1
|
Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN, Xie J, Jarmusch SA, Wibowo M, Kjeldgaard B, Surabhi S, Xu X, Jautzus T, Phippen CBW, Tyc O, Arentshorst M, Wang Y, Garbeva P, Larsen TO, Ram AFJ, van den Hondel CAM, Maróti G, Kovács ÁT. Enhanced surface colonisation and competition during bacterial adaptation to a fungus. Nat Commun 2024; 15:4486. [PMID: 38802389 PMCID: PMC11130161 DOI: 10.1038/s41467-024-48812-1] [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: 06/05/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.
Collapse
Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Felix Blei
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
| | - Jan W Schwitalla
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jiyu Xie
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Scott A Jarmusch
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Surabhi Surabhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Xinming Xu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Christopher B W Phippen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Olaf Tyc
- Netherlands Institute of Ecology, Wageningen, The Netherlands
- Department of Internal Medicine I, Goethe University Hospital, Frankfurt, Germany
| | - Mark Arentshorst
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Thomas Ostenfeld Larsen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Arthur F J Ram
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark.
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
2
|
Qiao J, Borriss R, Sun K, Zhang R, Chen X, Liu Y, Liu Y. Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review. Microb Cell Fact 2024; 23:100. [PMID: 38566071 PMCID: PMC10988940 DOI: 10.1186/s12934-024-02372-7] [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: 11/16/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Surfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. subtilis group and its closely related species, such as B. subtilis subsp subtilis, B. subtilis subsp spizizenii, B. subtilis subsp inaquosorum, B. atrophaeus, B. amyloliquefaciens, B. velezensis (Steinke mSystems 6: e00057, 2021) It functions as a biosurfactant and signaling molecule and has antibacterial, antiviral, antitumor, and plant disease resistance properties. The Bacillus lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing and pharmaceuticals, but the natural yield of surfactin synthesized by Bacillus is low. This paper reviews the regulatory pathways and mechanisms that affect surfactin synthesis and release, highlighting the regulatory genes involved in the transcription of the srfAA-AD operon. The several ways to enhance surfactin production, such as governing expression of the genes involved in synthesis and regulation of surfactin synthesis and transport, removal of competitive pathways, optimization of media, and fermentation conditions were commented. This review will provide a theoretical platform for the systematic genetic modification of high-yielding strains of surfactin.
Collapse
Affiliation(s)
- Junqing Qiao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Rainer Borriss
- Institute of Biology, Humboldt University Berlin, Berlin, Germany.
| | - Kai Sun
- College of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Xijun Chen
- College of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
| |
Collapse
|
3
|
Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA-mediated Multimerization of DegU and an Upstream Activation Sequence Enhance Flagellar Gene Expression in Bacillus subtilis. J Mol Biol 2024; 436:168419. [PMID: 38141873 DOI: 10.1016/j.jmb.2023.168419] [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: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
The earliest genes in bacterial flagellar assembly are activated by narrowly-conserved proteins called master regulators that often act as heteromeric complexes. A complex of SwrA and the response-regulator transcription factor DegU is thought to form the master flagellar regulator in Bacillus subtilis but how the two proteins co-operate to activate gene expression is poorly-understood. Here we find using ChIP-Seq that SwrA interacts with a subset of DegU binding sites in the chromosome and does so in a DegU-dependent manner. Using this information, we identify a DegU-specific inverted repeat DNA sequence in the Pflache promoter region and show that SwrA synergizes with DegU phosphorylation to increase binding affinity. We further demonstrate that the SwrA/DegU footprint extends from the DegU binding site towards the promoter, likely through SwrA-induced DegU multimerization. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription by disrupting a previously-unrecognized upstream activation sequence (UAS). Thus, the SwrA-DegU heteromeric complex likely enables both remote binding and interaction between the activator and RNA polymerase. Small co-activator proteins like SwrA may allow selective activation of subsets of genes where activator multimerization is needed. Why some promoters require activator multimerization and some require UAS sequences is unknown.
Collapse
Affiliation(s)
- Ayushi Mishra
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Anna C Hughes
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN 47408, USA.
| |
Collapse
|
4
|
Yu C, Qiao J, Ali Q, Jiang Q, Song Y, Zhu L, Gu Q, Borriss R, Dong S, Gao X, Wu H. degQ associated with the degS/degU two-component system regulates biofilm formation, antimicrobial metabolite production, and biocontrol activity in Bacillus velezensis DMW1. MOLECULAR PLANT PATHOLOGY 2023; 24:1510-1521. [PMID: 37731193 PMCID: PMC10632791 DOI: 10.1111/mpp.13389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
The gram-positive bacterium Bacillus velezensis strain DMW1 produces a high level of antimicrobial metabolites that can suppress the growth of phytopathogens. We investigated the mechanism used by degQ and the degS/degU two-component system to regulate the biocontrol characteristics of DMW1. When degQ and degU were deleted, the biofilm formation, cell motility, colonization activities, and antifungal abilities of ΔdegQ and ΔdegU were significantly reduced compared to wild-type DMW1. The expression levels of biofilm-related genes (epsA, epsB, epsC, and tasA) and swarming-related genes (swrA and swrB) were all down-regulated. We also evaluated the impact on secondary metabolites of these two genes. The degQ and degU genes reduced surfactin and macrolactin production and up-regulated the production of fengycin, iturin, bacillaene, and difficidin metabolites. The reverse transcription-quantitative PCR results were consistent with these observations. Electrophoretic mobility shift assay and microscale thermophoresis revealed that DegU can bind to the promoter regions of these six antimicrobial metabolite genes and regulate their synthesis. In conclusion, we provided systematic evidence to demonstrate that the degQ and degU genes are important regulators of multicellular behaviour and antimicrobial metabolic processes in B. velezensis DMW1 and suggested novel amenable strains to be used for the industrial production of antimicrobial metabolites.
Collapse
Affiliation(s)
- Chenjie Yu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Junqing Qiao
- Jiangsu Academy of Agricultural SciencesInstitute of Plant ProtectionNanjingChina
| | - Qurban Ali
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Qifan Jiang
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Yan Song
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Linli Zhu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Qin Gu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Rainer Borriss
- Institut für BiologieHumboldt University BerlinBerlinGermany
| | - Suomeng Dong
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Xuewen Gao
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| | - Huijun Wu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Sanya Institute of Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjingChina
| |
Collapse
|
5
|
Danevčič T, Spacapan M, Dragoš A, Kovács ÁT, Mandic-Mulec I. DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis. Microbiol Spectr 2023; 11:e0090823. [PMID: 37676037 PMCID: PMC10581247 DOI: 10.1128/spectrum.00908-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.
Collapse
Affiliation(s)
- Tjaša Danevčič
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Mihael Spacapan
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Ákos T. Kovács
- Department of Biotechnology and Biomedicine, Bacterial Interactions and Evolution Group, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ines Mandic-Mulec
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| |
Collapse
|
6
|
Paredes A, Iheacho C, Smith AT. Metal Messengers: Communication in the Bacterial World through Transition-Metal-Sensing Two-Component Systems. Biochemistry 2023; 62:2339-2357. [PMID: 37539997 PMCID: PMC10530140 DOI: 10.1021/acs.biochem.3c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Bacteria survive in highly dynamic and complex environments due, in part, to the presence of systems that allow the rapid control of gene expression in the presence of changing environmental stimuli. The crosstalk between intra- and extracellular bacterial environments is often facilitated by two-component signal transduction systems that are typically composed of a transmembrane histidine kinase and a cytosolic response regulator. Sensor histidine kinases and response regulators work in tandem with their modular domains containing highly conserved structural features to control a diverse array of genes that respond to changing environments. Bacterial two-component systems are widespread and play crucial roles in many important processes, such as motility, virulence, chemotaxis, and even transition metal homeostasis. Transition metals are essential for normal prokaryotic physiological processes, and the presence of these metal ions may also influence pathogenic virulence if their levels are appropriately controlled. To do so, bacteria use transition-metal-sensing two-component systems that bind and respond to rapid fluctuations in extracytosolic concentrations of transition metals. This perspective summarizes the structural and metal-binding features of bacterial transition-metal-sensing two-component systems and places a special emphasis on understanding how these systems are used by pathogens to establish infection in host cells and how these systems may be targeted for future therapeutic developments.
Collapse
Affiliation(s)
- Alexander Paredes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Chioma Iheacho
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| |
Collapse
|
7
|
Structural and biochemical analyses of the flagellar expression regulator DegU from Listeria monocytogenes. Sci Rep 2022; 12:10856. [PMID: 35798759 PMCID: PMC9263151 DOI: 10.1038/s41598-022-14459-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/07/2022] [Indexed: 11/24/2022] Open
Abstract
Listeria monocytogenes is a pathogenic bacterium that produces flagella, the locomotory organelles, in a temperature-dependent manner. At 37 °C inside humans, L. monocytogenes employs MogR to repress the expression of flagellar proteins, thereby preventing the production of flagella. However, in the low-temperature environment outside of the host, the antirepressor GmaR inactivates MogR, allowing flagellar formation. Additionally, DegU is necessary for flagellar expression at low temperatures. DegU transcriptionally activates the expression of GmaR and flagellar proteins by binding the operator DNA in the fliN-gmaR promoter as a response regulator of a two-component regulatory system. To determine the DegU-mediated regulation mechanism, we performed structural and biochemical analyses on the recognition of operator DNA by DegU. The DegU-DNA interaction is primarily mediated by a C-terminal DNA-binding domain (DBD) and can be fortified by an N-terminal receiver domain (RD). The DegU DBD adopts a tetrahelical helix-turn-helix structure and assembles into a dimer. The DegU DBD dimer recognizes the operator DNA using a positive patch. Unexpectedly, unlike typical response regulators, DegU interacts with operator DNA in both unphosphorylated and phosphorylated states with similar binding affinities. Therefore, we conclude that DegU is a noncanonical response regulator that is constitutively active irrespective of phosphorylation.
Collapse
|
8
|
Kawakami M, Matsuoka S. Galactolipids from <i>Arabidopsis thaliana</i> can replace the function of gluco lipids in <i>Bacillus subtilis</i>. J GEN APPL MICROBIOL 2022; 68:54-61. [DOI: 10.2323/jgam.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Manami Kawakami
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| | - Satoshi Matsuoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University
| |
Collapse
|
9
|
Matsuoka S, Shimizu Y, Nobe K, Matsumoto K, Asai K, Hara H. Glucolipids and lipoteichoic acids affect the activity of SigI, an alternative sigma factor, and WalKR, an essential two-component system, in Bacillus subtilis. Genes Cells 2021; 27:77-92. [PMID: 34910349 DOI: 10.1111/gtc.12912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
In a Bacillus subtilis ugtP mutant lacking glucolipids, SigI was activated in the log phase, and the activation of SigI in the mutant was suppressed by the expression of native ugtP. By contrast, SigI was inhibited in a yfnI mutant lacking one of the lipoteichoic acid (LTA) synthase genes, and the inhibition was suppressed by the expression of yfnI. A series of mutation analyses of the sigI promoter revealed that the two WalR binding sites were involved in the increase of PsigI -lacZ activity in the ugtP mutant and decrease of the lacZ activity in the yfnI mutant. Transcription from the SigI recognition sequence was enhanced in the ugtP mutant, whereas yfnI disruption inhibited the transcription from the SigA recognition sequence in the sigI promoter. We found that not only SigI but also WalKR, the essential two-component system, was activated in the ugtP mutant and inhibited in the yfnI mutant. The walK mutants with activated WalR exhibited abnormal morphology, but this phenotype was suppressed by the addition of MgSO4 . We conclude that glucolipids and LTA are key compounds in the maintenance of normal cell surface structure in B. subtilis.
Collapse
Affiliation(s)
- Satoshi Matsuoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yoko Shimizu
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kaori Nobe
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kouji Matsumoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kei Asai
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan.,Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiroshi Hara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| |
Collapse
|
10
|
Xu K, Tong Y, Li Y, Tao J, Rao S, Li J, Zhou J, Liu S. Efficient, Flexible Autoinduction Expression Systems with Broad Initiation in Bacillus subtilis. ACS Synth Biol 2021; 10:3084-3093. [PMID: 34699187 DOI: 10.1021/acssynbio.1c00369] [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] [Indexed: 01/15/2023]
Abstract
Low expression levels and inflexible induction initiation have been the main obstacles to produce proteins using bacterial quorum sensing (QS). The typical QS system in Bacillus subtilis, ComQXPA, activates the promoter PsrfA using ComX and ComA as an auto-inducer and a promoter activator, respectively. Here, we developed a series of flexible autoinduction expression systems in B. subtilis WB600 based on ComQXPA using a super-folder green fluorescent protein as the reporter. The -35 region of PsrfA was replaced with corresponding conserved sequences of σA-dependent promoters, yielding P1 with 85% enhanced strength. We then applied a semi-rational design within the spacer between the -35 and -15 regions of P1 to generate the QS promoter PS1E, which generated 8.22-fold more expression than PsrfA. Based on PS1E, we finally obtained three types of autoinduction expression systems with initiation ranging from 1.5-9.5 h by optimizing the combination of the promoters for ComX and ComA. The yield of Bacillus deramificans pullulanase generated using autoinduction expression systems in B. subtilis reached 80.2 U/mL, which was 36% more than that of the most powerful constitutive promoter P566. Flexible autoinduction expression systems with diverse dynamic features have considerable potential for improving protein expression and metabolite production in B. subtilis.
Collapse
Affiliation(s)
- Kuidong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yi Tong
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co. Ltd, Changchun 130033, China
| | - Yi Li
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co. Ltd, Changchun 130033, China
| | - Jin Tao
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemical Co. Ltd, Changchun 130033, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 214122 Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
11
|
Ermoli F, Bontà V, Vitali G, Calvio C. SwrA as global modulator of the two-component system DegSU in Bacillus subtilis. Res Microbiol 2021; 172:103877. [PMID: 34487843 DOI: 10.1016/j.resmic.2021.103877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/28/2022]
Abstract
The two-component system DegSU of Bacillus subtilis controls more than one hundred genes involved in several different cellular behaviours. Over the last four decades, the degU32Hy allele, supposedly encoding a constitutively active mutant of the response regulator DegU, was exploited to define the impact of this system on cell physiology. Those studies concluded that phosphorylated DegU (DegU∼P) induced degradative enzyme expression while repressing flagellar motility and competence. Recent experiments, however, demonstrated that flagella expression is enhanced by DegU∼P if SwrA, a protein only encoded by wild strains, is present. Yet, to promote motility, SwrA must interact with DegU∼P produced by a wild-type degU allele, as it cannot correctly cooperate with the mutant DegU32Hy protein. In this work, the impact of DegSU was reanalysed in the presence or absence of SwrA employing a DegS kinase mutant, degS200Hy, to force the activation of the TCS. Our results demonstrate that the role of SwrA in B. subtilis physiology is wider than expected and affects several other DegSU targets. SwrA reduces subtilisin, cellulases and xylanases production while, besides motility, it also positively modulates competence for DNA uptake, remarkably relieving the inhibition caused by DegU∼P alone and restoring transformability in degS200Hy strains.
Collapse
Affiliation(s)
- Francesca Ermoli
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Valeria Bontà
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Giulia Vitali
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Cinzia Calvio
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| |
Collapse
|
12
|
Luo C, Liu J, Bilal M, Liu X, Wang X, Dong F, Liu Y, Zang S, Yin X, Yang X, Zhu T, Zhang S, Zhang W, Li B. Extracellular lipopeptide bacillomycin L regulates serial expression of genes for modulating multicellular behavior in Bacillus velezensis Bs916. Appl Microbiol Biotechnol 2021; 105:6853-6870. [PMID: 34477941 DOI: 10.1007/s00253-021-11524-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
In wild strains of Bacillus, a handful of extracellular natural products act as signals that can regulate multicellular behavior, but relatively little is known about molecular mechanisms' detail. We proposed a previously unreported molecular mechanism for triggering multicellularity in B. velezensis Bs916 by an endogenous cyclic lipopeptide, bacillomycin L. The genome-wide effect on gene expression was caused by the disruption of bacillomycin L gene cluster, and 100 µg/mL bacillomycin L was revealed by quantitative transcriptomics. A total of 878 differentially expressed genes among Bs916, Δbl, and Δbl + 100BL were identified and grouped into 9 functional categories. The transcription levels of 40 candidate genes were further evaluated by RT-qPCR analysis. The expression of eight candidate genes regulated by bacillomycin L in a dose-dependent manner was revealed by LacZ fusion experiment. Although the addition of bacillomycin L could not completely restore the expression levels of the differentially regulated genes in △bl, our results strongly suggest that bacillomycin L acts as a tuning signal of swarming motility and complex biofilm formation by indirectly regulating the expression levels of some two-component systems (TCSs) connector genes, particularly including several Raps that potentially regulate the phosphorylation levels of three major regulators ComA, DegU, and Spo0A.Key points• Proposed model for bacillomycin L regulation in B. velezensis Bs916.• Bacillomycin L can act as an extracellular signal to regulate the phosphorylation levels of three major regulators, ComA, DegU, and Spo0A and control the multicellular processes of vegetative growth, competent, motility, matrix production, sporulation, and autolysis.
Collapse
Affiliation(s)
- Chuping Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Jiachen Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Muhammad Bilal
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xuehui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaohua Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Fei Dong
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Yuan Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China.,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shanshan Zang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiulian Yin
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xueting Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tao Zhu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Shuangyu Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Weifeng Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Bin Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| |
Collapse
|
13
|
Kobayashi K. Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms. PLoS Genet 2021; 17:e1009682. [PMID: 34280190 PMCID: PMC8321402 DOI: 10.1371/journal.pgen.1009682] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 07/29/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
Biofilms are multispecies communities, in which bacteria constantly compete with one another for resources and niches. Bacteria produce many antibiotics and toxins for competition. However, since biofilm cells exhibit increased tolerance to antimicrobials, their roles in biofilms remain controversial. Here, we showed that Bacillus subtilis produces multiple diverse polymorphic toxins, called LXG toxins, that contain N-terminal LXG delivery domains and diverse C-terminal toxin domains. Each B. subtilis strain possesses a distinct set of LXG toxin–antitoxin genes, the number and variation of which is sufficient to distinguish each strain. The B. subtilis strain NCIB3610 possesses six LXG toxin–antitoxin operons on its chromosome, and five of the toxins functioned as DNase. In competition assays, deletion mutants of any of the six LXG toxin–antitoxin operons were outcompeted by the wild-type strain. This phenotype was suppressed when the antitoxins were ectopically expressed in the deletion mutants. The fitness defect of the mutants was only observed in solid media that supported biofilm formation. Biofilm matrix polymers, exopolysaccharides and TasA protein polymers were required for LXG toxin function. These results indicate that LXG toxin-antitoxin systems specifically mediate intercellular competition between B. subtilis strains in biofilms. Mutual antagonism between some LXG toxin producers drove the spatial segregation of two strains in a biofilm, indicating that LXG toxins not only mediate competition in biofilms, but may also help to avoid warfare between strains in biofilms. LXG toxins from strain NCIB3610 were effective against some natural isolates, and thus LXG toxin–antitoxin systems have ecological impact. B. subtilis possesses another polymorphic toxin, WapA. WapA had toxic effects under planktonic growth conditions but not under biofilm conditions because exopolysaccharides and TasA protein polymers inhibited WapA function. These results indicate that B. subtilis uses two types of polymorphic toxins for competition, depending on the growth mode. Biofilms are surface-associated multispecies communities, in which bacteria are protected by self-produced extracellular polymeric substances. In biofilms, bacteria constantly engage in intra- and interspecies competition. To minimize exploitation by competitors, bacteria produce a variety of antibiotics and toxins for competition. However, since biofilm cells exhibit increased tolerance to antimicrobials, the function of antibiotics and toxins in biofilms remains controversial. Therefore, the mechanisms underlying bacterial competition in biofilms remain to be investigated. We found that the soil bacterium B. subtilis produces polymorphic toxins, termed LXG toxins. LXG toxins are highly diversified among B. subtilis strains, and each B. subtilis strain possesses three to nine different LXG toxins. LXG toxins specifically mediate intraspecies competition in biofilms. Competition between some LXG toxin producers resulted in the spatial segregation of strains in biofilms, indicating that LXG toxins not only mediate competition, but also help to minimize warfare in biofilms. LXG toxins were effective against natural isolates of B. subtilis, suggesting that LXG toxin–antitoxin systems have ecological impact. Our results provide new insights into how bacteria survive competition in biofilms.
Collapse
Affiliation(s)
- Kazuo Kobayashi
- Division of Biological Science, Department of Science and Technology, Nara Institute of Science & Technology, Ikoma, Nara, Japan
- * E-mail:
| |
Collapse
|
14
|
Nordgaard M, Mortensen RMR, Kirk NK, Gallegos‐Monterrosa R, Kovács ÁT. Deletion of Rap-Phr systems in Bacillus subtilis influences in vitro biofilm formation and plant root colonization. Microbiologyopen 2021; 10:e1212. [PMID: 34180604 PMCID: PMC8236291 DOI: 10.1002/mbo3.1212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
Natural isolates of the soil-dwelling bacterium Bacillus subtilis form robust biofilms under laboratory conditions and colonize plant roots. B. subtilis biofilm gene expression displays phenotypic heterogeneity that is influenced by a family of Rap-Phr regulatory systems. Most Rap-Phr systems in B. subtilis have been studied independently, in different genetic backgrounds and under distinct conditions, hampering true comparison of the Rap-Phr systems' impact on bacterial cell differentiation. Here, we investigated each of the 12 Rap-Phr systems of B.subtilis NCIB 3610 for their effect on biofilm formation. By studying single ∆rap-phr mutants, we show that despite redundancy between the cell-cell communication systems, deletion of each of the 12 Rap-Phr systems influences matrix gene expression. These Rap-Phr systems therefore enable fine-tuning of the timing and level of matrix production in response to specific conditions. Furthermore, some of the ∆rap-phr mutants demonstrated altered biofilm formation in vitro and colonization of Arabidopsis thaliana roots, but not necessarily similarly in both processes, indicating that the pathways regulating matrix gene expression and other factors important for biofilm formation may be differently regulated under these distinct conditions.
Collapse
Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Nikolaj Kaae Kirk
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Ákos T. Kovács
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| |
Collapse
|
15
|
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: 15] [Impact Index Per Article: 5.0] [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
|
16
|
Barreto HC, Cordeiro TN, Henriques AO, Gordo I. Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate. Sci Rep 2020; 10:18886. [PMID: 33144634 PMCID: PMC7642357 DOI: 10.1038/s41598-020-76017-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
Most model bacteria have been domesticated in laboratory conditions. Yet, the tempo with which a natural isolate diverges from its ancestral phenotype under domestication to a novel laboratory environment is poorly understood. Such knowledge, however is essential to understanding the rate of evolution, the time scale over which a natural isolate can be propagated without loss of its natural adaptive traits, and the reliability of experimental results across labs. Using experimental evolution, phenotypic assays, and whole-genome sequencing, we show that within a week of propagation in a common laboratory environment, a natural isolate of Bacillus subtilis acquires mutations that cause changes in a multitude of traits. A single adaptive mutational step in the gene coding for the transcriptional regulator DegU impairs a DegU-dependent positive autoregulatory loop and leads to loss of robust biofilm architecture, impaired swarming motility, reduced secretion of exoproteases, and to changes in the dynamics of sporulation across environments. Importantly, domestication also resulted in improved survival when the bacteria face pressure from cells of the innate immune system. These results show that degU is a target for mutations during domestication and underscores the importance of performing careful and extremely short-term propagations of natural isolates to conserve the traits encoded in their original genomes.
Collapse
Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
| |
Collapse
|
17
|
Mechanisms for Induction of Microbial Extracellular Proteases in Response to Exterior Proteins. Appl Environ Microbiol 2020; 86:AEM.01036-20. [PMID: 32709731 DOI: 10.1128/aem.01036-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteins are a main organic nitrogen source for microorganisms. Many heterotrophic microorganisms secrete extracellular proteases (ex-proteases) to efficiently decompose proteins into oligopeptides and amino acids when exterior proteins are required for growth. These ex-proteases not only play important roles in microbial nutrient acquisition or host infection but also contribute greatly to the global recycling of carbon and nitrogen. Moreover, may microbial ex-proteases have important applications in industrial, medical, and biotechnological areas. Therefore, uncovering the mechanisms by which microorganisms initiate the expression of ex-protease genes in response to exterior proteins is of great significance. In this review, the progress made in understanding the induction mechanisms of microbial ex-proteases in response to exterior proteins is summarized, with a focus on the inducer molecules, membrane sensors, and downstream pathways. Problems to be solved for better understanding of the induction mechanisms of microbial ex-proteases are also discussed.
Collapse
|
18
|
Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
Collapse
|
19
|
Špacapan M, Danevčič T, Štefanic P, Porter M, Stanley-Wall NR, Mandic-Mulec I. The ComX Quorum Sensing Peptide of Bacillus subtilis Affects Biofilm Formation Negatively and Sporulation Positively. Microorganisms 2020; 8:E1131. [PMID: 32727033 PMCID: PMC7463575 DOI: 10.3390/microorganisms8081131] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023] Open
Abstract
Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of Bacillus subtilis as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells. We confirm that ComX positively affects the transcriptional activity of the PepsA promoter, which controls the synthesis of the major matrix polysaccharide. In contrast, ComX negatively controls the PtapA promoter, which drives the production of TasA, a fibrous matrix protein. Overall, the biomass of the mutant biofilm lacking ComX accumulates more monosaccharide and protein content than the wild type. We conclude that this QS phenotype might be due to extended investment into growth rather than spore development. Consistent with this, the ComX deficient mutant shows a delayed activation of the pre-spore specific promoter, PspoIIQ, and a delayed, more synchronous commitment to sporulation. We conclude that ComX mediated early commitment to sporulation of the wild type slows down biofilm formation and modulates the coexistence of multiple biological states during the early stages of biofilm development.
Collapse
Affiliation(s)
- Mihael Špacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Polonca Štefanic
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| |
Collapse
|
20
|
Inhibition of nattokinase against the production of poly (γ-glutamic Acid) in Bacillus subtilis natto. Biotechnol Lett 2020; 42:2285-2291. [PMID: 32596743 DOI: 10.1007/s10529-020-02941-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/09/2020] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To study the effect of nattokinse (NK) on the synthesis of poly(γ-glutamic acid) (γ-PGA) in Bacillus subtilis natto. RESULTS γ-PGA yield significantly decreased as NK was added in the original medium. With the increment of NK dosage, the yield decreased increasingly, but biomass increased instead of decreasing. The fact that cell density triggers the synthesis of γ-PGA is a controversial issue. γ-PGA yield and biomass closely correlate with addition time of NK. The later the addition of NK, the more γ-PGA yield decreased but the more biomass increased. It is concluded that cell hunger is a key factor to trigger the transmission of the cell density signal, and NK may inhibit γ-PGA synthesis by alleviating cell hunger. Besides, NK may reduce γ-PGA yield by degrading extracellular γ-PGA molecules. The study of adding L-glutamate of 0-20 g/L to the original medium showed that low concentration of L-glutamate (less than 5 g/L) could promote the synthesis of NK and γ-PGA, and thus NK may inhibit γ-PGA synthesis through strengthening substrate competition. CONCLUSIONS NK mainly inhibits γ-PGA synthesis in Bacillus subtilis natto through alleviating cell starvation and strengthening substrate competition, and reduces γ-PGA yield through degrading extracellular γ-PGA molecules.
Collapse
|
21
|
Rajeev L, Garber ME, Mukhopadhyay A. Tools to map target genes of bacterial two-component system response regulators. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:267-276. [PMID: 32212247 PMCID: PMC7318608 DOI: 10.1111/1758-2229.12838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 05/05/2023]
Abstract
Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.
Collapse
Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Megan E. Garber
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| |
Collapse
|
22
|
Multiple and Overlapping Functions of Quorum Sensing Proteins for Cell Specialization in Bacillus Species. J Bacteriol 2020; 202:JB.00721-19. [PMID: 32071096 DOI: 10.1128/jb.00721-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In bacterial populations, quorum sensing (QS) systems participate in the regulation of specialization processes and regulate collective behaviors that mediate interactions and allow survival of the species. In Gram-positive bacteria, QS systems of the RRNPP family (Rgg, Rap, NprR, PlcR, and PrgX) consist of intracellular receptors and their cognate signaling peptides. Two of these receptors, Rap and NprR, have regained attention in Bacillus subtilis and the Bacillus cereus group. Some Rap proteins, such as RapH and Rap60, are multifunctional and/or redundant in function, linking the specialization processes of sporulation and competence, as well as global expression changes in the transition phase in B. subtilis NprR, an evolutionary intermediate between Rap and RRNPP transcriptional activators, is a bifunctional regulator that modulates sporulation initiation and activates nutrient scavenging genes. In this review, we discuss how these receptors switch between functions and connect distinct signaling pathways. Based on structural evidence, we propose that RapH and Rap60 should be considered moonlighting proteins. Additionally, we analyze an evolutionary and ecological perspective to understand the multifunctionality and functional redundancy of these regulators in both Bacillus spp. and non-Bacillus Firmicutes Understanding the mechanistic, structural, ecological, and evolutionary basis for the multifunctionality and redundancy of these QS systems is a key step for achieving the development of innovative technologies for health and agriculture.
Collapse
|
23
|
Hirooka K, Shioda S, Okada M. Identification of critical residues for the catalytic activity of ComQ, a Bacillus prenylation enzyme for quorum sensing, by using a simple bioassay system. Biosci Biotechnol Biochem 2020; 84:347-357. [DOI: 10.1080/09168451.2019.1685371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
Bacillus ComQ participates in the biosynthesis of a quorum-sensing signaling molecule (ComX pheromone) through catalyzing the prenylation at a Trp residue of the precursor peptide (pre-ComX) with geranyl diphosphate (C10 type) or farnesyl diphosphate (C15 type). We hypothesized that several residues specifically conserved among either type of ComQs are important for their substrate specificities. Using a simple bioassay, we revealed that Phe63, Asn186, and Gly190 in ComQRO-E-2 (C10 type) were nondisplaceable to Ser63, Gly186, and Val190, the corresponding residues in the C15-type ComQ, respectively. A three-dimensional model suggested that the 186th and 190th residues are involved in the pre-ComX binding. In vitro analysis showed that substitution of Phe63 with Ser in ComQRO-E-2 significantly reduced the geranylation activity but substantially enhanced the farnesylation activity, whereas substitution of Ser63 with Phe in ComQ168 (C15 type) reduced the farnesylation activity. Therefore, the 63rd residue was found to be significant for the prenyl-substrate preference.
Abbreviations: GPP: geranyl diphosphate; FPP: farnesyl diphosphate; IPP: isopentenyl diphosphate; GGPP: geranylgeranyl diphosphate; FARM: first aspartate-rich motif; SARM: second aspartate-rich motif; β-Gal: β-galactosidase; TBABG: tryptose blood agar base supplemented with glucose; X-gal: 5-bromo-4-chloro-3-indolyl-β-D-galactoside
Collapse
Affiliation(s)
- Kazutake Hirooka
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Saki Shioda
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Masahiro Okada
- Department of Material and Life Chemistry, Kanagawa University, Yokohama, Japan
| |
Collapse
|
24
|
New Insights into Multistep-Phosphorelay (MSP)/ Two-Component System (TCS) Regulation: Are Plants and Bacteria that Different? PLANTS 2019; 8:plants8120590. [PMID: 31835810 PMCID: PMC6963811 DOI: 10.3390/plants8120590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022]
Abstract
The Arabidopsis multistep-phosphorelay (MSP) is a signaling mechanism based on a phosphorelay that involves three different types of proteins: Histidine kinases, phosphotransfer proteins, and response regulators. Its bacterial equivalent, the two-component system (TCS), is the most predominant device for signal transduction in prokaryotes. The TCS has been extensively studied and is thus generally well-understood. In contrast, the MSP in plants was first described in 1993. Although great advances have been made, MSP is far from being completely comprehended. Focusing on the model organism Arabidopsis thaliana, this review summarized recent studies that have revealed many similarities with bacterial TCSs regarding how TCS/MSP signaling is regulated by protein phosphorylation and dephosphorylation, protein degradation, and dimerization. Thus, comparison with better-understood bacterial systems might be relevant for an improved study of the Arabidopsis MSP.
Collapse
|
25
|
Hong LTT, Hachiya T, Hase S, Shiwa Y, Yoshikawa H, Sakakibara Y, Nguyen SLT, Kimura K. Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene. J Biosci Bioeng 2019; 128:690-696. [PMID: 31272833 DOI: 10.1016/j.jbiosc.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023]
Abstract
Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (ΔdegQ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments including LacZ-fusion assay of γPGA synthetic operon confirmed that the suppressor mutation (yabJS103F) was responsible for the recovery of γPGA production. The yabJ itself was not essential for the γPGA production and the mutant allele enabled γPGA production of the ΔdegQ strain even in the presence of wild type yabJ. Thus, yabJS103F was a dominant positive allele. degU-lacZ fusion gene was hyper-expressed in cells carrying the yabJS103F, but disruption of yabJ did not affect the transcription level of the degU-lacZ. These observations suggested that YabJ acquired a function to stimulate expression of degU by the S103F mutation which is involved in the regulation of γPGA synthesis.
Collapse
Affiliation(s)
- Le Thi Thu Hong
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Tsuyoshi Hachiya
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sumitaka Hase
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Yasubumi Sakakibara
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sy Le Thanh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan.
| |
Collapse
|
26
|
Denham EL, Piersma S, Rinket M, Reilman E, de Goffau MC, van Dijl JM. Differential expression of a prophage-encoded glycocin and its immunity protein suggests a mutualistic strategy of a phage and its host. Sci Rep 2019; 9:2845. [PMID: 30808982 PMCID: PMC6391423 DOI: 10.1038/s41598-019-39169-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/31/2018] [Indexed: 01/12/2023] Open
Abstract
Sublancin 168 is a highly potent and stable antimicrobial peptide secreted by the Gram-positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major competitive growth advantage over a range of other bacteria thriving in the same ecological niches, the soil and plant rhizosphere. B. subtilis protects itself against sublancin by producing the cognate immunity protein SunI. Previous studies have shown that both the sunA gene for sublancin and the sunI immunity gene are encoded by the prophage SPβ. The sunA gene is under control of several transcriptional regulators. Here we describe the mechanisms by which sunA is heterogeneously expressed within a population, while the sunI gene encoding the immunity protein is homogeneously expressed. The key determinants in heterogeneous sunA expression are the transcriptional regulators Spo0A, AbrB and Rok. Interestingly, these regulators have only a minor influence on sunI expression and they have no effect on the homogeneous expression of sunI within a population of growing cells. Altogether, our findings imply that the homogeneous expression of sunI allows even cells that are not producing sublancin to protect themselves at all times from the active sublancin produced at high levels by their isogenic neighbors. This suggests a mutualistic evolutionary strategy entertained by the SPβ prophage and its Bacillus host, ensuring both stable prophage maintenance and a maximal competitive advantage for the host at minimal costs.
Collapse
Affiliation(s)
- Emma L Denham
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Sjouke Piersma
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marleen Rinket
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Ewoud Reilman
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marcus C de Goffau
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Wellcome Sanger Institute, Cambridge, UK
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
| |
Collapse
|
27
|
Wang J, Guo R, Wang W, Ma G, Li S. Insight into the surfactin production of Bacillus velezensis B006 through metabolomics analysis. ACTA ACUST UNITED AC 2018; 45:1033-1044. [PMID: 30203399 DOI: 10.1007/s10295-018-2076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/30/2018] [Indexed: 11/25/2022]
Abstract
Abstract
Bacillus velezensis B006 is a biocontrol agent which functions through effective colonization and surfactin production. To reveal the surfactin-producing mechanism, gas chromatography–mass spectrometry based untargeted metabolomics was performed to compare the metabolite profiles of strain B006 grown in industrial media M3 and M4. Based on the statistical and pathway topology analyses, a total of 31 metabolites with a fold change of less than − 1.0 were screened as the significantly altered metabolites, which distributed in 15 metabolic pathways. Fourteen amino acids involving in the metabolisms of alanine/aspartate/glutamate, glycine/serine/threonine, arginine/proline, glutathione/cysteine/methionine and valine/leucine/isoleucine as well as succinic acid in TCA cycle were identified to be the hub metabolites. Aminoacyl-tRNA biosynthesis, glycerolipid metabolism, and pantothenate/CoA biosynthesis also contributed to surfactin production. To the best of our knowledge, this study is the first to investigate the metabolic pathways of B. velezensis on surfactin production, and will benefit the optimization of commercial fermentation for higher surfactin yield.
Collapse
Affiliation(s)
- Junqiang Wang
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
- Jiangsu Frey Agrochemicals Co. Ltd 222005 Lianyungang Jiangsu China
| | - Rongjun Guo
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
| | - Wenchao Wang
- Shanghai ProfLeader Biotech Co. Ltd 200231 Shanghai China
| | - Guizhen Ma
- 0000 0004 1800 0658 grid.443480.f School of Chemical Engineering Huaihai Institute of Technology 222005 Lianyungang Jiangsu China
| | - Shidong Li
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
| |
Collapse
|
28
|
Gullón S, Mellado RP. The Cellular Mechanisms that Ensure an Efficient Secretion in Streptomyces. Antibiotics (Basel) 2018; 7:E33. [PMID: 29661993 PMCID: PMC6022935 DOI: 10.3390/antibiotics7020033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 01/01/2023] Open
Abstract
Gram-positive soil bacteria included in the genus Streptomyces produce a large variety of secondary metabolites in addition to extracellular hydrolytic enzymes. From the industrial and commercial viewpoints, the S. lividans strain has generated greater interest as a host bacterium for the overproduction of homologous and heterologous hydrolytic enzymes as an industrial application, which has considerably increased scientific interest in the characterization of secretion routes in this bacterium. This review will focus on the secretion machinery in S. lividans.
Collapse
Affiliation(s)
- Sonia Gullón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain.
| | - Rafael P Mellado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain.
| |
Collapse
|
29
|
The C-Terminal Region of Bacillus subtilis SwrA Is Required for Activity and Adaptor-Dependent LonA Proteolysis. J Bacteriol 2018; 200:JB.00659-17. [PMID: 29311275 DOI: 10.1128/jb.00659-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
SwrA is the master activator of flagellar biosynthesis in Bacillus subtilis, and SwrA activity is restricted by regulatory proteolysis in liquid environments. SwrA is proteolyzed by the LonA protease but requires a proteolytic adaptor protein, SmiA. Here, we show that SwrA and SmiA interact directly. To better understand SwrA activity, SwrA was randomly mutagenized and loss-of-function and gain-of-function mutants were localized primarily to the predicted unstructured C-terminal region. The loss-of-function mutations impaired swarming motility and activation from the Pfla-che promoter. The gain-of-function mutations increased protein stability but did not abolish SmiA binding, suggesting that SmiA association was a precursor to, but not sufficient for, LonA-dependent proteolysis. Finally, one allele abolished simultaneously SwrA activity and regulatory proteolysis, suggesting that the two functions may be in steric competition.IMPORTANCE SwrA is the master activator of flagellar biosynthesis in Bacillus subtilis, and its mechanism of activation is poorly understood. Moreover, SwrA levels are restricted by SmiA, the first adaptor protein reported for the Lon family of proteases. Here, we show that the C-terminal region of SwrA is important for both transcriptional activation and regulatory proteolysis. Competition between the two processes at this region may be critical for responding to cell contact with a solid surface and the initiation of swarming motility.
Collapse
|
30
|
Spacapan M, Danevčič T, Mandic-Mulec I. ComX-Induced Exoproteases Degrade ComX in Bacillus subtilis PS-216. Front Microbiol 2018; 9:105. [PMID: 29449835 PMCID: PMC5799266 DOI: 10.3389/fmicb.2018.00105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Gram-positive bacteria use peptides as auto-inducing (AI) signals to regulate the production of extracellular enzymes (e.g., proteases). ComX is an AI peptide, mostly known for its role in the regulation of bacterial competence and surfactant production in Bacillus subtilis. These two traits are regulated accordingly to the bacterial population size, thus classifying ComX as a quorum sensing signal. ComX also indirectly regulates exoprotease production through the intermediate transcriptional regulator DegQ. We here use this peptide-based AI system (the ComQXPA system) as a model to address exoprotease regulation by ComX in biofilms. We also investigate the potential of ComX regulated proteases to degrade the ComX AI peptide. Results indicate that ComX indeed induces the expression of aprE, the gene for the major serine protease subtilisin, and stimulates overall exoprotease production in biofilms of B. subtilis PS-216 and several other B. subtilis soil isolates. We also provide evidence that these exoproteases can degrade ComX. The ComX biological activity decay is reduced in the spent media of floating biofilms with low proteolytic activity found in the comP and degQ mutants. ComX biological activity decay can be restored by the addition of subtilisin to such media. In contrast, inhibition of metalloproteases by EDTA reduces ComX biological activity decay. This suggests that both serine and metalloproteases, which are induced by ComX, are ultimately capable of degrading this signaling peptide. This work brings novel information on regulation of exoproteases in B. subtilis floating biofilms and reveals that these proteolytic enzymes degrade the AI signaling peptide ComX, which is also a major determinant of their expression in biofilms.
Collapse
Affiliation(s)
- Mihael Spacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
31
|
Kleine B, Chattopadhyay A, Polen T, Pinto D, Mascher T, Bott M, Brocker M, Freudl R. The three-component system EsrISR regulates a cell envelope stress response in Corynebacterium glutamicum. Mol Microbiol 2017; 106:719-741. [PMID: 28922502 DOI: 10.1111/mmi.13839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 02/03/2023]
Abstract
When the cell envelope integrity is compromised, bacteria trigger signaling cascades resulting in the production of proteins that counteract these extracytoplasmic stresses. Here, we show that the two-component system EsrSR regulates a cell envelope stress response in the Actinobacterium Corynebacterium glutamicum. The sensor kinase EsrS possesses an amino-terminal phage shock protein C (PspC) domain, a property that sets EsrSR apart from all other two-component systems characterized so far. An integral membrane protein, EsrI, whose gene is divergently transcribed to the esrSR gene locus and which interestingly also possesses a PspC domain, acts as an inhibitor of EsrSR under non-stress conditions. The resulting EsrISR three-component system is activated among others by antibiotics inhibiting the lipid II cycle, such as bacitracin and vancomycin, and it orchestrates a broad regulon including the esrI-esrSR gene locus itself, genes encoding heat shock proteins, ABC transporters, and several putative membrane-associated or secreted proteins of unknown function. Among those, the ABC transporter encoded by cg3322-3320 was shown to be directly involved in bacitracin resistance of C. glutamicum. Since similar esrI-esrSR loci are present in a large number of actinobacterial genomes, EsrISR represents a novel type of stress-responsive system whose components are highly conserved in the phylum Actinobacteria.
Collapse
Affiliation(s)
- Britta Kleine
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Ava Chattopadhyay
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Tino Polen
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Daniela Pinto
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, Dresden D-01217, Germany
| | - Thorsten Mascher
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, Dresden D-01217, Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Melanie Brocker
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Roland Freudl
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| |
Collapse
|
32
|
Tiwari S, Jamal SB, Hassan SS, Carvalho PVSD, Almeida S, Barh D, Ghosh P, Silva A, Castro TLP, Azevedo V. Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview. Front Microbiol 2017; 8:1878. [PMID: 29067003 PMCID: PMC5641358 DOI: 10.3389/fmicb.2017.01878] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
The bacterial communities in a wide range of environmental niches sense and respond to numerous external stimuli for their survival. Primarily, a source they require to follow up this communication is the two-component signal transduction system (TCS), which typically comprises a sensor Histidine kinase for receiving external input signals and a response regulator that conveys a proper change in the bacterial cell physiology. For numerous reasons, TCSs have ascended as convincing targets for antibacterial drug design. Several studies have shown that TCSs are essential for the coordinated expression of virulence factors and, in some cases, for bacterial viability and growth. It has also been reported that the expression of antibiotic resistance determinants may be regulated by some TCSs. In addition, as a mode of signal transduction, phosphorylation of histidine in bacteria differs from normal serine/threonine and tyrosine phosphorylation in higher eukaryotes. Several studies have shown the molecular mechanisms by which TCSs regulate virulence and antibiotic resistance in pathogenic bacteria. In this review, we list some of the characteristics of the bacterial TCSs and their involvement in virulence and antibiotic resistance. Furthermore, this review lists and discusses inhibitors that have been reported to target TCSs in pathogenic bacteria.
Collapse
Affiliation(s)
- Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Syed B. Jamal
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Syed S. Hassan
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Biochemistry Group, Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Paulo V. S. D. Carvalho
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sintia Almeida
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Thiago L. P. Castro
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
33
|
Diethmaier C, Chawla R, Canzoneri A, Kearns DB, Lele PP, Dubnau D. Viscous drag on the flagellum activates Bacillus subtilis entry into the K-state. Mol Microbiol 2017; 106:367-380. [PMID: 28800172 DOI: 10.1111/mmi.13770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2017] [Indexed: 12/23/2022]
Abstract
Bacillus subtilis flagella are not only required for locomotion but also act as sensors that monitor environmental changes. Although how the signal transmission takes place is poorly understood, it has been shown that flagella play an important role in surface sensing by transmitting a mechanical signal to control the DegS-DegU two-component system. Here we report a role for flagella in the regulation of the K-state, which enables transformability and antibiotic tolerance (persistence). Mutations impairing flagellar synthesis are inferred to increase DegU-P, which inhibits the expression of ComK, the master regulator for the K-state, and reduces transformability. Tellingly, both deletion of the flagellin gene and straight filament (hagA233V ) mutations increased DegU phosphorylation despite the fact that both mutants had wild type numbers of basal bodies and the flagellar motors were functional. We propose that higher viscous loads on flagellar motors result in lower DegU-P levels through an unknown signaling mechanism. This flagellar-load based mechanism ensures that cells in the motile subpopulation have a tenfold enhanced likelihood of entering the K-state and taking up DNA from the environment. Further, our results suggest that the developmental states of motility and competence are related and most commonly occur in the same epigenetic cell type.
Collapse
Affiliation(s)
- Christine Diethmaier
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station Texas, TX, USA
| | | | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station Texas, TX, USA
| | - David Dubnau
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| |
Collapse
|
34
|
Habib C, Yu Y, Gozzi K, Ching C, Shemesh M, Chai Y. Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis. PLoS One 2017; 12:e0179761. [PMID: 28617843 PMCID: PMC5472308 DOI: 10.1371/journal.pone.0179761] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022] Open
Abstract
The soil bacterium Bacillus subtilis is often found in association with plants in the rhizosphere. Previously, plant polysaccharides have been shown to stimulate formation of root-associated multicellular communities, or biofilms, in this bacterium, yet the underlying mechanism is not fully understood. A five-gene gan operon (ganSPQAB) in B. subtilis has recently been shown to be involved in utilization of the plant-derived polysaccharide galactan. Despite these findings, molecular details about the regulation of the operon and the role of the operon in biofilm formation remain elusive. In this study, we performed comprehensive genetic analyses on the regulation of the gan operon. We show that this operon is regulated both by a LacI-like transcription repressor (GanR), which directly binds to pairs of inverted DNA repeats in the promoter region of the operon, and by the catabolite control protein A (CcpA). Derepression can be triggered by the presence of the inducer β-1,4-galactobiose, a hydrolysis product of galactan, or in situ when B. subtilis cells are associated with plant roots. In addition to the transcriptional regulation, the encoded ß-galactosidase GanA (by ganA), which hydrolyzes ß-1,4-galactobiose into galactose, is inhibited at the enzymatic level by the catalytic product galactose. Thus, the galactan utilization pathway is under complex regulation involving both positive and negative feedback mechanisms in B. subtilis. We discuss about the biological significance of such complex regulation as well as a hypothesis of biofilm induction by galactan via multiple mechanisms.
Collapse
Affiliation(s)
- Cameron Habib
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Yiyang Yu
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Kevin Gozzi
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Carly Ching
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Moshe Shemesh
- Agricultural Research Organization The Volcani Center, Rishon LeZion, Israel
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, United States of America
- * E-mail:
| |
Collapse
|
35
|
Rodriguez Ayala F, Bauman C, Bartolini M, Saball E, Salvarrey M, Leñini C, Cogliati S, Strauch M, Grau R. Transcriptional regulation of adhesive properties ofBacillus subtilisto extracellular matrix proteins through the fibronectin-binding protein YloA. Mol Microbiol 2017; 104:804-821. [DOI: 10.1111/mmi.13666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Facundo Rodriguez Ayala
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| | - Carlos Bauman
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| | - Marco Bartolini
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| | - Ester Saball
- Departamento de Bioquímica Clínica, Área Inmunología, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Rosario, Argentina
| | - Marcela Salvarrey
- Departamento de Bioquímica Clínica, Área Inmunología, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Rosario, Argentina
| | - Cecilia Leñini
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| | - Sebastián Cogliati
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| | - Mark Strauch
- Biomedical Sciences Department, Dental School; University of Maryland; Baltimore MD USA
| | - Roberto Grau
- Departamento de Microbiología, Área Microbiología Básica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, CONICET - Rosario; Rosario, Argentina
| |
Collapse
|
36
|
Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45. Sci Rep 2017; 7:40976. [PMID: 28112210 PMCID: PMC5256033 DOI: 10.1038/srep40976] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/13/2016] [Indexed: 11/23/2022] Open
Abstract
Natural Bacillus isolates generate limited amounts of surfactin (<10% of their biomass), which functions as an antibiotic or signalling molecule in inter-/intra-specific interactions. However, overproduction of surfactin in Bacillus amyloliquefaciens MT45 was observed at a titre of 2.93 g/l, which is equivalent to half of the maximum biomass. To systemically unravel this efficient biosynthetic process, the genome and transcriptome of this bacterium were compared with those of B. amyloliquefaciens type strain DSM7T. MT45 possesses a smaller genome while containing more unique transporters and resistance-associated genes. Comparative transcriptome analysis revealed notable enrichment of the surfactin synthesis pathway in MT45, including central carbon metabolism and fatty acid biosynthesis to provide sufficient quantities of building precursors. Most importantly, the modular surfactin synthase overexpressed (9 to 49-fold) in MT45 compared to DSM7T suggested efficient surfactin assembly and resulted in the overproduction of surfactin. Furthermore, based on the expression trends observed in the transcriptome, there are multiple potential regulatory genes mediating the expression of surfactin synthase. Thus, the results of the present study provide new insights regarding the synthesis and regulation of surfactin in high-producing strain and enrich the genomic and transcriptomic resources available for B. amyloliquefaciens.
Collapse
|
37
|
Roy EM, Griffith KL. Characterization of a Novel Iron Acquisition Activity That Coordinates the Iron Response with Population Density under Iron-Replete Conditions in Bacillus subtilis. J Bacteriol 2017; 199:e00487-16. [PMID: 27795321 PMCID: PMC5165090 DOI: 10.1128/jb.00487-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/24/2016] [Indexed: 01/10/2023] Open
Abstract
Iron is an essential micronutrient required for the viability of many organisms. Under oxidizing conditions, ferric iron is highly insoluble (∼10-9 to 10-18 M), yet bacteria typically require ∼10-6 M for survival. To overcome this disparity, many bacteria have adopted the use of extracellular iron-chelating siderophores coupled with specific iron-siderophore uptake systems. In the case of Bacillus subtilis, undomesticated strains produce the siderophore bacillibactin. However, many laboratory strains, e.g., JH642, have lost the ability to produce bacillibactin during the process of domestication. In this work, we identified a novel iron acquisition activity from strain JH642 that accumulates in the growth medium and coordinates the iron response with population density. The molecule(s) responsible for this activity was named elemental Fe(II/III) (Efe) acquisition factor because efeUOB (ywbLMN) is required for its activity. Unlike most iron uptake molecules, including siderophores and iron reductases, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur repressor. Restoring bacillibactin production in strain JH642 inhibits the activity of Efe acquisition factor, presumably by sequestering available iron. A similar iron acquisition activity is produced from a mutant of Escherichia coli unable to synthesize the siderophore enterobactin. Given the conservation of efeUOB and its regulation by catecholic siderophores in B. subtilis and E. coli, we speculate that Efe acquisition factor is utilized by many bacteria, serves as an alternative to Fur-mediated iron acquisition systems, and provides cells with biologically available iron that would normally be inaccessible during aerobic growth under iron-replete conditions. IMPORTANCE Iron is an essential micronutrient required for a variety of biological processes, yet ferric iron is highly insoluble during aerobic growth. In this work, we identified a novel iron acquisition activity that coordinates the iron response with population density in laboratory strains of Bacillus subtilis We named the molecule(s) responsible for this activity elemental Fe(II/III) (Efe) acquisition factor after the efeUOB (ywbLMN) operon required for its uptake into cells. Unlike most iron uptake systems, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur, the master regulator of the iron response. We speculate that Efe acquisition factor is highly conserved among bacteria and serves as a backup to Fur-mediated iron acquisition systems.
Collapse
Affiliation(s)
- Emily M Roy
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kevin L Griffith
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| |
Collapse
|
38
|
Fan B, Li YL, Mariappan A, Becker A, Wu XQ, Borriss R. New SigD-regulated genes identified in the rhizobacterium Bacillus amyloliquefaciens FZB42. Biol Open 2016; 5:1776-1783. [PMID: 27797724 PMCID: PMC5200910 DOI: 10.1242/bio.021501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The alternative sigma factor D is known to be involved in at least three biological processes in Bacilli: flagellin synthesis, methyl-accepting chemotaxis and autolysin synthesis. Although many Bacillus genes have been identified as SigD regulon, the list may be not be complete. With microarray-based systemic screening, we found a set of genes downregulated in the sigD knockout mutant of the plant growth-promoting rhizobacterium B. amyloliquefaciens subsp. plantarum FZB42. Eight genes (appA, blsA, dhaS, spoVG, yqgA, RBAM_004640, RBAM_018080 and ytk) were further confirmed by quantitative PCR and/or northern blot to be controlled by SigD at the transcriptional level. These genes are hitherto not reported to be controlled by SigD. Among them, four genes are of unknown function and two genes (RBAM_004640 and RBAM_018080), absent in the model strain B. subtilis 168, are unique to B. amyloliquefaciens stains. The eight genes are involved in sporulation, biofilm formation, metabolite transport and several other functions. These findings extend our knowledge of the regulatory network governed by SigD in Bacillus and will further help to decipher the roles of the genes.
Collapse
Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.,Institut für Biologie/Bakteriengenetik, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany
| | - Yu-Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Aruljothi Mariappan
- Institut für Biologie/Bakteriengenetik, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg an der Lahn, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Rainer Borriss
- Institut für Biologie/Bakteriengenetik, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany .,Fachgebiet Phytomedizin, Albrecht Daniel Thaer Institut für Agrar- und Gartenbauwissenschaften, Lebenswissenschaftliche Fakultät, Humboldt Universität zu Berlin, Berlin 14195, Germany
| |
Collapse
|
39
|
Matsuoka S, Seki T, Matsumoto K, Hara H. Suppression of abnormal morphology and extracytoplasmic function sigma activity in Bacillus subtilis ugtP mutant cells by expression of heterologous glucolipid synthases from Acholeplasma laidlawii. Biosci Biotechnol Biochem 2016; 80:2325-2333. [PMID: 27684739 DOI: 10.1080/09168451.2016.1217147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Glucolipids in Bacillus subtilis are synthesized by UgtP processively transferring glucose from UDP-glucose to diacylglycerol. Here we conclude that the abnormal morphology of a ugtP mutant is caused by lack of glucolipids, since the same morphology arises after abolition of glucolipid production by disruption of pgcA and gtaB, which are involved in UDP-glucose synthesis. Conversely, expression of a monoglucosyldiacylglycerol (MGlcDG) produced by 1,2-diacylglycerol 3-glucosyltransferase from Acholeplasma laidlawii (alMGS) almost completely suppressed the ugtP disruptant phenotype. Activation of extracytoplasmic function (ECF) sigmas (SigM, SigV, and SigX) in the ugtP mutant was decreased by alMGS expression, and was suppressed to low levels by MgSO4 addition. When alMGS and alDGS (A. laidlawii 1,2-diacylglycerol-3-glucose (1-2)-glucosyltransferase producing diglucosyldiacylglycerol (DGlcDG)) were simultaneously expressed, SigX activation was repressed to wild type level. These observations suggest that MGlcDG molecules are required for maintenance of B. subtilis cell shape and regulation of ECF sigmas, and DGlcDG regulates SigX activity.
Collapse
Affiliation(s)
- Satoshi Matsuoka
- a Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering , Saitama University , Saitama , Japan
| | - Takahiro Seki
- a Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering , Saitama University , Saitama , Japan
| | - Kouji Matsumoto
- a Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering , Saitama University , Saitama , Japan
| | - Hiroshi Hara
- a Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering , Saitama University , Saitama , Japan
| |
Collapse
|
40
|
Ogura M. Post-transcriptionally generated cell heterogeneity regulates biofilm formation in Bacillus subtilis. Genes Cells 2016; 21:335-49. [PMID: 26819068 DOI: 10.1111/gtc.12343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 12/22/2015] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis forms biofilms in appropriate environments by producing extracellular matrices. Genes required for matrix formation, for example tapA, are regulated by the SinI/SinR/SlrR system. SinR is the repressor for tapA. SinI and SlrR inhibit DNA-binding of SinR. sinI and sinR constitute two-gene operon, and sinR has its own promoter. During biofilm formation, a portion of the population differentiates into matrix-producing cells. This is thought to be caused by Spo0A-dependent, heterogeneous expression of the PsinI promoter, whereas the PsinR promoter is expressed homogeneously. However, we observed that at its original locus, overall sinI transcription was almost homogeneous, because upstream read-through transcription from PyqHG would overcome expression of PsinI. When we used translational sinI-gfp and sinR-mCherry reporters at their original loci, their fluorescence distribution patterns in the cell population were clearly bimodal. This bimodal expression might be caused by cell-to-cell variations of mRNA stability. This study shows that the post-transcriptionally regulated bimodal expression of SinI and SinR is important for bacterial cell-fate determination.
Collapse
Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, 3-20-1 Orido-Shimizu, Shizuoka, 424-8610, Japan
| |
Collapse
|
41
|
Interplay of CodY and ScoC in the Regulation of Major Extracellular Protease Genes of Bacillus subtilis. J Bacteriol 2016; 198:907-20. [PMID: 26728191 DOI: 10.1128/jb.00894-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED AprE and NprE are two major extracellular proteases in Bacillus subtilis whose expression is directly regulated by several pleiotropic transcriptional factors, including AbrB, DegU, ScoC, and SinR. In cells growing in a rich, complex medium, the aprE and nprE genes are strongly expressed only during the post-exponential growth phase; mutations in genes encoding the known regulators affect the level of post-exponential-phase gene expression but do not permit high-level expression during the exponential growth phase. Using DNA-binding assays and expression and mutational analyses, we have shown that the genes for both exoproteases are also under strong, direct, negative control by the global transcriptional regulator CodY. However, because CodY also represses scoC, little or no derepression of aprE and nprE was seen in a codY null mutant due to overexpression of scoC. Thus, CodY is also an indirect positive regulator of these genes by limiting the synthesis of a second repressor. In addition, in cells growing under conditions that activate CodY, a scoC null mutation had little effect on aprE or nprE expression; full effects of scoC or codY null mutations could be seen only in the absence of the other regulator. However, even the codY scoC double mutant did not show high levels of aprE and nprE gene expression during exponential growth phase in a rich, complex medium. Only a third mutation, in abrB, allowed such expression. Thus, three repressors can contribute to reducing exoprotease gene expression during growth in the presence of excess nutrients. IMPORTANCE The major Bacillus subtilis exoproteases, AprE and NprE, are important metabolic enzymes whose genes are subject to complex regulation by multiple transcription factors. We show here that expression of the aprE and nprE genes is also controlled, both directly and indirectly, by CodY, a global transcriptional regulator that responds to the intracellular pools of amino acids. Direct CodY-mediated repression explains a long-standing puzzle, that is, why exoproteases are not produced when cells are growing exponentially in a medium containing abundant quantities of proteins or their degradation products. Indirect regulation of aprE and nprE through CodY-mediated repression of the scoC gene, encoding another pleiotropic repressor, serves to maintain a significant level of repression of exoprotease genes when CodY loses activity.
Collapse
|
42
|
Rahmer R, Morabbi Heravi K, Altenbuchner J. Construction of a Super-Competent Bacillus subtilis 168 Using the P mtlA -comKS Inducible Cassette. Front Microbiol 2015; 6:1431. [PMID: 26732353 PMCID: PMC4685060 DOI: 10.3389/fmicb.2015.01431] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/01/2015] [Indexed: 11/16/2022] Open
Abstract
Competence is a physiological state that enables Bacillus subtilis 168 to take up and internalize extracellular DNA. In practice, only a small subpopulation of B. subtilis 168 cells becomes competent when they enter stationary phase. In this study, we developed a new transformation method to improve the transformation efficiency of B. subtilis 168, specially in rich media. At first, different competence genes, namely comK, comS, and dprA, were alone or together integrated into the chromosome of B. subtilis 168 under control of mannitol-inducible PmtlA promoter. Overexpression of both comK and comS increased the transformation efficiency of B. subtilis REG19 with plasmid DNA by 6.7-fold compared to the wild type strain 168. This transformation efficiency reached its maximal level after 1.5 h of induction by mannitol. Besides, transformability of the REG19 cells was saturated in the presence of 100 ng dimeric plasmid or 3000 ng chromosomal DNA. Studying the influence of global regulators on the development of competence pointed out that important competence development factors, such as Spo0A, ComQXPA, and DegU, could be removed in REG19. On the other hand, efficient REG19 transformation remained highly dependent on the original copies of comK and comS regardless of the presence of PmtlA-comKS. Finally, novel plasmid-free strategies were used for transformation of REG19 based on Gibson assembly.
Collapse
Affiliation(s)
- Regine Rahmer
- Institut für Industrielle Genetik, Universität Stuttgart Stuttgart, Germany
| | | | - Josef Altenbuchner
- Institut für Industrielle Genetik, Universität Stuttgart Stuttgart, Germany
| |
Collapse
|
43
|
Fukuhara T, Kobayashi K, Kanayama Y, Enomoto SI, Kondo T, Tsunekawa N, Nemoto M, Ogasawara N, Inagaki K, Tamura T. Identification and characterization of the zosA gene involved in copper uptake in Bacillus subtilis 168. Biosci Biotechnol Biochem 2015; 80:600-9. [PMID: 26566138 DOI: 10.1080/09168451.2015.1107462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
DL-Penicillamine, a copper-specific metal chelator, remarkably suppressed the growth of Bacillus subtilis 168 when added to a synthetic medium under Cu(2+) limitation. DNA microarray and screening of 2,602 knockout mutants showed that the zosA gene was de-repressed in the presence of 0.1% dl-penicillamine, and that the zosA mutant was sensitive to dl-penicillamine medium. The zosA mutant delayed the growth under Cu-limitation even without the chelator, and the sensitivity to dl-penicillamine was reversed by induction using 0.3 mM IPTG and the Pspac promoter inserted directly upstream of the zosA gene. Furthermore, the zosA mutant showed elevated tolerance of excessive Cu(2+) but not of excessive Zn(2+) added to LB and synthetic media. Homology modeling of the ZosA protein suggested that the protein can fold itself into essential domains for constituting a metal transporting ATPase. Our study suggests that zosA is a candidate gene involved in copper uptake.
Collapse
Affiliation(s)
- Takahiro Fukuhara
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Kazuo Kobayashi
- b Graduate School of Information Science , Nara Institute of Science & Technology , Ikoma , Japan
| | - Yousuke Kanayama
- c Laboratory of Multiple Molecular Imaging Research , Center for Molecular Imaging Science, RIKEN Kobe Institute , Hyogo , Japan
| | - Shu-ichi Enomoto
- c Laboratory of Multiple Molecular Imaging Research , Center for Molecular Imaging Science, RIKEN Kobe Institute , Hyogo , Japan
| | - Taeko Kondo
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Naoki Tsunekawa
- d Institute of Molecular and Cellular Biosciences , The University of Tokyo , Tokyo , Japan
| | - Michiko Nemoto
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Naotake Ogasawara
- b Graduate School of Information Science , Nara Institute of Science & Technology , Ikoma , Japan
| | - Kenji Inagaki
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan
| | - Takashi Tamura
- a Graduate School of Life and Environmental Science , Okayama University , Okayama , Japan.,e PRESTO, Japan Science and Technology Agency , Tokyo , Japan
| |
Collapse
|
44
|
Kalantari A, Derouiche A, Shi L, Mijakovic I. Serine/threonine/tyrosine phosphorylation regulates DNA binding of bacterial transcriptional regulators. Microbiology (Reading) 2015. [DOI: 10.1099/mic.0.000148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Chaire Agro-Biotechnologies Industrielles, AgroParisTech, Reims, France
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
45
|
van der Stel AX, van Mourik A, Łaniewski P, van Putten JPM, Jagusztyn-Krynicka EK, Wösten MMSM. The Campylobacter jejuni RacRS two-component system activates the glutamate synthesis by directly upregulating γ-glutamyltranspeptidase (GGT). Front Microbiol 2015; 6:567. [PMID: 26097472 PMCID: PMC4456614 DOI: 10.3389/fmicb.2015.00567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/24/2015] [Indexed: 11/15/2022] Open
Abstract
The highly conserved enzyme γ-glutamyltranspeptidase (GGT) plays an important role in metabolism of glutathione and glutamine. Yet, the regulation of ggt transcription in prokaryotes is poorly understood. In the human pathogen Campylobacter jejuni, GGT is important as it contributes to persistent colonization of the gut. Here we show that the GGT activity in C. jejuni is dependent on a functional RacRS (reduced ability to colonize) two-component system. Electrophoretic mobility shift and luciferase reporter assays indicate that the response regulator RacR binds to a promoter region ~80 bp upstream of the ggt transcriptional start site, which contains a recently identified RacR DNA binding consensus sequence. RacR needs to be phosphorylated to activate the transcription of the ggt gene, which is the case under low oxygen conditions in presence of alternative electron acceptors. A functional GGT and RacR are needed to allow C. jejuni to grow optimally on glutamine as sole carbon source under RacR inducing conditions. However, when additional carbon sources are present C. jejuni is capable of utilizing glutamine independently of GGT. RacR is the first prokaryotic transcription factor known to directly up-regulate both the cytoplasmic [glutamine-2-oxoglutarate aminotransferase (GOGAT)] as well as the periplasmic (GGT) production of glutamate.
Collapse
Affiliation(s)
| | - Andries van Mourik
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht Netherlands
| | - Paweł Łaniewski
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw Poland
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht Netherlands
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw Poland
| | - Marc M S M Wösten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht Netherlands
| |
Collapse
|
46
|
Yang Y, Wu HJ, Lin L, Zhu QQ, Borriss R, Gao XW. A plasmid-born Rap-Phr system regulates surfactin production, sporulation and genetic competence in the heterologous host, Bacillus subtilis OKB105. Appl Microbiol Biotechnol 2015; 99:7241-52. [PMID: 25921807 DOI: 10.1007/s00253-015-6604-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/16/2023]
Abstract
According to the change of environment, soil-dwelling Bacillus species differentiate into distinct subpopulations, such as spores and competent cells. Rap-Phr systems have been found to be involved in this differentiation circuit by interacting with major regulatory proteins, such as Spo0A, ComA, and DegU. In this study, we report that the plasmid-born RapQ-PhrQ system found in Bacillus amyloliquefaciens B3 affects three regulatory pathways in the heterologous host Bacillus subtilis. Expression of rapQ in B. subtilis OKB105 strongly suppressed its sporulation efficiency, transformation efficiency, and surfactin production. Co-expression of phrQ or addition of synthesized PhrQ pentapeptide in vitro could compensate for the suppressive effects caused by rapQ. We also found that expression of rapQ decreased the transcriptional level of the sporulation-related gene spoIIE and surfactin synthesis-related gene srfA; meanwhile, the transcriptional levels of these genes could be rescued by co-expression of phrQ and in vitro addition of PhrQ pentapeptide. Electrophoretic mobility shift (EMSA) result also showed that RapQ could bind to ComA without interacting with ComA binding to DNA, and PhrQ pentapeptide antagonized RapQ activity in vitro. These results indicate that this new plasmid-born RapQ-PhrQ system controls sporulation, competent cell formation, and surfactin production in B. subtilis OKB105.
Collapse
Affiliation(s)
- Yang Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | | | | | | | | | | |
Collapse
|
47
|
Tanaka K, Iwasaki K, Morimoto T, Matsuse T, Hasunuma T, Takenaka S, Chumsakul O, Ishikawa S, Ogasawara N, Yoshida KI. Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis. BMC Microbiol 2015; 15:43. [PMID: 25880922 PMCID: PMC4348106 DOI: 10.1186/s12866-015-0373-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Abstract
Background The two-component regulatory system, involving the histidine sensor kinase DegS and response regulator DegU, plays an important role to control various cell processes in the transition phase of Bacillus subtilis. The degU32 allele in strain 1A95 is characterized by the accumulation of phosphorylated form of DegU (DegU-P). Results Growing 1A95 cells elevated the pH of soytone-based medium more than the parental strain 168 after the onset of the transition phase. The rocG gene encodes a catabolic glutamate dehydrogenase that catalyzes one of the main ammonia-releasing reactions. Inactivation of rocG abolished 1A95-mediated increases in the pH of growth media. Thus, transcription of the rocG locus was examined, and a novel 3.7-kb transcript covering sivA, rocG, and rocA was found in 1A95 but not 168 cells. Increased intracellular fructose 1,6-bisphosphate (FBP) levels are known to activate the HPr kinase HPrK, and to induce formation of the P-Ser-HPr/CcpA complex, which binds to catabolite responsive elements (cre) and exerts CcpA-dependent catabolite repression. A putative cre found within the intergenic region between sivA and rocG, and inactivation of ccpA led to creation of the 3.7-kb transcript in 168 cells. Analyses of intermediates in central carbon metabolism revealed that intracellular FBP levels were lowered earlier in 1A95 than in 168 cells. A genome wide transcriptome analysis comparing 1A95 and 168 cells suggested similar events occurring in other catabolite repressive loci involving induction of lctE encoding lactate dehydrogenase. Conclusions Under physiological conditions the 3.7-kb rocG transcript may be tightly controlled by a roadblock mechanism involving P-Ser-HPr/CcpA in 168 cells, while in 1A95 cells abolished repression of the 3.7-kb transcript. Accumulation of DegU-P in 1A95 affects central carbon metabolism involving lctE enhanced by unknown mechanisms, downregulates FBP levels earlier, and inactivates HPrK to allow the 3.7-kb transcription, and thus similar events may occur in other catabolite repressive loci. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0373-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan.
| | - Kana Iwasaki
- Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
| | - Takuya Morimoto
- Biological Science Laboratories, Kao Corporation, Haga, Tochigi, Japan. .,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | | | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan.
| | - Shinji Takenaka
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. .,Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Ken-ichi Yoshida
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan. .,Department of Agrobioscience, Kobe University, Kobe, Hyogo, Japan.
| |
Collapse
|
48
|
Boguslawski KM, Hill PA, Griffith KL. Novel mechanisms of controlling the activities of the transcription factors Spo0A and ComA by the plasmid-encoded quorum sensing regulators Rap60-Phr60 in Bacillus subtilis. Mol Microbiol 2015; 96:325-48. [PMID: 25598361 DOI: 10.1111/mmi.12939] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2015] [Indexed: 01/09/2023]
Abstract
Bacillus subtilis and its closest relatives have multiple rap-phr quorum sensing gene pairs that coordinate a variety of physiological processes with population density. Extra-chromosomal rap-phr genes are also present on mobile genetic elements, yet relatively little is known about their function. In this work, we demonstrate that Rap60-Phr60 from plasmid pTA1060 coordinates a variety of biological processes with population density including sporulation, cannibalism, biofilm formation and genetic competence. Similar to other Rap proteins that control sporulation, Rap60 modulates phosphorylation of the transcription factor Spo0A by acting as a phosphatase of Spo0F∼P, an intermediate of the sporulation phosphorelay system. Additionally, Rap60 plays a noncanonical role in regulating the autophosphorylation of the sporulation-specific kinase KinA, a novel activity for Rap proteins. In contrast, Rap proteins that modulate genetic competence interfere with DNA binding by the transcription factor ComA. Rap60 regulates the activity of ComA in a unique manner by forming a Rap60-ComA-DNA ternary complex that inhibits transcription of target genes. Taken together, this work provides new insight into two novel mechanisms of regulating Spo0A and ComA by Rap60 and expands our general understanding of how plasmid-encoded quorum sensing pairs regulate important biological processes.
Collapse
Affiliation(s)
- Kristina M Boguslawski
- Medical Scientist Training Program, New York University School of Medicine, 550 First Avenue, New York, NY, 10016, USA
| | | | | |
Collapse
|
49
|
CodY regulates expression of the Bacillus subtilis extracellular proteases Vpr and Mpr. J Bacteriol 2015; 197:1423-32. [PMID: 25666135 DOI: 10.1128/jb.02588-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED CodY is a global transcriptional regulator in low-G+C Gram-positive bacteria that is responsive to GTP and branched-chain amino acids. By interacting with its two cofactors, it is able to sense the nutritional and energetic status of the cell and respond by regulating expression of adaptive genetic programs. In Bacillus subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. In this study, we demonstrated that expression of two extracellular proteases, Vpr and Mpr, is negatively controlled by CodY. By gel mobility shift and DNase I footprinting assays, we showed that CodY binds to the regulatory regions of both genes, in the vicinity of their transcription start points. The mpr gene is also characterized by the presence of a second, higher-affinity CodY-binding site located at the beginning of its coding sequence. Using strains carrying vpr- or mpr-lacZ transcriptional fusions in which CodY-binding sites were mutated, we demonstrated that repression of both protease genes is due to the direct effect by CodY and that the mpr internal site is required for regulation. The vpr promoter is a rare example of a sigma H-dependent promoter that is regulated by CodY. In a codY null mutant, Vpr became one of the more abundant proteins of the B. subtilis exoproteome. IMPORTANCE CodY is a global transcriptional regulator of metabolism and virulence in low-G+C Gram-positive bacteria. In B. subtilis, more than 200 genes, including those for peptide transporters, intracellular proteolytic enzymes, and amino acid degradative pathways, are controlled by CodY. However, no role for B. subtilis CodY in regulating expression of extracellular proteases has been established to date. In this work, we demonstrate that by binding to the regulatory regions of the corresponding genes, B. subtilis CodY negatively controls expression of Vpr and Mpr, two extracellular proteases. Thus, in B. subtilis, CodY can now be seen to regulate the entire protein utilization pathway.
Collapse
|
50
|
Kierul K, Voigt B, Albrecht D, Chen XH, Carvalhais LC, Borriss R. Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology (Reading) 2015; 161:131-147. [DOI: 10.1099/mic.0.083576-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Kinga Kierul
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Greifswald, Germany
| | - Dirk Albrecht
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Greifswald, Germany
| | - Xiao-Hua Chen
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Lilia C. Carvalhais
- Molecular Plant Nutrition, University of Hohenheim, Stuttgart, Germany
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Rainer Borriss
- ABiTEP GmbH, Berlin, Germany
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| |
Collapse
|