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Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
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2
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Expression of the Bacillus subtilis TasA signal peptide leads to cell death in Escherichia coli due to inefficient cleavage by LepB. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183768. [PMID: 34492253 DOI: 10.1016/j.bbamem.2021.183768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/21/2021] [Accepted: 08/30/2021] [Indexed: 11/22/2022]
Abstract
Bacillus subtilis has five type I signal peptidases, one of these, SipW, is an archaeal-like peptidase. SipW is expressed in an operon (tapA-sipW-tasA) and is responsible for removing the signal peptide from two proteins: TapA and TasA. It is unclear from the signal peptide sequence of TasA and TapA, why an archaeal-like signal peptidase is required for their processing. Bioinformatic analysis of TasA and TapA indicates that both contain highly similar signal peptide cleavage sites, both predicted to be cleaved by Escherichia coli signal peptidase I, LepB. We show that expressing full length TasA in E. coli is toxic and leads to cell death. To determine if this phenotype is due to the inability of the E. coli LepB to process the TasA signal peptide, we fused the TasA signal peptide and two amino acids of mature TasA (up to P2') to both maltose binding protein (MBP) and β-lactamase (Bla). We observed a defect in secretion, indicated by an abundance of unprocessed protein with both TasA-MBP and TasA-Bla fusions. A series of mutations in both TasA-MBP and TasA-Bla were made around the junction of the TasA signal peptide and the fusion protein. Both of these studies indicate that residues around the predicted TasA signal sequence cleavage site, particularly the sequence from P3 to P2', inhibit processing by LepB. The cell death observed when TasA and TasA signal sequence fusion proteins are expressed is likely due to the TasA signal peptide blocking LepB and thereby the general secretion pathway.
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3
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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4
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Verma N, Srivastava S, Malik R, Yadav JK, Goyal P, Pandey J. Computational investigation for modeling the protein-protein interaction of TasA (28-261)-TapA (33-253): a decisive process in biofilm formation by Bacillus subtilis. J Mol Model 2020; 26:226. [PMID: 32779018 DOI: 10.1007/s00894-020-04507-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/04/2020] [Indexed: 01/27/2023]
Abstract
Biofilms have a significant role in microbial persistence, antibiotic resistance, and chronic infections; consequently, there is a pressing need for development of novel "anti-biofilm strategies." One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of "amyloid-like proteins" (ALPs) in the extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of structural features the of protein-protein interaction with conventional structure biology tools including X-ray diffraction and nuclear magnetic resonance is technically challenging, expensive, and time-consuming. In contrast, modeling such interactions is time-efficient and economical, and might provide deeper understanding of structural basis of interactions. Although it is often acknowledged that molecular modeling methods have varying accuracy, their careful implementation with supplementary verification methods can provide valuable insight and directions for future studies. With this reasoning, during the present study, the protein-protein interaction of TasA(28-261)-TapA(33-253) (which is a decisive process for biofilm formation by Bacillus subtilis) was modeled using in silico approaches, viz., molecular modeling, protein-protein docking, and molecular dynamics simulations. Results obtained here identified amino acid residues present within intrinsically disordered regions of both proteins to be critical for interaction. These results were further supported with principal component analyses (PCA) and free energy landscape (FEL) analyses. Results presented here represent novel finding, and we hypothesize that amino acid residues identified during the present study could be targeted for inhibition of biofilm formation by B. subtilis.
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Affiliation(s)
- Nidhi Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Pankaj Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Janmejay Pandey
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India.
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5
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Isticato R, Lanzilli M, Petrillo C, Donadio G, Baccigalupi L, Ricca E. Bacillus subtilisbuilds structurally and functionally different spores in response to the temperature of growth. Environ Microbiol 2019; 22:170-182. [DOI: 10.1111/1462-2920.14835] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Rachele Isticato
- Department of BiologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
| | - Mariamichela Lanzilli
- Department of BiologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
| | - Claudia Petrillo
- Department of BiologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
| | - Giuliana Donadio
- Department of BiologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
| | - Loredana Baccigalupi
- Department of Molecular Medicine and Medical BiotechnologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
| | - Ezio Ricca
- Department of BiologyFederico II University of Naples, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 80126 Naples Italy
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6
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Sayer CV, Barat B, Popham DL. Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq. PLoS One 2019; 14:e0218220. [PMID: 31199835 PMCID: PMC6568419 DOI: 10.1371/journal.pone.0218220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/28/2019] [Indexed: 11/18/2022] Open
Abstract
Bacterial endospores can survive harsh environmental conditions and long-term dormancy in the absence of nutrients, but can rapidly germinate under favorable conditions. In the present study, we employed transposon sequencing (Tn-seq) to identify genes with previously uncharacterized roles in spore germination. Identified genes that encoded spore inner membrane proteins were chosen for study of defined mutants, which exhibited delayed germination in several assays in response to varying germinants. Significantly slowed release of DPA indicated that mutants were affected in Stage I of germination. Several mutants exhibited phenotypic traits consistent with failure of a GerA germinant receptor-mediated response, while others appeared to have a more general loss of response to varied germinants. Use of a gerA-lacZ transcriptional fusion and quantitative western blotting of GerAC allowed mutants to be classified based upon normal or decreased gerA transcription and normal or reduced GerA accumulation. Fourteen genes were identified to have newly described roles within Bacillus spore germination. A more complete understanding of this process can contribute to the development of better spore decontamination procedures.
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Affiliation(s)
- Cameron V. Sayer
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Bidisha Barat
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
- * E-mail:
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7
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Shanmugam N, Baker MODG, Ball SR, Steain M, Pham CLL, Sunde M. Microbial functional amyloids serve diverse purposes for structure, adhesion and defence. Biophys Rev 2019; 11:287-302. [PMID: 31049855 PMCID: PMC6557962 DOI: 10.1007/s12551-019-00526-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The functional amyloid state of proteins has in recent years garnered much attention for its role in serving crucial and diverse biological roles. Amyloid is a protein fold characterised by fibrillar morphology, binding of the amyloid-specific dyes Thioflavin T and Congo Red, insolubility and underlying cross-β structure. Amyloids were initially characterised as an aberrant protein fold associated with mammalian disease. However, in the last two decades, functional amyloids have been described in almost all biological systems, from viruses, to bacteria and archaea, to humans. Understanding the structure and role of these amyloids elucidates novel and potentially ancient mechanisms of protein function throughout nature. Many of these microbial functional amyloids are utilised by pathogens for invasion and maintenance of infection. As such, they offer novel avenues for therapies. This review examines the structure and mechanism of known microbial functional amyloids, with a particular focus on the pathogenicity conferred by the production of these structures and the strategies utilised by microbes to interfere with host amyloid structures. The biological importance of microbial amyloid assemblies is highlighted by their ubiquity and diverse functionality.
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Affiliation(s)
- Nirukshan Shanmugam
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Max O D G Baker
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Sarah R Ball
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Megan Steain
- Infectious Diseases and Immunology, Central Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Chi L L Pham
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia.
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8
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Transcriptional Regulation of icaADBC by both IcaR and TcaR in Staphylococcus epidermidis. J Bacteriol 2019; 201:JB.00524-18. [PMID: 30602488 DOI: 10.1128/jb.00524-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022] Open
Abstract
S. epidermidis is a primary cause of biofilm-mediated infections in humans due to adherence to foreign bodies. A major staphylococcal biofilm accumulation molecule is polysaccharide intracellular adhesin (PIA), which is synthesized by enzymes encoded by the icaADBC operon. Expression of PIA is highly variable among clinical isolates, suggesting that PIA expression levels are selected in certain niches of the host. However, the mechanisms that govern enhanced icaADBC transcription and PIA synthesis in these isolates are not known. We hypothesized that enhanced PIA synthesis in these isolates was due to function of IcaR and/or TcaR. Thus, two S. epidermidis isolates (1457 and CSF41498) with different icaADBC transcription and PIA expression levels were studied. Constitutive expression of both icaR and tcaR demonstrated that both repressors are functional and can completely repress icaADBC transcription in both 1457 and CSF41498. However, it was found that IcaR was the primary repressor for CSF41498 and TcaR was the primary repressor for 1457. Further analysis demonstrated that icaR transcription was repressed in 1457 in comparison to CSF41498, suggesting that TcaR functions as a repressor only in the absence of IcaR. Indeed, DNase I footprinting suggests IcaR and TcaR may bind to the same site within the icaR-icaA intergenic region. Lastly, we found mutants expressing variable amounts of PIA could rapidly be selected from both 1457 and CSF41498. Collectively, we propose that strains producing enhanced PIA synthesis are selected within certain niches of the host through several genetic mechanisms that function to repress icaR transcription, thus increasing PIA synthesis.IMPORTANCE Staphylococcus epidermidis is a commensal bacterium that resides on our skin. As a commensal, it protects humans from bacterial pathogens through a variety of mechanisms. However, it is also a significant cause of biofilm infections due to its ability to bind to plastic. Polysaccharide intercellular adhesin is a significant component of biofilm, and we propose that the expression of this polysaccharide is beneficial in certain host niches, such as providing extra strength when the bacterium is colonizing the lumen of a catheter, and detrimental in others, such as colonization of the skin surface. We show here that fine-tuning of icaADBC transcription, and thus PIA synthesis, is mediated via two transcriptional repressors, IcaR and TcaR.
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9
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Alves Feliciano C, Douché T, Giai Gianetto Q, Matondo M, Martin-Verstraete I, Dupuy B. CotL, a new morphogenetic spore coat protein of Clostridium difficile. Environ Microbiol 2019; 21:984-1003. [PMID: 30556639 DOI: 10.1111/1462-2920.14505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/07/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023]
Abstract
The strict anaerobe Clostridium difficile is the most common cause of antibiotic-associated diarrhoea. The oxygen-resistant C. difficile spores play a central role in the infectious cycle, contributing to transmission, infection and recurrence. The spore surface layers, the coat and exosporium, enable the spores to resist physical and chemical stress. However, little is known about the mechanisms of their assembly. In this study, we characterized a new spore protein, CotL, which is required for the assembly of the spore coat. The cotL gene was expressed in the mother cell compartment under the dual control of the RNA polymerase sigma factors, σE and σK . CotL was localized in the spore coat, and the spores of the cotL mutant had a major morphologic defect at the level of the coat/exosporium layers. Therefore, the mutant spores contained a reduced amount of several coat/exosporium proteins and a defect in their localization in sporulating cells. Finally, cotL mutant spores were more sensitive to lysozyme and were impaired in germination, a phenotype likely to be associated with the structurally altered coat. Collectively, these results strongly suggest that CotL is a morphogenetic protein essential for the assembly of the spore coat in C. difficile.
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Affiliation(s)
- Carolina Alves Feliciano
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Thibaut Douché
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour La Biologie, CNRS USR 2000, Institut Pasteur, Paris, France
| | - Quentin Giai Gianetto
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour La Biologie, CNRS USR 2000, Institut Pasteur, Paris, France.,Bioinformatics and Biostatistics HUB, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Spectrométrie de Masse pour La Biologie, CNRS USR 2000, Institut Pasteur, Paris, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Paris, France
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10
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Erskine E, Morris RJ, Schor M, Earl C, Gillespie RMC, Bromley KM, Sukhodub T, Clark L, Fyfe PK, Serpell LC, Stanley‐Wall NR, MacPhee CE. Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA. Mol Microbiol 2018; 110:897-913. [PMID: 29802781 PMCID: PMC6334530 DOI: 10.1111/mmi.13985] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2018] [Indexed: 01/06/2023]
Abstract
Bacterial biofilms are communities of microbial cells encased within a self-produced polymeric matrix. In the Bacillus subtilis biofilm matrix, the extracellular fibres of TasA are essential. Here, a recombinant expression system allows interrogation of TasA, revealing that monomeric and fibre forms of TasA have identical secondary structure, suggesting that fibrous TasA is a linear assembly of globular units. Recombinant TasA fibres form spontaneously, and share the biological activity of TasA fibres extracted from B. subtilis, whereas a TasA variant restricted to a monomeric form is inactive and subjected to extracellular proteolysis. The biophysical properties of both native and recombinant TasA fibres indicate that they are not functional amyloid-like fibres. A gel formed by TasA fibres can recover after physical shear force, suggesting that the biofilm matrix is not static and that these properties may enable B. subtilis to remodel its local environment in response to external cues. Using recombinant fibres formed by TasA orthologues we uncover species variability in the ability of heterologous fibres to cross-complement the B. subtilis tasA deletion. These findings are indicative of specificity in the biophysical requirements of the TasA fibres across different species and/or reflect the precise molecular interactions needed for biofilm matrix assembly.
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Affiliation(s)
- Elliot Erskine
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Ryan J. Morris
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Marieke Schor
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Rachel M. C. Gillespie
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Keith M. Bromley
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Lauren Clark
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Paul K. Fyfe
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | | | - Nicola R. Stanley‐Wall
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Cait E. MacPhee
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
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11
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Van Gerven N, Van der Verren SE, Reiter DM, Remaut H. The Role of Functional Amyloids in Bacterial Virulence. J Mol Biol 2018; 430:3657-3684. [PMID: 30009771 PMCID: PMC6173799 DOI: 10.1016/j.jmb.2018.07.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets. Functional amyloids are widespread in bacteria, pathogenic and non-pathogenic. Bacterial biofilms most commonly function as structural support in the extracellular matrix of biofilms or spore coats, and in cell–cell and cell-surface adherence. The amyloid state can be the sole structured and functional state, or can be facultative, as a secondary state to folded monomeric subunits. Bacterial amyloids can enhance virulence by increasing persistence, cell adherence and invasion, intracellular survival, and pathogen spread by increased environmental survival. Bacterial amyloids may indirectly inflict disease by triggering inflammation, contact phase activation and possibly induce or aggravate human pathological aggregation disorders.
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Affiliation(s)
- Nani Van Gerven
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sander E Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Dirk M Reiter
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
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12
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Abstract
Understanding the formation and structure of protective bacterial biofilms will help to design and identify antimicrobial strategies. Our experiments with the secreted major biofilm protein TasA characterize on a molecular level in vivo the transition of a folded protein into protease-resistant biofilm-stabilizing fibrils. Such conformational changes from a globular state into fibrillar structures are so far not seen for other biofilm-forming proteins. In this context, TasA can serve as a model system to study functional fibril formation from a globular state. Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics. Bacillus subtilis biofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, β-sheet–rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level.
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13
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Dragoš A, Kovács ÁT, Claessen D. The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria. Biomolecules 2017; 7:biom7030060. [PMID: 28783117 PMCID: PMC5618241 DOI: 10.3390/biom7030060] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023] Open
Abstract
Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles.
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Affiliation(s)
- Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Dennis Claessen
- Institute of Biology, Leiden University, 2333BE Leiden, The Netherlands.
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14
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Fakhry SS, Jessim AI, Azeez AZ, Alwash SJ, Abdulbaqi AA. Protein binding pigment by Bacillus pumilus SF214. KARBALA INTERNATIONAL JOURNAL OF MODERN SCIENCE 2017. [DOI: 10.1016/j.kijoms.2017.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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Khezri M, Jouzani GS, Ahmadzadeh M. Fusarium culmorum affects expression of biofilm formation key genes in Bacillus subtilis. Braz J Microbiol 2016; 47:47-54. [PMID: 26887226 PMCID: PMC4822762 DOI: 10.1016/j.bjm.2015.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 07/28/2015] [Indexed: 11/03/2022] Open
Abstract
It is known that there is correlation between biofilm formation and antagonistic activities of Bacillus subtilis strains; but, the mechanism of this correlation is not clear. So, the effect of the plant pathogen (Fusarium culmorum) on the biofilm formation in a B. subtilis strain with high antagonistic and biofilm formation activities was studied. The expression of sinR and tasA genes involved in the biofilm formation was studied in both single culture of bacterium (B) and co-culture with F. culmorum (FB) using real-time PCR. The results revealed that the expression of the sinR gene in both B and FB conditions was continuously decreased during the biofilm formation period and, after 24h (B4 and FB4), it reached 1% and 0.3% at the planktonic phase (B1), respectively, whereas the expression of the tasA was continuously increased and was 5.27 and 30 times more than that at the planktonic phase (B1) after 24h, respectively. So, the expression reduction rate for sinR (3 times) and the expression increasing rate for tasA (6 times) were significantly higher in FB conditions than the B ones. The relative expression of sinR in FB1 (planktonic phase), FB2 (8h), FB3(12h), and FB4 (24h) times was 0.65, 0.44, 0.35, and 0.29, whereas the tasA gene expression was 2.98, 3.44, 4.37, and 5.63-fold of the one at coordinate time points in B conditions, respectively. The significant expression reduction of sinR and increase of tasA confirmed that the presence of pathogen could stimulate biofilm formation in the antagonistic bacterium.
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Affiliation(s)
- Maryam Khezri
- Microbial Biotechnology and Biosafety Department, Agriculture Biotechnology Research Institute of Iran (ABRII), AREEO, 3135933151, Karaj, Iran; Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran; Department of Plant Protection, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology and Biosafety Department, Agriculture Biotechnology Research Institute of Iran (ABRII), AREEO, 3135933151, Karaj, Iran.
| | - Masoud Ahmadzadeh
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran
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16
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Zhang Y, Zhou L, Zhang Y. Investigation of UV-TiO2 photocatalysis and its mechanism in Bacillus subtilis spore inactivation. J Environ Sci (China) 2014; 26:1943-1948. [PMID: 25193846 DOI: 10.1016/j.jes.2014.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/11/2014] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
The inactivation levels of Bacillus subtilis spores for various disinfection processes (ultraviolet (UV), TiO2 and UV-TiO2) were compared. The results showed that the inactivation effect of B. subtilis spores by UV treatment alone was far below that for bacteria without endospores. TiO2 alone in the dark, as a control experiment, exhibited almost no inactivation effect. Compared with UV treatment alone, the inactivation effect increased significantly with the addition of TiO2. Increases of the UV irradiance and TiO2 concentration both contributed to the increase of the inactivation effect. Lipid peroxidation was found to be the underlying mechanism of inactivation. Malondialdehyde (MDA), the degradation product of lipid peroxidation, was used as an index to determine the extent of the reaction. The MDA concentration surged surprisingly to 3.24nmol/mg dry cell with the combination disinfection for 600sec (0.10mW/cm(2) irradiance and 10mg/L TiO2). In contrast, for UV alone or TiO2 in the dark, the MDA concentration was 0.38 and 0.25nmol/mg dry cell, respectively, under the same conditions. This indicated that both UV and TiO2 were essential for lipid peroxidation. Changes in cell ultrastructure were observed by transmission electron microscopy. The cell membrane was heavily damaged and cellular contents were completely lysed with the UV-TiO2 process, suggesting that lipid peroxidation was the root of the enhancement in inactivation efficiency.
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Affiliation(s)
- Yiqing Zhang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai 200092, China.
| | - Lingling Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science & Engineering, Tongji University, Shanghai 200092, China
| | - Yongji Zhang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai 200092, China.
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17
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Abhyankar W, de Koning LJ, Brul S, de Koster CG. Spore proteomics: the past, present and the future. FEMS Microbiol Lett 2014; 358:137-44. [PMID: 25110127 DOI: 10.1111/1574-6968.12568] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/30/2022] Open
Abstract
Endospores are metabolically dormant, multi-layered cellular structures formed by Gram-positive bacteria belonging to the genera Bacillus, Clostridium and related organisms. Their external layers are composed of proteins which in part play a role in the resistance behaviour of spores to varied chemical and environmental assaults. Thus, protein analysis is of major interest in spore biology. Spore proteomic studies have been carried out previously but these studies have focused on the soluble coat protein fraction. Using gel-based techniques, protein identification and analysis were performed. Mass spectrometry-driven proteomics has opened new avenues to resolve in particular the insoluble part of the spore layer proteomes. Mass spectrometry-based qualitative and quantitative proteomics methods expand the knowledge about both the actual composition and the amount of proteins in their various layers. The techniques can also be used to study the integrity of the layers as well as spore biology in general. This notion is explored concisely in this mini-review.
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Affiliation(s)
- Wishwas Abhyankar
- Department of Mass Spectrometry of BioMacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands; Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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18
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Asadishad B, Olsson ALJ, Dusane DH, Ghoshal S, Tufenkji N. Transport, motility, biofilm forming potential and survival of Bacillus subtilis exposed to cold temperature and freeze-thaw. WATER RESEARCH 2014; 58:239-247. [PMID: 24768703 DOI: 10.1016/j.watres.2014.03.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 02/27/2014] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
In cold climate regions, microorganisms in upper layers of soil are subject to low temperatures and repeated freeze-thaw (FT) conditions during the winter. We studied the effects of cold temperature and FT cycles on the viability and survival strategies (namely motility and biofilm formation) of the common soil bacterium and model pathogen Bacillus subtilis. We also examined the effect of FT on the transport behavior of B. subtilis at two solution ionic strengths (IS: 10 and 100 mM) in quartz sand packed columns. Finally, to study the mechanical properties of the bacteria-surface bond, a quartz crystal microbalance with dissipation monitoring (QCM-D) was used to monitor changes in bond stiffness when B. subtilis attached to a quartz substrate (model sand surface) under different environmental conditions. We observed that increasing the number of FT cycles decreased bacterial viability and that B. subtilis survived for longer time periods in higher IS solution. FT treatment decreased bacterial swimming motility and the transcription of flagellin encoding genes. Although FT exposure had no significant effect on the bacterial growth rate, it substantially decreased B. subtilis biofilm formation and correspondingly decreased the transcription of matrix production genes in higher IS solution. As demonstrated with QCM-D, the bond stiffness between B. subtilis and the quartz surface decreased after FT. Moreover, column transport studies showed higher bacterial retention onto sand grains after exposure to FT. This investigation demonstrates how temperature variations around the freezing point in upper layers of soil can influence key bacterial properties and behavior, including survival and subsequent transport.
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Affiliation(s)
- Bahareh Asadishad
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Adam L J Olsson
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Devendra H Dusane
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 2B2, Canada.
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19
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Zhang Y, Zhou L, Zhang Y, Tan C. Inactivation ofBacillus subtilisSpores Using Various Combinations of Ultraviolet Treatment with Addition of Hydrogen Peroxide. Photochem Photobiol 2014; 90:609-14. [DOI: 10.1111/php.12210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Yiqing Zhang
- Key Laboratory of Yangtze River Water Environment; Ministry of Education (Tongji University); Shanghai China
| | - Lingling Zhou
- State Key Laboratory of Pollution Control and Resources Reuse; College of Environmental Science & Engineering; Tongji University; Shanghai China
| | - Yongji Zhang
- Key Laboratory of Yangtze River Water Environment; Ministry of Education (Tongji University); Shanghai China
| | - Chaoqun Tan
- Key Laboratory of Yangtze River Water Environment; Ministry of Education (Tongji University); Shanghai China
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20
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Saujet L, Pereira FC, Serrano M, Soutourina O, Monot M, Shelyakin PV, Gelfand MS, Dupuy B, Henriques AO, Martin-Verstraete I. Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile. PLoS Genet 2013; 9:e1003756. [PMID: 24098137 PMCID: PMC3789822 DOI: 10.1371/journal.pgen.1003756] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/12/2013] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile, a Gram positive, anaerobic, spore-forming bacterium is an emergent pathogen and the most common cause of nosocomial diarrhea. Although transmission of C. difficile is mediated by contamination of the gut by spores, the regulatory cascade controlling spore formation remains poorly characterized. During Bacillus subtilis sporulation, a cascade of four sigma factors, σ(F) and σ(G) in the forespore and σ(E) and σ(K) in the mother cell governs compartment-specific gene expression. In this work, we combined genome wide transcriptional analyses and promoter mapping to define the C. difficile σ(F), σ(E), σ(G) and σ(K) regulons. We identified about 225 genes under the control of these sigma factors: 25 in the σ(F) regulon, 97 σ(E)-dependent genes, 50 σ(G)-governed genes and 56 genes under σ(K) control. A significant fraction of genes in each regulon is of unknown function but new candidates for spore coat proteins could be proposed as being synthesized under σ(E) or σ(K) control and detected in a previously published spore proteome. SpoIIID of C. difficile also plays a pivotal role in the mother cell line of expression repressing the transcription of many members of the σ(E) regulon and activating sigK expression. Global analysis of developmental gene expression under the control of these sigma factors revealed deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We showed that the expression of the σ(E) regulon in the mother cell was not strictly under the control of σ(F) despite the fact that the forespore product SpoIIR was required for the processing of pro-σ(E). In addition, the σ(K) regulon was not controlled by σ(G) in C. difficile in agreement with the lack of pro-σ(K) processing. This work is one key step to obtain new insights about the diversity and evolution of the sporulation process among Firmicutes.
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Affiliation(s)
- Laure Saujet
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Fátima C. Pereira
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Monica Serrano
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Pavel V. Shelyakin
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny per, 19, Moscow, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny per, 19, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Biengineering and Bioinformatics, Vorobievy Gory 1-73, Moscow, Russia
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Adriano O. Henriques
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
- * E-mail:
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21
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Romero D. Bacterial determinants of the social behavior of Bacillus subtilis. Res Microbiol 2013; 164:788-98. [PMID: 23791621 DOI: 10.1016/j.resmic.2013.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
Abstract
Bacteria utilize sophisticated cellular machinery to sense environmental changes and coordinate the most appropriate response. Fine sensors located on cell surfaces recognize a myriad of triggers and initiate genetic cascades leading to activation or repression of certain groups of genes. Structural elements such as pilli, exopolysaccharides and flagella are also exposed at the cell surface and contribute to modulating the intimate interaction with surfaces and host cells. This review will cover the latest advances in our understanding of the biology and functionality of these bacterial determinants within the context of biofilm formation of Bacillus subtilis.
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Affiliation(s)
- Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain.
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22
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Manzo N, Di Luccia B, Isticato R, D’Apuzzo E, De Felice M, Ricca E. Pigmentation and sporulation are alternative cell fates in Bacillus pumilus SF214. PLoS One 2013; 8:e62093. [PMID: 23634224 PMCID: PMC3636246 DOI: 10.1371/journal.pone.0062093] [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: 01/28/2013] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
Abstract
Bacillus pumilus SF214 is a spore forming bacterium, isolated from a marine sample, able to produce a matrix and a orange-red, water soluble pigment. Pigmentation is strictly regulated and high pigment production was observed during the late stationary growth phase in a minimal medium and at growth temperatures lower than the optimum. Only a subpopulation of stationary phase cells produced the pigment, indicating that the stationary culture contains a heterogeneous cell population and that pigment synthesis is a bimodal phenomenon. The fraction of cells producing the pigment varied in the different growth conditions and occured only in cells not devoted to sporulation. Only some of the pigmented cells were also able to produce a matrix. Pigment and matrix production in SF214 appear then as two developmental fates both alternative to sporulation. Since the pigment had an essential role in the cell resistance to oxidative stress conditions, we propose that within the heterogeneous population different survival strategies can be followed by the different cells.
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Affiliation(s)
- Nicola Manzo
- Department of Biology, Federico II University, Napoli, Italy
| | | | | | - Enrica D’Apuzzo
- Department of Biology, Federico II University, Napoli, Italy
| | | | - Ezio Ricca
- Department of Biology, Federico II University, Napoli, Italy
- * E-mail:
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23
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Biofilm research uncovers a novel nonenzymatic signal peptidase function in Bacillus. J Bacteriol 2012; 194:2779-80. [PMID: 22427624 DOI: 10.1128/jb.00270-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Identification of Bacillus subtilis SipW as a bifunctional signal peptidase that controls surface-adhered biofilm formation. J Bacteriol 2012; 194:2781-90. [PMID: 22328672 DOI: 10.1128/jb.06780-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms of microbial cells encased in an exopolymeric matrix can form on solid surfaces, but how bacteria sense a solid surface and upregulate biofilm genes is largely unknown. We investigated the role of the Bacillus subtilis signal peptidase, SipW, which has a unique role in forming biofilms on a solid surface and is not required at an air-liquid interface. Surprisingly, we found that the signal peptidase activity of SipW was not required for solid-surface biofilms. Furthermore, a SipW mutant protein was constructed that lacks the ability to form a solid-surface biofilm but still retains signal peptidase activity. Through genetic and gene expression tests, the non-signal peptidase role of SipW was found to activate biofilm matrix genes specifically when cells were on a solid surface. These data provide the first evidence that a signal peptidase is bifunctional and that SipW has a regulatory role in addition to its role as a signal peptidase.
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25
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Serrano M, Real G, Santos J, Carneiro J, Moran CP, Henriques AO. A negative feedback loop that limits the ectopic activation of a cell type-specific sporulation sigma factor of Bacillus subtilis. PLoS Genet 2011; 7:e1002220. [PMID: 21935351 PMCID: PMC3174212 DOI: 10.1371/journal.pgen.1002220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 06/18/2011] [Indexed: 11/18/2022] Open
Abstract
Two highly similar RNA polymerase sigma subunits, σF and σG, govern the early and late phases of forespore-specific gene expression during spore differentiation in Bacillus subtilis. σF drives synthesis of σG but the latter only becomes active once engulfment of the forespore by the mother cell is completed, its levels rising quickly due to a positive feedback loop. The mechanisms that prevent premature or ectopic activation of σG while discriminating between σF and σG in the forespore are not fully comprehended. Here, we report that the substitution of an asparagine by a glutamic acid at position 45 of σG (N45E) strongly reduced binding by a previously characterized anti-sigma factor, CsfB (also known as Gin), in vitro, and increased the activity of σG in vivo. The N45E mutation caused the appearance of a sub-population of pre-divisional cells with strong activity of σG. CsfB is normally produced in the forespore, under σF control, but sigGN45E mutant cells also expressed csfB and did so in a σG-dependent manner, autonomously from σF. Thus, a negative feedback loop involving CsfB counteracts the positive feedback loop resulting from ectopic σG activity. N45 is invariant in the homologous position of σG orthologues, whereas its functional equivalent in σF proteins, E39, is highly conserved. While CsfB does not bind to wild-type σF, a E39N substitution in σF resulted in efficient binding of CsfB to σF. Moreover, under certain conditions, the E39N alteration strongly restrains the activity of σF in vivo, in a csfB-dependent manner, and the efficiency of sporulation. Therefore, a single amino residue, N45/E39, is sufficient for the ability of CsfB to discriminate between the two forespore-specific sigma factors in B. subtilis. Positive auto-regulation of a transcriptional activator during cell differentiation or development often allows the rapid and robust deployment of cell- and stage-specific genes and the routing of the differentiating cell down a specific path. Positive auto-regulation however, raises the potential for inappropriate activity of the transcription factor. Here we unravel the role of a previously characterized anti-sigma factor, CsfB, in a negative feedback loop that prevents ectopic expression of the sporulation-specific sigma factor σG of Bacillus subtilis. σG is activated in the forespore, one of the two chambers of the developing cell, at an intermediate stage in spore development. Once active, a positive feedback loop allows the rapid accumulation of σG. Synthesis of both σG and CsfB is under the control of the early forespore regulator σF, and CsfB may help prevent the premature activity of σG in the forespore. However, CsfB is also produced under σG control in non-sporulating cells, setting a negative feedback loop that we show limits its ectopic activation. We further show that an asparagine residue conserved among σG orthologues is critical for binding and inhibition by CsfB, whereas the exclusion of asparagine from the homologous position in σF confers immunity to CsfB.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gonçalo Real
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Joana Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Charles P. Moran
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Adriano O. Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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26
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Yu WB, Gao SH, Yin CY, Zhou Y, Ye BC. Comparative transcriptome analysis of Bacillus subtilis responding to dissolved oxygen in adenosine fermentation. PLoS One 2011; 6:e20092. [PMID: 21625606 PMCID: PMC3097244 DOI: 10.1371/journal.pone.0020092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 04/12/2011] [Indexed: 12/20/2022] Open
Abstract
Dissolved oxygen (DO) is an important factor for adenosine fermentation. Our previous experiments have shown that low oxygen supply in the growth period was optimal for high adenosine yield. Herein, to better understand the link between oxygen supply and adenosine productivity in B. subtilis (ATCC21616), we sought to systematically explore the effect of DO on genetic regulation and metabolism through transcriptome analysis. The microarrays representing 4,106 genes were used to study temporal transcript profiles of B. subtilis fermentation in response to high oxygen supply (agitation 700 r/min) and low oxygen supply (agitation 450 r/min). The transcriptome data analysis revealed that low oxygen supply has three major effects on metabolism: enhance carbon metabolism (glucose metabolism, pyruvate metabolism and carbon overflow), inhibit degradation of nitrogen sources (glutamate family amino acids and xanthine) and purine synthesis. Inhibition of xanthine degradation was the reason that low oxygen supply enhanced adenosine production. These provide us with potential targets, which can be modified to achieve higher adenosine yield. Expression of genes involved in energy, cell type differentiation, protein synthesis was also influenced by oxygen supply. These results provided new insights into the relationship between oxygen supply and metabolism.
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Affiliation(s)
- Wen-Bang Yu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shu-Hong Gao
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chun-Yun Yin
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- * E-mail:
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27
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Driks A. Tapping into the biofilm: insights into assembly and disassembly of a novel amyloid fibre in Bacillus subtilis. Mol Microbiol 2011; 80:1133-6. [PMID: 21488983 DOI: 10.1111/j.1365-2958.2011.07666.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Bacillus subtilis biofilm matrix harbours a functionally important amyloid fibre network composed of the protein TasA. Previous studies showed that the protein TapA (formerly YqxM) plays roles in TasA fibre formation and disassembly. In this issue, Romero et al., 2011 show that TapA is a component of the fibre and links it to the peptidoglycan. Therefore, TapA directs TasA fibre formation, links it to the cell wall and, most likely, participates in fibre dispersal. These results provide important insights into the control of biofilm formation in B. subtilis and, potentially, the regulation of amyloid fibre formation in diverse species.
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Affiliation(s)
- Adam Driks
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
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28
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Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci U S A 2010; 107:2230-4. [PMID: 20080671 DOI: 10.1073/pnas.0910560107] [Citation(s) in RCA: 532] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bacillus subtilis forms biofilms whose constituent cells are held together by an extracellular matrix. Previous studies have shown that the protein TasA and an exopolysaccharide are the main components of the matrix. Given the importance of TasA in biofilm formation, we characterized the physicochemical properties of this protein. We report that purified TasA forms fibers of variable length and 10-15 nm in width. Biochemical analyses, in combination with the use of specific dyes and microscopic analyses, indicate that TasA forms amyloid fibers. Consistent with this hypothesis, TasA fibers required harsh treatments (e.g., formic acid) to be depolymerized. When added to a culture of a tasA mutant, purified TasA restored wild-type biofilm morphology, indicating that the purified protein retained biological activity. We propose that TasA forms amyloid fibers that bind cells together in the biofilm.
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29
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Processing of a membrane protein required for cell-to-cell signaling during endospore formation in Bacillus subtilis. J Bacteriol 2008; 190:7786-96. [PMID: 18820020 DOI: 10.1128/jb.00715-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activation of the late prespore-specific RNA polymerase sigma factor sigma(G) during Bacillus subtilis sporulation coincides with completion of the engulfment process, when the prespore becomes a protoplast fully surrounded by the mother cell cytoplasm and separated from it by a double membrane system. Activation of sigma(G) also requires expression of spoIIIJ, coding for a membrane protein translocase of the YidC/Oxa1p/Alb3 family, and of the mother cell-specific spoIIIA operon. Here we present genetic and biochemical evidence indicating that SpoIIIAE, the product of one of the spoIIIA cistrons, and SpoIIIJ interact in the membrane, thereby linking the function of the spoIIIJ and spoIIIA loci in the activation of sigma(G). We also show that SpoIIIAE has a functional Sec-type signal peptide, which is cleaved during sporulation. Furthermore, mutations that reduce or eliminate processing of the SpoIIIAE signal peptide arrest sporulation following engulfment completion and prevent activation of sigma(G). SpoIIIJ-type proteins can function in cooperation with or independently of the Sec system. In one model, SpoIIIJ interacts with SpoIIIAE in the context of the Sec translocon to promote its correct localization and/or topology in the membrane, so that it can signal the activation of sigma(G) following engulfment completion.
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Abstract
Spores of Bacillus subtilis have a thick outer layer of relatively insoluble protein called the coat, which protects spores against a number of treatments and may also play roles in spore germination. However, elucidation of precise roles of the coat in spore properties has been hampered by the inability to prepare spores lacking all or most coat material. In this work, we show that spores of a strain with mutations in both the cotE and gerE genes, which encode proteins involved in coat assembly and expression of genes encoding coat proteins, respectively, lack most extractable coat protein as seen by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, as well as the great majority of the coat as seen by atomic force microscopy. However, the cotE gerE spores did retain a thin layer of insoluble coat material that was most easily seen by microscopy following digestion of these spores with lysozyme. These severely coat-deficient spores germinated relatively normally with nutrients and even better with dodecylamine but not with a 1:1 chelate of Ca(2+) and dipicolinic acid. These spores were also quite resistant to wet heat, to mechanical disruption, and to treatment with detergents at an elevated temperature and pH but were exquisitely sensitive to killing by sodium hypochlorite. These results provide new insight into the role of the coat layer in spore properties.
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Abstract
Our understanding of the molecular mechanisms involved in biofilm formation has increased tremendously in recent years. From research on diverse bacteria, a general model of bacterial biofilm development has emerged. This model can be adjusted to fit either of two common modes of unicellular existence: nonmotile and motile. Here we provide a detailed review of what is currently known about biofilm formation by the motile bacterium Bacillus subtilis. While the ability of bacteria to form a biofilm appears to be almost universal and overarching themes apply, the combination of molecular events necessary varies widely, and this is reflected in the other chapters of this book.
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Zhukhlistova NE, Zhukova YN, Lyashenko AV, Zaĭtsev VN, Mikhaĭlov AM. Three-dimensional organization of three-domain copper oxidases: A review. CRYSTALLOGR REP+ 2008. [DOI: 10.1134/s1063774508010124] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Endospores formed by Bacillus, Clostridia, and related genera are encased in a protein shell called the coat. In many species, including B. subtilis, the coat is the outermost spore structure, and in other species, such as the pathogenic organisms B. anthracis and B. cereus, the spore is encased in an additional layer called the exosporium. Both the coat and the exosporium have roles in protection of the spore and in its environmental interactions. Assembly of both structures is a function of the mother cell, one of two cellular compartments of the developing sporangium. Studies in B. subtilis have revealed that the timing of coat protein production, the guiding role of a small group of morphogenetic proteins, and several types of posttranslational modifications are essential for the fidelity of the assembly process. Assembly of the exosporium requires a set of novel proteins as well as homologues of proteins found in the outermost layers of the coat and of some of the coat morphogenetic factors, suggesting that the exosporium is a more specialized structure of a multifunctional coat. These and other insights into the molecular details of spore surface morphogenesis provide avenues for exploitation of the spore surface layers in applications for biotechnology and medicine.
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Affiliation(s)
- Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras Codex, Portugal.
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CotC-CotU heterodimerization during assembly of the Bacillus subtilis spore coat. J Bacteriol 2007; 190:1267-75. [PMID: 18065538 DOI: 10.1128/jb.01425-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report evidence that CotC and CotU, two previously identified components of the Bacillus subtilis spore coat, are produced concurrently in the mother cell chamber of the sporulating cell under the control of sigmaK and GerE and immediately assembled around the forming spore. In the coat, the two proteins interact to form a coat component of 23 kDa. The CotU-CotC interaction was not detected in two heterologous hosts, suggesting that it occurs only in B. subtilis. Monomeric forms of both CotU and CotC failed to be assembled at the surface of the developing spore and accumulated in the mother cell compartment of cells mutant for cotE. In contrast, neither CotU nor CotC accumulated in the mother cell compartment of cells mutant for cotH. These results suggest that CotH is required to protect both CotU and CotC in the mother cell compartment of the sporangium and that CotE is needed to allow their assembly and subsequent interaction at the spore surface.
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Steichen CT, Kearney JF, Turnbough CL. Non-uniform assembly of the Bacillus anthracis exosporium and a bottle cap model for spore germination and outgrowth. Mol Microbiol 2007; 64:359-67. [PMID: 17493122 DOI: 10.1111/j.1365-2958.2007.05658.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Spores of Bacillus anthracis are enclosed by an exosporium composed of a basal layer and an external hair-like nap. The nap is formed by a collagen-like glycoprotein called BclA, while the basal layer contains many different proteins, one of which is a spore-specific alanine racemase (Alr). In this study, we employed fluorescence microscopy and a fluorescently labelled anti-Alr monoclonal antibody (mAb) to examine the distribution of Alr within the exosporium. Binding of the mAb occurred over approximately three-quarters of the exosporium but not in a cap-like region at one end of the spore, indicating the absence or inaccessibility of Alr in this region. We also determined that the cap-like region, or cap, corresponds to the first part of the exosporium assembled within the mother cell during sporulation and the only part of the exosporium assembled in a DeltaexsY mutant strain of B. anthracis. Our results provide the first direct evidence that exosporium assembly is a non-uniform process and suggest that exosporium formation is discontinuous. Finally, we demonstrated that during spore germination and outgrowth, the outgrowing cell always escapes from its exosporium shell by popping through the cap, suggesting that the cap is designed to facilitate the emergence of the outgrowing cell.
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Affiliation(s)
- Christopher T Steichen
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Costa T, Serrano M, Steil L, Völker U, Moran CP, Henriques AO. The timing of cotE expression affects Bacillus subtilis spore coat morphology but not lysozyme resistance. J Bacteriol 2006; 189:2401-10. [PMID: 17172339 PMCID: PMC1899386 DOI: 10.1128/jb.01353-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis of structural components and morphogenetic factors required for the assembly of the Bacillus subtilis spore coat is governed by a mother cell-specific transcriptional cascade. The first two temporal classes of gene expression, which involve RNA polymerase sigma sigma(E) factor and the ancillary regulators GerR and SpoIIID, are deployed prior to engulfment of the prespore by the mother cell. The two last classes rely on sigma(K), whose activation follows engulfment completion, and GerE. The cotE gene codes for a morphogenetic protein essential for the assembly of the outer coat layer and spore resistance to lysozyme. cotE is expressed first from a sigma(E)-dependent promoter and, in a second stage, from a promoter that additionally requires SpoIIID and that remains active under sigma(K) control. CotE localizes prior to engulfment completion close to the surface of the developing spore, but formation of the outer coat is a late, sigma(K)-controlled event. We have transplanted cotE to progressively later classes of mother cell gene expression. This created an early class of mutants in which cotE is expressed prior to engulfment completion and a late class in which expression of cotE follows the complete engulfment of the prespore. Mutants of the early class assemble a nearly normal outer coat structure, whereas mutants of the late class do not. Hence, the early expression of CotE is essential for outer coat assembly. Surprisingly, however, all mutants were fully resistant to lysozyme. The results suggest that CotE has genetically separable functions in spore resistance to lysozyme and spore outer coat assembly.
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Affiliation(s)
- Teresa Costa
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
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Escutia MR, Val G, Palacín A, Geukens N, Anné J, Mellado RP. Compensatory effect of the minorStreptomyces lividans type I signal peptidases on the SipY major signal peptidase deficiency as determined by extracellular proteome analysis. Proteomics 2006; 6:4137-46. [PMID: 16786486 DOI: 10.1002/pmic.200500927] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The developmentally complex bacterium Streptomyces lividans has the ability to produce and secrete a significant amount of protein and possesses four different type I signal peptidase genes (sipW, sipX, sipY and sipZ) that are unusually clustered in its chromosome. 2-DE and subsequent MS of extracellular proteins showed that proteins with typical export signals for type I and type II signal peptidases are the main components of the S. lividans secretome. Secretion of extracellular proteins is severely reduced in a strain deficient in the major type I signal peptidase (SipY). This deficiency was efficiently compensated by complementation with any of the other three signal peptidases as deduced from a comparison of the corresponding 2-D PAGE patterns with that of the wild-type strain.
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Affiliation(s)
- Marta R Escutia
- Centro Nacional de Biotecnología, Campus de la Universidad Autónoma, Cantoblanco, Madrid, Spain
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38
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Stein C, Jones GW, Chalmers T, Berry C. Transcriptional analysis of the toxin-coding plasmid pBtoxis from Bacillus thuringiensis subsp. israelensis. Appl Environ Microbiol 2006; 72:1771-6. [PMID: 16517621 PMCID: PMC1393223 DOI: 10.1128/aem.72.3.1771-1776.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Bacillus thuringiensis subsp. israelensis all of the insecticidal toxins are encoded on a single, large plasmid, pBtoxis. Sequencing of this plasmid revealed 125 potential coding sequences, many of which have predicted functions in gene regulation and physiological processes, such as germination. As a first step in understanding the possible role of pBtoxis in its host bacterium, a survey of the transcription of genes with predicted functions was carried out. Whereas many coding sequences, including those previously identified as probable pseudogenes, were not transcribed, mRNA was detected for 29 of the 40 sequences surveyed. Several of these sequences, including eight with similarities to the sequences of known transcriptional regulators, may influence wider gene regulation and thus may alter the phenotype of the host bacterium.
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Affiliation(s)
- Claudia Stein
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3US, United Kingdom
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Real G, Henriques AO. Localization of the Bacillus subtilis murB gene within the dcw cluster is important for growth and sporulation. J Bacteriol 2006; 188:1721-32. [PMID: 16484183 PMCID: PMC1426548 DOI: 10.1128/jb.188.5.1721-1732.2006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis murB gene, encoding UDP-N-acetylenolpyruvoylglucosamine reductase, a key enzyme in the peptidoglycan (PG) biosynthetic pathway, is embedded in the dcw (for "division and cell wall") cluster immediately upstream of divIB. Previous attempts to inactivate murB were unsuccessful, suggesting its essentiality. Here we show that the cell morphology, growth rate, and resistance to cell wall-active antibiotics of murB conditional mutants is a function of the expression level of murB. In one mutant, in which murB was insertionally inactivated in a merodiploid bearing a second xylose-inducible PxylA-murB allele, DivIB levels were reduced and a normal growth rate was achieved only if MurB levels were threefold that of the wild-type strain. However, expression of an extra copy of divIB restored normal growth at wild-type levels of MurB. In contrast, DivIB levels were normal in a second mutant containing an in-frame deletion of murB (DeltamurB) in the presence of the PxylA-murB gene. Furthermore, this strain grew normally with wild-type levels of MurB. During sporulation, the levels of MurB were highest at the time of synthesis of the spore cortex PG. Interestingly, the DeltamurB PxylA-murB mutant did not sporulate efficiently even at high concentrations of inducer. Since high levels of inducer did not interfere with sporulation of a murB(+)PxylA-murB strain, it appears that ectopic expression of murB fails to support efficient sporulation. These data suggest that coordinate expression of divIB and murB is important for growth and sporulation. The genetic context of the murB gene within the dcw cluster is unique to the Bacillus group and, taken together with our data, suggests that in these species it contributes to the optimal expression of cell division and PG biosynthetic functions during both vegetative growth and spore development.
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Affiliation(s)
- Gonçalo Real
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras Codex, Portugal.
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Chu F, Kearns DB, Branda SS, Kolter R, Losick R. Targets of the master regulator of biofilm formation in Bacillus subtilis. Mol Microbiol 2006; 59:1216-28. [PMID: 16430695 DOI: 10.1111/j.1365-2958.2005.05019.x] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wild strains of the spore-forming bacterium Bacillus subtilis are capable of forming architecturally complex communities of cells. The formation of these biofilms is mediated in part by the 15-gene exopolysaccharide operon, epsA-O, which is under the direct negative control of the SinR repressor. We report the identification of an additional operon, yqxM-sipW-tasA, that is required for biofilm formation and is under the direct negative control of SinR. We now show that all three members of the operon are required for the formation of robust biofilms and that SinR is a potent repressor of the operon that acts by binding to multiple sites in the promoter region. Genome-wide analysis of SinR-controlled transcription indicates that the epsA-O and yqxM-sipW-tasA operons constitute many of the most strongly controlled genes in the SinR regulon. These findings reinforce the view that SinR is a master regulator for biofilm formation and further suggest that a principal biological function of SinR is to govern the assembly of complex multicellular communities.
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Affiliation(s)
- Frances Chu
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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41
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Branda SS, Chu F, Kearns DB, Losick R, Kolter R. A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol 2006; 59:1229-38. [PMID: 16430696 DOI: 10.1111/j.1365-2958.2005.05020.x] [Citation(s) in RCA: 520] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbes construct structurally complex multicellular communities (biofilms) through production of an extracellular matrix. Here we present evidence from scanning electron microscopy showing that a wild strain of the Gram positive bacterium Bacillus subtilis builds such a matrix. Genetic, biochemical and cytological evidence indicates that the matrix is composed predominantly of a protein component, TasA, and an exopolysaccharide component. The absence of TasA or the exopolysaccharide resulted in a residual matrix, while the absence of both components led to complete failure to form complex multicellular communities. Extracellular complementation experiments revealed that a functional matrix can be assembled even when TasA and the exopolysaccharide are produced by different cells, reinforcing the view that the components contribute to matrix formation in an extracellular manner. Having defined the major components of the biofilm matrix and the control of their synthesis by the global regulator SinR, we present a working model for how B. subtilis switches between nomadic and sedentary lifestyles.
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Affiliation(s)
- Steven S Branda
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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Stecchini ML, Del Torre M, Venir E, Morettin A, Furlan P, Maltini E. Glassy state in Bacillus subtilis spores analyzed by differential scanning calorimetry. Int J Food Microbiol 2006; 106:286-90. [PMID: 16257078 DOI: 10.1016/j.ijfoodmicro.2005.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Revised: 04/01/2005] [Accepted: 06/30/2005] [Indexed: 10/25/2022]
Abstract
Thermal properties of dried spores of Bacillus subtilis, investigated by differential scanning calorimetry (DSC), were studied. A reversible heat capacity shift ascribable to glass-rubber transition was observed at 90-115 degrees C. The transition was found to be a pressure-inhibited volume-activated event. The decoated spores and the extracted peptidoglycan material exhibited glass transition, suggesting that the cortex could be involved in the event. Furthermore, the glass transition was evident when spores were treated with strong acid, and when the isogenic strain PS578 was scanned, indicating that core integrity and core components are not involved in the occurrence of the event. These results suggest that in the dried B. subtilis spores an amorphous biomaterial, possibly the cortex peptidoglycan, is present as a glass.
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Affiliation(s)
- Mara Lucia Stecchini
- Department of Food Science, University of Udine, Via Marangoni n. 97, 33100 Udine, Italy.
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43
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Zilhão R, Isticato R, Martins LO, Steil L, Völker U, Ricca E, Moran CP, Henriques AO. Assembly and function of a spore coat-associated transglutaminase of Bacillus subtilis. J Bacteriol 2005; 187:7753-64. [PMID: 16267299 PMCID: PMC1280291 DOI: 10.1128/jb.187.22.7753-7764.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The assembly of a multiprotein coat around the Bacillus subtilis spore confers resistance to lytic enzymes and noxious chemicals and ensures normal germination. Part of the coat is cross-linked and resistant to solubilization. The coat contains epsilon-(gamma-glutamyl)lysyl cross-links, and the expression of the gene (tgl) for a spore-associated transglutaminase was shown before to be required for the cross-linking of coat protein GerQ. Here, we have investigated the assembly and function of Tgl. We found that Tgl associates, albeit at somewhat reduced levels, with the coats of mutants that are unable to assemble the outer coat (cotE), that are missing the inner coat and with a greatly altered outer coat (gerE), or that are lacking discernible inner and outer coat structures (cotE gerE double mutant). This suggests that Tgl is present at various levels within the coat lattice. The assembly of Tgl occurs independently of its own activity, as a single amino acid substitution of a cysteine to an alanine (C116A) at the active site of Tgl does not affect its accumulation or assembly. However, like a tgl insertional mutation, the tglC116A allele causes increased extractability of polypeptides of about 40, 28, and 16 kDa in addition to GerQ (20 kDa) and affects the structural integrity of the coat. We show that most Tgl is assembled onto the spore surface soon after its synthesis in the mother cell under sigma(K) control but that the complete insolubilization of at least two of the Tgl-controlled polypeptides occurs several hours later. We also show that a multicopy allele of tgl causes increased assembly of Tgl and affects the assembly, structure, and functional properties of the coat.
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Affiliation(s)
- Rita Zilhão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras Codex, Portugal
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Balaban N, Gabdrakhmanova L, Sharipova M, Sokolova E, Malikova L, Mardanova A, Rudenskaya G, Leshchinskaya I. Selection of cultivation medium for production of late stationary phase serine proteinases from Bacillus intermedius. J Basic Microbiol 2005; 44:415-23. [PMID: 15558822 DOI: 10.1002/jobm.200410426] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
B. intermedius have been shown previously to secrete two serine proteinases: glutamyl endopeptidase 2 and subtilisin 2 during the late stationary phase, with maximal levels of the enzymes activities recorded at the 40th and 44th hours of growth, respectively. In the current study, we analyzed the impact of various culture medium components on biosynthesis of these proteinases. Yeast extract and gelatin did not stimulate the enzymes biosynthesis. However, on the medium containing 0.1% casein subtilisin 2 production increased to reach 140%. Biosynthesis of both serine proteinases, produced by B. intermedius at the late stationary phase, were found to be inhibited by individual amino acids, and to be insensitive to catabolite repression. In order to maximise enzyme production, the presence of Ca(2+) and Mg(2+) at concentration of 5 mM was shown to be necessary. Based on the results of this work, the composition of a complex culture media for the effective production of late stationary phase proteinases by B. intermedius was developed.
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Affiliation(s)
- Nelly Balaban
- Department of Microbiology, Kazan State University, Kremlievskaya str. 18, 420008 Kazan, Russia
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Hamon MA, Stanley NR, Britton RA, Grossman AD, Lazazzera BA. Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis. Mol Microbiol 2004; 52:847-60. [PMID: 15101989 PMCID: PMC1409746 DOI: 10.1111/j.1365-2958.2004.04023.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacillus subtilis is a ubiquitous soil bacterium that forms biofilms in a process that is negatively controlled by the transcription factor AbrB. To identify the AbrB-regulated genes required for biofilm formation by B. subtilis, genome-wide expression profiling studies of biofilms formed by spo0A abrB and sigH abrB mutant strains were performed. These data, in concert with previously published DNA microarray analysis of spo0A and sigH mutant strains, led to the identification of 39 operons that appear to be repressed by AbrB. Eight of these operons had previously been shown to be repressed by AbrB, and we confirmed AbrB repression for a further six operons by reverse transcription-PCR. The AbrB-repressed genes identified in this study are involved in processes known to be regulated by AbrB, such as extracellular degradative enzyme production and amino acid metabolism, and processes not previously known to be regulated by AbrB, such as membrane bioenergetics and cell wall functions. To determine whether any of these AbrB-regulated genes had a role in biofilm formation, we tested 23 mutants, each with a disruption in a different AbrB-regulated operon, for the ability to form biofilms. Two mutants had a greater than twofold defect in biofilm formation. A yoaW mutant exhibited a biofilm structure with reduced depth, and a sipW mutant exhibited only surface-attached cells and did not form a mature biofilm. YoaW is a putative secreted protein, and SipW is a signal peptidase. This is the first evidence that secreted proteins have a role in biofilm formation by Bacillus subtilis.
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Affiliation(s)
- Mélanie A. Hamon
- Department of Microbiology, Immunology and Molecular Genetics University of California Los Angeles 1602 Molecular Sciences Building 405 Hilgard Avenue Los Angeles, CA 90095, USA
| | - Nicola R. Stanley
- Department of Microbiology, Immunology and Molecular Genetics University of California Los Angeles 1602 Molecular Sciences Building 405 Hilgard Avenue Los Angeles, CA 90095, USA
| | - Robert A. Britton
- Department of Biology Massachusetts Institute of Technology Cambridge, MA 02139, USA
| | - Alan. D. Grossman
- Department of Biology Massachusetts Institute of Technology Cambridge, MA 02139, USA
| | - Beth A. Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California Los Angeles 1602 Molecular Sciences Building 405 Hilgard Avenue Los Angeles, CA 90095, USA
- *For correspondence. E-mail; Tel (+1) 310 794 4804; Fax (+1) 310 206 5231
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Branda SS, González-Pastor JE, Dervyn E, Ehrlich SD, Losick R, Kolter R. Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol 2004; 186:3970-9. [PMID: 15175311 PMCID: PMC419949 DOI: 10.1128/jb.186.12.3970-3979.2004] [Citation(s) in RCA: 222] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The spore-forming bacterium Bacillus subtilis is capable of assembling multicellular communities (biofilms) that display a high degree of spatiotemporal organization. Wild strains that have not undergone domestication in the laboratory produce particularly robust biofilms with complex architectural features, such as fruiting-body-like aerial projections whose tips serve as preferential sites for sporulation. To discover genes involved in this multicellular behavior and to do so on a genome-wide basis, we took advantage of a large collection of mutants which have disruptions of most of the uncharacterized genes in the B. subtilis genome. This collection, which was generated with a laboratory strain, was screened for mutants that were impaired in biofilm formation. This subset of mutated genes was then introduced into the wild strain NCIB 3610 to study their effects on biofilm formation in liquid and solid media. In this way we identified six genes that are involved in the development of multicellular communities. These are yhxB (encoding a putative phosphohexomutase that may mediate exopolysaccharide synthesis), sipW (encoding a signal peptidase), ecsB (encoding an ABC transporter subunit), yqeK (encoding a putative phosphatase), ylbF (encoding a regulatory protein), and ymcA (a gene of unknown function). Further analysis revealed that these six genes play different roles in B. subtilis community development.
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Affiliation(s)
- Steven S Branda
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
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Rhee KJ, Sethupathi P, Driks A, Lanning DK, Knight KL. Role of commensal bacteria in development of gut-associated lymphoid tissues and preimmune antibody repertoire. THE JOURNAL OF IMMUNOLOGY 2004; 172:1118-24. [PMID: 14707086 DOI: 10.4049/jimmunol.172.2.1118] [Citation(s) in RCA: 271] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intestinal bacteria are required for development of gut-associated lymphoid tissues (GALT), which mediate a variety of host immune functions, such as mucosal immunity and oral tolerance. In rabbits, the intestinal microflora are also required for developing the preimmune Ab repertoire by promoting somatic diversification of Ig genes in B cells that have migrated to GALT. We studied the mechanism of bacteria-induced GALT development. Bacteria were introduced into rabbits in which the appendix had been rendered germfree by microsurgery (we refer to these rabbits as germfree-appendix rabbits). We then identified specific members of the intestinal flora that promote GALT development. The combination of Bacteroides fragilis and Bacillus subtilis consistently promoted GALT development and led to development of the preimmune Ab repertoire, as shown by an increase in somatic diversification of VDJ-C micro genes in appendix B cells. Neither species alone consistently induced GALT development, nor did Clostridium subterminale, Escherichia coli, or Staphylococcus epidermidis. B. fragilis, which by itself is immunogenic, did not promote GALT development; hence, GALT development in rabbits does not appear to be the result of an Ag-specific immune response. To identify bacterial pathways required for GALT development, we introduced B. fragilis along with stress-response mutants of B. subtilis into germfree-appendix rabbits. We identified two Spo0A-controlled stress responses, sporulation and secretion of the protein YqxM, which are required for GALT development. We conclude that specific members of the commensal, intestinal flora drive GALT development through a specific subset of stress responses.
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Affiliation(s)
- Ki-Jong Rhee
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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Costa T, Steil L, Martins LO, Völker U, Henriques AO. Assembly of an oxalate decarboxylase produced under sigmaK control into the Bacillus subtilis spore coat. J Bacteriol 2004; 186:1462-74. [PMID: 14973022 PMCID: PMC344410 DOI: 10.1128/jb.186.5.1462-1474.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Over 30 polypeptides are synthesized at various times during sporulation in Bacillus subtilis, and they are assembled at the surface of the developing spore to form a multilayer protein structure called the coat. The coat consists of three main layers, an amorphous undercoat close to the underlying spore cortex peptidoglycan, a lamellar inner layer, and an electron-dense striated outer layer. The product of the B. subtilis oxdD gene was previously shown to have oxalate decarboxylase activity when it was produced in Escherichia coli and to be a spore constituent. In this study, we found that OxdD specifically associates with the spore coat structure, and in this paper we describe regulation of its synthesis and assembly. We found that transcription of oxdD is induced during sporulation as a monocistronic unit under the control of sigma(K) and is negatively regulated by GerE. We also found that localization of a functional OxdD-green fluorescent protein (GFP) at the surface of the developing spore depends on the SafA morphogenetic protein, which localizes at the interface between the spore cortex and coat layers. OxdD-GFP localizes around the developing spore in a cotE mutant, which does not assemble the spore outer coat layer, but it does not persist in spores produced by the mutant. Together, the data suggest that OxdD-GFP is targeted to the interior layers of the coat. Additionally, we found that expression of a multicopy allele of oxdD resulted in production of spores with increased levels of OxdD that were able to degrade oxalate but were sensitive to lysozyme.
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Affiliation(s)
- Teresa Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras Codex, Portugal
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Zilhão R, Serrano M, Isticato R, Ricca E, Moran CP, Henriques AO. Interactions among CotB, CotG, and CotH during assembly of the Bacillus subtilis spore coat. J Bacteriol 2004; 186:1110-9. [PMID: 14762006 PMCID: PMC344205 DOI: 10.1128/jb.186.4.1110-1119.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spores formed by wild-type Bacillus subtilis are encased in a multilayered protein structure (called the coat) formed by the ordered assembly of over 30 polypeptides. One polypeptide (CotB) is a surface-exposed coat component that has been used as a vehicle for the display of heterologous antigens at the spore surface. The cotB gene was initially identified by reverse genetics as encoding an abundant coat component. cotB is predicted to code for a 43-kDa polypeptide, but the form that prevails in the spore coat has a molecular mass of about 66 kDa (herein designated CotB-66). Here we show that in good agreement with its predicted size, expression of cotB in Escherichia coli results in the accumulation of a 46-kDa protein (CotB-46). Expression of cotB in sporulating cells of B. subtilis also results in a 46-kDa polypeptide which appears to be rapidly converted into CotB-66. These results suggest that soon after synthesis, CotB undergoes a posttranslational modification. Assembly of CotB-66 has been shown to depend on expression of both the cotH and cotG loci. We found that CotB-46 is the predominant form found in extracts prepared from sporulating cells or in spore coat preparations of cotH or cotG mutants. Therefore, both cotH and cotG are required for the efficient conversion of CotB-46 into CotB-66 but are dispensable for the association of CotB-46 with the spore coat. We also show that CotG does not accumulate in sporulating cells of a cotH mutant, suggesting that CotH (or a CotH-controlled factor) stabilizes the otherwise unstable CotG. Thus, the need for CotH for formation of CotB-66 results in part from its role in the stabilization of CotG. We also found that CotB-46 is present in complexes with CotG at the time when formation of CotB-66 is detected. Moreover, using a yeast two-hybrid system, we found evidence that CotB directly interacts with CotG and that both CotB and CotG self-interact. We suggest that an interaction between CotG and CotB is required for the formation of CotB-66, which may represent a multimeric form of CotB.
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Affiliation(s)
- Rita Zilhão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras Codex, Portugal
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Isticato R, Esposito G, Zilhão R, Nolasco S, Cangiano G, De Felice M, Henriques AO, Ricca E. Assembly of multiple CotC forms into the Bacillus subtilis spore coat. J Bacteriol 2004; 186:1129-35. [PMID: 14762008 PMCID: PMC344207 DOI: 10.1128/jb.186.4.1129-1135.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report evidence that the CotC polypeptide, a previously identified component of the Bacillus subtilis spore coat, is assembled into at least four distinct forms. Two of these, having molecular masses of 12 and 21 kDa, appeared 8 h after the onset of sporulation and were probably assembled on the forming spore immediately after their synthesis, since no accumulation of either of them was detected in the mother cell compartment, where their synthesis occurs. The other two components, 12.5 and 30 kDa, were generated 2 h later and were probably the products of posttranslational modifications of the two early forms occurring directly on the coat surface during spore maturation. None of the CotC forms was found either on the spore coat or in the mother cell compartment of a cotH mutant. This indicates that CotH serves a dual role of stabilizing the early forms of CotC and promoting the assembly of both early and late forms on the spore surface.
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Affiliation(s)
- Rachele Isticato
- Dipartimento di Fisiologia Generale ed Ambientale, Università Federico II, Naples, Italy
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