation at 4 μg/ml, and prevented SB formation and eliminated planktonic cells at 8 μg/ml. In contrast, the nanocomposites ZEO-CuNPs and ZEO-ZnNPs affect V. cholerae viability but did not completely avoid bacterial growth. At transcriptional level, depending on the nanoparticles and biofilm type, nanocomposites modified the relative expression of the vpsL, rbmA and bap1, genes involved in biofilm formation. Furthermore, the relative abundance of the outer membrane proteins OmpT, OmpU, OmpA and OmpW also differs among treatments in PB and SB. This work provides a basis for further study of the nanomaterials effect at structural, genetic and proteomic levels to understand the response mechanisms of V. cholerae against metallic nanoparticles.
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Affiliation(s)
- Anaid Meza-Villezcas
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
| | - Ana L. Gallego-Hernández
- Microbiology and Environmental Toxicology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (ALGH); (AHS)
| | - Fitnat H. Yildiz
- Microbiology and Environmental Toxicology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Oscar E. Jaime-Acuña
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
| | - Oscar Raymond-Herrera
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
| | - Alejandro Huerta-Saquero
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
- * E-mail: (ALGH); (AHS)
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16
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Kemter FS, Messerschmidt SJ, Schallopp N, Sobetzko P, Lang E, Bunk B, Spröer C, Teschler JK, Yildiz FH, Overmann J, Waldminghaus T. Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae. PLoS Genet 2018; 14:e1007251. [PMID: 29505558 PMCID: PMC5854411 DOI: 10.1371/journal.pgen.1007251] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae, the causative agent of the cholera disease, is commonly used as a model organism for the study of bacteria with multipartite genomes. Its two chromosomes of different sizes initiate their DNA replication at distinct time points in the cell cycle and terminate in synchrony. In this study, the time-delayed start of Chr2 was verified in a synchronized cell population. This replication pattern suggests two possible regulation mechanisms for other Vibrio species with different sized secondary chromosomes: Either all Chr2 start DNA replication with a fixed delay after Chr1 initiation, or the timepoint at which Chr2 initiates varies such that termination of chromosomal replication occurs in synchrony. We investigated these two models and revealed that the two chromosomes of various Vibrionaceae species terminate in synchrony while Chr2-initiation timing relative to Chr1 is variable. Moreover, the sequence and function of the Chr2-triggering crtS site recently discovered in V. cholerae were found to be conserved, explaining the observed timing mechanism. Our results suggest that it is beneficial for bacterial cells with multiple chromosomes to synchronize their replication termination, potentially to optimize chromosome related processes as dimer resolution or segregation.
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Affiliation(s)
- Franziska S. Kemter
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Sonja J. Messerschmidt
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Schallopp
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Elke Lang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jennifer K. Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States of America
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner Site Hannover–Braunschweig, Braunschweig, Germany
| | - Torsten Waldminghaus
- LOEWE Center for Synthetic Microbiology–SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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17
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Warner CJA, Salinas M, Zamorano-Sánchez D, Bray WM, Lokey RS, Yildiz FH, Linington RG. The Bioactive Lipid (S)-Sebastenoic Acid Impacts Motility and Dispersion in Vibrio cholerae. CAN J CHEM 2018; 96:196-203. [PMID: 34158674 DOI: 10.1139/cjc-2017-0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although Gram-negative bacterial pathogens continue to impart a substantial burden on global healthcare systems, much remains to be understood about aspects of basic physiology in these organisms. In recent years, cyclic-diguanylate (c-di-GMP) has emerged as a key regulator of a number of important processes related to pathogenicity, including biofilm formation, motility and virulence. In an effort to discover chemical genetic probes for studying V. cholerae we have developed a new motility-based high-throughput screen to identify compounds that modulate c-di-GMP levels. Using this new screening platform, we tested a library of microbially-derived marine natural products extracts, leading to the discovery of the bioactive lipid (S)-sebastenoic acid. Evaluation of the effect of this new compound on bacterial motility, vpsL expression and biofilm formation implied that (S)-sebastenoic acid may alter phenotypes associated to c-di-GMP signaling in V. cholerae.
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Affiliation(s)
- Christopher J A Warner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mauro Salinas
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Zamorano-Sánchez
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Walter M Bray
- Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, Canada
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18
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Fong JC, Rogers A, Michael AK, Parsley NC, Cornell WC, Lin YC, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife 2017; 6:26163. [PMID: 28762945 PMCID: PMC5605196 DOI: 10.7554/elife.26163] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 07/31/2017] [Indexed: 01/10/2023] Open
Abstract
Biofilm formation is critical for the infection cycle of Vibrio cholerae. Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are required for the development of biofilm architecture. We demonstrate that RbmA binds VPS directly and uses a binary structural switch within its first fibronectin type III (FnIII-1) domain to control RbmA structural dynamics and the formation of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates interactions in trans with the FnIII-2 domain, leading to open (monomeric) or closed (dimeric) interfaces. The ability of RbmA to switch between open and closed states is important for V. cholerae biofilm formation, as RbmA variants with switches that are locked in either of the two states lead to biofilms with altered architecture and structural integrity.
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Affiliation(s)
- Jiunn Cn Fong
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States
| | - Andrew Rogers
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States
| | - Alicia K Michael
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - Nicole C Parsley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | | | - Yu-Cheng Lin
- Department of Biological Sciences, Columbia University, New York, United States
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Lars Ep Dietrich
- Department of Biological Sciences, Columbia University, New York, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, United States
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19
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Joshi A, Kostiuk B, Rogers A, Teschler J, Pukatzki S, Yildiz FH. Rules of Engagement: The Type VI Secretion System in Vibrio cholerae. Trends Microbiol 2017; 25:267-279. [PMID: 28027803 PMCID: PMC5365375 DOI: 10.1016/j.tim.2016.12.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 11/16/2022]
Abstract
Microbial species often exist in complex communities where they must avoid predation and compete for favorable niches. The type VI secretion system (T6SS) is a contact-dependent bacterial weapon that allows for direct killing of competitors through the translocation of proteinaceous toxins. Vibrio cholerae is a Gram-negative pathogen that can use its T6SS during antagonistic interactions with neighboring prokaryotic and eukaryotic competitors. The T6SS not only promotes V. cholerae's survival during its aquatic and host life cycles, but also influences its evolution by facilitating horizontal gene transfer. This review details the recent insights regarding the structure and function of the T6SS as well as the diverse signals and regulatory pathways that control its activation in V. cholerae.
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Affiliation(s)
- Avatar Joshi
- Department of Microbiology and Environmental Toxicology, University of Santa Cruz, Santa Cruz, California, USA
| | - Benjamin Kostiuk
- Department of Medical Microbiology and Immunology, University of Alberta, Alberta, Canada
| | - Andrew Rogers
- Department of Microbiology and Environmental Toxicology, University of Santa Cruz, Santa Cruz, California, USA
| | - Jennifer Teschler
- Department of Microbiology and Environmental Toxicology, University of Santa Cruz, Santa Cruz, California, USA
| | - Stefan Pukatzki
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of Santa Cruz, Santa Cruz, California, USA.
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20
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Bennett RR, Lee CK, De Anda J, Nealson KH, Yildiz FH, O'Toole GA, Wong GCL, Golestanian R. Species-dependent hydrodynamics of flagellum-tethered bacteria in early biofilm development. J R Soc Interface 2016; 13:20150966. [PMID: 26864892 DOI: 10.1098/rsif.2015.0966] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monotrichous bacteria on surfaces exhibit complex spinning movements. Such spinning motility is often a part of the surface detachment launch sequence of these cells. To understand the impact of spinning motility on bacterial surface interactions, we develop a hydrodynamic model of a surface-bound bacterium, which reproduces behaviours that we observe in Pseudomonas aeruginosa, Shewanella oneidensis and Vibrio cholerae, and provides a detailed dictionary for connecting observed spinning behaviour to bacteria-surface interactions. Our findings indicate that the fraction of the flagellar filament adhered to the surface, the rotation torque of this appendage, the flexibility of the flagellar hook and the shape of the bacterial cell dictate the likelihood that a microbe will detach and the optimum orientation that it should have during detachment. These findings are important for understanding species-specific reversible attachment, the key transition event between the planktonic and biofilm lifestyle for motile, rod-shaped organisms.
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Affiliation(s)
- Rachel R Bennett
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, UK Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Calvin K Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Jaime De Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Kenneth H Nealson
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095-1600, USA
| | - Ramin Golestanian
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3NP, UK
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21
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Wang YC, Chin KH, Tu ZL, He J, Jones CJ, Sanchez DZ, Yildiz FH, Galperin MY, Chou SH. Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat Commun 2016; 7:12481. [PMID: 27578558 PMCID: PMC5013675 DOI: 10.1038/ncomms12481] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/06/2016] [Indexed: 12/28/2022] Open
Abstract
C-di-GMP is a bacterial second messenger regulating various cellular functions. Many bacteria contain c-di-GMP-metabolizing enzymes but lack known c-di-GMP receptors. Recently, two MshE-type ATPases associated with bacterial type II secretion system and type IV pilus formation were shown to specifically bind c-di-GMP. Here we report crystal structure of the MshE N-terminal domain (MshEN1-145) from Vibrio cholerae in complex with c-di-GMP at a 1.37 Å resolution. This structure reveals a unique c-di-GMP-binding mode, featuring a tandem array of two highly conserved binding motifs, each comprising a 24-residue sequence RLGxx(L/V/I)(L/V/I)xxG(L/V/I)(L/V/I)xxxxLxxxLxxQ that binds half of the c-di-GMP molecule, primarily through hydrophobic interactions. Mutating these highly conserved residues markedly reduces c-di-GMP binding and biofilm formation by V. cholerae. This c-di-GMP-binding motif is present in diverse bacterial proteins exhibiting binding affinities ranging from 0.5 μM to as low as 14 nM. The MshEN domain contains the longest nucleotide-binding motif reported to date. Cyclic-di-GMP is a bacterial second messenger that binds to the regulatory domain of ATPases of some bacteria. Here, the authors report the crystal structure of this interaction, identify a cyclic-di-GMP binding mode, and show that this interaction might be important for bacterial biofilm formation.
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Affiliation(s)
- Yu-Chuan Wang
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - Ko-Hsin Chin
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - Zhi-Le Tu
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Christopher J Jones
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - David Zamorano Sanchez
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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22
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Jones CJ, Utada A, Davis KR, Thongsomboon W, Zamorano Sanchez D, Banakar V, Cegelski L, Wong GCL, Yildiz FH. C-di-GMP Regulates Motile to Sessile Transition by Modulating MshA Pili Biogenesis and Near-Surface Motility Behavior in Vibrio cholerae. PLoS Pathog 2015; 11:e1005068. [PMID: 26505896 PMCID: PMC4624765 DOI: 10.1371/journal.ppat.1005068] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023] Open
Abstract
In many bacteria, including Vibrio cholerae, cyclic dimeric guanosine monophosphate (c-di-GMP) controls the motile to biofilm life style switch. Yet, little is known about how this occurs. In this study, we report that changes in c-di-GMP concentration impact the biosynthesis of the MshA pili, resulting in altered motility and biofilm phenotypes in V. cholerae. Previously, we reported that cdgJ encodes a c-di-GMP phosphodiesterase and a ΔcdgJ mutant has reduced motility and enhanced biofilm formation. Here we show that loss of the genes required for the mannose-sensitive hemagglutinin (MshA) pilus biogenesis restores motility in the ΔcdgJ mutant. Mutations of the predicted ATPase proteins mshE or pilT, responsible for polymerizing and depolymerizing MshA pili, impair near surface motility behavior and initial surface attachment dynamics. A ΔcdgJ mutant has enhanced surface attachment, while the ΔcdgJmshA mutant phenocopies the high motility and low attachment phenotypes observed in a ΔmshA strain. Elevated concentrations of c-di-GMP enhance surface MshA pilus production. MshE, but not PilT binds c-di-GMP directly, establishing a mechanism for c-di-GMP signaling input in MshA pilus production. Collectively, our results suggest that the dynamic nature of the MshA pilus established by the assembly and disassembly of pilin subunits is essential for transition from the motile to sessile lifestyle and that c-di-GMP affects MshA pilus assembly and function through direct interactions with the MshE ATPase.
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Affiliation(s)
- Christopher J. Jones
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew Utada
- Department of Bioengineering, Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kimberly R. Davis
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Wiriya Thongsomboon
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - David Zamorano Sanchez
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Vinita Banakar
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California, United States of America
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23
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Warner CJA, Cheng AT, Yildiz FH, Linington RG. Development of benzo[1,4]oxazines as biofilm inhibitors and dispersal agents against Vibrio cholerae. Chem Commun (Camb) 2015; 51:1305-8. [PMID: 25479128 PMCID: PMC4288701 DOI: 10.1039/c4cc07003h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthesis of a library of natural product-inspired biofilm inhibitors has revealed a compound with selective and potent anti-biofilm activity against V. cholerae.
Bacterial biofilms are estimated to be associated with over 65 percent of all nosocomial infections. However, no therapeutics have been approved by the FDA which directly mediate biofilm formation or persistence. Herein we report oxazine 25 as a highly potent inhibitor, disperser and in the presence of the appropriate antibiotic eradicator of V. cholerae biofilms.
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Affiliation(s)
- Christopher J A Warner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, California, 95064, USA.
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24
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Ruhe ZC, Townsley L, Wallace AB, King A, Van der Woude MW, Low DA, Yildiz FH, Hayes CS. CdiA promotes receptor-independent intercellular adhesion. Mol Microbiol 2015; 98:175-92. [PMID: 26135212 DOI: 10.1111/mmi.13114] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 01/02/2023]
Abstract
CdiB/CdiA proteins mediate inter-bacterial competition in a process termed contact-dependent growth inhibition (CDI). Filamentous CdiA exoproteins extend from CDI(+) cells and bind specific receptors to deliver toxins into susceptible target bacteria. CDI has also been implicated in auto-aggregation and biofilm formation in several species, but the contribution of CdiA-receptor interactions to these multi-cellular behaviors has not been examined. Using Escherichia coli isolate EC93 as a model, we show that cdiA and bamA receptor mutants are defective in biofilm formation, suggesting a prominent role for CdiA-BamA mediated cell-cell adhesion. However, CdiA also promotes auto-aggregation in a BamA-independent manner, indicating that the exoprotein possesses an additional adhesin activity. Cells must express CdiA in order to participate in BamA-independent aggregates, suggesting that adhesion could be mediated by homotypic CdiA-CdiA interactions. The BamA-dependent and BamA-independent interaction domains map to distinct regions within the CdiA filament. Thus, CdiA orchestrates a collective behavior that is independent of its growth-inhibition activity. This adhesion should enable 'greenbeard' discrimination, in which genetically unrelated individuals cooperate with one another based on a single shared trait. This kind-selective social behavior could provide immediate fitness benefits to bacteria that acquire the systems through horizontal gene transfer.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Loni Townsley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Adam B Wallace
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Andrew King
- Centre for Immunology and Infection, Hull York Medical School and the Department of Biology, University of York, York, YO10 5DD, UK
| | - Marjan W Van der Woude
- Centre for Immunology and Infection, Hull York Medical School and the Department of Biology, University of York, York, YO10 5DD, UK
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106-9625, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106-9625, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106-9625, USA
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25
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Hollenbeck EC, Fong JCN, Lim JY, Yildiz FH, Fuller GG, Cegelski L. Molecular determinants of mechanical properties of V. cholerae biofilms at the air-liquid interface. Biophys J 2015; 107:2245-52. [PMID: 25418293 DOI: 10.1016/j.bpj.2014.10.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/23/2014] [Accepted: 10/01/2014] [Indexed: 12/13/2022] Open
Abstract
Biofilm formation increases both the survival and infectivity of Vibrio cholerae, the causative agent of cholera. V. cholerae is capable of forming biofilms on solid surfaces and at the air-liquid interface, termed pellicles. Known components of the extracellular matrix include the matrix proteins Bap1, RbmA, and RbmC, an exopolysaccharide termed Vibrio polysaccharide, and DNA. In this work, we examined a rugose strain of V. cholerae and its mutants unable to produce matrix proteins by interfacial rheology to compare the evolution of pellicle elasticity in real time to understand the molecular basis of matrix protein contributions to pellicle integrity and elasticity. Together with electron micrographs, visual inspection, and contact angle measurements of the pellicles, we defined distinct contributions of the matrix proteins to pellicle morphology, microscale architecture, and mechanical properties. Furthermore, we discovered that Bap1 is uniquely required for the maintenance of the mechanical strength of the pellicle over time and contributes to the hydrophobicity of the pellicle. Thus, Bap1 presents an important matrix component to target in the prevention and dispersal of V. cholerae biofilms.
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Affiliation(s)
- Emily C Hollenbeck
- Department of Chemical Engineering, Stanford University, Stanford, California
| | - Jiunn C N Fong
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California
| | - Ji Youn Lim
- Department of Chemistry, Stanford University, Stanford, California
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California
| | - Gerald G Fuller
- Department of Chemical Engineering, Stanford University, Stanford, California
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, California.
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26
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Teschler JK, Zamorano-Sánchez D, Utada AS, Warner CJA, Wong GCL, Linington RG, Yildiz FH. Living in the matrix: assembly and control of Vibrio cholerae biofilms. Nat Rev Microbiol 2015; 13:255-68. [PMID: 25895940 DOI: 10.1038/nrmicro3433] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nearly all bacteria form biofilms as a strategy for survival and persistence. Biofilms are associated with biotic and abiotic surfaces and are composed of aggregates of cells that are encased by a self-produced or acquired extracellular matrix. Vibrio cholerae has been studied as a model organism for understanding biofilm formation in environmental pathogens, as it spends much of its life cycle outside of the human host in the aquatic environment. Given the important role of biofilm formation in the V. cholerae life cycle, the molecular mechanisms underlying this process and the signals that trigger biofilm assembly or dispersal have been areas of intense investigation over the past 20 years. In this Review, we discuss V. cholerae surface attachment, various matrix components and the regulatory networks controlling biofilm formation.
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Affiliation(s)
- Jennifer K Teschler
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064, USA
| | - David Zamorano-Sánchez
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064, USA
| | - Andrew S Utada
- Bioengineering Department, Chemistry and Biochemistry Department, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Christopher J A Warner
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Gerard C L Wong
- Bioengineering Department, Chemistry and Biochemistry Department, California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064, USA
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27
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Townsley L, Yildiz FH. Temperature affects c-di-GMP signalling and biofilm formation in Vibrio cholerae. Environ Microbiol 2015; 17:4290-305. [PMID: 25684220 DOI: 10.1111/1462-2920.12799] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/19/2015] [Accepted: 01/31/2015] [Indexed: 02/04/2023]
Abstract
Biofilm formation is crucial to the environmental survival and transmission of Vibrio cholerae, the facultative human pathogen responsible for the disease cholera. During its infectious cycle, V. cholerae experiences fluctuations in temperature within the aquatic environment and during the transition between human host and aquatic reservoirs. In this study, we report that biofilm formation is induced at low temperatures through increased levels of the signalling molecule, cyclic diguanylate (c-di-GMP). Strains harbouring in frame deletions of all V. cholerae genes that are predicted to encode diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) were screened for their involvement in low-temperature-induced biofilm formation and Vibrio polysaccharide gene expression. Of the 52 mutants tested, deletions of six DGCs and three PDEs were found to affect these phenotypes at low temperatures. Unlike wild type, a strain lacking all six DGCs did not exhibit a low-temperature-dependent increase in c-di-GMP, indicating that these DGCs are required for temperature modulation of c-di-GMP levels. We also show that temperature modulates c-di-GMP levels in a similar fashion in the Gram-negative pathogen Pseudomonas aeruginosa but not in the Gram-positive pathogen Listeria monocytogenes. This study uncovers the role of temperature in environmental regulation of biofilm formation and c-di-GMP signalling.
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Affiliation(s)
- Loni Townsley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
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Song T, Sabharwal D, Gurung JM, Cheng AT, Sjöström AE, Yildiz FH, Uhlin BE, Wai SN. Vibrio cholerae utilizes direct sRNA regulation in expression of a biofilm matrix protein. PLoS One 2014; 9:e101280. [PMID: 25054332 PMCID: PMC4108314 DOI: 10.1371/journal.pone.0101280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/05/2014] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae biofilms contain exopolysaccharide and three matrix proteins RbmA, RbmC and Bap1. While much is known about exopolysaccharide regulation, little is known about the mechanisms by which the matrix protein components of biofilms are regulated. VrrA is a conserved, 140-nt sRNA of V. cholerae, whose expression is controlled by sigma factor σE. In this study, we demonstrate that VrrA negatively regulates rbmC translation by pairing to the 5′ untranslated region of the rbmC transcript and that this regulation is not stringently dependent on the RNA chaperone protein Hfq. These results point to VrrA as a molecular link between the σE-regulon and biofilm formation in V. cholerae. In addition, VrrA represents the first example of direct regulation of sRNA on biofilm matrix component, by-passing global master regulators.
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Affiliation(s)
- Tianyan Song
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Dharmesh Sabharwal
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jyoti Mohan Gurung
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Andrew T. Cheng
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Annika E. Sjöström
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- * E-mail:
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Peach KC, Cheng AT, Oliver AG, Yildiz FH, Linington RG. Discovery and biological characterization of the auromomycin chromophore as an inhibitor of biofilm formation in Vibrio cholerae. Chembiochem 2013; 14:2209-15. [PMID: 24106077 DOI: 10.1002/cbic.201300131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Indexed: 11/06/2022]
Abstract
Bacterial biofilms pose a significant challenge in clinical environments due to their inherent lack of susceptibility to antibiotic treatment. It is widely recognized that most pathogenic bacterial strains in the clinical setting persist in the biofilm state, and are the root cause of many recrudescent infections. The discovery and development of compounds capable of either inhibiting biofilm formation or initiating biofilm dispersal might provide new therapeutic avenues for reducing the number of hospital-acquired, biofilm-mediated infections. We detail here the application of our recently reported image-based, high-throughput screen to the discovery of microbially derived natural products with inhibitory activity against Vibrio cholerae biofilm. Examination of a prefractionated library of microbially derived marine natural products has led to the identification of a new biofilm inhibitor that is structurally unrelated to previously reported inhibitors and is one of the most potent inhibitors of V. cholerae reported to date. Combination of this compound with sub-MIC concentrations of a number of clinically relevant antibiotics was shown to improve the inhibitory efficacy of this new compound compared to monotherapy treatments, and provides evidence for the potential therapeutic benefit of biofilm inhibitors in treating persistent biofilm-mediated infections.
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Affiliation(s)
- Kelly C Peach
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 (USA)
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León B, Fong JCN, Peach KC, Wong WR, Yildiz FH, Linington RG. Development of quinoline-based disruptors of biofilm formation against Vibrio cholerae. Org Lett 2013; 15:1234-7. [PMID: 23461487 DOI: 10.1021/ol400150z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biofilm formation is a major cause of bacterial persistence in nosocomial infections, leading to extended treatment times and increased rates of morbidity and mortality. Despite this, there are currently no biofilm inhibitors approved for clinical use. The synthesis and biological evaluation of a library of amino alcohol quinolines as lead compounds for the disruption of biofilm formation in Vibrio cholerae is now reported. Application of selective metal-halogen exchange chemistry installed both stereocenters in one step, to afford a simpler scaffold than the initial lead molecule, with an EC50 < 10 μM.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
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Berk V, Fong JCN, Dempsey GT, Develioglu ON, Zhuang X, Liphardt J, Yildiz FH, Chu S. Molecular architecture and assembly principles of Vibrio cholerae biofilms. Science 2012; 337:236-9. [PMID: 22798614 DOI: 10.1126/science.1222981] [Citation(s) in RCA: 266] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In their natural environment, microbes organize into communities held together by an extracellular matrix composed of polysaccharides and proteins. We developed an in vivo labeling strategy to allow the extracellular matrix of developing biofilms to be visualized with conventional and superresolution light microscopy. Vibrio cholerae biofilms displayed three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Multiresolution imaging of living V. cholerae biofilms revealed the complementary architectural roles of the four essential matrix constituents: RbmA provided cell-cell adhesion; Bap1 allowed the developing biofilm to adhere to surfaces; and heterogeneous mixtures of Vibrio polysaccharide, RbmC, and Bap1 formed dynamic, flexible, and ordered envelopes that encased the cell clusters.
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Affiliation(s)
- Veysel Berk
- Department of Physics, University of California, Berkeley, CA 94720, USA.
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32
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Shikuma NJ, Davis KR, Fong JNC, Yildiz FH. The transcriptional regulator, CosR, controls compatible solute biosynthesis and transport, motility and biofilm formation in Vibrio cholerae. Environ Microbiol 2012; 15:1387-99. [PMID: 22690884 DOI: 10.1111/j.1462-2920.2012.02805.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Vibrio cholerae inhabits aquatic environments and colonizes the human digestive tract to cause the disease cholera. In these environments, V. cholerae copes with fluctuations in salinity and osmolarity by producing and transporting small, organic, highly soluble molecules called compatible solutes, which counteract extracellular osmotic pressure. Currently, it is unclear how V. cholerae regulates the expression of genes important for the biosynthesis or transport of compatible solutes in response to changing salinity or osmolarity conditions. Through a genome-wide transcriptional analysis of the salinity response of V. cholerae, we identified a transcriptional regulator we name CosR for compatible solute regulator. The expression of cosR is regulated by ionic strength and not osmolarity. A transcriptome analysis of a ΔcosR mutant revealed that CosR represses genes involved in ectoine biosynthesis and compatible solute transport in a salinity-dependent manner. When grown in salinities similar to estuarine environments, CosR activates biofilm formation and represses motility independently of its function as an ectoine regulator. This is the first study to characterize a compatible solute regulator in V. cholerae and couples the regulation of osmotic tolerance with biofilm formation and motility.
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Affiliation(s)
- Nicholas J Shikuma
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Berk V, Fong JC, Dempsey GT, Develioglu ON, Zhuang X, Liphardt J, Yildiz FH, Chu S. Molecular Architecture and Assembly Principles of Vibrio Cholerae Biofilms. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Abstract
MOTIVATION Accurate prediction of genes encoding small proteins (on the order of 50 amino acids or less) remains an elusive open problem in bioinformatics. Some of the best methods for gene prediction use either sequence composition analysis or sequence similarity to a known protein coding sequence. These methods often fail for small proteins, however, either due to a lack of experimentally verified small protein coding genes or due to the limited statistical significance of statistics on small sequences. Our approach is based upon the hypothesis that true small proteins will be under selective pressure for encoding the particular amino acid sequence, for ease of translation by the ribosome and for structural stability. This stability can be achieved either independently or as part of a larger protein complex. Given this assumption, it follows that small proteins should display conserved local protein structure properties much like larger proteins. Our method incorporates neural-net predictions for three local structure alphabets within a comparative genomic approach using a genomic alignment of 22 closely related bacteria genomes to generate predictions for whether or not a given open reading frame (ORF) encodes for a small protein. RESULTS We have applied this method to the complete genome for Escherichia coli strain K12 and looked at how well our method performed on a set of 60 experimentally verified small proteins from this organism. Out of a total of 11 407 possible ORFs, we found that 6 of the top 10 and 27 of the top 100 predictions belonged to the set of 60 experimentally verified small proteins. We found 35 of all the true small proteins within the top 200 predictions. We compared our method to Glimmer, using a default Glimmer protocol and a modified small ORF Glimmer protocol with a lower minimum size cutoff. The default Glimmer protocol identified 16 of the true small proteins (all in the top 200 predictions), but failed to predict on 34 due to size cutoffs. The small ORF Glimmer protocol made predictions for all the experimentally verified small proteins but only contained 9 of the 60 true small proteins within the top 200 predictions. CONTACT jsamayoa@jhu.edu
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Affiliation(s)
- Josue Samayoa
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.
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35
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Peach KC, Bray WM, Shikuma NJ, Gassner NC, Lokey RS, Yildiz FH, Linington RG. An image-based 384-well high-throughput screening method for the discovery of biofilm inhibitors in Vibrio cholerae. Mol Biosyst 2011; 7:1176-84. [PMID: 21246108 PMCID: PMC8216101 DOI: 10.1039/c0mb00276c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial biofilms are assemblages of bacterial cells and extracellular matrix that result in the creation of surface-associated macrocolony formation. Most bacteria are capable of forming biofilms under suitable conditions. Biofilm formation by pathogenic bacteria on medical implant devices has been linked to implant rejection in up to 10% of cases, due to biofilm-related secondary infections. In addition, biofilm formation has been implicated in both bacterial persistence and antibiotic resistance. In this study, a method has been developed for the discovery of small molecule inhibitors of biofilm formation in Vibrio cholerae, through the use of high-throughput epifluorescence microscopy imaging. Adaptation of a strategy for the growth of bacterial biofilms in wellplates, and the subsequent quantification of biofilm coverage within these wells, provides the first example of an image-based 384-well format system for the evaluation of biofilm inhibition in V. cholerae. Application of this method to the high-throughput screening of small molecule libraries has lead to the discovery of 29 biofilm lead structures, many of which eliminate biofilm formation without altering bacterial cell viability.
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Affiliation(s)
- Kelly C Peach
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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36
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Fong JCN, Syed KA, Klose KE, Yildiz FH. Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis. Microbiology (Reading) 2010; 156:2757-2769. [PMID: 20466768 PMCID: PMC3068689 DOI: 10.1099/mic.0.040196-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biofilm formation enhances the survival and persistence of the facultative human pathogen Vibrio cholerae in natural ecosystems and its transmission during seasonal cholera outbreaks. A major component of the V. cholerae biofilm matrix is the Vibrio polysaccharide (VPS), which is essential for development of three-dimensional biofilm structures. The vps genes are clustered in two regions, the vps-I cluster (vpsU, vpsA–K, VC0916–27) and the vps-II cluster (vpsL–Q, VC0934–39), separated by an intergenic region containing the rbm gene cluster that encodes biofilm matrix proteins. In-frame deletions of the vps clusters and genes encoding matrix proteins drastically altered biofilm formation phenotypes. To determine which genes within the vps gene clusters are required for biofilm formation and VPS synthesis, we generated in-frame deletion mutants for all the vps genes. Many of these mutants exhibited reduced capacity to produce VPS and biofilms. Infant mouse colonization assays revealed that mutants lacking either vps clusters or rbmA (encoding secreted matrix protein RbmA) exhibited a defect in intestinal colonization compared to the wild-type. Understanding the roles of the various vps gene products will aid in the biochemical characterization of the VPS biosynthetic pathway and elucidate how vps gene products contribute to VPS biosynthesis, biofilm formation and virulence in V. cholerae.
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Affiliation(s)
- Jiunn C N Fong
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Khalid A Syed
- Department of Biology, The University of Texas at San Antonio, South Texas Center for Emerging Infectious Diseases, San Antonio, TX 78249, USA
| | - Karl E Klose
- Department of Biology, The University of Texas at San Antonio, South Texas Center for Emerging Infectious Diseases, San Antonio, TX 78249, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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37
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Krasteva PV, Fong JCN, Shikuma NJ, Beyhan S, Navarro MVAS, Yildiz FH, Sondermann H. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 2010; 327:866-8. [PMID: 20150502 DOI: 10.1126/science.1181185] [Citation(s) in RCA: 325] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.
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Affiliation(s)
- Petya V Krasteva
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Abstract
Vibrio cholerae's capacity to cause outbreaks of cholera is linked to its survival and adaptability to changes in aquatic environments. One of the environmental conditions that can vary in V. cholerae's natural aquatic habitats is calcium (Ca(+2)). In this study, we investigated the response of V. cholerae to changes in extracellular Ca(2+) levels. Whole-genome expression profiling revealed that Ca(2+) decreased the expression of genes required for biofilm matrix production. Luria-Bertani (LB) medium supplemented with Ca(2+) (LBCa(2+)) caused V. cholerae to form biofilms with decreased thickness and increased roughness, as compared with biofilms formed in LB. Furthermore, addition of Ca(2+) led to dissolution in biofilms. Transcription of two genes encoding a two-component regulatory system pair, now termed calcium-regulated sensor (carS) and regulator (carR), was decreased in cells grown in LBCa(2+). Analysis of null and overexpression alleles of carS and carR revealed that expression of vps (Vibriopolysaccharide) genes and biofilm formation are negatively regulated by the CarRS two-component regulatory system. Through epistasis analysis we determined that CarR acts in parallel with HapR, the negative regulator of vps gene expression.
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Affiliation(s)
- Kivanc Bilecen
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA
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39
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Kanabar PN, Vaske CJ, Yeang CH, Yildiz FH, Stuart JM. Inferring disease-related pathways using a probabilistic epistasis model. Pac Symp Biocomput 2009:480-491. [PMID: 19209724 DOI: 10.1142/9789812836939_0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We present a probabilistic model called a Joint Intervention Network (JIN) for inferring interactions among a chosen set of regulator genes. The input to the method are expression changes of downstream indicator genes observed under the knock-out of the regulators. JIN can use any number of perturbation combinations for model inference (e.g. single, double, and triple knock-outs). RESUITS/CONCLUSIONS: We applied JIN to a Vibrio cholerae regulatory network to uncover mechanisms critical to its environmental persistence. V. cholerae is a facultative human pathogen that causes cholera in humans and responsible for seven pandemics. We analyzed the expression response of 17 V. cholerae biofilm indicator genes under various single and multiple knock-outs of three known biofilm regulators. Using the inferred network, we were able to identify new genes involved in biofilm formation more accurately than clustering expression profiles.
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Affiliation(s)
- P N Kanabar
- Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95062, USA
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40
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Beyhan S, Yildiz FH. Smooth to rugose phase variation in Vibrio cholerae can be mediated by a single nucleotide change that targets c-di-GMP signalling pathway. Mol Microbiol 2007; 63:995-1007. [PMID: 17233827 DOI: 10.1111/j.1365-2958.2006.05568.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Microorganisms use phase variation to increase population diversity to maximize evolutionary success. One such variation is the smooth to rugose phenotype change in Vibrio cholerae. We determined that the variation between smooth and rugose phenotypes can be controlled by a single nucleotide change in a gene (vpvC) predicted to encode a diguanylate cyclase. The vpvC allele found in the rugose genetic background is more active at producing c-di-GMP while that in smooth genetic background is less active. In support of this finding, disruption of vpvC in the rugose genetic variant decreases cellular c-di-GMP levels, diminishes rugose-associated phenotypes and yields a smooth variant. Furthermore, the frequency of phase variation decreases dramatically when the vpvC locus is deleted in the smooth genetic background. Evidence is presented that the rugose variant is less susceptible to phage infection than the smooth variant. As phage infection is known to control populations of V. cholerae and thus outbreaks of cholera, phase variation may increase the evolutionary success of the pathogen.
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Affiliation(s)
- Sinem Beyhan
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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41
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Yildiz FH. Processes controlling the transmission of bacterial pathogens in the environment. Res Microbiol 2007; 158:195-202. [PMID: 17350808 DOI: 10.1016/j.resmic.2006.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 11/27/2006] [Accepted: 12/01/2006] [Indexed: 11/20/2022]
Abstract
Many pathogens in the environment can be transmitted to human populations and cause outbreaks and epidemics. Transmission is a multifactorial process influenced by the physiology of the pathogen as it exits its initial host, the mechanisms it uses for surviving outside the host, the physiology of the pathogen as it enters the next susceptible host and its ability to establish a successful infection. Few studies so far have focused on the processes responsible for modulating microbial survival in non-host environments and the transmission dynamics between infected and susceptible hosts, as well as the interplay between hosts. A better understanding of these mechanisms is thus necessary for predicting and preventing future outbreaks.
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Affiliation(s)
- Fitnat H Yildiz
- Department of Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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42
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Abstract
Vibrio cholerae, the causative agent of cholera, can undergo phenotypic variation generating rugose and smooth variants. The rugose variant forms corrugated colonies and well-developed biofilms and exhibits increased levels of resistance to several environmental stresses. Many of these phenotypes are mediated in part by increased expression of the vps genes, which are organized into vps-I and vps-II coding regions, separated by an intergenic region. In this study, we generated in-frame deletions of the five genes located in the vps intergenic region, termed rbmB to -F (rugosity and biofilm structure modulators B to F) in the rugose genetic background, and characterized the mutants for rugose colony development and biofilm formation. Deletion of rbmB, which encodes a protein with low sequence similarity to polysaccharide hydrolases, resulted in an increase in colony corrugation and accumulation of exopolysaccharides relative to the rugose variant. RbmC and its homolog Bap1 are predicted to encode proteins with carbohydrate-binding domains. The colonies of the rbmC bap1 double deletion mutant and bap1 single deletion mutant exhibited a decrease in colony corrugation. Furthermore, the rbmC bap1 double deletion mutant was unable to form biofilms at the air-liquid interface after 2 days, while the biofilms formed on solid surfaces detached readily. Although the colony morphology of rbmDEF mutants was similar to that of the rugose variant, their biofilm structure and cell aggregation phenotypes were different than those of the rugose variant. Taken together, these results indicate that vps intergenic region genes encode proteins that are involved in biofilm matrix production and maintenance of biofilm structure and stability.
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Affiliation(s)
- Jiunn C N Fong
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Lim B, Beyhan S, Yildiz FH. Regulation of Vibrio polysaccharide synthesis and virulence factor production by CdgC, a GGDEF-EAL domain protein, in Vibrio cholerae. J Bacteriol 2006; 189:717-29. [PMID: 17122338 PMCID: PMC1797307 DOI: 10.1128/jb.00834-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In Vibrio cholerae, the second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) regulates several cellular processes, such as formation of corrugated colony morphology, biofilm formation, motility, and virulence factor production. Both synthesis and degradation of c-di-GMP in the cell are modulated by proteins containing GGDEF and/or EAL domains, which function as a diguanylate cyclase and a phosphodiesterase, respectively. The expression of two genes, cdgC and mbaA, which encode proteins harboring both GGDEF and EAL domains is higher in the rugose phase variant of V. cholerae than in the smooth variant. In this study, we carried out gene expression analysis to determine the genes regulated by CdgC in the rugose and smooth phase variants of V. cholerae. We determined that CdgC regulates expression of genes required for V. cholerae polysaccharide synthesis and of the transcriptional regulator genes vpsR, vpsT, and hapR. CdgC also regulates expression of genes involved in extracellular protein secretion, flagellar biosynthesis, and virulence factor production. We then compared the genes regulated by CdgC and by MbaA, during both exponential and stationary phases of growth, to elucidate processes regulated by them. Identification of the regulons of CdgC and MbaA revealed that the regulons overlap, but the timing of regulation exerted by CdgC and MbaA is different, suggesting the interplay and complexity of the c-di-GMP signal transduction pathways operating in V. cholerae.
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Affiliation(s)
- Bentley Lim
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Beyhan S, Bilecen K, Salama SR, Casper-Lindley C, Yildiz FH. Regulation of rugosity and biofilm formation in Vibrio cholerae: comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR. J Bacteriol 2006; 189:388-402. [PMID: 17071756 PMCID: PMC1797413 DOI: 10.1128/jb.00981-06] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vibrio cholerae undergoes phenotypic variation that generates two morphologically different variants, termed smooth and rugose. The transcriptional profiles of the two variants differ greatly, and many of the differentially regulated genes are controlled by a complex regulatory circuitry that includes the transcriptional regulators VpsR, VpsT, and HapR. In this study, we identified the VpsT regulon and compared the VpsT and VpsR regulons to elucidate the contribution of each positive regulator to the rugose variant transcriptional profile and associated phenotypes. We have found that although the VpsT and VpsR regulons are very similar, the magnitude of the gene regulation accomplished by each regulator is different. We also determined that cdgA, which encodes a GGDEF domain protein, is partially responsible for the altered vps gene expression between the vpsT and vpsR mutants. Analysis of epistatic relationships among hapR, vpsT, and vpsR with respect to a whole-genome expression profile, colony morphology, and biofilm formation revealed that vpsR is epistatic to hapR and vpsT. Expression of virulence genes was increased in a vpsR hapR double mutant relative to a hapR mutant, suggesting that VpsR negatively regulates virulence gene expression in the hapR mutant. These results show that a complex regulatory interplay among VpsT, VpsR, HapR, and GGDEF/EAL family proteins controls transcription of the genes required for Vibrio polysaccharide and virulence factor production in V. cholerae.
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Affiliation(s)
- Sinem Beyhan
- Department of Environmental Toxicology, University of California, Santa Cruz, CA 95064, USA
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Abstract
Cyclic di-guanylic acid (c-diGMP) is a second messenger that modulates the cell surface properties of several microorganisms. Concentrations of c-diGMP in the cell are controlled by the opposing activities of diguanylate cyclases and phosphodiesterases, which are carried out by proteins harbouring GGDEF and EAL domains respectively. In this study, we report that the cellular levels of c-diGMP are higher in the Vibrio cholerae rugose variant compared with the smooth variant. Modulation of cellular c-diGMP levels by overexpressing proteins with GGDEF or EAL domains increased or decreased colony rugosity respectively. Several genes encoding proteins with either GGDEF or EAL domains are differentially expressed between the two V. cholerae variants. The generation and characterization of null mutants of these genes (cdgA-E, rocS and mbaA) revealed that rugose colony formation, exopolysaccharide production, motility and biofilm formation are controlled by their action. Furthermore, epistasis analysis suggested that cdgC, rocS and mbaA act in convergent pathways to regulate the phenotypic properties of the rugose and smooth variants, and are part of the VpsR, VpsT and HapR signal transduction pathway.
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Affiliation(s)
- Bentley Lim
- Department of Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Abstract
Vibrio cholerae, the causative agent of cholera, is a facultative human pathogen with intestinal and aquatic life cycles. The capacity of V. cholerae to recognize and respond to fluctuating parameters in its environment is critical to its survival. In many microorganisms, the second messenger, 3',5'-cyclic diguanylic acid (c-di-GMP), is believed to be important for integrating environmental stimuli that affect cell physiology. Sequence analysis of the V. cholerae genome has revealed an abundance of genes encoding proteins with either GGDEF domains, EAL domains, or both, which are predicted to modulate cellular c-di-GMP concentrations. To elucidate the cellular processes controlled by c-di-GMP, whole-genome transcriptome responses of the El Tor and classical V. cholerae biotypes to increased c-di-GMP concentrations were determined. The results suggest that V. cholerae responds to an elevated level of c-di-GMP by increasing the transcription of the vps, eps, and msh genes and decreasing that of flagellar genes. The functions of other c-di-GMP-regulated genes in V. cholerae are yet to be identified.
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Affiliation(s)
- Sinem Beyhan
- Department of Environmental Toxicology, University of California, Santa Cruz, 95064, USA
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Abstract
Differences in whole-genome expression patterns between the classical and El Tor biotypes of Vibrio cholerae O1 were determined under conditions that induce virulence gene expression in the classical biotype. A total of 524 genes (13.5% of the genome) were found to be differentially expressed in the two biotypes. The expression of genes encoding proteins required for biofilm formation, chemotaxis, and transport of amino acids, peptides, and iron was higher in the El Tor biotype. These gene expression differences may contribute to the enhanced survival capacity of the El Tor biotype in environmental reservoirs. The expression of genes encoding virulence factors was higher in the classical than in the El Tor biotype. In addition, the vieSAB genes, which were originally identified as regulators of ctxA transcription, were expressed at a fivefold higher level in the classical biotype. We determined the VieA regulon in both biotypes by transcriptome comparison of wild-type and vieA deletion mutant strains. VieA predominantly regulates gene expression in the classical biotype; 401 genes (10.3% of the genome), including those encoding proteins required for virulence, exopolysaccharide biosynthesis, and flagellum production as well as those regulated by sigmaE, are differentially expressed in the classical vieA deletion mutant. In contrast, only five genes were regulated by VieA in the El Tor biotype. A large fraction (20.8%) of the genes that are differentially expressed in the classical versus the El Tor biotype are controlled by VieA in the classical biotype. Thus, VieA is a major regulator of genes in the classical biotype under virulence gene-inducing conditions.
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Affiliation(s)
- Sinem Beyhan
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Fong JCN, Karplus K, Schoolnik GK, Yildiz FH. Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae. J Bacteriol 2006; 188:1049-59. [PMID: 16428409 PMCID: PMC1347326 DOI: 10.1128/jb.188.3.1049-1059.2006] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phase variation between smooth and rugose colony variants of Vibrio cholerae is predicted to be important for the pathogen's survival in its natural aquatic ecosystems. The rugose variant forms corrugated colonies, exhibits increased levels of resistance to osmotic, acid, and oxidative stresses, and has an enhanced capacity to form biofilms. Many of these phenotypes are mediated in part by increased production of an exopolysaccharide termed VPS. In this study, we compared total protein profiles of the smooth and rugose variants using two-dimensional gel electrophoresis and identified one protein that is present at a higher level in the rugose variant. A mutation in the gene encoding this protein, which does not have any known homologs in the protein databases, causes cells to form biofilms that are more fragile and sensitive to sodium dodecyl sulfate than wild-type biofilms. The results indicate that the gene, termed rbmA (rugosity and biofilm structure modulator A), is required for rugose colony formation and biofilm structure integrity in V. cholerae. Transcription of rbmA is positively regulated by the response regulator VpsR but not VpsT.
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Affiliation(s)
- Jiunn C N Fong
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Matz C, McDougald D, Moreno AM, Yung PY, Yildiz FH, Kjelleberg S. Biofilm formation and phenotypic variation enhance predation-driven persistence of Vibrio cholerae. Proc Natl Acad Sci U S A 2005; 102:16819-24. [PMID: 16267135 PMCID: PMC1283802 DOI: 10.1073/pnas.0505350102] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Persistence of the opportunistic bacterial pathogen Vibrio cholerae in aquatic environments is the principal cause for seasonal occurrence of cholera epidemics. This causality has been explained by postulating that V. cholerae forms biofilms in association with animate and inanimate surfaces. Alternatively, it has been proposed that bacterial pathogens are an integral part of the natural microbial food web and thus their survival is constrained by protozoan predation. Here, we report that both explanations are interrelated. Our data show that biofilms are the protective agent enabling V. cholerae to survive protozoan grazing while their planktonic counterparts are eliminated. Grazing on planktonic V. cholerae was found to select for the biofilm-enhancing rugose phase variant, which is adapted to the surface-associated niche by the production of exopolymers. Interestingly, grazing resistance in V. cholerae biofilms was not attained by exopolymer production alone but was accomplished by the secretion of an antiprotozoal factor that inhibits protozoan feeding activity. We identified that the cell density-dependent regulator hapR controls the production of this factor in biofilms. The inhibitory effect of V. cholerae biofilms was found to be widespread among toxigenic and nontoxigenic isolates. Our results provide a mechanistic explanation for the adaptive advantage of surface-associated growth in the environmental persistence of V. cholerae and suggest an important contribution of protozoan predation in the selective enrichment of biofilm-forming strains in the out-of-host environment.
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Affiliation(s)
- Carsten Matz
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Sydney, Australia.
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Abstract
Reversible phase variation between the rugose and smooth colony variants is predicted to be important for the survival of Vibrio cholerae in natural aquatic habitats. Microarray expression profiling studies of the rugose and smooth variants of the same strain led to the identification of 124 differentially regulated genes. Further expression profiling experiments showed how these genes are regulated by the VpsR and HapR transcription factors, which, respectively, positively and negatively regulate production of VPS(El Tor), a rugose-associated extracellular polysaccharide. The study of mutants of rpoN and rpoS demonstrated the effects of these alternative sigma factors on phase variation-specific gene expression. Bioinformatics analysis of these expression data shows that 'rugosity' and 'smoothness' are determined by a complex hierarchy of positive and negative regulators, which also affect the biofilm, surface hydrophobicity and motility phenotypes of the organism.
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Affiliation(s)
- Fitnat H Yildiz
- Department of Environmental Toxicology, University of California, Santa Cruz, 269 Jack Baskin Engineering Bldg, Santa Cruz, CA 95064, USA.
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