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Cámara-Almirón J, Domínguez-García L, El Mammeri N, Lends A, Habenstein B, de Vicente A, Loquet A, Romero D. Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation. NPJ Biofilms Microbiomes 2023; 9:68. [PMID: 37739955 PMCID: PMC10516879 DOI: 10.1038/s41522-023-00437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Biofilms are bacterial communities that result from a cell differentiation process leading to the secretion of an extracellular matrix (ECM) by part of the population. In Bacillus subtilis, the main protein component of the ECM is TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved among Bacillus species and contains a protein domain, the rigid core (RcTasA), which is critical for the structural and functional properties of the recombinant protein. In this study, we demonstrate that recombinantly purified RcTasA in vitro retains biochemical properties previously observed for the entire protein. Further analysis of the RcTasA amino acid sequence revealed two aggregation-prone stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these stretches found in RcTasA revealed their amyloid-like capacity in vitro, contributing to the amyloid nature of RcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA. Experiments with versions of TasA carrying the substitutions D64A and K68AD69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid-like properties. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of protein filaments in bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Nadia El Mammeri
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV, 1006, Latvia
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Antonio de Vicente
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain.
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Functional amyloid in a lipid-like environment: a merry dance of many steps. Essays Biochem 2022; 66:1035-1046. [PMID: 36205438 DOI: 10.1042/ebc20220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Functional amyloid, which unlike its pathological counterpart serves a biological purpose, is produced in a carefully orchestrated sequence of events. In bacteria, the major amyloid component is transported over the periplasm and through the outer membrane to assemble on the bacterial cell surface. During its life time, the amyloid protein may be exposed to both membrane lipids and extracellular surfactant, making it relevant to study its interactions with these components in vitro. Particularly for charged surfactants, the interaction is quite complex and highly dependent on the surfactant:protein molar ratio. Low ratios typically promote aggregation, likely by binding the proteins to micelles and thus increasing the local concentration of proteins, while higher concentrations see an inhibition of the same process as the protein is diluted out and immobilized on individual micelles. This is particularly pronounced for strongly anionic surfactants like SDS; the naturally occurring biosurfactant rhamnolipid interacts more weakly with the protein, which still not only allows aggregation but also leads to less detrimental effects at higher ratios. Similarly, anionic vesicle-forming lipids largely stimulate aggregation likely because of weaker interactions. Anionic lysolipids, thanks to their micelle-forming properties, resemble SDS in their impact on fibrillation. There are also examples of systems where membrane binding sequesters an otherwise amyloidogenic sequence and prevents fibrillation or-quite the opposite- liberates another part of the protein to engage in self-assembly. Thus, membranes and surfactants have very varied roles to play in the biogenesis and function of bacterial amyloid.
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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: 161] [Impact Index Per Article: 53.7] [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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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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Levkovich SA, Gazit E, Laor Bar-Yosef D. Two Decades of Studying Functional Amyloids in Microorganisms. Trends Microbiol 2020; 29:251-265. [PMID: 33041179 DOI: 10.1016/j.tim.2020.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
In the past two decades, amyloids, typically associated with human diseases, have been described to play various functional roles in nearly all life forms. The structural and functional diversity of microbial 'functional amyloids' has dramatically increased in recent years, expanding the canonical definition of these assembled molecules. Here, we provide a broad review of the current understanding of microbial functional amyloids and their diverse roles, putting the spotlight on recent discoveries in the field. We discuss their functions as structural scaffolds, surface-tension modulators, adhesion molecules, cell-cycle and gametogenesis regulators, toxins, and mediators of host-pathogen interactions. We outline how noncanonical amyloid morphologies and sophisticated regulatory mechanisms underlie their functional diversity and emphasize their therapeutic and biotechnological implications and applications.
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Affiliation(s)
- Shon A Levkovich
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ehud Gazit
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; Sagol Interdisciplinary School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
| | - Dana Laor Bar-Yosef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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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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Earl C, Arnaouteli S, Bamford NC, Porter M, Sukhodub T, MacPhee CE, Stanley-Wall NR. The majority of the matrix protein TapA is dispensable for Bacillus subtilis colony biofilm architecture. Mol Microbiol 2020; 114:920-933. [PMID: 32491277 DOI: 10.1111/mmi.14559] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 01/08/2023]
Abstract
Biofilm formation is a co-operative behaviour, where microbial cells become embedded in an extracellular matrix. This biomolecular matrix helps manifest the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the principles of biofilm formation. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease-resistant fibres needed for structuring. TapA is a secreted protein also needed for biofilm formation and helps in vivo TasA-fibre formation but is dispensable for in vitro TasA-fibre assembly. We show that TapA is subjected to proteolytic cleavage in the colony biofilm and that only the first 57 amino acids of the 253-amino acid protein are required for colony biofilm architecture. Through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesised at 253 amino acids when the first 57 are sufficient for colony biofilm structuring; the findings do not exclude the core conserved region of TapA having a second role beyond structuring the B. subtilis colony biofilm.
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Affiliation(s)
- Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - 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
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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8
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Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins. J Biosci 2020. [DOI: 10.1007/s12038-020-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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Mammeri NE, Hierrezuelo J, Tolchard J, Cámara‐Almirón J, Caro‐Astorga J, Álvarez‐Mena A, Dutour A, Berbon M, Shenoy J, Morvan E, Grélard A, Kauffmann B, Lecomte S, Vicente A, Habenstein B, Romero D, Loquet A. Molecular architecture of bacterial amyloids in
Bacillus
biofilms. FASEB J 2019; 33:12146-12163. [DOI: 10.1096/fj.201900831r] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nadia El Mammeri
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | | | - James Tolchard
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | | | | | | | - Antoine Dutour
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Melanie Berbon
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Jayakrishna Shenoy
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie (IECB)Unité Mixte de Service (UMS) 3033 Unité de Soutien (US) 001Centre National de la Recherche (CNRS)University of BordeauxPessacFrance
| | - Axelle Grélard
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (IECB)Unité Mixte de Service (UMS) 3033 Unité de Soutien (US) 001Centre National de la Recherche (CNRS)University of BordeauxPessacFrance
| | - Sophie Lecomte
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Antonio Vicente
- Departamento de MicrobiologíaUniversidad de MálagaMálagaSpain
| | - Birgit Habenstein
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Diego Romero
- Departamento de MicrobiologíaUniversidad de MálagaMálagaSpain
| | - Antoine Loquet
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
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