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Gallegos-Monterrosa R, Christensen MN, Barchewitz T, Koppenhöfer S, Priyadarshini B, Bálint B, Maróti G, Kempen PJ, Dragoš A, Kovács ÁT. Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis. Commun Biol 2021; 4:468. [PMID: 33850233 PMCID: PMC8044106 DOI: 10.1038/s42003-021-01983-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Mathilde Nordgaard Christensen
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tino Barchewitz
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sonja Koppenhöfer
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.25055.370000 0000 9130 6822Present Address: Department of Biology, Memorial University of Newfoundland, St. John’s, NL Canada
| | - B. Priyadarshini
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Balázs Bálint
- grid.475919.7Seqomics Biotechnology Ltd., Mórahalom, Hungary
| | - Gergely Maróti
- grid.5018.c0000 0001 2149 4407Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Paul J. Kempen
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Dragoš
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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Presence of Calcium Lowers the Expansion of Bacillus subtilis Colony Biofilms. Microorganisms 2017; 5:microorganisms5010007. [PMID: 28212310 PMCID: PMC5374384 DOI: 10.3390/microorganisms5010007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 11/17/2022] Open
Abstract
Robust colony formation by Bacillus subtilis is recognized as one of the sessile, multicellular lifestyles of this bacterium. Numerous pathways and genes are responsible for the architecturally complex colony structure development. Cells in the biofilm colony secrete extracellular polysaccharides (EPS) and protein components (TasA and the hydrophobin BslA) that hold them together and provide a protective hydrophobic shield. Cells also secrete surfactin with antimicrobial as well as surface tension reducing properties that aid cells to colonize the solid surface. Depending on the environmental conditions, these secreted components of the colony biofilm can also promote the flagellum-independent surface spreading of B. subtilis, called sliding. In this study, we emphasize the influence of Ca2+ in the medium on colony expansion of B. subtilis. Interestingly, the availability of Ca2+ has no major impact on the induction of complex colony morphology. However, in the absence of this divalent ion, peripheral cells of the colony expand radially at later stages of development, causing colony size to increase. We demonstrate that the secreted extracellular compounds, EPS, BslA, and surfactin facilitate colony expansion after biofilm maturation. We propose that Ca2+ hinders biofilm colony expansion by modifying the amphiphilic properties of surfactin.
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Kovács ÁT, Eckhardt TH, van Kranenburg R, Kuipers OP. Functional analysis of the ComK protein of Bacillus coagulans. PLoS One 2013; 8:e53471. [PMID: 23301076 PMCID: PMC3536758 DOI: 10.1371/journal.pone.0053471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/29/2012] [Indexed: 11/27/2022] Open
Abstract
The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B.subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis.
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Affiliation(s)
- Ákos T. Kovács
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Tom H. Eckhardt
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | - Oscar P. Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
- * E-mail:
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Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence. Cell 2012; 150:792-802. [DOI: 10.1016/j.cell.2012.06.036] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 03/03/2012] [Accepted: 06/25/2012] [Indexed: 11/23/2022]
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Abstract
Natural competence is the ability of certain microbes to take up exogenous DNA from the environment and integrate it in their genome. Competence development has been described for a variety of bacteria, but has so far not been shown to occur in Bacillus cereus. However, orthologues of most proteins involved in natural DNA uptake in Bacillus subtilis could be identified in B. cereus. Here, we report that B. cereus ATCC14579 can become naturally competent. When expressing the B. subtilis ComK protein using an IPTG-inducible system in B. cereus ATCC14579, cells grown in minimal medium displayed natural competence, as either genomic DNA or plasmid DNA was shown to be taken up by the cells and integrated into the genome or stably maintained respectively. This work proves that a sufficient structural system for DNA uptake exists in B. cereus. Bacillus cereus can be employed as a model system to investigate the mechanism of DNA uptake in related bacteria such as Bacillus anthracis and Bacillus thuringiensis. Moreover, natural competence provides an important tool for biotechnology, as it will allow more efficient transformation of B. cereus and related organisms, e.g. to knockout genes in a high-throughput way.
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Affiliation(s)
- Aleksandra M Mirończuk
- Groningen Biomolecular Sciences and Biotechnology Institute, Department of Genetics, University of Groningen, Kerklaan 30, 9751NN Haren, the Netherlands
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Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits. Cell 2009; 139:512-22. [DOI: 10.1016/j.cell.2009.07.046] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 06/06/2009] [Accepted: 07/21/2009] [Indexed: 11/18/2022]
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van Hijum SAFT, Medema MH, Kuipers OP. Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev 2009; 73:481-509, Table of Contents. [PMID: 19721087 PMCID: PMC2738135 DOI: 10.1128/mmbr.00037-08] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been very innovative in creating intricate mechanisms by which different regulatory signals operate and interact at promoters to drive gene expression. The regulation of target gene expression by transcription factors (TFs) is governed by control logic brought about by the interaction of regulators with TF binding sites (TFBSs) in cis-regulatory regions. A factor that in large part determines the strength of the response of a target to a given TF is motif stringency, the extent to which the TFBS fits the optimal TFBS sequence for a given TF. Advances in high-throughput technologies and computational genomics allow reconstruction of transcriptional regulatory networks in silico. To optimize the prediction of transcriptional regulatory networks, i.e., to separate direct regulation from indirect regulation, a thorough understanding of the control logic underlying the regulation of gene expression is required. This review summarizes the state of the art of the elements that determine the functionality of TFBSs by focusing on the molecular biological mechanisms and evolutionary origins of cis-regulatory regions.
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Affiliation(s)
- Sacha A F T van Hijum
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
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Leisner M, Stingl K, Frey E, Maier B. Stochastic switching to competence. Curr Opin Microbiol 2008; 11:553-9. [PMID: 18955155 DOI: 10.1016/j.mib.2008.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 09/24/2008] [Accepted: 09/28/2008] [Indexed: 11/15/2022]
Abstract
Distinct modes of gene expression enable isogenic populations of bacteria to maintain a diversity of phenotypes and to rapidly adapt to environmental changes. Competence development for DNA transformation in Bacillus subtilis has become a paradigm for a multimodal system which implements a genetic switch through a nonlinear positive feedback of a transcriptional master regulator. Recent advances in quantitative analysis at the single cell level in conjunction with mathematical modeling allowed a molecular level understanding of the switching probability between the noncompetent state and the competent state. It has been discovered that the genetic switching probability may be tuned by controlling noise in the transcription of the master regulator of competence, by timing of its expression, and by rewiring of the control circuit.
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Affiliation(s)
- Madeleine Leisner
- Institut für Allgemeine Zoologie und Genetik, Westfälische Wilhelms Universität, Schlossplatz 5, 48149 Münster, Germany
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