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Nair ZJ, Gao IH, Firras A, Chong KKL, Hill ED, Choo PY, Colomer-Winter C, Chen Q, Manzano C, Pethe K, Kline KA. An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalis. Mol Microbiol 2024; 121:1021-1038. [PMID: 38527904 DOI: 10.1111/mmi.15253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Daptomycin is a last-line antibiotic commonly used to treat vancomycin-resistant Enterococci, but resistance evolves rapidly and further restricts already limited treatment options. While genetic determinants associated with clinical daptomycin resistance (DAPR) have been described, information on factors affecting the speed of DAPR acquisition is limited. The multiple peptide resistance factor (MprF), a phosphatidylglycerol-modifying enzyme involved in cationic antimicrobial resistance, is linked to DAPR in pathogens such as methicillin-resistant Staphylococcus aureus. Since Enterococcus faecalis encodes two paralogs of mprF and clinical DAPR mutations do not map to mprF, we hypothesized that functional redundancy between the paralogs prevents mprF-mediated resistance and masks other evolutionary pathways to DAPR. Here, we performed in vitro evolution to DAPR in mprF mutant background. We discovered that the absence of mprF results in slowed DAPR evolution and is associated with inactivating mutations in ftsH, resulting in the depletion of the chaperone repressor HrcA. We also report that ftsH is essential in the parental, but not in the ΔmprF, strain where FtsH depletion results in growth impairment in the parental strain, a phenotype associated with reduced extracellular acidification and reduced ability for metabolic reduction. This presents FtsH and HrcA as enticing targets for developing anti-resistance strategies.
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Affiliation(s)
- Zeus Jaren Nair
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Iris Hanxing Gao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aslam Firras
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cristina Colomer-Winter
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Qingyan Chen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kevin Pethe
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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2
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Bramkamp M, Scheffers DJ. Bacterial membrane dynamics: Compartmentalization and repair. Mol Microbiol 2023; 120:490-501. [PMID: 37243899 DOI: 10.1111/mmi.15077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
In every bacterial cell, the plasma membrane plays a key role in viability as it forms a selective barrier between the inside of the cell and its environment. This barrier function depends on the physical state of the lipid bilayer and the proteins embedded or associated with the bilayer. Over the past decade or so, it has become apparent that many membrane-organizing proteins and principles, which were described in eukaryote systems, are ubiquitous and play important roles in bacterial cells. In this minireview, we focus on the enigmatic roles of bacterial flotillins in membrane compartmentalization and bacterial dynamins and ESCRT-like systems in membrane repair and remodeling.
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Affiliation(s)
- Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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3
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Dupuy P, Gutierrez C, Neyrolles O. Modulation of bacterial membrane proteins activity by clustering into plasma membrane nanodomains. Mol Microbiol 2023; 120:502-507. [PMID: 37303242 DOI: 10.1111/mmi.15105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Recent research has demonstrated specific protein clustering within membrane subdomains in bacteria, challenging the long-held belief that prokaryotes lack these subdomains. This mini review provides examples of bacterial membrane protein clustering, discussing the benefits of protein assembly in membranes and highlighting how clustering regulates protein activity.
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Affiliation(s)
- Pierre Dupuy
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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4
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Kado T, Akbary Z, Motooka D, Sparks IL, Melzer ES, Nakamura S, Rojas ER, Morita YS, Siegrist MS. A cell wall synthase accelerates plasma membrane partitioning in mycobacteria. eLife 2023; 12:e81924. [PMID: 37665120 PMCID: PMC10547480 DOI: 10.7554/elife.81924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/02/2023] [Indexed: 09/05/2023] Open
Abstract
Lateral partitioning of proteins and lipids shapes membrane function. In model membranes, partitioning can be influenced both by bilayer-intrinsic factors like molecular composition and by bilayer-extrinsic factors such as interactions with other membranes and solid supports. While cellular membranes can departition in response to bilayer-intrinsic or -extrinsic disruptions, the mechanisms by which they partition de novo are largely unknown. The plasma membrane of Mycobacterium smegmatis spatially and biochemically departitions in response to the fluidizing agent benzyl alcohol, then repartitions upon fluidizer washout. By screening for mutants that are sensitive to benzyl alcohol, we show that the bifunctional cell wall synthase PonA2 promotes membrane partitioning and cell growth during recovery from benzyl alcohol exposure. PonA2's role in membrane repartitioning and regrowth depends solely on its conserved transglycosylase domain. Active cell wall polymerization promotes de novo membrane partitioning and the completed cell wall polymer helps to maintain membrane partitioning. Our work highlights the complexity of membrane-cell wall interactions and establishes a facile model system for departitioning and repartitioning cellular membranes.
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Affiliation(s)
- Takehiro Kado
- Department of Microbiology, University of Massachusetts AmherstAmherstUnited States
| | - Zarina Akbary
- Department of Biology, New York UniversityNew YorkUnited States
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka UniversityOsakaJapan
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts AmherstAmherstUnited States
| | - Emily S Melzer
- Department of Microbiology, University of Massachusetts AmherstAmherstUnited States
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka UniversityOsakaJapan
| | - Enrique R Rojas
- Department of Biology, New York UniversityNew YorkUnited States
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Graduate Program, University of Massachusetts AmherstAmherstUnited States
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Graduate Program, University of Massachusetts AmherstAmherstUnited States
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5
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Wessel AK, Yoshii Y, Reder A, Boudjemaa R, Szczesna M, Betton JM, Bernal-Bayard J, Beloin C, Lopez D, Völker U, Ghigo JM. Escherichia coli SPFH Membrane Microdomain Proteins HflKC Contribute to Aminoglycoside and Oxidative Stress Tolerance. Microbiol Spectr 2023; 11:e0176723. [PMID: 37347165 PMCID: PMC10434171 DOI: 10.1128/spectrum.01767-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Many eukaryotic membrane-dependent functions are often spatially and temporally regulated by membrane microdomains (FMMs), also known as lipid rafts. These domains are enriched in polyisoprenoid lipids and scaffolding proteins belonging to the stomatin, prohibitin, flotillin, and HflK/C (SPFH) protein superfamily that was also identified in Gram-positive bacteria. In contrast, little is still known about FMMs in Gram-negative bacteria. In Escherichia coli K-12, 4 SPFH proteins, YqiK, QmcA, HflK, and HflC, were shown to localize in discrete polar or lateral inner membrane locations, raising the possibility that E. coli SPFH proteins could contribute to the assembly of inner membrane FMMs and the regulation of cellular processes. Here, we studied the determinant of the localization of QmcA and HflC and showed that FMM-associated cardiolipin lipid biosynthesis is required for their native localization pattern. Using Biolog phenotypic arrays, we showed that a mutant lacking all SPFH genes displayed increased sensitivity to aminoglycosides and oxidative stress that is due to the absence of HflKC. Our study therefore provides further insights into the contribution of SPFH proteins to stress tolerance in E. coli. IMPORTANCE Eukaryotic cells often segregate physiological processes in cholesterol-rich functional membrane microdomains. These domains are also called lipid rafts and contain proteins of the stomatin, prohibitin, flotillin, and HflK/C (SPFH) superfamily, which are also present in prokaryotes but have been mostly studied in Gram-positive bacteria. Here, we showed that the cell localization of the SPFH proteins QmcA and HflKC in the Gram-negative bacterium E. coli is altered in the absence of cardiolipin lipid synthesis. This suggests that cardiolipins contribute to E. coli membrane microdomain assembly. Using a broad phenotypic analysis, we also showed that HflKC contribute to E. coli tolerance to aminoglycosides and oxidative stress. Our study, therefore, provides new insights into the cellular processes associated with SPFH proteins in E. coli.
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Affiliation(s)
- Aimee K. Wessel
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Alexander Reder
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | - Magdalena Szczesna
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
- Centre for Bacteriology Resistance Biology, Imperial College London, London, United Kingdom
| | - Jean-Michel Betton
- Institut Pasteur, Université de Paris-Cité, UMR UMR6047, Stress adaptation and metabolism in enterobacteria, Paris, France
| | - Joaquin Bernal-Bayard
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Christophe Beloin
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
| | - Daniel Lopez
- Universidad Autonoma de Madrid, Centro Nacional de Biotecnologia, Madrid, Spain
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris-Cité, CNRS UMR6047, Genetics of Biofilms Laboratory, Paris, France
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6
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Mitchison-Field LM, Belin BJ. Bacterial lipid biophysics and membrane organization. Curr Opin Microbiol 2023; 74:102315. [PMID: 37058914 PMCID: PMC10523990 DOI: 10.1016/j.mib.2023.102315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The formation of lateral microdomains is emerging as a central organizing principle in bacterial membranes. These microdomains are targets of antibiotic development and have the potential to enhance natural product synthesis, but the rules governing their assembly are unclear. Previous studies have suggested that microdomain formation is promoted by lipid phase separation, particularly by cardiolipin (CL) and isoprenoid lipids, and there is strong evidence that CL biosynthesis is required for recruitment of membrane proteins to cell poles and division sites. New work demonstrates that additional bacterial lipids may mediate membrane protein localization and function, opening the field for mechanistic evaluation of lipid-driven membrane organization in vivo.
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Affiliation(s)
- Lorna My Mitchison-Field
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Brittany J Belin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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7
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Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. Nat Commun 2023; 14:3510. [PMID: 37316519 PMCID: PMC10267222 DOI: 10.1038/s41467-023-39121-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Jia Yan
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Xiandong Meng
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- University of California San Francisco, San Francisco, CA, USA.
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8
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Xu F, Liu C, Xia M, Li S, Tu R, Wang S, Jin H, Zhang D. Characterization of a Riboflavin-Producing Mutant of Bacillus subtilis Isolated by Droplet-Based Microfluidics Screening. Microorganisms 2023; 11:microorganisms11041070. [PMID: 37110496 PMCID: PMC10146818 DOI: 10.3390/microorganisms11041070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Bacillus subtilis is one of the commonly used industrial strains for riboflavin production. High-throughput screening is useful in biotechnology, but there are still an insufficient number of articles focusing on improving the riboflavin production of B. subtilis by this powerful tool. With droplet-based microfluidics technology, single cells can be encapsulated in droplets. The screening can be carried out by detecting the fluorescence intensity of secreted riboflavin. Thus, an efficient and high-throughput screening method suitable for riboflavin production strain improvement could be established. In this study, droplet-based microfluidics screening was applied, and a more competitive riboflavin producer U3 was selected from the random mutation library of strain S1. The riboflavin production and biomass of U3 were higher than that of S1 in flask fermentation. In addition, the results of fed-batch fermentation showed that the riboflavin production of U3 was 24.3 g/L, an 18% increase compared with the parent strain S1 (20.6 g/L), and the yield (g riboflavin/100 g glucose) increased by 19%, from 7.3 (S1) to 8.7 (U3). Two mutations of U3 (sinRG89R and icdD28E) were identified through whole genome sequencing and comparison. Then they were introduced into BS168DR (parent of S1) for further analysis, which also caused riboflavin production to increase. This paper provides protocols for screening riboflavin-producing B. subtilis with droplet-based microfluidics technology and reveals mutations in riboflavin overproduction strains.
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Affiliation(s)
- Fan Xu
- School of Chemical Engineering, Hebei University of Technology, Tianjin 300131, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chuan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miaomiao Xia
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shixin Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Biological Engineering, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Sijia Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Hongxing Jin
- School of Chemical Engineering, Hebei University of Technology, Tianjin 300131, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Gupta S, Mandal T. Simulation study of domain formation in a model bacterial membrane. Phys Chem Chem Phys 2022; 24:18133-18143. [PMID: 35856570 DOI: 10.1039/d2cp01873j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental studies revealed that functional membrane microdomains (FMMs) are formed in prokaryotic cells which are structurally and functionally similar to the lipid rafts formed in eukaryotic cells. In this study, we employ coarse-grained molecular dynamics simulations to investigate the mechanism of domain formation and its physiochemical properties in a model methicillin-resistant staphylococcus aureus (MRSA) cell membrane. We find that domains are formed through lateral segregation of staphyloxanthin (STX), a carotenoid which shields the bacteria from the host's immune because of its antioxidant nature. Simulation results suggest that membrane integrity increases with the size of the domain, which is assessed by computing bond order parameter of the lipid tails, membrane expansion modulus and water permeability across the membrane. Various membrane domain proteins such as flotillin-like protein floA and penicillin binding protein (PBP2a) preferentially bind with the STX and accumulate in the membrane domain which is consistent with the recent experimental results.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
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10
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Czolkoss S, Safronov X, Rexroth S, Knoke LR, Aktas M, Narberhaus F. Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes. Front Microbiol 2021; 12:754486. [PMID: 34899640 PMCID: PMC8656257 DOI: 10.3389/fmicb.2021.754486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cell membranes are not homogenous but compartmentalized into lateral microdomains, which are considered as biochemical reaction centers for various physiological processes in eukaryotes and prokaryotes. Due to their special lipid and protein composition, some of these microdomains are resistant to treatment with non-ionic detergents and can be purified as detergent-resistant membranes (DRMs). Here we report the proteome of DRMs from the Gram-negative phytopathogen Agrobacterium tumefaciens. Using label-free liquid chromatography-tandem mass spectrometry, we identified proteins enriched in DRMs isolated under normal and virulence-mimicking growth conditions. Prominent microdomain marker proteins such as the SPFH (stomatin/prohibitin/flotillin/HflKC) proteins HflK, HflC and Atu3772, along with the protease FtsH were highly enriched in DRMs isolated under any given condition. Moreover, proteins involved in cell envelope biogenesis, transport and secretion, as well as motility- and chemotaxis-associated proteins were overrepresented in DRMs. Most strikingly, we found virulence-associated proteins such as the VirA/VirG two-component system, and the membrane-spanning type IV and type VI secretion systems enriched in DRMs. Fluorescence microscopy of the cellular localization of both secretion systems and of marker proteins was in agreement with the results from the proteomics approach. These findings suggest that virulence traits are micro-compartmentalized into functional microdomains in A. tumefaciens.
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Affiliation(s)
- Simon Czolkoss
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Xenia Safronov
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Sascha Rexroth
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Lisa R Knoke
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Meriyem Aktas
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Department of Microbial Biology, Ruhr University Bochum, Bochum, Germany
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11
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Sharipova MR, Mardanova AM, Rudakova NL, Pudova DS. Bistability and Formation of the Biofilm Matrix as Adaptive Mechanisms during the Stationary Phase of Bacillus subtilis. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172006017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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12
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Zielińska A, Savietto A, de Sousa Borges A, Martinez D, Berbon M, Roelofsen JR, Hartman AM, de Boer R, Van der Klei IJ, Hirsch AKH, Habenstein B, Bramkamp M, Scheffers DJ. Flotillin-mediated membrane fluidity controls peptidoglycan synthesis and MreB movement. eLife 2020; 9:e57179. [PMID: 32662773 PMCID: PMC7360373 DOI: 10.7554/elife.57179] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
The bacterial plasma membrane is an important cellular compartment. In recent years it has become obvious that protein complexes and lipids are not uniformly distributed within membranes. Current hypotheses suggest that flotillin proteins are required for the formation of complexes of membrane proteins including cell-wall synthetic proteins. We show here that bacterial flotillins are important factors for membrane fluidity homeostasis. Loss of flotillins leads to a decrease in membrane fluidity that in turn leads to alterations in MreB dynamics and, as a consequence, in peptidoglycan synthesis. These alterations are reverted when membrane fluidity is restored by a chemical fluidizer. In vitro, the addition of a flotillin increases membrane fluidity of liposomes. Our data support a model in which flotillins are required for direct control of membrane fluidity rather than for the formation of protein complexes via direct protein-protein interactions.
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Affiliation(s)
- Aleksandra Zielińska
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Abigail Savietto
- Biozentrum, Ludwig-Maximilians-Universität MünchenMünchenGermany
- Institute for General Microbiology, Christian-Albrechts-UniversityKielGermany
| | - Anabela de Sousa Borges
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Melanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Joël R Roelofsen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Alwin M Hartman
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany
- Department of Pharmacy, Saarland UniversitySaarbrückenGermany
- Stratingh Institute for Chemistry, University of GroningenGroningenNetherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Ida J Van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Anna KH Hirsch
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany
- Department of Pharmacy, Saarland UniversitySaarbrückenGermany
- Stratingh Institute for Chemistry, University of GroningenGroningenNetherlands
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Marc Bramkamp
- Biozentrum, Ludwig-Maximilians-Universität MünchenMünchenGermany
- Institute for General Microbiology, Christian-Albrechts-UniversityKielGermany
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
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13
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Dual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane. Nat Commun 2020; 11:1859. [PMID: 32313019 PMCID: PMC7171179 DOI: 10.1038/s41467-020-15758-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria can form biofilms that consist of multicellular communities embedded in an extracellular matrix (ECM). In Bacillus subtilis, the main protein component of the ECM is the functional amyloid TasA. Here, we study further the roles played by TasA in B. subtilis physiology and biofilm formation on plant leaves and in vitro. We show that ΔtasA cells exhibit a range of cytological symptoms indicative of excessive cellular stress leading to increased cell death. TasA associates to the detergent-resistant fraction of the cell membrane, and the distribution of the flotillin-like protein FloT is altered in ΔtasA cells. We propose that, in addition to a structural function during ECM assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics as cells enter stationary phase. The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.
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14
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Cell Membrane and Electron Transfer Engineering for Improved Synthesis of Menaquinone-7 in Bacillus subtilis. iScience 2020; 23:100918. [PMID: 32109677 PMCID: PMC7044751 DOI: 10.1016/j.isci.2020.100918] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
The formation of biofilm facilitates the synthesis of valuable natural product menaquinone-7 (MK-7) in static culture of Bacillus subtilis, whereas the essential role and mechanism of biofilm in MK-7 synthesis have not been revealed. Herein, comparative transcriptomics show that the formation of biofilm affected MK-7 synthesis by changing the transcription levels of signal receptor (BSU02010), transmembrane transporter (BSU29340, BSU03070), and signal transduction (BSU02630). Moreover, we also found that oxalate decarboxylase OxdC has an important effect on electron generation and MK-7 synthesis, when the transcriptional level of NADH dehydrogenase decreases in static culture. Our results revealed that cell membrane and electron transfer are important factors in promoting MK-7 synthesis. Transcriptome analysis shows the relationship between biofilm and MK-7 synthesis Electron transfer significantly affects the synthesis of MK-7 Oxalate decarboxylase OxdC plays a role in electron generation and MK-7 synthesis
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15
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Culp EJ, Waglechner N, Wang W, Fiebig-Comyn AA, Hsu YP, Koteva K, Sychantha D, Coombes BK, Van Nieuwenhze MS, Brun YV, Wright GD. Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling. Nature 2020; 578:582-587. [DOI: 10.1038/s41586-020-1990-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022]
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16
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Proteomic analysis of Escherichia coli detergent-resistant membranes (DRM). PLoS One 2019; 14:e0223794. [PMID: 31603938 PMCID: PMC6788730 DOI: 10.1371/journal.pone.0223794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Membrane microdomains or lipid rafts compartmentalize cellular processes by laterally organizing membrane components. Such sub-membrane structures were mainly described in eukaryotic cells, but, recently, also in bacteria. Here, the protein content of lipid rafts in Escherichia coli was explored by mass spectrometry analyses of Detergent Resistant Membranes (DRM). We report that at least three of the four E. coli flotillin homologous proteins were found to reside in DRM, along with 77 more proteins. Moreover, the proteomic data were validated by subcellular localization, using immunoblot assays and fluorescence microscopy of selected proteins. Our results confirm the existence of lipid raft-like microdomains in the inner membrane of E. coli and represent the first comprehensive profiling of proteins in these bacterial membrane platforms.
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17
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Fleitas Martínez O, Cardoso MH, Ribeiro SM, Franco OL. Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition. Front Cell Infect Microbiol 2019; 9:74. [PMID: 31001485 PMCID: PMC6454102 DOI: 10.3389/fcimb.2019.00074] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.
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Affiliation(s)
- Osmel Fleitas Martínez
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon Henrique Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Suzana Meira Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Octavio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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18
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The Multifaceted Antibacterial Mechanisms of the Pioneering Peptide Antibiotics Tyrocidine and Gramicidin S. mBio 2018; 9:mBio.00802-18. [PMID: 30301848 PMCID: PMC6178620 DOI: 10.1128/mbio.00802-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Cyclic β-sheet decapeptides, such as tyrocidines and gramicidin S, were among the first antibiotics in clinical application. Although they have been used for such a long time, there is virtually no resistance to them, which has led to a renewed interest in this peptide class. Both tyrocidines and gramicidin S are thought to disrupt the bacterial membrane. However, this knowledge is mainly derived from in vitro studies, and there is surprisingly little knowledge about how these long-established antibiotics kill bacteria. Our results shed new light on the antibacterial mechanism of β-sheet peptide antibiotics and explain why they are still so effective and why there is so little resistance to them. Cyclic β-sheet decapeptides from the tyrocidine group and the homologous gramicidin S were the first commercially used antibiotics, yet it remains unclear exactly how they kill bacteria. We investigated their mode of action using a bacterial cytological profiling approach. Tyrocidines form defined ion-conducting pores, induce lipid phase separation, and strongly reduce membrane fluidity, resulting in delocalization of a broad range of peripheral and integral membrane proteins. Interestingly, they also cause DNA damage and interfere with DNA-binding proteins. Despite sharing 50% sequence identity with tyrocidines, gramicidin S causes only mild lipid demixing with minor effects on membrane fluidity and permeability. Gramicidin S delocalizes peripheral membrane proteins involved in cell division and cell envelope synthesis but does not affect integral membrane proteins or DNA. Our results shed a new light on the multifaceted antibacterial mechanisms of these antibiotics and explain why resistance to them is virtually nonexistent.
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19
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Yu Y, Yan F, He Y, Qin Y, Chen Y, Chai Y, Guo JH. The ClpY-ClpQ protease regulates multicellular development in Bacillus subtilis. Microbiology (Reading) 2018; 164:848-862. [DOI: 10.1099/mic.0.000658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yiyang Yu
- Department of Plant Pathology, Nanjing Agricultural University; Engineering Center of Bioresource Pesticide in Jiangsu Province; Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing 210095, PR China
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Fang Yan
- Department of Plant Pathology, Nanjing Agricultural University; Engineering Center of Bioresource Pesticide in Jiangsu Province; Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing 210095, PR China
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yinghao He
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yuxuan Qin
- Department of Biology, Northeastern University, Boston, MA 02115, USA
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Yun Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Jian-hua Guo
- Department of Plant Pathology, Nanjing Agricultural University; Engineering Center of Bioresource Pesticide in Jiangsu Province; Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing 210095, PR China
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20
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Pandit S, Ravikumar V, Abdel-Haleem AM, Derouiche A, Mokkapati VRSS, Sihlbom C, Mineta K, Gojobori T, Gao X, Westerlund F, Mijakovic I. Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms. Front Microbiol 2017; 8:2599. [PMID: 29317857 PMCID: PMC5748153 DOI: 10.3389/fmicb.2017.02599] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 11/13/2022] Open
Abstract
Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS matrix is primarily composed of polysaccharides, proteins and extracellular DNA. In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, it shields the bacterial cells inside the biofilm, by preventing antimicrobial agents from getting in contact with them, thereby reducing their killing effect. New strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of existing antimicrobials. Here we examined the mechanism of the known effect of vitamin C (sodium ascorbate) on enhancing the activity of various antibacterial agents. Our quantitative proteomics analysis shows that non-lethal concentrations of vitamin C inhibit bacterial quorum sensing and other regulatory mechanisms underpinning biofilm development. As a result, the EPS biosynthesis in reduced, and especially the polysaccharide component of the matrix is depleted. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antimicrobials or treatments.
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Affiliation(s)
- Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vaishnavi Ravikumar
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alyaa M Abdel-Haleem
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - V R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Fredrik Westerlund
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Mielich-Süss B, Wagner RM, Mietrach N, Hertlein T, Marincola G, Ohlsen K, Geibel S, Lopez D. Flotillin scaffold activity contributes to type VII secretion system assembly in Staphylococcus aureus. PLoS Pathog 2017; 13:e1006728. [PMID: 29166667 PMCID: PMC5718613 DOI: 10.1371/journal.ppat.1006728] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/06/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022] Open
Abstract
Scaffold proteins are ubiquitous chaperones that promote efficient interactions between partners of multi-enzymatic protein complexes; although they are well studied in eukaryotes, their role in prokaryotic systems is poorly understood. Bacterial membranes have functional membrane microdomains (FMM), a structure homologous to eukaryotic lipid rafts. Similar to their eukaryotic counterparts, bacterial FMM harbor a scaffold protein termed flotillin that is thought to promote interactions between proteins spatially confined to the FMM. Here we used biochemical approaches to define the scaffold activity of the flotillin homolog FloA of the human pathogen Staphylococcus aureus, using assembly of interacting protein partners of the type VII secretion system (T7SS) as a case study. Staphylococcus aureus cells that lacked FloA showed reduced T7SS function, and thus reduced secretion of T7SS-related effectors, probably due to the supporting scaffold activity of flotillin. We found that the presence of flotillin mediates intermolecular interactions of T7SS proteins. We tested several small molecules that interfere with flotillin scaffold activity, which perturbed T7SS activity in vitro and in vivo. Our results suggest that flotillin assists in the assembly of S. aureus membrane components that participate in infection and influences the infective potential of this pathogen. The recently discovered functional membrane microdomains (FMM) of prokaryotic cells contain a protein homologous to the scaffold protein flotillin found in eukaryotic lipid rafts. It remains to be elucidated whether, like their eukaryotic counterparts, flotillin homolog proteins have a scaffold function in bacteria. Here we show that the Staphylococcus aureus flotillin FloA acts as a scaffold protein, to promote more efficient assembly of membrane-associated protein interacting partners of multi-enzyme complexes. In a case study, we provide biochemical evidence that FloA participates in assembly of the Type VII secretion system and thus contributes to S. aureus infective potential. Targeted dispersion of FMM-related processes using anti-FMM molecules opens up new perspectives for microbial therapies to treat persistent S. aureus infections.
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Affiliation(s)
- Benjamin Mielich-Süss
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Rabea M. Wagner
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Nicole Mietrach
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- Rudolf Virchow Center - DFG Research Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Gabriella Marincola
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Sebastian Geibel
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- Rudolf Virchow Center - DFG Research Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- * E-mail:
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22
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Senpuku H, Yonezawa H, Yoneda S, Suzuki I, Nagasawa R, Narisawa N. SMU.940 regulates dextran-dependent aggregation and biofilm formation in Streptococcus mutans. Mol Oral Microbiol 2017; 33:47-58. [PMID: 28845576 DOI: 10.1111/omi.12196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/30/2022]
Abstract
The oral bacterium Streptococcus mutans is the principal agent in the development of dental caries. Biofilm formation by S. mutans requires bacterial attachment, aggregation, and glucan formation on the tooth surface under sucrose supplementation conditions. Our previous microarray analysis of clinical strains identified 74 genes in S. mutans that were related to biofilm morphology; however, the roles of almost all of these genes in biofilm formation are poorly understood. We investigated the effects of 21 genes randomly selected from our previous study regarding S. mutans biofilm formation, regulation by the complement pathway, and responses to competence-stimulating peptide. Eight competence-stimulating peptide-dependent genes were identified, and their roles in biofilm formation and aggregation were examined by mutational analyses of the S. mutansUA159 strain. Of these eight genes, the inactivation of the putative hemolysin III family SMU.940 gene of S. mutansUA159 promoted rapid dextran-dependent aggregation and biofilm formation in tryptic soy broth without dextrose (TSB) with 0.25% glucose and slightly reduced biofilm formation in TSB with 0.25% sucrose. The SMU.940 mutant showed higher expression of GbpC and gbpC gene than wild-type. GbpC is known to be involved in the dextran-dependent aggregation of S. mutans. An SMU.940-gbpC double mutant strain was constructed in the SMU.940 mutant background. The gbpC mutation completely abolished the dextran-dependent aggregation of the SMU.940 mutant. In addition, the aggregation of the mutant was abrogated by dextranase. These findings suggest that SMU.940 controls GbpC expression, and contributes to the regulation of dextran-dependent aggregation and biofilm formation.
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Affiliation(s)
- Hidenobu Senpuku
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hideo Yonezawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.,Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka, Tokyo, Japan
| | - Saori Yoneda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.,Department of Microbiology, Faculty of Medicine, Kagawa University, Takamatsu, Japan
| | - Itaru Suzuki
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.,Department of Pediatric Dentistry, Nihon University at Matsudo, Chiba, Japan
| | - Ryo Nagasawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.,Graduate School of Science and Engineering, Hosei University, Shinjuku-ku, Tokyo, Japan
| | - Naoki Narisawa
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.,Department of Food Science and Technology, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
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23
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Linearmycins Activate a Two-Component Signaling System Involved in Bacterial Competition and Biofilm Morphology. J Bacteriol 2017; 199:JB.00186-17. [PMID: 28461449 DOI: 10.1128/jb.00186-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria use two-component signaling systems to adapt and respond to their competitors and changing environments. For instance, competitor bacteria may produce antibiotics and other bioactive metabolites and sequester nutrients. To survive, some species of bacteria escape competition through antibiotic production, biofilm formation, or motility. Specialized metabolite production and biofilm formation are relatively well understood for bacterial species in isolation. How bacteria control these functions when competitors are present is not well studied. To address fundamental questions relating to the competitive mechanisms of different species, we have developed a model system using two species of soil bacteria, Bacillus subtilis and Streptomyces sp. strain Mg1. Using this model, we previously found that linearmycins produced by Streptomyces sp. strain Mg1 cause lysis of B. subtilis cells and degradation of colony matrix. We identified strains of B. subtilis with mutations in the two-component signaling system yfiJK operon that confer dual phenotypes of specific linearmycin resistance and biofilm morphology. We determined that expression of the ATP-binding cassette (ABC) transporter yfiLMN operon, particularly yfiM and yfiN, is necessary for biofilm morphology. Using transposon mutagenesis, we identified genes that are required for YfiLMN-mediated biofilm morphology, including several chaperones. Using transcriptional fusions, we found that YfiJ signaling is activated by linearmycins and other polyene metabolites. Finally, using a truncated YfiJ, we show that YfiJ requires its transmembrane domain to activate downstream signaling. Taken together, these results suggest coordinated dual antibiotic resistance and biofilm morphology by a single multifunctional ABC transporter promotes competitive fitness of B. subtilisIMPORTANCE DNA sequencing approaches have revealed hitherto unexplored diversity of bacterial species in a wide variety of environments that includes the gastrointestinal tract of animals and the rhizosphere of plants. Interactions between different species in bacterial communities have impacts on our health and industry. However, many approaches currently used to study whole bacterial communities do not resolve mechanistic details of interspecies interactions, including how bacteria sense and respond to their competitors. Using a competition model, we have uncovered dual functions for a previously uncharacterized two-component signaling system involved in specific antibiotic resistance and biofilm morphology. Insights gleaned from signaling within interspecies interaction models build a more complete understanding of gene functions important for bacterial communities and will enhance community-level analytical approaches.
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24
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Abstract
The bacterial cytoplasmic membrane is composed of roughly equal proportions of lipids and proteins. The main lipid components are phospholipids, which vary in acyl chain length, saturation, and branching and carry head groups that vary in size and charge. Phospholipid variants determine membrane properties such as fluidity and charge that in turn modulate interactions with membrane-associated proteins. We summarize recent advances in understanding bacterial membrane structure and function, focusing particularly on the possible existence and significance of specialized membrane domains. We review the role of membrane curvature as a spatial cue for recruitment and regulation of proteins involved in morphogenic functions, especially elongation and division. Finally, we examine the role of the membrane, especially regulation of synthesis and fluid properties, in the life cycle of cell wall-deficient L-form bacteria.
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Affiliation(s)
- Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX United Kingdom; ,
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX United Kingdom; ,
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25
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Koch G, Wermser C, Acosta IC, Kricks L, Stengel ST, Yepes A, Lopez D. Attenuating Staphylococcus aureus Virulence by Targeting Flotillin Protein Scaffold Activity. Cell Chem Biol 2017; 24:845-857.e6. [PMID: 28669526 DOI: 10.1016/j.chembiol.2017.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 01/13/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S. aureus toxin expression. Small molecules that altered FloA oligomerization also reduced Rny function and decreased the virulence potential of S. aureus in vitro, as well as in vivo, using invertebrate and murine infection models. Our results suggest that flotillin assists in the assembly of protein complexes involved in S. aureus virulence, and could thus be an attractive target for the development of new antimicrobial therapies.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ivan C Acosta
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Lara Kricks
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany; National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain.
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26
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Vega-Cabrera LA, Wood CD, Pardo-López L. Spo0M: structure and function beyond regulation of sporulation. Curr Genet 2017; 64:17-23. [PMID: 28577219 DOI: 10.1007/s00294-017-0718-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
In this mini-review, we present a perspective on the recent findings relating Spo0M structure and function that will stimulate and guide further studies in the characterization of this interesting protein. Cell division and sporulation constitute two of the best studied processes in the model organism Bacillus subtilis; however, there are many missing pieces in the giant regulatory puzzle that governs the independent and shared networks between them. Spo0M is a little studied protein that has been related to both, cell division and sporulation, but its biochemical function and its direct interactions have not been yet defined. Structural analysis of Spo0M revealed the presence of an arrestin-like domain and an FP domain (a dimerization domain present in proteasome elements), motifs more commonly found in eukaryotic proteins. The aim of this perspective is to present open questions regarding the functional and structural features of Spo0M that make this protein a good candidate for the ancestor of arrestins in bacteria and an important element in developmental and differentiation processes of Bacillus subtilis.
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Affiliation(s)
- Luz Adriana Vega-Cabrera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Christopher D Wood
- Laboratorio Nacional de Microscopía Avanzada, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico.
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Rashid R, Cazenave-Gassiot A, Gao IH, Nair ZJ, Kumar JK, Gao L, Kline KA, Wenk MR. Comprehensive analysis of phospholipids and glycolipids in the opportunistic pathogen Enterococcus faecalis. PLoS One 2017; 12:e0175886. [PMID: 28423018 PMCID: PMC5397010 DOI: 10.1371/journal.pone.0175886] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 04/02/2017] [Indexed: 02/07/2023] Open
Abstract
Enterococcus faecalis is a Gram-positive, opportunistic, pathogenic bacterium that causes a significant number of antibiotic-resistant infections in hospitalized patients. The development of antibiotic resistance in hospital-associated pathogens is a formidable public health threat. In E. faecalis and other Gram-positive pathogens, correlations exist between lipid composition and antibiotic resistance. Resistance to the last-resort antibiotic daptomycin is accompanied by a decrease in phosphatidylglycerol (PG) levels, whereas multiple peptide resistance factor (MprF) converts anionic PG into cationic lysyl-PG via a trans-esterification reaction, providing resistance to cationic antimicrobial peptides. Unlike previous studies that relied on thin layer chromatography and spectrophotometry, we have performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) directly on lipids extracted from E. faecalis, and quantified the phospholipids through multiple reaction monitoring (MRM). In the daptomycin-sensitive E. faecalis strain OG1RF, we have identified 17 PGs, 8 lysyl-PGs (LPGs), 23 cardiolipins (CL), 3 glycerophospho-diglucosyl-diacylglycerols (GPDGDAG), 5 diglucosyl-diacylglycerols (DGDAG), 3 diacylglycerols (DAGs), and 4 triacylglycerols (TAGs). We have quantified PG and shown that PG levels vary during growth of E. faecalis in vitro. We also show that two daptomycin-resistant (DapR) strains of E. faecalis have substantially lower levels of PG and LPG levels. Since LPG levels in these strains are lower, daptomycin resistance is likely due to the reduction in PG. This lipidome map is the first comprehensive analysis of membrane phospholipids and glycolipids in the important human pathogen E. faecalis, for which antimicrobial resistance and altered lipid homeostasis have been intimately linked.
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Affiliation(s)
- Rafi Rashid
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Iris H. Gao
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zeus J. Nair
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jaspal K. Kumar
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Liang Gao
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Kimberly A. Kline
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (KAK); (MRW)
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- * E-mail: (KAK); (MRW)
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Omar A, Wright JB, Schultz G, Burrell R, Nadworny P. Microbial Biofilms and Chronic Wounds. Microorganisms 2017; 5:microorganisms5010009. [PMID: 28272369 PMCID: PMC5374386 DOI: 10.3390/microorganisms5010009] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/04/2017] [Indexed: 12/14/2022] Open
Abstract
Background is provided on biofilms, including their formation, tolerance mechanisms, structure, and morphology within the context of chronic wounds. The features of biofilms in chronic wounds are discussed in detail, as is the impact of biofilm on wound chronicity. Difficulties associated with the use of standard susceptibility tests (minimum inhibitory concentrations or MICs) to determine appropriate treatment regimens for, or develop new treatments for use in, chronic wounds are discussed, with alternate test methods specific to biofilms being recommended. Animal models appropriate for evaluating biofilm treatments are also described. Current and potential future therapies for treatment of biofilm-containing chronic wounds, including probiotic therapy, virulence attenuation, biofilm phenotype expression attenuation, immune response suppression, and aggressive debridement combined with antimicrobial dressings, are described.
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Affiliation(s)
- Amin Omar
- Innovotech Inc., Suite 101, 2011 94 Street, Edmonton, Alberta T6N 1H1, Canada.
| | - J Barry Wright
- Harkynn Consulting, P.O. Box 104, Albertville, Saskatchewan S0J 0A0, Canada.
| | - Gregory Schultz
- Department of Obstetrics and Gynecology, Institute for Wound Research, University of Florida, 1600 South West Archer Road, Room M337F, Gainesville, FL 32610-0294, USA.
| | - Robert Burrell
- Department of Biomedical Engineering, Faculties of Engineering and Medicine & Dentistry, 1101 Research Transition Facility, University of Alberta, Edmonton, Alberta T6G 2G6, Canada.
| | - Patricia Nadworny
- Innovotech Inc., Suite 101, 2011 94 Street, Edmonton, Alberta T6N 1H1, Canada.
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Vega-Cabrera LA, Guerrero A, Rodríguez-Mejía JL, Tabche ML, Wood CD, Gutiérrez-Rios RM, Merino E, Pardo-López L. Analysis of Spo0M function in Bacillus subtilis. PLoS One 2017; 12:e0172737. [PMID: 28234965 PMCID: PMC5325327 DOI: 10.1371/journal.pone.0172737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/08/2017] [Indexed: 12/22/2022] Open
Abstract
Spo0M has been previously reported as a regulator of sporulation in Bacillus subtilis; however, little is known about the mechanisms through which it participates in sporulation, and there is no information to date that relates this protein to other processes in the bacterium. In this work we present evidence from proteomic, protein-protein interaction, morphological, subcellular localization microscopy and bioinformatics studies which indicate that Spo0M function is not necessarily restricted to sporulation, and point towards its involvement in other stages of the vegetative life cycle. In the current study, we provide evidence that Spo0M interacts with cytoskeletal proteins involved in cell division, which suggest a function additional to that previously described in sporulation. Spo0M expression is not restricted to the transition phase or sporulation; rather, its expression begins during the early stages of growth and Spo0M localization in B. subtilis depends on the bacterial life cycle and could be related to an additional proposed function. This is supported by our discovery of homologs in a broad distribution of bacterial genera, even in non-sporulating species. Our work paves the way for re-evaluation of the role of Spo0M in bacterial cell.
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Affiliation(s)
- Luz Adriana Vega-Cabrera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Avenida Universidad 2001, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - José Luis Rodríguez-Mejía
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
| | - María Luisa Tabche
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
| | - Christopher D. Wood
- Laboratorio Nacional de Microscopía Avanzada, Avenida Universidad 2001, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Rosa-María Gutiérrez-Rios
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
| | - Liliana Pardo-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, Cuernavaca, Morelos, México
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Lopez D, Koch G. Exploring functional membrane microdomains in bacteria: an overview. Curr Opin Microbiol 2017; 36:76-84. [PMID: 28237903 DOI: 10.1016/j.mib.2017.02.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/01/2017] [Indexed: 01/08/2023]
Abstract
Recent studies show that internal organization of bacterial cells is more complex than previously appreciated. A clear example of this is the assembly of the nanoscale membrane platforms termed functional membrane microdomains. The lipid composition of these regions differs from that of the surrounding membrane; these domains confine a set of proteins involved in specific cellular processes such as protease secretion and signal transduction. It is currently thought that functional membrane microdomains act as oligomerization platforms and promote efficient oligomerization of interacting protein partners in bacterial membranes. In this review, we highlight the most noteworthy achievements, challenges and controversies of this emerging research field over the past five years.
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Affiliation(s)
- Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany; Spanish National Centre for Biotechnology (CNB), Madrid 28049, Spain.
| | - Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
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31
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Arends J, Thomanek N, Kuhlmann K, Marcus K, Narberhaus F. In vivo trapping of FtsH substrates by label-free quantitative proteomics. Proteomics 2016; 16:3161-3172. [DOI: 10.1002/pmic.201600316] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Arends
- Ruhr-Universität Bochum; Lehrstuhl Biologie der Mikroorganismen; Bochum Germany
| | - Nikolas Thomanek
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Katja Kuhlmann
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Katrin Marcus
- Ruhr-Universität Bochum; Medizinisches Proteom-Center; Bochum Germany
| | - Franz Narberhaus
- Ruhr-Universität Bochum; Lehrstuhl Biologie der Mikroorganismen; Bochum Germany
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Zwick JV, Noble S, Ellaicy YK, Coe GD, Hakey DJ, King AN, Sadauskas AJ, Faulkner MJ. AhpA is a peroxidase expressed during biofilm formation in Bacillus subtilis. Microbiologyopen 2016; 6. [PMID: 27683249 PMCID: PMC5300871 DOI: 10.1002/mbo3.403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 11/10/2022] Open
Abstract
Organisms growing aerobically generate reactive oxygen species such as hydrogen peroxide. These reactive oxygen molecules damage enzymes and DNA, potentially causing cell death. In response, Bacillus subtilis produces at least nine potential peroxide-scavenging enzymes; two belong to the alkylhydroperoxide reductase (Ahp) class of peroxidases. Here, we explore the role of one of these Ahp homologs, AhpA. While previous studies demonstrated that AhpA can scavenge peroxides and thus defend cells against peroxides, they did not clarify when during growth the cell produces AhpA. The results presented here show that the expression of ahpA is regulated in a manner distinct from that of the other peroxide-scavenging enzymes in B. subtilis. While the primary Ahp, AhpC, is expressed during exponential growth and stationary phase, these studies demonstrate that the expression of ahpA is dependent on the transition-state regulator AbrB and the sporulation and biofilm formation transcription factor Spo0A. Furthermore, these results show that ahpA is specifically expressed during biofilm formation, and not during sporulation or stationary phase, suggesting that derepression of ahpA by AbrB requires a signal other than those present upon entry into stationary phase. Despite this expression pattern, ahpA mutant strains still form and maintain robust biofilms, even in the presence of peroxides. Thus, the role of AhpA with regard to protecting cells within biofilms from environmental stresses is still uncertain. These studies highlight the need to further study the Ahp homologs to better understand how they differ from one another and the unique roles they may play in oxidative stress resistance.
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Affiliation(s)
- Joelie V Zwick
- Department of Biology, Bradley University, Peoria, IL, USA
| | - Sarah Noble
- Department of Biology, Bradley University, Peoria, IL, USA
| | | | | | - Dylan J Hakey
- Department of Biology, Bradley University, Peoria, IL, USA
| | - Alyssa N King
- Department of Biology, Bradley University, Peoria, IL, USA
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Mamani S, Moinier D, Denis Y, Soulère L, Queneau Y, Talla E, Bonnefoy V, Guiliani N. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog. Front Microbiol 2016; 7:1365. [PMID: 27683573 PMCID: PMC5021923 DOI: 10.3389/fmicb.2016.01365] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/17/2016] [Indexed: 12/13/2022] Open
Abstract
While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270(T) and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidans (T), the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidans (T) cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270(T) genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis.
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Affiliation(s)
- Sigde Mamani
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche ScientifiqueMarseille, France; Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de ChileSantiago, Chile
| | - Danielle Moinier
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Yann Denis
- Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Laurent Soulère
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Yves Queneau
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Nicolas Guiliani
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de Chile Santiago, Chile
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Functional Membrane Microdomains Organize Signaling Networks in Bacteria. J Membr Biol 2016; 250:367-378. [PMID: 27566471 DOI: 10.1007/s00232-016-9923-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/16/2016] [Indexed: 11/27/2022]
Abstract
Membrane organization is usually associated with the correct function of a number of cellular processes in eukaryotic cells as diverse as signal transduction, protein sorting, membrane trafficking, or pathogen invasion. It has been recently discovered that bacterial membranes are able to compartmentalize their signal transduction pathways in functional membrane microdomains (FMMs). In this review article, we discuss the biological significance of the existence of FMMs in bacteria and comment on possible beneficial roles that FMMs play on the harbored signal transduction cascades. Moreover, four different membrane-associated signal transduction cascades whose functions are linked to the integrity of FMMs are introduced, and the specific role that FMMs play in stabilizing and promoting interactions of their signaling components is discussed. Altogether, FMMs seem to play a relevant role in promoting more efficient activation of signal transduction cascades in bacterial cells and show that bacteria are more sophisticated organisms than previously appreciated.
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Dempwolff F, Schmidt FK, Hervás AB, Stroh A, Rösch TC, Riese CN, Dersch S, Heimerl T, Lucena D, Hülsbusch N, Stuermer CAO, Takeshita N, Fischer R, Eckhardt B, Graumann PL. Super Resolution Fluorescence Microscopy and Tracking of Bacterial Flotillin (Reggie) Paralogs Provide Evidence for Defined-Sized Protein Microdomains within the Bacterial Membrane but Absence of Clusters Containing Detergent-Resistant Proteins. PLoS Genet 2016; 12:e1006116. [PMID: 27362352 PMCID: PMC4928834 DOI: 10.1371/journal.pgen.1006116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 05/20/2016] [Indexed: 12/14/2022] Open
Abstract
Biological membranes have been proposed to contain microdomains of a specific lipid composition, in which distinct groups of proteins are clustered. Flotillin-like proteins are conserved between pro—and eukaryotes, play an important function in several eukaryotic and bacterial cells, and define in vertebrates a type of so-called detergent-resistant microdomains. Using STED microscopy, we show that two bacterial flotillins, FloA and FloT, form defined assemblies with an average diameter of 85 to 110 nm in the model bacterium Bacillus subtilis. Interestingly, flotillin microdomains are of similar size in eukaryotic cells. The soluble domains of FloA form higher order oligomers of up to several hundred kDa in vitro, showing that like eukaryotic flotillins, bacterial assemblies are based in part on their ability to self-oligomerize. However, B. subtilis paralogs show significantly different diffusion rates, and consequently do not colocalize into a common microdomain. Dual colour time lapse experiments of flotillins together with other detergent-resistant proteins in bacteria show that proteins colocalize for no longer than a few hundred milliseconds, and do not move together. Our data reveal that the bacterial membrane contains defined-sized protein domains rather than functional microdomains dependent on flotillins. Based on their distinct dynamics, FloA and FloT confer spatially distinguishable activities, but do not serve as molecular scaffolds. Many membrane proteins are not uniformly distributed within biological membranes, and may prefer specific lipid environments to function optimally. Using super resolution fluorescence microscopy, we show that several Bacillus subtilis membrane proteins indeed cluster into structures of 60 to 110 nm, verifying the existence of defined-size protein microdomains. Biochemical co-isolation of specific membrane proteins and flotillins, a family of proteins highly conserved between eukaryotic and bacterial cells, suggested that common “functional” microdomains exist, containing so-called “detergent-resistant” membrane proteins, that are centered by flotillins. Through high speed tracking of Bacillus subtilis FloA and FloT we show that both proteins are not present in the same microdomain, but move through the membrane with different velocities. Dual colour time lapse microscopy showed that contrarily to vertebrate flotillins, bacterial flotillins do not move together with detergent-resistant proteins, ruling out the existence of coclusters. The lack of both flotillins, but not of a single one, leads to striking defects in cell shape and in cell growth, indicating important overlapping functions of flotillin paralogs. Our data show that FloA and FloT perform spatially distinct functions, possibly in the insertion of membrane proteins that require a specific lipid environment, based on a close connection between FloA and FloT with the Sec membrane insertion machinery, but do not act as scaffolds for detergent resistant proteins. Our tracking analyses provide an important basis for the understanding of interactions between membrane proteins in living cells.
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Affiliation(s)
- Felix Dempwolff
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Felix K. Schmidt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Physics, Philipps Universität Marburg, Marburg, Germany
| | - Ana B. Hervás
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Alex Stroh
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Thomas C. Rösch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Cornelius N. Riese
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Biology, Philipps Universität Marburg, Marburg, Germany
| | - Simon Dersch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Thomas Heimerl
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Biology, Philipps Universität Marburg, Marburg, Germany
| | - Daniella Lucena
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Nikola Hülsbusch
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Norio Takeshita
- University of Tsukuba, Faculty of Life and Environmental Sciences, Tsukuba, Ibaraki, Japan
- Department of Microbiology, Institute for Applied Bioscience, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Bioscience, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Bruno Eckhardt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Physics, Philipps Universität Marburg, Marburg, Germany
| | - Peter L. Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
- * E-mail:
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36
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Lopez D. Molecular composition of functional microdomains in bacterial membranes. Chem Phys Lipids 2015; 192:3-11. [PMID: 26320704 DOI: 10.1016/j.chemphyslip.2015.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/10/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022]
Abstract
Membranes of eukaryotic cells organize a number of proteins related to signal transduction and membrane trafficking into microdomains, which are enriched in particular lipids, like cholesterol and sphingolipids and are commonly referred as to lipid rafts or membrane rafts. The existence of this type of signaling platforms was traditionally associated with eukaryotic membranes because prokaryotic cells were considered too simple organisms to require a sophisticated organization of their signaling networks. However, the research that have been performed during last years have shown that bacteria organize many signaling transduction processes in Functional Membrane Microdomains (FMMs), which are similar to the lipid rafts that are found in eukaryotic cells. The current knowledge of the existence of FMMs in bacteria is described in this review and the specific structural and biological properties of these membrane microdomains are introduced. The organization of FMMs in bacterial membranes reveals an unexpected level of sophistication in signaling transduction and membrane organization that is unprecedented in bacteria, suggesting that bacteria as more complex organisms than previously considered.
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Affiliation(s)
- Daniel Lopez
- Research Center for Infectious Diseases (ZINF), Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider Strasse (2), 97080 Würzburg, Germany; Spanish National Center for Biotechnology (CNB), Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain.
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Schneider J, Mielich-Süss B, Böhme R, Lopez D. In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1871-1887. [PMID: 26297017 DOI: 10.1099/mic.0.000137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind to proteins and facilitate the physical interaction of the components of signal transduction pathways or multi-enzymic complexes. In this study, we used a biochemical approach to dissect the molecular mechanism of a membrane-associated scaffold protein, FloT, a flotillin-homologue protein that is localized in functional membrane microdomains of the bacterium Bacillus subtilis. This study provides unambiguous evidence that FloT physically binds to and interacts with the membrane-bound sensor kinase KinC. This sensor kinase activates biofilm formation in B. subtilis in response to the presence of the self-produced signal surfactin. Furthermore, we have characterized the mechanism by which the interaction of FloT with KinC benefits the activity of KinC. Two separate and synergistic effects constitute this mechanism: first, the scaffold activity of FloT promotes more efficient self-interaction of KinC and facilitates dimerization into its active form. Second, the selective binding of FloT to KinC prevents the occurrence of unspecific aggregation between KinC and other proteins that may generate dead-end intermediates that could titrate the activity of KinC. Flotillin proteins appear to play an important role in prokaryotes in promoting effective binding of signalling proteins with their correct protein partners.
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Affiliation(s)
- Johannes Schneider
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Benjamin Mielich-Süss
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Richard Böhme
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
- National Center for Biotechnology (CNB), Spanish Research Council (CSIC), Madrid 28050, Spain
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
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López D. Connection of KinC to flotillins and potassium leakage in Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1180-1. [PMID: 25934647 DOI: 10.1099/mic.0.000089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daniel López
- Research Centre for Infectious Diseases - Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Schneider J, Klein T, Mielich-Süss B, Koch G, Franke C, Kuipers OP, Kovács ÁT, Sauer M, Lopez D. Spatio-temporal remodeling of functional membrane microdomains organizes the signaling networks of a bacterium. PLoS Genet 2015; 11:e1005140. [PMID: 25909364 PMCID: PMC4409396 DOI: 10.1371/journal.pgen.1005140] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
Lipid rafts are membrane microdomains specialized in the regulation of numerous cellular processes related to membrane organization, as diverse as signal transduction, protein sorting, membrane trafficking or pathogen invasion. It has been proposed that this functional diversity would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known. We recently discovered that bacterial membranes organize their signal transduction pathways in functional membrane microdomains (FMMs) that are structurally and functionally similar to the eukaryotic lipid rafts. In this report, we took advantage of the tractability of the prokaryotic model Bacillus subtilis to provide evidence for the coexistence of two distinct families of FMMs in bacterial membranes, displaying a distinctive distribution of proteins specialized in different biological processes. One family of microdomains harbors the scaffolding flotillin protein FloA that selectively tethers proteins specialized in regulating cell envelope turnover and primary metabolism. A second population of microdomains containing the two scaffolding flotillins, FloA and FloT, arises exclusively at later stages of cell growth and specializes in adaptation of cells to stationary phase. Importantly, the diversification of membrane microdomains does not occur arbitrarily. We discovered that bacterial cells control the spatio-temporal remodeling of microdomains by restricting the activation of FloT expression to stationary phase. This regulation ensures a sequential assembly of functionally specialized membrane microdomains to strategically organize signaling networks at the right time during the lifespan of a bacterium. Cellular membranes organize proteins related to signal transduction, protein sorting and membrane trafficking into the so-called lipid rafts. It has been proposed that the functional diversity of lipid rafts would require a heterogeneous population of raft domains with varying compositions. However, a mechanism for such diversification is not known due in part to the complexity that entails the manipulation of eukaryotic cells. The recent discovery that bacteria organize many cellular processes in membrane microdomains (FMMs), functionally similar to the eukaryotic lipid rafts, prompted us to explore FMMs diversity in the bacterial model Bacillus subtilis. We show that diversification of FMMs occurs in cells and gives rise to functionally distinct microdomains, which compartmentalize distinct signal transduction pathways and regulate the expression of different genetic programs. We discovered that FMMs diversification does not occur randomly. Cells sequentially regulate the specialization of the FMMs during cell growth to ensure an effective and diverse activation of signaling processes.
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Affiliation(s)
- Johannes Schneider
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Teresa Klein
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Benjamin Mielich-Süss
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Gudrun Koch
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
| | - Christian Franke
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Oscar P. Kuipers
- Molecular Genetics Group,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T. Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- * E-mail:
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Farnoud AM, Toledo AM, Konopka JB, Del Poeta M, London E. Raft-like membrane domains in pathogenic microorganisms. CURRENT TOPICS IN MEMBRANES 2015; 75:233-68. [PMID: 26015285 DOI: 10.1016/bs.ctm.2015.03.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The lipid bilayer of the plasma membrane is thought to be compartmentalized by the presence of lipid-protein microdomains. In eukaryotic cells, microdomains composed of sterols and sphingolipids, commonly known as lipid rafts, are believed to exist, and reports on the presence of sterol- or protein-mediated microdomains in bacterial cell membranes are also appearing. Despite increasing attention, little is known about microdomains in the plasma membrane of pathogenic microorganisms. This review attempts to provide an overview of the current state of knowledge of lipid rafts in pathogenic fungi and bacteria. The current literature on characterization of microdomains in pathogens is reviewed, and their potential role in growth, pathogenesis, and drug resistance is discussed. Better insight into the structure and function of membrane microdomains in pathogenic microorganisms might lead to a better understanding of their pathogenesis and development of raft-mediated approaches for therapy.
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Affiliation(s)
- Amir M Farnoud
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Alvaro M Toledo
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - James B Konopka
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
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Abstract
An interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. Membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. The assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria and archaea were organisms too simple to require such a sophisticated organization of their cellular membranes. However, it was recently discovered that bacteria organize many signal transduction, protein secretion, and transport processes in functional membrane microdomains, which are equivalent to the lipid rafts of eukaryotic cells. This review contains the most significant advances during the last 4 years in understanding the structural and biological role of lipid rafts in bacteria. Furthermore, this review shows a detailed description of a number of molecular and genetic approaches related to the discovery of bacterial lipid rafts as well as an overview of the group of tentative lipid-protein and protein-protein interactions that give consistency to these sophisticated signaling platforms. Additional data suggesting that lipid rafts are widely distributed in bacteria are presented in this review. Therefore, we discuss the available techniques and optimized protocols for the purification and analysis of raft-associated proteins in various bacterial species to aid in the study of bacterial lipid rafts in other laboratories that could be interested in this topic. Overall, the discovery of lipid rafts in bacteria reveals a new level of sophistication in signal transduction and membrane organization that was unexpected for bacteria and shows that bacteria are more complex than previously appreciated.
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Affiliation(s)
- Marc Bramkamp
- Department of Biology I, University of Munich (LMU), Planegg/Martinsried, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
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Mielich-Süss B, Lopez D. Molecular mechanisms involved in Bacillus subtilis biofilm formation. Environ Microbiol 2015; 17:555-65. [PMID: 24909922 PMCID: PMC4188541 DOI: 10.1111/1462-2920.12527] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/01/2014] [Indexed: 02/02/2023]
Abstract
Biofilms are the predominant lifestyle of bacteria in natural environments, and they severely impact our societies in many different fashions. Therefore, biofilm formation is a topic of growing interest in microbiology, and different bacterial models are currently studied to better understand the molecular strategies that bacteria undergo to build biofilms. Among those, biofilms of the soil-dwelling bacterium Bacillus subtilis are commonly used for this purpose. Bacillus subtilis biofilms show remarkable architectural features that are a consequence of sophisticated programmes of cellular specialization and cell-cell communication within the community. Many laboratories are trying to unravel the biological role of the morphological features of biofilms, as well as exploring the molecular basis underlying cellular differentiation. In this review, we present a general perspective of the current state of knowledge of biofilm formation in B. subtilis and thereby placing a special emphasis on summarizing the most recent discoveries in the field.
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Affiliation(s)
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF). University of Würzburg, Germany
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Devi SN, Vishnoi M, Kiehler B, Haggett L, Fujita M. In vivo functional characterization of the transmembrane histidine kinase KinC in Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1092-1104. [PMID: 25701730 DOI: 10.1099/mic.0.000054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
In response to starvation, Bacillus subtilis cells differentiate into different subsets, undergoing cannibalism, biofilm formation or sporulation. These processes require a multiple component phosphorelay, wherein the master regulator Spo0A is activated upon phosphorylation by one or a combination of five histidine kinases (KinA-KinE) via two intermediate phosphotransferases, Spo0F and Spo0B. In this study, we focused on KinC, which was originally identified as a sporulation kinase and was later shown to regulate cannibalism and biofilm formation. First, genetic experiments using both the domesticated and undomesticated (biofilm forming) strains revealed that KinC activity and the membrane localization are independent of both the lipid raft marker proteins FloTA and cytoplasmic potassium concentration, which were previously shown to be required for the kinase activity. Next, we demonstrated that KinC controls cannibalism and biofilm formation in a manner dependent on phosphorelay. For further detailed characterization of KinC, we established an IPTG-inducible expression system in the domesticated strain, in which biofilm formation is defective, for simplicity of study. Using this system, we found that the N-terminal transmembrane domain is dispensable but the PAS domain is needed for the kinase activity. An in vivo chemical cross-linking experiment demonstrated that the soluble and functional KinC (KinC(ΔTM1+2)) forms a tetramer. Based on these results, we propose a revised model in which KinC becomes active by forming a homotetramer via the N-terminal PAS domain, but its activity is independent of both the lipid raft and the potassium leakage, which was previously suggested to be induced by surfactin.
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Affiliation(s)
- Seram Nganbiton Devi
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Monika Vishnoi
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Brittany Kiehler
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Lindsey Haggett
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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Bach JN, Bramkamp M. Dissecting the molecular properties of prokaryotic flotillins. PLoS One 2015; 10:e0116750. [PMID: 25635948 PMCID: PMC4312047 DOI: 10.1371/journal.pone.0116750] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/14/2014] [Indexed: 01/13/2023] Open
Abstract
Flotillins are universally conserved proteins that are present in all kingdoms of life. Recently it was demonstrated that the B. subtilis flotillin YuaG (FloT) has a direct influence on membrane domain formation by orchestrating lipid domains. Thereby it allocates a proper environment for diverse cellular machineries. YuaG creates platforms for signal transduction, processes crucial for biofilm formation, sporulation, competence, secretion, and others. Even though, flotillins are an emerging topic of research in the field of microbiology little is known about the molecular architecture of prokaryotic flotillins. All flotillins share common structural elements and are tethered to the membrane N’- terminally, followed by a so called PHB domain and a flotillin domain. We show here that prokaryotic flotillins are, similarly to eukaryotic flotillins, tethered to the membrane via a hairpin loop. Further it is demonstrated by sedimentation assays that B. subtilis flotillins do not bind to the membrane via their PHB domain contrary to eukaryotic flotillins. Size exclusion chromatography experiments, blue native PAGE and cross linking experiments revealed that B. subtilis YuaG can oligomerize into large clusters via the PHB domain. This illustrates an important difference in the setup of prokaryotic flotillins compared to the organization of eukaryotic flotillins.
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Affiliation(s)
- Juri Niño Bach
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
- * E-mail:
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Mhatre E, Monterrosa RG, Kovács AT. From environmental signals to regulators: modulation of biofilm development in Gram-positive bacteria. J Basic Microbiol 2014; 54:616-32. [PMID: 24771632 DOI: 10.1002/jobm.201400175] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/30/2014] [Indexed: 12/22/2022]
Abstract
Bacterial lifestyle is influenced by environmental signals, and many differentiation processes in bacteria are governed by the threshold concentrations of molecules present in their niche. Biofilm is one such example where bacteria in their sessile state adapt to a lifestyle that causes several adaptive alterations in the population. Here, a brief overview is given on a variety of environmental signals that bias biofilm development in Gram-positive bacteria, including nutrient conditions, self- and heterologously produced substances, like quorum sensing and host produced molecules. The Gram-positive model organism, Bacillus subtilis is a superb example to illustrate how distinct signals activate sensor proteins that integrate the environmental signals towards global regulators related to biofilm formation. The role of reduced oxygen level, polyketides, antimicrobials, plant secreted carbohydrates, plant cell derived polymers, glycerol, and osmotic conditions are discussed during the transcriptional activation of biofilm related genes in B. subtilis.
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Affiliation(s)
- Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Abstract
Small proteins, here defined as proteins of 50 amino acids or fewer in the absence of processing, have traditionally been overlooked due to challenges in their annotation and biochemical detection. In the past several years, however, increasing numbers of small proteins have been identified either through the realization that mutations in intergenic regions are actually within unannotated small protein genes or through the discovery that some small, regulatory RNAs encode small proteins. These insights, together with comparative sequence analysis, indicate that tens if not hundreds of small proteins are synthesized in a given organism. This review summarizes what has been learned about the functions of several of these bacterial small proteins, most of which act at the membrane, illustrating the astonishing range of processes in which these small proteins act and suggesting several general conclusions. Important questions for future studies of these overlooked proteins are also discussed.
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Affiliation(s)
- Gisela Storz
- Cell Biology and Metabolism Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-5430;
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Mann JM, Carabetta VJ, Cristea IM, Dubnau D. Complex formation and processing of the minor transformation pilins of Bacillus subtilis. Mol Microbiol 2013; 90:1201-15. [PMID: 24164455 PMCID: PMC5687075 DOI: 10.1111/mmi.12425] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2013] [Indexed: 01/06/2023]
Abstract
Transformation in most bacteria is dependent on orthologues of Type 2 secretion and Type 4 pilus system proteins. In each system, pilin proteins (major and minor) are required to make the pilus structure and are essential to the process, although the precise roles of the minor pilins remain unclear. We have explored protein-protein interactions among the competence minor pilins of Bacillus subtilis through in vitro binding studies, immunopurification and mass spectrometry. We demonstrate that the minor pilins directly interact, and the minor pilin ComGG interacts with most of the known proteins required for transformation. We find that ComGG requires other ComG proteins for its stabilization and for processing by the pre-pilin peptidase. These observations, C-terminal mutations in ComGG that prevent processing and the inaccessibility of pre-ComGG to externally added protease suggest a model in which pre-ComGG must be associated with other minor pilins for processing to take place. We propose that ComGG does not become a transmembrane protein until after processing. These behaviours contrast with that of pre-ComGC, the major pilin, which is accessible to externally added protease and requires only the peptidase to be processed. The roles of the pilins and of the pilus in transformation are discussed.
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Affiliation(s)
- Jessica M. Mann
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Valerie J. Carabetta
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David Dubnau
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 07103, USA
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48
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Abstract
UNLABELLED Bacteria organize many membrane-related signaling processes in functional microdomains that are structurally and functionally similar to the lipid rafts of eukaryotic cells. An important structural component of these microdomains is the protein flotillin, which seems to act as a chaperone in recruiting other proteins to lipid rafts to facilitate their interaction. In eukaryotic cells, the occurrence of severe diseases is often observed in combination with an overproduction of flotillin, but a functional link between these two phenomena is yet to be demonstrated. In this work, we used the bacterial model Bacillus subtilis as a tractable system to study the physiological alterations that occur in cells that overproduce flotillin. We discovered that an excess of flotillin altered specific signal transduction pathways that are associated with the membrane microdomains of bacteria. As a consequence of this, we detected significant defects in cell division and cell differentiation. These physiological alterations were in part caused by an unusual stabilization of the raft-associated protease FtsH. This report opens the possibility of using bacteria as a working model to better understand fundamental questions related to the functionality of lipid rafts. IMPORTANCE The identification of signaling platforms in the membrane of bacteria that are functionally and structurally equivalent to eukaryotic lipid rafts reveals a level of sophistication in signal transduction and membrane organization unexpected in bacteria. It opens new and promising venues to address intricate questions related to the functionality of lipid rafts by using bacteria as a more tractable system. This is the first report that uses bacteria as a working model to investigate a fundamental question that was previously raised while studying the role of eukaryotic lipid rafts. It also provides evidence of the critical role of these signaling platforms in orchestrating diverse physiological processes in prokaryotic cells.
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Pelchovich G, Omer-Bendori S, Gophna U. Menaquinone and iron are essential for complex colony development in Bacillus subtilis. PLoS One 2013; 8:e79488. [PMID: 24223955 PMCID: PMC3817097 DOI: 10.1371/journal.pone.0079488] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
Cells of undomesticated species of Bacillus subtilis frequently form complex colonies during spreading on agar surfaces. Given that menaquinone is involved in another form of coordinated behavior, namely, sporulation, we looked for a possible role for menaquinone in complex colony development (CCD) in the B. subtilis strain NCIB 3610. Here we show that inhibition of menaquinone biosynthesis in B. subtilis indeed abolished its ability to develop complex colonies. Additionally some mutations of B. subtilis which confer defective CCD could be suppressed by menaquinone derivatives. Several such mutants mapped to the dhb operon encoding the genes responsible for the biosynthesis of the iron siderophore, bacillibactin. Our results demonstrate that both menaquinone and iron are essential for CCD in B. subtilis.
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Affiliation(s)
- Gidi Pelchovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Shira Omer-Bendori
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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50
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Small molecules are natural triggers for the disassembly of biofilms. Trends Microbiol 2013; 21:594-601. [DOI: 10.1016/j.tim.2013.08.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 01/27/2023]
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