1
|
Oliva RL, Khadka UB, Camenzind T, Dyckmans J, Joergensen RG. Constituent of extracellular polymeric substances (EPS) produced by a range of soil bacteria and fungi. BMC Microbiol 2025; 25:298. [PMID: 40375143 DOI: 10.1186/s12866-025-04034-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Accepted: 05/08/2025] [Indexed: 05/18/2025] Open
Abstract
Extracellular polymeric substances (EPS) produced by soil bacteria and fungi are crucial for microbial growth and provide many functions for the soil and its microbes. EPS composition may depend on microbial community composition and the soil physical and chemical environment, nevertheless, not much is known about the EPS constituents' specific roles nor how they interact to alter biofilm's functions. We hypothesized that EPS production would be enhanced with the presence of a surface and with a more labile carbon source. Also, that even though carbohydrates and proteins are the main constituents of EPS, we could still find quantifiable amounts of mannosamine and galactosamine (two amino sugars previously shown to be part of microbial biofilms). Ten soil bacterial and ten soil fungal species were cultured with glycerol or starch and with or without a quartz matrix. After a 4-day cultivation, EPS were extracted, and seven constituents were determined: carbohydrates, DNA, proteins, muramic acid, mannosamine, galactosamine, and glucosamine. We found EPS composition was strongly modified by microbial type, whereas differences in EPS production were driven mostly by environmental conditions. The EPS-carbohydrate/protein ratio was higher for cultures grown in starch media than in glycerol and increased in the presence of quartz. EPS-carbohydrate concentration reflected environmental changes of substrate quality and surface presence. Contrastingly, changes in the other EPS constituent composition are likely due to intrinsic microbial characteristics. Our findings open the pathway to study microbial biofilms in more complex environments (such as soils) and shed light to the importance of extracellular structures to microbial processes.
Collapse
Affiliation(s)
- Rebeca Leme Oliva
- Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, Witzenhausen, 37213, Germany.
| | - Umesh B Khadka
- Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, Witzenhausen, 37213, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
| | - Jens Dyckmans
- Centre for Stable Isotope Research and Analysis, University of Göttingen, Büsgenweg 2, Göttingen, 37077, Germany
| | - Rainer Georg Joergensen
- Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, Witzenhausen, 37213, Germany
| |
Collapse
|
2
|
Zarazúa-Osorio B, Srivastava P, Marathe A, Zahid SH, Fujita M. Autoregulation of the Master Regulator Spo0A Controls Cell-Fate Decisions in Bacillus subtilis. Mol Microbiol 2025; 123:305-329. [PMID: 39812382 DOI: 10.1111/mmi.15341] [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: 10/29/2024] [Revised: 12/30/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]
Abstract
Spo0A in Bacillus subtilis is activated by phosphorylation (Spo0A~P) upon starvation and differentially controls a set of genes involved in biofilm formation and sporulation. The spo0A gene is transcribed by two distinct promoters, a σA-recognized upstream promoter Pv during growth, and a σH-recognized downstream promoter Ps during starvation, and appears to be autoregulated by four Spo0A~P binding sites (0A1-4 boxes) localized between two promoters. However, the autoregulatory mechanisms and their impact on differentiation remain elusive. Here, we determined the relative affinity of Spo0A~P for each 0A box and dissected each promoter in combination with the systematic 0A box mutations. The data revealed that (1) the Pv and Ps promoters are on and off, respectively, under nutrient-rich conditions without Spo0A~P, (2) the Ps promoter is activated by first 0A3 and then 0A1 during early starvation with low Spo0A~P, (3) during later starvation with high Spo0A~P, the Pv promoter is repressed by first 0A1 and then 0A2 and 0A4, and (4) during prolonged starvation, both promoters are silenced by all 0A boxes with very high Spo0A~P. Our results indicate that the autoregulation of spo0A is one of the key determinants to achieve a developmental increase in Spo0A~P, leading to a temporal window for entry into biofilm formation or sporulation.
Collapse
Affiliation(s)
| | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Syeda Hira Zahid
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| |
Collapse
|
3
|
Squyres GR, Newman DK. Biofilms as more than the sum of their parts: lessons from developmental biology. Curr Opin Microbiol 2024; 82:102537. [PMID: 39241276 DOI: 10.1016/j.mib.2024.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 09/09/2024]
Abstract
Although our understanding of both bacterial cell physiology and the complex behaviors exhibited by bacterial biofilms is expanding rapidly, we cannot yet sum the behaviors of individual cells to understand or predict biofilm behavior. This is both because cell physiology in biofilms is different from planktonic growth and because cell behavior in biofilms is spatiotemporally patterned. We use developmental biology as a guide to examine this phenotypic patterning, discussing candidate cues that may encode spatiotemporal information and possible roles for phenotypic patterning in biofilms. We consider other questions that arise from the comparison between biofilm and eukaryotic development, including what defines normal biofilm development and the nature of biofilm cell types and fates. We conclude by discussing what biofilm development can tell us about developmental processes, emphasizing the additional challenges faced by bacteria in biofilm development compared with their eukaryotic counterparts.
Collapse
Affiliation(s)
- Georgia R Squyres
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA; Division of Geological and Planetary Sciences, Caltech, Pasadena, CA 91125, USA.
| |
Collapse
|
4
|
Bamford NC, Morris RJ, Prescott A, Murphy P, Erskine E, MacPhee CE, Stanley-Wall NR. TasA Fibre Interactions Are Necessary for Bacillus subtilis Biofilm Structure. Mol Microbiol 2024; 122:598-609. [PMID: 39344640 DOI: 10.1111/mmi.15315] [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: 06/28/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 10/01/2024]
Abstract
The extracellular matrix of biofilms provides crucial structural support to the community and protection from environmental perturbations. TasA, a key Bacillus subtilis biofilm matrix protein, forms both amyloid and non-amyloid fibrils. Non-amyloid TasA fibrils are formed via a strand-exchange mechanism, whereas the amyloid-like form involves non-specific self-assembly. We performed mutagenesis of the N-terminus to assess the role of non-amyloid fibrils in biofilm development. We find that the N-terminal tail is essential for the formation of structured biofilms, providing evidence that the strand-exchange fibrils are the active form in the biofilm matrix. Furthermore, we demonstrate that fibre formation alone is not sufficient to give structure to the biofilm. We build an interactome of TasA with other extracellular protein components, and identify important interaction sites. Our results provide insight into how protein-matrix interactions modulate biofilm development.
Collapse
Affiliation(s)
- Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ryan J Morris
- National Biofilms Innovation Centre, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Alan Prescott
- Centre for Advanced Scientific Technologies, School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul Murphy
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Elliot Erskine
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Cait E MacPhee
- National Biofilms Innovation Centre, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| |
Collapse
|
5
|
Xue Y, Yu C, Ouyang H, Huang J, Kang X. Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy. J Am Chem Soc 2024; 146:11906-11923. [PMID: 38629727 DOI: 10.1021/jacs.4c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.
Collapse
Affiliation(s)
- Yi Xue
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Yu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Han Ouyang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Kang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| |
Collapse
|
6
|
Morris RJ, Bamford NC, Bromley KM, Erskine E, Stanley-Wall NR, MacPhee CE. Bacillus subtilis Matrix Protein TasA is Interfacially Active, but BslA Dominates Interfacial Film Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:4164-4173. [PMID: 38351711 PMCID: PMC10905994 DOI: 10.1021/acs.langmuir.3c03163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/28/2024]
Abstract
Microbial growth often occurs within multicellular communities called biofilms, where cells are enveloped by a protective extracellular matrix. Bacillus subtilis serves as a model organism for biofilm research and produces two crucial secreted proteins, BslA and TasA, vital for biofilm matrix formation. BslA exhibits surface-active properties, spontaneously self-assembling at hydrophobic/hydrophilic interfaces to form an elastic protein film, which renders B. subtilis biofilm surfaces water-repellent. TasA is traditionally considered a fiber-forming protein with multiple matrix-related functions. In our current study, we investigate whether TasA also possesses interfacial properties and whether it has any impact on BslA's ability to form an interfacial protein film. Our research demonstrates that TasA indeed exhibits interfacial activity, partitioning to hydrophobic/hydrophilic interfaces, stabilizing emulsions, and forming an interfacial protein film. Interestingly, TasA undergoes interface-induced restructuring similar to BslA, showing an increase in β-strand secondary structure. Unlike BslA, TasA rapidly reaches the interface and forms nonelastic films that rapidly relax under pressure. Through mixed protein pendant drop experiments, we assess the influence of TasA on BslA film formation, revealing that TasA and other surface-active molecules can compete for interface space, potentially preventing BslA from forming a stable elastic film. This raises a critical question: how does BslA self-assemble to form the hydrophobic "raincoat" observed in biofilms in the presence of other potentially surface-active species? We propose a model wherein surface-active molecules, including TasA, initially compete with BslA for interface space. However, under lateral compression or pressure, BslA retains its position, expelling other molecules into the bulk. This resilience at the interface may result from structural rearrangements and lateral interactions between BslA subunits. This combined mechanism likely explains BslA's role in forming a stable film integral to B. subtilis biofilm hydrophobicity.
Collapse
Affiliation(s)
- Ryan J. Morris
- School
of Physics & Astronomy, University of
Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, U.K.
- National
Biofilms Innovation Centre, Southampton SO17 1GB, U.K.
| | - Natalie C. Bamford
- National
Biofilms Innovation Centre, Southampton SO17 1GB, U.K.
- Division
of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Keith M. Bromley
- School
of Physics & Astronomy, University of
Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, U.K.
| | - Elliot Erskine
- Division
of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Nicola R. Stanley-Wall
- Division
of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Cait E. MacPhee
- School
of Physics & Astronomy, University of
Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, U.K.
- National
Biofilms Innovation Centre, Southampton SO17 1GB, U.K.
| |
Collapse
|
7
|
Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LEP. Cellular arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Biol 2024; 22:e3002205. [PMID: 38300958 PMCID: PMC10833521 DOI: 10.1371/journal.pbio.3002205] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.
Collapse
Affiliation(s)
- Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Julie Kiss
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Emily LaMarre
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - William Cole Cornell
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Chase J. Morgan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Anuradha Janakiraman
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Jasmine A. Nirody
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| |
Collapse
|
8
|
Arnaouteli S, Bamford NC, Brandani GB, Morris RJ, Schor M, Carrington JT, Hobley L, van Aalten DMF, Stanley-Wall NR, MacPhee CE. Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA. Proc Natl Acad Sci U S A 2023; 120:e2312022120. [PMID: 37903266 PMCID: PMC7615278 DOI: 10.1073/pnas.2312022120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023] Open
Abstract
The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the crystal structure of the BslA paralogue YweA that we determined. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2-dimensional lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.
Collapse
Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Natalie C. Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Giovanni B. Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto606 8501, Japan
| | - Ryan J. Morris
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EdinburghEH9 3FD, United Kingdom
| | - Marieke Schor
- UB Education, Content & Support, Maastricht University, Maastricht6211 LK, Netherlands
| | - Jamie T. Carrington
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Laura Hobley
- School of Biosciences, University of Nottingham, NottinghamNG7 2RD, United Kingdom
| | - Daan M. F. van Aalten
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus8000, Denmark
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, DundeeDD5 4EH, United Kingdom
| | - Cait E. MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EdinburghEH9 3FD, United Kingdom
| |
Collapse
|
9
|
Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LE. Cell arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.20.545666. [PMID: 37645902 PMCID: PMC10462148 DOI: 10.1101/2023.06.20.545666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.
Collapse
Affiliation(s)
- Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Julie Kiss
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Emily LaMarre
- Program in Biology, The Graduate Center, City University of New York, New York, NY 10016
| | | | - Chase J. Morgan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Anuradha Janakiraman
- Program in Biology, The Graduate Center, City University of New York, New York, NY 10016
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Jasmine A Nirody
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois 60637
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10025
| |
Collapse
|
10
|
Sun H, Si F, Zhao X, Li F, Qi G. The cellular redox state in Bacillus amyloliquefaciens WH1 affects biofilm formation indirectly in a surfactant direct manner. J Basic Microbiol 2023. [PMID: 37189223 DOI: 10.1002/jobm.202300064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Surfactin is a signal to trigger biofilm formation against harsh environments. Generally, harsh environments can result in change of the cellular redox state to induce biofilm formation, but we know little about whether the cellular redox state influences biofilm formation via surfactin. Here, the reductant glucose could reduce surfactin and enhance biofilm formation by a surfactin-indirect way. The oxidant H2 O2 led to a decrease of surfactin accompanying with weakened biofilm formation. Spx and PerR were both necessary for surfactin production and biofilm formation. H2 O2 improved surfactin production but inhibited biofilm formation by a surfactin-indirect manner in Δspx, while it reduced surfactin production without obvious influence on biofilm formation in ΔperR. The ability against H2 O2 stress was enhanced in Δspx, but weakened in ΔperR. Thereby, PerR was favorable for resisting oxidative stress, while Spx played a negative role in this action. Knockout and compensation of rex also supported that the cells could form biofilm by a surfactin-indirect way. Collectively, surfactin is not a unique signal to trigger biofilm formation, and the cellular redox state can influence biofilm formation by a surfactin-direct or -indirect way in Bacillus amyloliquefaciens WH1.
Collapse
Affiliation(s)
- Huiwan Sun
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengmei Si
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
11
|
Gilmour KA, Aljannat M, Markwell C, James P, Scott J, Jiang Y, Torun H, Dade-Robertson M, Zhang M. Biofilm inspired fabrication of functional bacterial cellulose through ex-situ and in-situ approaches. Carbohydr Polym 2023; 304:120482. [PMID: 36641190 DOI: 10.1016/j.carbpol.2022.120482] [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: 09/12/2022] [Revised: 12/11/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Bacterial cellulose (BC) has been explored for use in a range of applications including tissue engineering and textiles. BC can be produced from waste streams, but sustainable approaches are needed for functionalisation. To this end, BslA, a B. subtilis biofilm protein was produced recombinantly with and without a cellulose binding module (CBM) and the cell free extract was used to treat BC either ex-situ, through drip coating or in-situ, by incorporating during fermentation. The results showed that ex-situ modified BC increased the hydrophobicity and water contact angle reached 120°. In-situ experiments led to a BC film morphological change and mechanical testing demonstrated that addition of BslA with CBM resulted in a stronger, more elastic material. This study presents a nature inspired approach to functionalise BC using a biofilm hydrophobin, and we demonstrate that recombinant proteins could be effective and sustainable molecules for functionalisation of BC materials.
Collapse
Affiliation(s)
- Katie A Gilmour
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Mahab Aljannat
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Christopher Markwell
- Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Paul James
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Jane Scott
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Yunhong Jiang
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Hamdi Torun
- Department of Mathematics, Physics and Electrical Engineering, Faculty of Environment and Engineering, Northumbria University at Newcastle, NE1 8ST, UK.
| | - Martyn Dade-Robertson
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, NE1 7RU, UK.
| | - Meng Zhang
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University at Newcastle, NE1 8ST, UK.
| |
Collapse
|
12
|
Luo S, Liu Y, Luo H, Jing G. Glycerol Droplet Spreading on Growing Bacillus Subtilis Biofilms. MICROMACHINES 2023; 14:599. [PMID: 36985005 PMCID: PMC10055872 DOI: 10.3390/mi14030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Bacterial biofilm is a three-dimensional matrix composed of a large number of living bacterial individuals. The strong bio-interaction between the bacteria and its self-secreted matrix environment strengthens the mechanical integrity of the biofilm and the sustainable resistance of bacteria to antibiotics. As a soft surface, the biofilm is expected to present different dynamical wetting behavior in response to shear stress, which is, however, less known. Here, the spreading of liquid droplet on Bacillus subtilis biofilm at its different growing phases was experimentally investigated. Due to the viscoelastic response of the biofilm to fast spreading of the droplet, three stages were identified as inertial, viscous stages, and a longer transition in between. The physical heterogeneity of growing biofilm correlates with the spreading scaling within the inertial stage, followed by the possible chemical variation after a critical growing time. By using the duration of inertial spreading, the characteristic time scale was successfully linked to the shear modulus of the elastic dissipation of the biofilm. This measurement suggests a facile, non-destructive and in vivo method to understand the mechanical instability of this living matter.
Collapse
Affiliation(s)
| | | | - Hao Luo
- Correspondence: (Y.L.); (H.L.)
| | | |
Collapse
|
13
|
Martín-Rodríguez AJ. Respiration-induced biofilm formation as a driver for bacterial niche colonization. Trends Microbiol 2023; 31:120-134. [PMID: 36075785 DOI: 10.1016/j.tim.2022.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.
Collapse
|
14
|
Eigentler L, Davidson FA, Stanley-Wall NR. Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective. Open Biol 2022; 12:220194. [PMID: 36514980 PMCID: PMC9748781 DOI: 10.1098/rsob.220194] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.
Collapse
Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK,Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Fordyce A. Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| |
Collapse
|
15
|
Lin Y, Briandet R, Kovács ÁT. Bacillus cereus sensu lato biofilm formation and its ecological importance. Biofilm 2022; 4:100070. [PMID: 35243332 PMCID: PMC8861577 DOI: 10.1016/j.bioflm.2022.100070] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/20/2022] Open
Abstract
Biofilm formation is a ubiquitous process of bacterial communities that enables them to survive and persist in various environmental niches. The Bacillus cereus group includes phenotypically diversified species that are widely distributed in the environment. Often, B. cereus is considered a soil inhabitant, but it is also commonly isolated from plant roots, nematodes, and food products. Biofilms differ in their architecture and developmental processes, reflecting adaptations to specific niches. Importantly, some B. cereus strains are foodborne pathogens responsible for two types of gastrointestinal diseases, diarrhea and emesis, caused by distinct toxins. Thus, the persistency of biofilms is of particular concern for the food industry, and understanding the underlying mechanisms of biofilm formation contributes to cleaning procedures. This review focuses on the genetic background underpinning the regulation of biofilm development, as well as the matrix components associated with biofilms. We also reflect on the correlation between biofilm formation and the development of highly resistant spores. Finally, advances in our understanding of the ecological importance and evolution of biofilm formation in the B. cereus group are discussed.
Collapse
Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| |
Collapse
|
16
|
Imai T, Tobe R, Honda K, Tanaka M, Kawamoto J, Mihara H. Group II truncated haemoglobin YjbI prevents reactive oxygen species-induced protein aggregation in Bacillus subtilis. eLife 2022; 11:70467. [PMID: 36125244 PMCID: PMC9536834 DOI: 10.7554/elife.70467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/19/2022] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress-mediated formation of protein hydroperoxides can induce irreversible fragmentation of the peptide backbone and accumulation of cross-linked protein aggregates, leading to cellular toxicity, dysfunction, and death. However, how bacteria protect themselves from damages caused by protein hydroperoxidation is unknown. Here, we show that YjbI, a group II truncated haemoglobin from Bacillus subtilis, prevents oxidative aggregation of cell-surface proteins by its protein hydroperoxide peroxidase-like activity, which removes hydroperoxide groups from oxidised proteins. Disruption of the yjbI gene in B. subtilis lowered biofilm water repellence, which associated with the cross-linked aggregation of the biofilm matrix protein TasA. YjbI was localised to the cell surface or the biofilm matrix, and the sensitivity of planktonically grown cells to generators of reactive oxygen species was significantly increased upon yjbI disruption, suggesting that YjbI pleiotropically protects labile cell-surface proteins from oxidative damage. YjbI removed hydroperoxide residues from the model oxidised protein substrate bovine serum albumin and biofilm component TasA, preventing oxidative aggregation in vitro. Furthermore, the replacement of Tyr63 near the haem of YjbI with phenylalanine resulted in the loss of its protein peroxidase-like activity, and the mutant gene failed to rescue biofilm water repellency and resistance to oxidative stress induced by hypochlorous acid in the yjbI-deficient strain. These findings provide new insights into the role of truncated haemoglobin and the importance of hydroperoxide removal from proteins in the survival of aerobic bacteria.
Collapse
Affiliation(s)
- Takeshi Imai
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Ryuta Tobe
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Koji Honda
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Mai Tanaka
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Hisaaki Mihara
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| |
Collapse
|
17
|
Eigentler L, Kalamara M, Ball G, MacPhee CE, Stanley-Wall NR, Davidson FA. Founder cell configuration drives competitive outcome within colony biofilms. THE ISME JOURNAL 2022; 16:1512-1522. [PMID: 35121821 PMCID: PMC9122948 DOI: 10.1038/s41396-022-01198-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 11/19/2022]
Abstract
Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells' potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.
Collapse
Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK
| | - Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK
| | - Cait E MacPhee
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK.
| |
Collapse
|
18
|
Fessia A, Barra P, Barros G, Nesci A. Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere? J Appl Microbiol 2022; 133:2148-2166. [PMID: 35476896 DOI: 10.1111/jam.15596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/30/2022]
Abstract
Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.
Collapse
Affiliation(s)
- Aluminé Fessia
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Paula Barra
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Germán Barros
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Andrea Nesci
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| |
Collapse
|
19
|
Choi Y, Kim YH. Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13. J Microbiol 2022; 60:411-418. [DOI: 10.1007/s12275-022-2018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
|
20
|
Jo J, Price-Whelan A, Dietrich LEP. Gradients and consequences of heterogeneity in biofilms. Nat Rev Microbiol 2022; 20:593-607. [PMID: 35149841 DOI: 10.1038/s41579-022-00692-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/15/2022]
Abstract
Historically, appreciation for the roles of resource gradients in biology has fluctuated inversely to the popularity of genetic mechanisms. Nevertheless, in microbiology specifically, widespread recognition of the multicellular lifestyle has recently brought new emphasis to the importance of resource gradients. Most microorganisms grow in assemblages such as biofilms or spatially constrained communities with gradients that influence, and are influenced by, metabolism. In this Review, we discuss examples of gradient formation and physiological differentiation in microbial assemblages growing in diverse settings. We highlight consequences of physiological heterogeneity in microbial assemblages, including division of labour and increased resistance to stress. Our impressions of microbial behaviour in various ecosystems are not complete without complementary maps of the chemical and physical geographies that influence cellular activities. A holistic view, incorporating these geographies and the genetically encoded functions that operate within them, will be essential for understanding microbial assemblages in their many roles and potential applications.
Collapse
Affiliation(s)
- Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| |
Collapse
|
21
|
Yoon J, Shin M, Kim D, Lim J, Kim HW, Kang T, Choi JW. Bionanohybrid composed of metalloprotein/DNA/MoS 2/peptides to control the intracellular redox states of living cells and its applicability as a cell-based biomemory device. Biosens Bioelectron 2022; 196:113725. [PMID: 34678652 DOI: 10.1016/j.bios.2021.113725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/17/2021] [Indexed: 12/13/2022]
Abstract
The development of cell-based bioelectronic devices largely depends on the direct control of intracellular redox states. However, most related studies have focused on the accurate measurement of electrical signals from living cells, whereas direct intracellular state control remains largely unexplored. Here, we developed a biocompatible transmembranal bionanohybrid structure composed of a recombinant metalloprotein, DNA, molybdenum disulfide nanoparticles (MoS2), and peptides to control intracellular redox states, which can be used as a cell-based biomemory device. Using the capacitance of MoS2 located inside the cell, the bionanohybrid controled the intracellular redox states of living cells by recording and extracting intracellular charges, which inturn was achieved by activating (writing) and deactivating (erasing) the cells. As a proof of concept, cell-based biomemory functions including writing, reading, and erasing were successfully demonstrated and confirmed via electrochemical methods and patch-clamp analyses, resulting in the development of the first in vitro cell-based biomemory device. This newly developed bionanohybrid provides a novel approach to control cellular redox states for cell-based bioelectronic applications, and can be applicable in a wide range of biological fields including bioelectronic medicine and intracellular redox status regulation.
Collapse
Affiliation(s)
- Jinho Yoon
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Minkyu Shin
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Dongyeon Kim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Joungpyo Lim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Hyun-Woong Kim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Taewook Kang
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea.
| |
Collapse
|
22
|
Pani A, Valeria L, Dugnani S, Scaglione F. Erdosteine enhances antibiotic activity against bacteria within biofilm. Int J Antimicrob Agents 2022; 59:106529. [DOI: 10.1016/j.ijantimicag.2022.106529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 11/05/2022]
|
23
|
Ramamirtham S, Whitby CP, Zare D, Weeks M, Williams MA. The rheological properties of bovine β-Lactoglobulin stabilized oil/water interfaces depend on the protein's quaternary structure. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
24
|
Structural and functional characterization of the bacterial biofilm activator RemA. Nat Commun 2021; 12:5707. [PMID: 34588455 PMCID: PMC8481266 DOI: 10.1038/s41467-021-26005-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022] Open
Abstract
Bacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the structure of the RemA homologue from Geobacillus thermodenitrificans, showing a unique octameric ring with the potential to form a 16-meric superstructure. These results, together with further biochemical and in vivo characterization of B. subtilis RemA, suggests that the protein can wrap DNA around its ring-like structure through a LytTR-related domain. Biofilm formation in Bacillus subtilis requires expression of matrix production genes, which are upregulated by transcriptional activator RemA. Here, the authors show that RemA forms octameric rings with the potential to form a 16-meric superstructure, suggesting that the protein can wrap DNA through a LytTR-related domain.
Collapse
|
25
|
Kalamara M, Abbott JC, MacPhee CE, Stanley-Wall NR. Biofilm hydrophobicity in environmental isolates of Bacillus subtilis. MICROBIOLOGY-SGM 2021; 167. [PMID: 34486975 DOI: 10.1099/mic.0.001082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our novel isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason for the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.
Collapse
Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - James C Abbott
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Cait E MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| |
Collapse
|
26
|
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: 225] [Impact Index Per Article: 56.3] [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.
Collapse
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.
| |
Collapse
|
27
|
Pedre B, Barayeu U, Ezeriņa D, Dick TP. The mechanism of action of N-acetylcysteine (NAC): The emerging role of H 2S and sulfane sulfur species. Pharmacol Ther 2021; 228:107916. [PMID: 34171332 DOI: 10.1016/j.pharmthera.2021.107916] [Citation(s) in RCA: 244] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Initially adopted as a mucolytic about 60 years ago, the cysteine prodrug N-acetylcysteine (NAC) is the standard of care to treat paracetamol intoxication, and is included on the World Health Organization's list of essential medicines. Additionally, NAC increasingly became the epitome of an "antioxidant". Arguably, it is the most widely used "antioxidant" in experimental cell and animal biology, as well as clinical studies. Most investigators use and test NAC with the idea that it prevents or attenuates oxidative stress. Conventionally, it is assumed that NAC acts as (i) a reductant of disulfide bonds, (ii) a scavenger of reactive oxygen species and/or (iii) a precursor for glutathione biosynthesis. While these mechanisms may apply under specific circumstances, they cannot be generalized to explain the effects of NAC in a majority of settings and situations. In most cases the mechanism of action has remained unclear and untested. In this review, we discuss the validity of conventional assumptions and the scope of a newly discovered mechanism of action, namely the conversion of NAC into hydrogen sulfide and sulfane sulfur species. The antioxidative and cytoprotective activities of per- and polysulfides may explain many of the effects that have previously been ascribed to NAC or NAC-derived glutathione.
Collapse
Affiliation(s)
- Brandán Pedre
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Uladzimir Barayeu
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Daria Ezeriņa
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.
| |
Collapse
|
28
|
A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
Collapse
|
29
|
Sharipova MR, Mardanova AM, Rudakova NL, Pudova DS. Bistability and Formation of the Biofilm Matrix as Adaptive Mechanisms during the Stationary Phase of Bacillus subtilis. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172006017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
30
|
Azeredo J, García P, Drulis-Kawa Z. Targeting biofilms using phages and their enzymes. Curr Opin Biotechnol 2021; 68:251-261. [PMID: 33714050 DOI: 10.1016/j.copbio.2021.02.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 02/08/2023]
Abstract
The complex biofilm architecture composed of extracellular polymeric structures (EPS) provides a protective shield to physiologically diverse bacterial cells immersed in its structure. The evolutionary interplay between bacteria and their viruses (phages) forced the latter ones to develop specific strategies to overcome the biofilm defensive barriers and kill sessile cells. Phages are equipped with a wide panel of enzyme-degrading EPS macromolecules which together are powerful weapons to combat biofilms. Antibiofilm performance can be achieved by combining phages or phage-borne enzymes with other antimicrobials such as antibiotics. Nevertheless, a variety of enzymes encoded in phage genomes still need to be explored. To advance in biofilm control strategies we must deepen the understanding of the biofilm biology itself, as well as discover and better exploit the unlimited antibacterial potential of phages.
Collapse
Affiliation(s)
- Joana Azeredo
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares sn. 33300, Villaviciosa, Asturias, Spain.
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
| |
Collapse
|
31
|
Peptide signaling without feedback in signal production operates as a true quorum sensing communication system in Bacillus subtilis. Commun Biol 2021; 4:58. [PMID: 33420264 PMCID: PMC7794433 DOI: 10.1038/s42003-020-01553-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial quorum sensing (QS) is based on signal molecules (SM), which increase in concentration with cell density. At critical SM concentration, a variety of adaptive genes sharply change their expression from basic level to maximum level. In general, this sharp transition, a hallmark of true QS, requires an SM dependent positive feedback loop, where SM enhances its own production. Some communication systems, like the peptide SM-based ComQXPA communication system of Bacillus subtilis, do not have this feedback loop and we do not understand how and if the sharp transition in gene expression is achieved. Based on experiments and mathematical modeling, we observed that the SM peptide ComX encodes the information about cell density, specific cell growth rate, and even oxygen concentration, which ensure power-law increase in SM production. This enables together with the cooperative response to SM (ComX) a sharp transition in gene expression level and this without the SM dependent feedback loop. Due to its ultra-sensitive nature, the ComQXPA can operate at SM concentrations that are 100-1000 times lower than typically found in other QS systems, thereby substantially reducing the total metabolic cost of otherwise expensive ComX peptide.
Collapse
|
32
|
Pandit S, Fazilati M, Gaska K, Derouiche A, Nypelö T, Mijakovic I, Kádár R. The Exo-Polysaccharide Component of Extracellular Matrix is Essential for the Viscoelastic Properties of Bacillus subtilis Biofilms. Int J Mol Sci 2020; 21:ijms21186755. [PMID: 32942569 PMCID: PMC7555405 DOI: 10.3390/ijms21186755] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteria are known to form biofilms on various surfaces. Biofilms are multicellular aggregates, held together by an extracellular matrix, which is composed of biological polymers. Three principal components of the biofilm matrix are exopolysaccharides (EPS), proteins, and nucleic acids. The biofilm matrix is essential for biofilms to remain organized under mechanical stress. Thanks to their polymeric nature, biofilms exhibit both elastic and viscous mechanical characteristics; therefore, an accurate mechanical description needs to take into account their viscoelastic nature. Their viscoelastic properties, including during their growth dynamics, are crucial for biofilm survival in many environments, particularly during infection processes. How changes in the composition of the biofilm matrix affect viscoelasticity has not been thoroughly investigated. In this study, we used interfacial rheology to study the contribution of the EPS component of the matrix to viscoelasticity of Bacillus subtilis biofilms. Two strategies were used to specifically deplete the EPS component of the biofilm matrix, namely (i) treatment with sub-lethal doses of vitamin C and (ii) seamless inactivation of the eps operon responsible for biosynthesis of the EPS. In both cases, the obtained results suggest that the EPS component of the matrix is essential for maintaining the viscoelastic properties of bacterial biofilms during their growth. If the EPS component of the matrix is depleted, the mechanical stability of biofilms is compromised and the biofilms become more susceptible to eradication by mechanical stress.
Collapse
Affiliation(s)
- Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
| | - Mina Fazilati
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden;
| | - Karolina Gaska
- Department of Aerospace Engineering, University of Bristol, Bristol BS8 1TR, UK;
| | - Abderahmane Derouiche
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
| | - Tiina Nypelö
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Wallenberg Wood Science Center, Chalmers, 412 96 Göteborg, Sweden
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
- Correspondence: (I.M.); (R.K.)
| | - Roland Kádár
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Wallenberg Wood Science Center, Chalmers, 412 96 Göteborg, Sweden
- Correspondence: (I.M.); (R.K.)
| |
Collapse
|
33
|
Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm Matrixome: Extracellular Components in Structured Microbial Communities. Trends Microbiol 2020; 28:668-681. [PMID: 32663461 DOI: 10.1016/j.tim.2020.03.016] [Citation(s) in RCA: 698] [Impact Index Per Article: 139.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 02/04/2023]
Abstract
Biofilms consist of microbial communities embedded in a 3D extracellular matrix. The matrix is composed of a complex array of extracellular polymeric substances (EPS) that contribute to the unique attributes of biofilm lifestyle and virulence. This ensemble of chemically and functionally diverse biomolecules is termed the 'matrixome'. The composition and mechanisms of EPS matrix formation, and its role in biofilm biology, function, and microenvironment are being revealed. This perspective article highlights recent advances about the multifaceted role of the 'matrixome' in the development, physical-chemical properties, and virulence of biofilms. We emphasize that targeting biofilm-specific conditions such as the matrixome could lead to precise and effective antibiofilm approaches. We also discuss the limited knowledge in the context of polymicrobial biofilms, and the need for more in-depth analyses of the EPS matrix in mixed communities that are associated with many human infectious diseases.
Collapse
Affiliation(s)
- L Karygianni
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine University of Zurich, Zurich, Switzerland
| | - Z Ren
- Department of Orthodontics, Divisions of Pediatric Dentistry and Community of Oral Health, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - H Koo
- Department of Orthodontics, Divisions of Pediatric Dentistry and Community of Oral Health, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA; Center for Innovation and Precision Dentistry, University of Pennsylvania School of Dental Medicine, School of Engineering and Applied Sciences, Philadelphia, PA, USA
| | - T Thurnheer
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine University of Zurich, Zurich, Switzerland.
| |
Collapse
|
34
|
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms. Nat Commun 2020; 11:950. [PMID: 32075967 PMCID: PMC7031267 DOI: 10.1038/s41467-020-14431-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σB in individual cells during biofilm development. Both σB and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σB represses sporulation. As predicted by a simple mathematical model, increasing σB expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development. Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.
Collapse
|
35
|
Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus. NPJ Biofilms Microbiomes 2020; 6:3. [PMID: 31969984 PMCID: PMC6962202 DOI: 10.1038/s41522-019-0112-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
Biofilm formation is a strategy of many bacterial species to adapt to a variety of stresses and has become a part of infections, contaminations, or beneficial interactions. In this study, we demonstrate that profound physiological changes permit Bacillus cereus to switch from a floating to a sessile lifestyle, to undergo further maturation of the biofilm and to differentiate into the offensive or defensive features. We report that floating and biofilm cells are populations that differentiate metabolically, with members of each subpopulation developing different branches of certain metabolic pathways. Secondly, biofilm populations rearrange nucleotides, sugars, amino acids, and energy metabolism. Thirdly, this metabolic rearrangement coexists with: the synthesis of the extracellular matrix, sporulation, reinforcement of the cell wall, activation of the ROS detoxification machinery and production of secondary metabolites. This strategy contributes to defend biofilm cells from competitors. However, floating cells maintain a fermentative metabolic status that ensures a higher aggressiveness against hosts, evidenced by the production of toxins. The maintenance of the two distinct subpopulations is an effective strategy to face different environmental conditions found in the life styles of B. cereus.
Collapse
|
36
|
Falcón García C, Kretschmer M, Lozano-Andrade CN, Schönleitner M, Dragoŝ A, Kovács ÁT, Lieleg O. Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms. NPJ Biofilms Microbiomes 2020; 6:1. [PMID: 31908831 PMCID: PMC6941983 DOI: 10.1038/s41522-019-0111-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023] Open
Abstract
Surface superhydrophobicity makes bacterial biofilms very difficult to fight, and it is a combination of their matrix composition and complex surface roughness which synergistically protects these biomaterials from wetting. Although trying to eradicate biofilms with aqueous (antibiotic) solutions is common practice, this can be a futile approach if the biofilms have superhydrophobic properties. To date, there are not many options available to reduce the liquid repellency of biofilms or to prevent this material property from developing. Here, we present a solution to this challenge. We demonstrate how the addition of metal ions such as copper and zinc during or after biofilm formation can render the surface of otherwise superhydrophobic B. subtilis NCIB 3610 biofilms completely wettable. As a result of this procedure, these smoother, hydrophilic biofilms are more susceptible to aqueous antibiotics solutions. Our strategy proposes a scalable and widely applicable step in a multi-faceted approach to eradicate biofilms.
Collapse
Affiliation(s)
- Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Martin Kretschmer
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Carlos N. Lozano-Andrade
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Markus Schönleitner
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Anna Dragoŝ
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| |
Collapse
|
37
|
Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP. Regulating, Measuring, and Modeling the Viscoelasticity of Bacterial Biofilms. J Bacteriol 2019; 201:e00101-19. [PMID: 31182499 PMCID: PMC6707926 DOI: 10.1128/jb.00101-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biofilms occur in a broad range of environments under heterogeneous physicochemical conditions, such as in bioremediation plants, on surfaces of biomedical implants, and in the lungs of cystic fibrosis patients. In these scenarios, biofilms are subjected to shear forces, but the mechanical integrity of these aggregates often prevents their disruption or dispersal. Biofilms' physical robustness is the result of the multiple biopolymers secreted by constituent microbial cells which are also responsible for numerous biological functions. A better understanding of the role of these biopolymers and their response to dynamic forces is therefore crucial for understanding the interplay between biofilm structure and function. In this paper, we review experimental techniques in rheology, which help quantify the viscoelasticity of biofilms, and modeling approaches from soft matter physics that can assist our understanding of the rheological properties. We describe how these methods could be combined with synthetic biology approaches to control and investigate the effects of secreted polymers on the physical properties of biofilms. We argue that without an integrated approach of the three disciplines, the links between genetics, composition, and interaction of matrix biopolymers and the viscoelastic properties of biofilms will be much harder to uncover.
Collapse
Affiliation(s)
- Samuel G V Charlton
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A White
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Saikat Jana
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - J Grant Burgess
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anil Wipat
- Interdisciplinary Computing & Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
38
|
Abstract
Understanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition is critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance to modulate their local environment to maximize colonization, and therefore survival. Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a nonexpanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe3+ from the growth medium in a nonenzymatic reaction. Utilizing mathematical modeling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated with pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion by neighboring communities through the generation of an “iron-free” zone, thereby addressing the paradox of pulcherriminic acid production by B. subtilis.
Collapse
|
39
|
Abstract
The cytoplasm of bacterial cells is a highly crowded cellular compartment that possesses considerable osmotic potential. As a result, and owing to the semipermeable nature of the cytoplasmic membrane and the semielastic properties of the cell wall, osmotically driven water influx will generate turgor, a hydrostatic pressure considered critical for growth and viability. Both increases and decreases in the external osmolarity inevitably trigger water fluxes across the cytoplasmic membrane, thus impinging on the degree of cellular hydration, molecular crowding, magnitude of turgor, and cellular integrity. Here, we assess mechanisms that permit the perception of osmotic stress by bacterial cells and provide an overview of the systems that allow them to genetically and physiologically cope with this ubiquitous environmental cue. We highlight recent developments implicating the secondary messenger c-di-AMP in cellular adjustment to osmotic stress and the role of osmotic forces in the life of bacteria-assembled in biofilms.
Collapse
Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology; and Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany;
| |
Collapse
|
40
|
Candela T, Fagerlund A, Buisson C, Gilois N, Kolstø AB, Økstad OA, Aymerich S, Nielsen-Leroux C, Lereclus D, Gohar M. CalY is a major virulence factor and a biofilm matrix protein. Mol Microbiol 2019; 111:1416-1429. [PMID: 30548239 DOI: 10.1111/mmi.14184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 12/16/2022]
Abstract
The extracellular biofilm matrix often contains a network of amyloid fibers which, in the human opportunistic pathogen Bacillus cereus, includes the two homologous proteins TasA and CalY. We show here, in the closely related entomopathogenic species Bacillus thuringiensis, that CalY also displays a second function. In the early stationary phase of planktonic cultures, CalY was located at the bacterial cell-surface, as shown by immunodetection. Deletion of calY revealed that this protein plays a major role in adhesion to HeLa epithelial cells, to the insect Galleria mellonella hemocytes and in the bacterial virulence against larvae of this insect, suggesting that CalY is a cell-surface adhesin. In mid-stationary phase and in biofilms, the location of CalY shifted from the cell surface to the extracellular medium, where it was found as fibers. The transcription study and the deletion of sipW suggested that CalY change of location is due to a delayed activity of the SipW signal peptidase. Using purified CalY, we found that the protein polymerization occurred only in the presence of cell-surface components. CalY is, therefore, a bifunctional protein, which switches from a cell-surface adhesin activity in early stationary phase, to the production of fibers in mid-stationary phase and in biofilms.
Collapse
Affiliation(s)
- Thomas Candela
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Annette Fagerlund
- Laboratory for Microbial Dynamics, School of Pharmacy and Centre for Integrative Microbial Evolution, University of Oslo, Oslo, Norway
| | - Christophe Buisson
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Nathalie Gilois
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics, School of Pharmacy and Centre for Integrative Microbial Evolution, University of Oslo, Oslo, Norway
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics, School of Pharmacy and Centre for Integrative Microbial Evolution, University of Oslo, Oslo, Norway
| | - Stéphane Aymerich
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | | | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Michel Gohar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| |
Collapse
|
41
|
Zheng C, Guo S, Tennant WG, Pradhan PK, Black KA, Dos Santos PC. The Thioredoxin System Reduces Protein Persulfide Intermediates Formed during the Synthesis of Thio-Cofactors in Bacillus subtilis. Biochemistry 2019; 58:1892-1904. [PMID: 30855939 DOI: 10.1021/acs.biochem.9b00045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthesis of Fe-S clusters and other thio-cofactors requires the participation of redox agents. A shared feature in these pathways is the formation of transient protein persulfides, which are susceptible to reduction by artificial reducing agents commonly used in reactions in vitro. These agents modulate the reactivity and catalytic efficiency of biosynthetic reactions and, in some cases, skew the enzymes' kinetic behavior, bypassing sulfur acceptors known to be critical for the functionality of these pathways in vivo. Here, we provide kinetic evidence for the selective reactivity of the Bacillus subtilis Trx (thioredoxin) system toward protein-bound persulfide intermediates. Our results demonstrate that the redox flux of the Trx system modulates the rate of sulfide production in cysteine desulfurase assays. Likewise, the activity of the Trx system is dependent on the rate of persulfide formation, suggesting the occurrence of coupled reaction schemes between both enzymatic systems in vitro. Inactivation of TrxA (thioredoxin) or TrxR (thioredoxin reductase) impairs the activity of Fe-S enzymes in B. subtilis, indicating the involvement of the Trx system in Fe-S cluster metabolism. Surprisingly, biochemical characterization of TrxA reveals that this enzyme is able to coordinate Fe-S species, resulting in the loss of its reductase activity. The inactivation of TrxA through the coordination of a labile cluster, combined with its proposed role as a physiological reducing agent in sulfur transfer pathways, suggests a model for redox regulation. These findings provide a potential link between redox regulation and Fe-S metabolism.
Collapse
Affiliation(s)
- Chenkang Zheng
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Selina Guo
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - William G Tennant
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Pradyumna K Pradhan
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Chemistry and Biochemistry , The University of North Carolina at Greensboro , Greensboro , North Carolina 27412 , United States
| | - Katherine A Black
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States.,Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Patricia C Dos Santos
- Department of Chemistry , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| |
Collapse
|
42
|
Kovács ÁT, Dragoš A. Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles. J Mol Biol 2019; 431:4749-4759. [PMID: 30769118 DOI: 10.1016/j.jmb.2019.02.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/21/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022]
Abstract
For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis, the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid-air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of "ON" cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the "generalist" wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature.
Collapse
Affiliation(s)
- Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| |
Collapse
|
43
|
Klotz M, Kretschmer M, Goetz A, Ezendam S, Lieleg O, Opitz M. Importance of the biofilm matrix for the erosion stability of Bacillus subtilis NCIB 3610 biofilms. RSC Adv 2019; 9:11521-11529. [PMID: 35520264 PMCID: PMC9063333 DOI: 10.1039/c9ra01955c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022] Open
Abstract
Erosion of bacterial biofilms is dependent on the composition of the biofilm matrix and the surrounding chemical environment.
Collapse
Affiliation(s)
- M. Klotz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - M. Kretschmer
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - A. Goetz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - S. Ezendam
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - O. Lieleg
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - M. Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| |
Collapse
|
44
|
Falcón García C, Stangl F, Götz A, Zhao W, Sieber SA, Opitz M, Lieleg O. Topographical alterations render bacterial biofilms susceptible to chemical and mechanical stress. Biomater Sci 2019; 7:220-232. [DOI: 10.1039/c8bm00987b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Treatment with concentrated ethanol, saline or glucose solutions smoothens biofilm surface topography and initially superhydrophobic/omniphobic biofilms are rendered hydrophilic.
Collapse
Affiliation(s)
- Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technical University of Munich
- 85748 Garching
- Germany
| | - Felix Stangl
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technical University of Munich
- 85748 Garching
- Germany
| | - Alexandra Götz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - Weining Zhao
- Department of Chemistry
- Chair for Organic Chemistry II
- Technical University of Munich
- 85748 Garching
- Germany
| | - Stephan A. Sieber
- Department of Chemistry
- Chair for Organic Chemistry II
- Technical University of Munich
- 85748 Garching
- Germany
| | - Madeleine Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering
- Technical University of Munich
- 85748 Garching
- Germany
| |
Collapse
|
45
|
Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nat Chem Biol 2018; 15:34-41. [PMID: 30510190 DOI: 10.1038/s41589-018-0169-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.
Collapse
|
46
|
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: 29] [Impact Index Per Article: 4.1] [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.
Collapse
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
| |
Collapse
|
47
|
Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT. Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 2018; 93:4604779. [PMID: 29126191 DOI: 10.1093/femsec/fix155] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.
Collapse
Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Nivedha Lakshmanan
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Balázs Horváth
- Seqomics Biotechnology Ltd, Vállalkozók útja 7, Mórahalom 6782, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| |
Collapse
|
48
|
Collapse of genetic division of labour and evolution of autonomy in pellicle biofilms. Nat Microbiol 2018; 3:1451-1460. [PMID: 30297741 DOI: 10.1038/s41564-018-0263-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 09/05/2018] [Indexed: 11/08/2022]
Abstract
Closely related microorganisms often cooperate, but the prevalence and stability of cooperation between different genotypes remain debatable. Here, we track the evolution of pellicle biofilms formed through genetic division of labour and ask whether partially deficient partners can evolve autonomy. Pellicles of Bacillus subtilis rely on an extracellular matrix composed of exopolysaccharide (EPS) and the fibre protein TasA. In monocultures, ∆eps and ∆tasA mutants fail to form pellicles, but, facilitated by cooperation, they succeed in co-culture. Interestingly, cooperation collapses on an evolutionary timescale and ∆tasA gradually outcompetes its partner ∆eps. Pellicle formation can evolve independently from division of labour in ∆eps and ∆tasA monocultures, by selection acting on the residual matrix component, TasA or EPS, respectively. Using a set of interdisciplinary tools, we unravel that the TasA producer (∆eps) evolves via an unconventional but reproducible substitution in TasA that modulates the biochemical properties of the protein. Conversely, the EPS producer (ΔtasA) undergoes genetically variable adaptations, all leading to enhanced EPS secretion and biofilms with different biomechanical properties. Finally, we revisit the collapse of division of labour between Δeps and ΔtasA in light of a strong frequency versus exploitability trade-off that manifested in the solitarily evolving partners. We propose that such trade-off differences may represent an additional barrier to evolution of division of labour between genetically distinct microorganisms.
Collapse
|
49
|
von Bronk B, Götz A, Opitz M. Complex microbial systems across different levels of description. Phys Biol 2018; 15:051002. [PMID: 29757151 DOI: 10.1088/1478-3975/aac473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Complex biological systems offer a variety of interesting phenomena at the different physical scales. With increasing abstraction, details of the microscopic scales can often be extrapolated to average or typical macroscopic properties. However, emergent properties and cross-scale interactions can impede naïve abstractions and necessitate comprehensive investigations of these complex systems. In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2) single cells, (3) populations, and (4) emergent multi-cellular properties. Second, we employ two illustrating examples, microbial competition and biofilm formation, to elucidate how cross-scale interactions and emergent properties enrich the observed multi-cellular behavior in these systems. Finally, we conclude with pointing out the necessity of multi-scale investigations to understand complex biological systems and discuss recent investigations.
Collapse
Affiliation(s)
- Benedikt von Bronk
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, D-80539 Munich, Germany
| | | | | |
Collapse
|
50
|
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: 25] [Impact Index Per Article: 3.1] [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.
Collapse
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.
| |
Collapse
|