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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [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: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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2
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George NL, Bennett EC, Orlando BJ. Guarding the walls: the multifaceted roles of Bce modules in cell envelope stress sensing and antimicrobial resistance. J Bacteriol 2024; 206:e0012324. [PMID: 38869304 PMCID: PMC11270860 DOI: 10.1128/jb.00123-24] [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] [Indexed: 06/14/2024] Open
Abstract
Bacteria have developed diverse strategies for defending their cell envelopes from external threats. In Firmicutes, one widespread strategy is to use Bce modules-membrane protein complexes that unite a peptide-detoxifying ABC transporter with a stress response coordinating two-component system. These modules provide specific, front-line defense for a wide variety of antimicrobial peptides and small molecule antibiotics as well as coordinate responses for heat, acid, and oxidative stress. Because of these abilities, Bce modules play important roles in virulence and the development of antibiotic resistance in a variety of pathogens, including Staphylococcus, Streptococcus, and Enterococcus species. Despite their importance, Bce modules are still poorly understood, with scattered functional data in only a small number of species. In this review, we will discuss Bce module structure in light of recent cryo-electron microscopy structures of the B. subtilis BceABRS module and explore the common threads and variations-on-a-theme in Bce module mechanisms across species. We also highlight the many remaining questions about Bce module function. Understanding these multifunctional membrane complexes will enhance our understanding of bacterial stress sensing and may point toward new therapeutic targets for highly resistant pathogens.
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Affiliation(s)
- Natasha L. George
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ellen C. Bennett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Benjamin J. Orlando
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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3
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Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food. Microorganisms 2022; 10:microorganisms10020252. [PMID: 35208707 PMCID: PMC8876208 DOI: 10.3390/microorganisms10020252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEADAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.
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4
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DnaJ and ClpX are required for HitRS and HssRS two-component system signaling in Bacillus anthracis. Infect Immun 2021; 90:e0056021. [PMID: 34748369 DOI: 10.1128/iai.00560-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis is the causative agent of anthrax. This Gram-positive bacterium poses a substantial risk to human health due to high mortality rates and the potential for malicious use as a bioterror weapon. To survive within the vertebrate host, B. anthracis relies on two-component system (TCS) signaling to sense host-induced stresses and respond to alterations in the environment through changes in target gene expression. HitRS and HssRS are cross-regulating TCSs in B. anthracis that respond to cell envelope disruptions and high heme levels, respectively. In this study, an unbiased and targeted genetic selection was designed to identify gene products that are involved in HitRS and HssRS signaling. This selection led to the identification of inactivating mutations within dnaJ and clpX that disrupt HitRS- and HssRS-dependent gene expression. DnaJ and ClpX are the substrate-binding subunits of the DnaJK protein chaperone and ClpXP protease, respectively. DnaJ regulates the levels of HitR and HitS to facilitate signal transduction, while ClpX specifically regulates HitS levels. Together these results reveal that the protein homeostasis regulators, DnaJ and ClpX, function to maintain B. anthracis signal transduction activities through TCS regulation. One sentence summary: Use of a genetic selection strategy to identify modulators of two-component system signaling in Bacillus anthracis.
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5
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Ortet P, Fochesato S, Bitbol AF, Whitworth DE, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M. Evolutionary history expands the range of signaling interactions in hybrid multikinase networks. Sci Rep 2021; 11:11763. [PMID: 34083699 PMCID: PMC8175716 DOI: 10.1038/s41598-021-91260-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions (‘phylogenetic promiscuity’). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS–GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.
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Affiliation(s)
- Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Anne-Florence Bitbol
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR8237), Sorbonne Université, 75005, Paris, France.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - David Lalaouna
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.,CNRS, ARN UPR 9002, Université de Strasbourg, 67000, Strasbourg, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.
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Laut CL, Perry WJ, Metzger AL, Weiss A, Stauff DL, Walker S, Caprioli RM, Skaar EP. Bacillus anthracis Responds to Targocil-Induced Envelope Damage through EdsRS Activation of Cardiolipin Synthesis. mBio 2020; 11:e03375-19. [PMID: 32234818 PMCID: PMC7157781 DOI: 10.1128/mbio.03375-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/27/2020] [Indexed: 01/08/2023] Open
Abstract
Bacillus anthracis is a spore-forming bacterium that causes devastating infections and has been used as a bioterror agent. This pathogen can survive hostile environments through the signaling activity of two-component systems, which couple environmental sensing with transcriptional activation to initiate a coordinated response to stress. In this work, we describe the identification of a two-component system, EdsRS, which mediates the B. anthracis response to the antimicrobial compound targocil. Targocil is a cell envelope-targeting compound that is toxic to B. anthracis at high concentrations. Exposure to targocil causes damage to the cellular barrier and activates EdsRS to induce expression of a previously uncharacterized cardiolipin synthase, which we have named ClsT. Both EdsRS and ClsT are required for protection against targocil-dependent damage. Induction of clsT by EdsRS during targocil treatment results in an increase in cardiolipin levels, which protects B. anthracis from envelope damage. Together, these results reveal that a two-component system signaling response to an envelope-targeting antimicrobial induces production of a phospholipid associated with stabilization of the membrane. Cardiolipin is then used to repair envelope damage and promote B. anthracis viability.IMPORTANCE Compromising the integrity of the bacterial cell barrier is a common action of antimicrobials. Targocil is an antimicrobial that is active against the bacterial envelope. We hypothesized that Bacillus anthracis, a potential weapon of bioterror, senses and responds to targocil to alleviate targocil-dependent cell damage. Here, we show that targocil treatment increases the permeability of the cellular envelope and is particularly toxic to B. anthracis spores during outgrowth. In vegetative cells, two-component system signaling through EdsRS is activated by targocil. This results in an increase in the production of cardiolipin via a cardiolipin synthase, ClsT, which restores the loss of barrier function, thereby reducing the effectiveness of targocil. By elucidating the B. anthracis response to targocil, we have uncovered an intrinsic mechanism that this pathogen employs to resist toxicity and have revealed therapeutic targets that are important for bacterial defense against structural damage.
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Affiliation(s)
- Clare L Laut
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Devin L Stauff
- Department of Biology, Grove City College, Grove City, Pennsylvania, USA
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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7
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Zhang R, Slamti L, Tong L, Verplaetse E, Ma L, Lemy C, Peng Q, Guo S, Zhang J, Song F, Lereclus D. The stationary phase regulator CpcR activates cry gene expression in non-sporulating cells of Bacillus thuringiensis. Mol Microbiol 2019; 113:740-754. [PMID: 31793098 DOI: 10.1111/mmi.14439] [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: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022]
Abstract
Cell differentiation within an isogenic population allows the specialisation of subpopulations and a division of labour. Bacillus thuringiensis is a spore-forming bacterium that produces insecticidal crystal proteins (Cry proteins) in sporulating cells. We recently reported that strain B. thuringiensis LM1212 presents the unique ability to differentiate into two subpopulations during the stationary phase: spore-formers and crystal-producers. Here, we characterised the transcriptional regulator CpcR responsible for this differentiation and the expression of the cry genes. cpcR is located on a plasmid that also harbours cry genes. The alignment of LM1212 cry gene promoters revealed the presence of a conserved DNA sequence upstream from the -35 region. This presumed CpcR box was also found in the promoter of cpcR and we showed that cpcR transcription is positively autoregulated. Electrophoretic mobility shift assays suggested that CpcR directly controls the transcription of its target genes by binding to the CpcR box. We showed that CpcR was able to direct the production of a crystal consisting of a heterologous insecticidal Cry protein in non-sporulating cells of a typical B. thuringiensis kurstaki strain. Moreover, the expression of cpcR induced a reduction in the sporulation of this B. thuringiensis strain, suggesting an interaction between CpcR and the sporulation regulatory networks.
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Affiliation(s)
- Ruibin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Leyla Slamti
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lei Tong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Emilie Verplaetse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lixia Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,Beijing Institute of Technology, Beijing, P. R. China
| | - Christelle Lemy
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shuyuan Guo
- Beijing Institute of Technology, Beijing, P. R. China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Didier Lereclus
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Identification and Characterization of the Two-Component System HK8700-RR8701 of Kocuria rhizophila DC2201. Protein J 2019; 38:683-692. [PMID: 31302850 DOI: 10.1007/s10930-019-09853-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two-component systems (TCSs) are highly conserved in prokaryotes, endowing cells with multiple physiological functions to respond to changes in the ambient environment. The signaling pathway of a typical TCS consists of a sensory histidine kinase and a response regulator. The TCSs of Kocuria rhizophila, which is usually used as a target strain for various antibiotics and other adverse factors, have captured our interest due to their potential roles in bacterial adaptation for survival. Herein, the distribution and putative biological functions of the TCSs of K. rhizophila DC2201 were analyzed by using bioinformatics, and a preliminary TCS regulatory network was constructed. A representative and important TCS (i.e., HK8700-RR8701 system), which is homologous to the LiaS-LiaR system previously discovered in Bacillus subtilis, was identified and characterized through yeast two-hybrid screening and phosphorylation assays. Detailed information of TCSs is expected to offer novel insights into the adaptation mechanism of K. rhizophila and thus boost its application.
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9
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Gupta V, Jain K, Garg R, Malik A, Gulati P, Bhatnagar R. Characterization of a two component system, Bas1213-1214, important for oxidative stress in Bacillus anthracis. J Cell Biochem 2018. [PMID: 29537101 DOI: 10.1002/jcb.26751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microbial colonization is an outcome of appropriate sensing and regulation of its gene expression. Bacillus anthracis adapts and thrives in its environment through complex regulatory mechanisms, among them, the two component systems (TCS). Many bacteria respond to the oxygen fluctuations via TCS. In the present work, a previously uncharacterized TCS, Bas1213-1214, of B. anthracis with a probable role in oxygen sensing has been characterized as a functional TCS. A substantial increase in the expression of Bas1213 was observed during the stationary growth phase, in presence of bicarbonate ions, and under oxidative stress thereby speculating the role of Bas1213 in toxin production and adaptive responses. Electrophoretic mobility shift assay (EMSA) and ANS assay highlighted autoregulation of the system. Identification of Bas1213 regulon further suggested its regulatory function in metabolism and adaptive responses. A marked reduction in sporulation was observed on overexpression of Bas1213 in B. anthracis which can be correlated with the augmented expression of sporulation kinase D. Additionally, Bas1213 was shown to regulate catalase, and ABC transporter (mntH) further implicating its essential role during oxidative stress. Finally, crucial residues involved in the DNA binding activity of Bas1213 were also identified. This study reports that the role of Bas1213-1214 in the regulation of metabolism and adaptive responses during oxidative stress. Both sporulation and response to environmental oxygen are important for the maintenance of B. anthracis lifecycle, therefore, characterization of Bas1213-1214 provides a step closer toward understanding the regulatory network governing in B. anthracis.
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Affiliation(s)
- Vatika Gupta
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Kanika Jain
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rajni Garg
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Anshu Malik
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Li Y, Li C, Qin H, Yang M, Ye J, Long Y, Ou H. Proteome and phospholipid alteration reveal metabolic network of Bacillus thuringiensis under triclosan stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:508-516. [PMID: 28988086 DOI: 10.1016/j.scitotenv.2017.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/30/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Triclosan is a common antibacterial agent widely applied in various household and personal care products. The molecule, cell, organ and organism-level understanding of its toxicity pose to some target organisms has been investigated, whereas, the alteration of a single metabolic reaction, gene or protein cannot reflect the impact of triclosan on metabolic network. To clarify the interaction between triclosan stress and metabolism at network and system levels, phospholipid synthesis, and cellular proteome and metabolism of Bacillus thuringiensis under 1μM of triclosan stress were investigated through omics approaches. The results showed that C14:0, C16:1ω7, C16:0 and C18:2ω6 were significantly up-produced, and 19 proteins were differentially expressed. Whereas, energy supply, protein repair and the synthesis of DNA, RNA and protein were down-regulated. PyrH and Eno could be biomarkers to reflect triclosan stress. At network level, the target proteins ACOX1, AHR, CAR, CYP1A, CYP1B1, DNMT1, ENO, HSP60, HSP70, SLC5A5, TPO and UGT expressed in different species shared high sequence homology with the same function proteins found in Homo sapiens not only validated their role as biomarkers but also implied the potential impact of triclosan on the metabolic pathways and network of humans. These findings provided novel insights into the metabolic influence of triclosan at network levels, and developed an omics approach to evaluate the safety of target compound.
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Affiliation(s)
- Yi Li
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Chongshu Li
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huaming Qin
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Meng Yang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek 94598, CA, USA.
| | - Yan Long
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huase Ou
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
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11
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Gupta V, Chaudhary N, Aggarwal S, Adlakha N, Gulati P, Bhatnagar R. Functional analysis of BAS2108-2109 two component system: Evidence for protease regulation in Bacillus anthracis. Int J Biochem Cell Biol 2017; 89:71-84. [PMID: 28602714 DOI: 10.1016/j.biocel.2017.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND Bacillus anthracis (BA) is a major bioterrorism concern which has evolved complex regulatory mechanisms for its virulence factors. Secreted proteases play an imperative role in the pathogenesis of BA, however their regulation remains elusive. Two component systems (TCS) are often employed by bacteria to sense and adapt to the environmental perturbations. In several pathogens, TCS are commonly associated with the regulation of virulence factors including proteases. The genome of BA encodes 41 TCS pairs, however, the role of any TCS in regulation of its proteases is not known. PRINCIPAL FINDINGS The study established BAS2108-2109 as a prototypical TCS where BAS2108 functions as a histidine kinase and BAS2109 as the response regulator. The expression of BAS2109 was found to be elevated under host simulated conditions and in pellicle forming cells. Electrophoretic mobility shift assay (EMSA) and lacZ reporter assay revealed positive autoregulation of the BAS2108-2109 operon by BAS2109. Collective analysis of ANS assay and EMSA demonstrated Lys167, Thr179 and Thr182 residues are crucial for the DNA binding activity of BAS2109. EMSA analysis further highlighted BAS2109 as the transcriptional regulator for different genes of BA, particularly proteases. Upregulation of proteases in BA overexpressing BAS2109 further strengthen its role in protease regulation. SIGNIFICANCE This is the first report to identify a TCS pair for its role in the regulation of proteases of BA. Importance of proteases in the pathogenesis of BA is well documented, therefore, studying the regulatory networks governing their expression will help in identification of new drug targets.
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Affiliation(s)
- Vatika Gupta
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India, India; Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Neha Chaudhary
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India, India
| | - Somya Aggarwal
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India, India
| | - Nidhi Adlakha
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India, India.
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Dhiman A, Rahi A, Gopalani M, Bajpai S, Bhatnagar S, Bhatnagar R. Role of the recognition helix of response regulator WalR from Bacillus anthracis in DNA binding and specificity. Int J Biol Macromol 2017; 96:257-264. [DOI: 10.1016/j.ijbiomac.2016.12.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
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13
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Cabrera R, Rodríguez-Romero A, Guarneros G, de la Torre M. New insights into the interaction between the quorum-sensing receptor NprR and its DNA target, or the response regulator Spo0F. FEBS Lett 2016; 590:3243-53. [PMID: 27543719 DOI: 10.1002/1873-3468.12371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 11/08/2022]
Abstract
The NprR protein and NprRB signaling peptide comprise a bifunctional quorum-sensing system from the Bacillus cereus group that is involved in transcriptional activation through DNA-binding and in sporulation initiation by binding to Spo0F. We characterized in vitro the direct interactions established by NprR that may be relevant for performing its two functions. Apo-NprR interacted with Spo0F, but not with the target DNA. The NprRB signaling peptide SSKPDIVG that binds strongly to Apo-NprR, failed to bind and disrupt the NprR-Spo0F complex. Finally, the NprR-NprRB complex bound both to Spo0F and the target DNA with similar affinity. Based on our findings, we propose that rather than a switch triggered by NprRB, the NprR/NprRB ratio and the availability of Spo0F binding sites define the function of NprR.
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Affiliation(s)
- Rosina Cabrera
- Centro de Investigación en Alimentación y Desarrollo A. C., Hermosillo, Mexico
| | - Adela Rodríguez-Romero
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Gabriel Guarneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Mayra de la Torre
- Centro de Investigación en Alimentación y Desarrollo A. C., Hermosillo, Mexico.
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14
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Diomandé SE, Doublet B, Vasaï F, Guinebretière MH, Broussolle V, Brillard J. Expression of the genes encoding the CasK/R two-component system and the DesA desaturase during Bacillus cereus cold adaptation. FEMS Microbiol Lett 2016; 363:fnw174. [PMID: 27435329 DOI: 10.1093/femsle/fnw174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 11/13/2022] Open
Abstract
Two-component systems (TCS) allow a cell to elaborate a variety of adaptive responses to environment changes. The recently discovered CasK/R TCS plays a role in the optimal unsaturation of fatty acids necessary for cold adaptation of the foodborne-pathogen Bacillus cereus Here, we showed that the promoter activity of the operon encoding this TCS was repressed during growth at low temperature in the stationary phase in the parental strain when compared to the casK/R mutant, suggesting that CasR negatively regulates the activity of its own promoter in these conditions. The promoter activity of the desA gene encoding the Δ5 fatty acid desaturase, providing unsaturated fatty acids (UFAs) required for low temperature adaptation, was repressed in the casK/R mutant grown at 12°C versus 37°C. This result suggests that CasK/R activates desA expression during B. cereus growth at low temperature, allowing an optimal unsaturation of the fatty acids. In contrast, desA expression was repressed during the lag phase at low temperature in presence of UFAs, in a CasK/R-independent manner. Our findings confirm that the involvement of this major TCS in B. cereus cold adaptation is linked to the upregulation of a fatty acid desaturase.
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Affiliation(s)
| | | | | | | | | | - Julien Brillard
- SQPOV, INRA, Univ. Avignon, 84000 Avignon, France DGIMI, INRA, Univ. Montpellier, 34095 Montpellier, France
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15
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Gopalani M, Dhiman A, Rahi A, Kandari D, Bhatnagar R. Identification, Functional Characterization and Regulon Prediction of a Novel Two Component System Comprising BAS0540-BAS0541 of Bacillus anthracis. PLoS One 2016; 11:e0158895. [PMID: 27392063 PMCID: PMC4938410 DOI: 10.1371/journal.pone.0158895] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 06/23/2016] [Indexed: 12/22/2022] Open
Abstract
Two component systems (TCSs) can be envisaged as complex molecular devices that help the bacteria to sense its environment and respond aptly. 41 TCSs are predicted in Bacillus anthracis, a potential bioterrorism agent, of which only four have been studied so far. Thus, the intricate signaling network contributed by TCSs remains largely unmapped in B. anthracis and needs comprehensive exploration. In this study, we functionally characterized one such system composed of BAS0540 (Response regulator) and BAS0541 (Histidine kinase). BAS0540-BAS0541, the closest homolog of CiaRH of Streptococcus in B. anthracis, forms a functional TCS with BAS0541 displaying autophosphorylation and subsequent phosphotransfer to BAS0540. BAS0540 was also found to accept phosphate from physiologically relevant small molecule phosphodonors like acetyl phosphate and carbamoyl phosphate. Results of qRT-PCR and immunoblotting demonstrated that BAS0540 exhibits a constitutive expression throughout the growth of B. anthracis. Regulon prediction for BAS0540 in B. anthracis was done in silico using the consensus DNA binding sequence of CiaR of Streptococcus. The predicted regulon of BAS0540 comprised of 23 genes, which could be classified into 8 functionally diverse categories. None of the proven virulence factors were a part of the predicted regulon, an observation contrasting with the regulon of CiaRH in Streptococci. Electrophoretic mobility shift assay was used to show direct binding of purified BAS0540 to the upstream regions of 5 putative regulon candidates- BAS0540 gene itself; a gene predicted to encode cell division protein FtsA; a self–immunity gene; a RND family transporter gene and a gene encoding stress (heat) responsive protein. A significant enhancement in the DNA binding ability of BAS0540 was observed upon phosphorylation. Overexpression of response regulator BAS0540 in B. anthracis led to a prodigious increase of ~6 folds in the cell length, thereby conferring it a filamentous phenotype. Furthermore, the sporulation titer of the pathogen also decreased markedly by ~16 folds. Thus, this study characterizes a novel TCS of B. anthracis and elucidates its role in two of the most important physiological processes of the pathogen: cell division and sporulation.
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Affiliation(s)
- Monisha Gopalani
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
| | - Alisha Dhiman
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
| | - Amit Rahi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
| | - Divya Kandari
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
- * E-mail:
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16
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Majed R, Faille C, Kallassy M, Gohar M. Bacillus cereus Biofilms-Same, Only Different. Front Microbiol 2016; 7:1054. [PMID: 27458448 PMCID: PMC4935679 DOI: 10.3389/fmicb.2016.01054] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/23/2016] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus displays a high diversity of lifestyles and ecological niches and include beneficial as well as pathogenic strains. These strains are widespread in the environment, are found on inert as well as on living surfaces and contaminate persistently the production lines of the food industry. Biofilms are suspected to play a key role in this ubiquitous distribution and in this persistency. Indeed, B. cereus produces a variety of biofilms which differ in their architecture and mechanism of formation, possibly reflecting an adaptation to various environments. Depending on the strain, B. cereus has the ability to grow as immersed or floating biofilms, and to secrete within the biofilm a vast array of metabolites, surfactants, bacteriocins, enzymes, and toxins, all compounds susceptible to act on the biofilm itself and/or on its environment. Within the biofilm, B. cereus exists in different physiological states and is able to generate highly resistant and adhesive spores, which themselves will increase the resistance of the bacterium to antimicrobials or to cleaning procedures. Current researches show that, despite similarities with the regulation processes and effector molecules involved in the initiation and maturation of the extensively studied Bacillus subtilis biofilm, important differences exists between the two species. The present review summarizes the up to date knowledge on biofilms produced by B. cereus and by two closely related pathogens, Bacillus thuringiensis and Bacillus anthracis. Economic issues caused by B. cereus biofilms and management strategies implemented to control these biofilms are included in this review, which also discuss the ecological and functional roles of biofilms in the lifecycle of these bacterial species and explore future developments in this important research area.
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Affiliation(s)
- Racha Majed
- Micalis Institute, INRA, AgroParisTech, CNRS, Université Paris-SaclayJouy-en-Josas, France; Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-JosephBeirut, Lebanon
| | - Christine Faille
- UMR UMET: Unité Matériaux et Transformations, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lille Villeneuve d'Ascq, France
| | - Mireille Kallassy
- Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-Joseph Beirut, Lebanon
| | - Michel Gohar
- Micalis Institute, INRA, AgroParisTech, CNRS, Université Paris-SaclayJouy-en-Josas, France; Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-JosephBeirut, Lebanon
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17
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Ortet P, Whitworth DE, Santaella C, Achouak W, Barakat M. P2CS: updates of the prokaryotic two-component systems database. Nucleic Acids Res 2014; 43:D536-41. [PMID: 25324303 PMCID: PMC4384028 DOI: 10.1093/nar/gku968] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and homologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes. HK and RR trees are annotated with gene organization and domain architecture, providing insights into the evolutionary origin of the contemporary gene set. The majority of TCSs are encoded by adjacent HK and RR genes, however, ‘orphan’ unpaired TCS genes are also abundant and identifying their partner proteins is challenging. P2CS now provides paired HK and RR trees with proteins from the same genetic locus indicated. This allows the appraisal of evolutionary relationships across entire TCSs and in some cases the identification of candidate partners for orphan TCS proteins.
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Affiliation(s)
- Philippe Ortet
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - Catherine Santaella
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Wafa Achouak
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Mohamed Barakat
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
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18
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Yu S, Peng Y, Chen W, Deng Y, Guo Y. Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei. Indian J Microbiol 2014; 54:293-301. [PMID: 24891736 DOI: 10.1007/s12088-014-0456-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/05/2014] [Indexed: 02/06/2023] Open
Abstract
Lactobacillus casei has traditionally been recognized as a probiotic, thus needing to survive the industrial production processes and transit through the gastrointestinal tract before providing benefit to human health. The two-component signal transduction system (TCS) plays important roles in sensing and reacting to environmental changes, which consists of a histidine kinase (HK) and a response regulator (RR). In this study we identified HKs and RRs of six sequenced L. casei strains. Ortholog analysis revealed 15 TCS clusters (HK-RR pairs), one orphan HKs and three orphan RRs, of which 12 TCS clusters were common to all six strains, three were absent in one strain. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. Some TCS clusters are involved with the response under the stress of the bile salts, acid, or oxidative, which contribute to survive the difficult journey through the human gastrointestinal tract. Computational predictions of 15 TCSs were verified by PCR experiments. This genomic level study of TCSs should provide valuable insights into the conservation and divergence of TCS proteins in the L. casei strains.
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Affiliation(s)
- Shuijing Yu
- State Key Laboratory of Dairy Biotechnology, Bright Dairy & Food Co. Ltd, Shanghai, 200436 People's Republic of China ; Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, No. 86, Hongqi Ave., Ganzhou, 341000 Jiangxi People's Republic of China
| | - Yanping Peng
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, No. 86, Hongqi Ave., Ganzhou, 341000 Jiangxi People's Republic of China
| | - Wanyi Chen
- State Key Laboratory of Dairy Biotechnology, Bright Dairy & Food Co. Ltd, Shanghai, 200436 People's Republic of China
| | - Yangwu Deng
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, No. 86, Hongqi Ave., Ganzhou, 341000 Jiangxi People's Republic of China
| | - Yanhua Guo
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, No. 86, Hongqi Ave., Ganzhou, 341000 Jiangxi People's Republic of China
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19
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Exploration of a Possible Partnership among Orphan Two-Component System Proteins in CyanobacteriumSynechococcus elongatusPCC 7942. Biosci Biotechnol Biochem 2014; 76:1484-91. [DOI: 10.1271/bbb.120172] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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The CasKR two-component system is required for the growth of mesophilic and psychrotolerant Bacillus cereus strains at low temperatures. Appl Environ Microbiol 2014; 80:2493-503. [PMID: 24509924 DOI: 10.1128/aem.00090-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The different strains of Bacillus cereus can grow at temperatures covering a very diverse range. Some B. cereus strains can grow in chilled food and consequently cause food poisoning. We have identified a new sensor/regulator mechanism involved in low-temperature B. cereus growth. Construction of a mutant of this two-component system enabled us to show that this system, called CasKR, is required for growth at the minimal temperature (Tmin). CasKR was also involved in optimal cold growth above Tmin and in cell survival below Tmin. Microscopic observation showed that CasKR plays a key role in cell shape during cold growth. Introducing the casKR genes in a ΔcasKR mutant restored its ability to grow at Tmin. Although it was first identified in the ATCC 14579 model strain, this mechanism has been conserved in most strains of the B. cereus group. We show that the role of CasKR in cold growth is similar in other B. cereus sensu lato strains with different growth temperature ranges, including psychrotolerant strains.
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21
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Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. FEBS Open Bio 2014; 4:65-76. [PMID: 24490131 PMCID: PMC3907690 DOI: 10.1016/j.fob.2013.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/24/2013] [Accepted: 12/24/2013] [Indexed: 12/20/2022] Open
Abstract
Two-component signal transduction systems (TCS), consisting of a sensor histidine protein kinase and its cognate response regulator, are an important mode of environmental sensing in bacteria. Additionally, they have been found to regulate virulence determinants in several pathogens. Bacillus anthracis, the causative agent of anthrax and a bioterrorism agent, harbours 41 pairs of TCS. However, their role in its pathogenicity has remained largely unexplored. Here, we show that WalRK of B. anthracis forms a functional TCS which exhibits some species-specific functions. Biochemical studies showed that domain variants of WalK, the histidine kinase, exhibit classical properties of autophosphorylation and phosphotransfer to its cognate response regulator WalR. Interestingly, these domain variants also show phosphatase activity towards phosphorylated WalR, thereby making WalK a bifunctional histidine kinase/phosphatase. An in silico regulon determination approach, using a consensus binding sequence from Bacillus subtilis, provided a list of 30 genes that could form a putative WalR regulon in B. anthracis. Further, electrophoretic mobility shift assay was used to show direct binding of purified WalR to the upstream regions of three putative regulon candidates, an S-layer protein EA1, a cell division ABC transporter FtsE and a sporulation histidine kinase KinB3. Our work lends insight into the species-specific functions and mode of action of B. anthracis WalRK. WalRK forms a functional TCS in B. anthracis, expressed throughout the growth phase. WalK variants exhibit autophosphorylation and phosphotransfer to WalR. WalKc variants also show phosphatase activity towards phosphorylated WalR. A potential WalR regulon in B. anthracis was predicted in silico. DNA binding ability was demonstrated for WalR.
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Affiliation(s)
- Alisha Dhiman
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi 110078, India
| | - Parul Kulshreshtha
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
- Corresponding author. Tel.: +91 1126704079/1126742040; fax: +91 1126742040.
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22
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Wang J, Mei H, Qian H, Tang Q, Liu X, Yu Z, He J. Expression profile and regulation of spore and parasporal crystal formation-associated genes in Bacillus thuringiensis. J Proteome Res 2013; 12:5487-501. [PMID: 24215520 DOI: 10.1021/pr4003728] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus thuringiensis, a Gram-positive endospore-forming bacterium, is characterized by the formation of parasporal crystals consisting of insecticidal crystal proteins (ICPs) during sporulation. We reveal gene expression profiles and regulatory mechanisms associated with spore and parasporal crystal formation based on transcriptomics and proteomics data of B. thuringiensis strain CT-43. During sporulation, five ICP genes encoded by CT-43 were specifically transcribed; moreover, most of the spore structure-, assembly-, and maturation-associated genes were specifically expressed or significantly up-regulated, with significant characteristics of temporal regulation. These findings suggest that it is essential for the cell to maintain efficient operation of transcriptional and translational machinery during sporulation. Our results indicate that the RNA polymerase complex δ and ω subunits, cold shock proteins, sigma factors, and transcriptional factors as well as the E2 subunit of the pyruvate dehydrogenase complex could cooperatively participate in transcriptional regulation via different mechanisms. In particular, differences in processing and modification of ribosomal proteins, rRNA, and tRNA combined with derepression of translational inhibition could boost the rate of ribosome recycling and assembly as well as translation initiation, elongation, and termination efficiency, thereby compensating for the reduction in ribosomal levels. The efficient operation of translational machineries and powerful protein-quality controlling systems would thus ensure biosyntheses of a large quantity of proteins with normal biological functions during sporulation.
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Affiliation(s)
- Jieping Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan, Hubei 430070, China
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23
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Arora G, Sajid A, Arulanandh MD, Singhal A, Mattoo AR, Pomerantsev AP, Leppla SH, Maiti S, Singh Y. Unveiling the novel dual specificity protein kinases in Bacillus anthracis: identification of the first prokaryotic dual specificity tyrosine phosphorylation-regulated kinase (DYRK)-like kinase. J Biol Chem 2012; 287:26749-63. [PMID: 22711536 PMCID: PMC3411013 DOI: 10.1074/jbc.m112.351304] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/14/2012] [Indexed: 12/23/2022] Open
Abstract
Dual specificity protein kinases (DSPKs) are unique enzymes that can execute multiple functions in the cell, which are otherwise performed exclusively by serine/threonine and tyrosine protein kinases. In this study, we have characterized the protein kinases Bas2152 (PrkD) and Bas2037 (PrkG) from Bacillus anthracis. Transcriptional analyses of these kinases showed that they are expressed in all phases of growth. In a serendipitous discovery, both kinases were found to be DSPKs. PrkD was found to be similar to the eukaryotic dual specificity Tyr phosphorylation-regulated kinase class of dual specificity kinases, which autophosphorylates on Ser, Thr, and Tyr residues and phosphorylates Ser and Thr residues on substrates. PrkG was found to be a bona fide dual specificity protein kinase that mediates autophosphorylation and substrate phosphorylation on Ser, Thr, and Tyr residues. The sites of phosphorylation in both of the kinases were identified through mass spectrometry. Phosphorylation on Tyr residues regulates the kinase activity of PrkD and PrkG. PrpC, the only known Ser/Thr protein phosphatase, was also found to possess dual specificity. Genistein, a known Tyr kinase inhibitor, was found to inhibit the activities of PrkD and PrkG and affect the growth of B. anthracis cells, indicating a possible role of these kinases in cell growth and development. In addition, the glycolytic enzyme pyruvate kinase was found to be phosphorylated by PrkD on Ser and Thr residues but not by PrkG. Thus, this study provides the first evidence of DSPKs in B. anthracis that belong to different classes and have different modes of regulation.
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Affiliation(s)
- Gunjan Arora
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Andaleeb Sajid
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Mary Diana Arulanandh
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Anshika Singhal
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Abid R. Mattoo
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Andrei P. Pomerantsev
- the Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892-3202
| | - Stephen H. Leppla
- the Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892-3202
| | - Souvik Maiti
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Yogendra Singh
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
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24
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Song F, Peng Q, Brillard J, Buisson C, Been M, Abee T, Broussolle V, Huang D, Zhang J, Lereclus D, Nielsen‐LeRoux C. A multicomponent sugar phosphate sensor system specifically induced in
Bacillus cereus
during infection of the insect gut. FASEB J 2012; 26:3336-50. [DOI: 10.1096/fj.11-197681] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fuping Song
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1319 MicalisGénétique Microbienne et Environnement Guyancourt France
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection Beijing China
| | - Qi Peng
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1319 MicalisGénétique Microbienne et Environnement Guyancourt France
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection Beijing China
| | - Julien Brillard
- INRA Avignon France
- Université d'Avignon et des Pays de Vaucluse, UMR408, Sécurité et Qualité des Produits d'Origine Végétale Avignon France
| | - Christophe Buisson
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1319 MicalisGénétique Microbienne et Environnement Guyancourt France
| | - Mark Been
- Top Institute (TI) Food and Nutrition and Laboratory of Food Microbiology Wageningen The Netherlands
| | - Tjakko Abee
- Top Institute (TI) Food and Nutrition and Laboratory of Food Microbiology Wageningen The Netherlands
| | - Véronique Broussolle
- INRA Avignon France
- Université d'Avignon et des Pays de Vaucluse, UMR408, Sécurité et Qualité des Produits d'Origine Végétale Avignon France
| | - Dafang Huang
- Biotechnology Research InstituteChinese Academy of Agricultural Sciences (CAAS) Beijing China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection Beijing China
| | - Didier Lereclus
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1319 MicalisGénétique Microbienne et Environnement Guyancourt France
| | - Christina Nielsen‐LeRoux
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1319 MicalisGénétique Microbienne et Environnement Guyancourt France
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection Beijing China
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25
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Kristoffersen SM, Haase C, Weil MR, Passalacqua KD, Niazi F, Hutchison SK, Desany B, Kolstø AB, Tourasse NJ, Read TD, Økstad OA. Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biol 2012; 13:R30. [PMID: 22537947 PMCID: PMC3446304 DOI: 10.1186/gb-2012-13-4-r30] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 04/15/2012] [Accepted: 04/26/2012] [Indexed: 11/23/2022] Open
Abstract
Background Recent years have shown a marked increase in the use of next-generation sequencing technologies for quantification of gene expression (RNA sequencing, RNA-Seq). The expression level of a gene is a function of both its rate of transcription and RNA decay, and the influence of mRNA decay rates on gene expression in genome-wide studies of Gram-positive bacteria is under-investigated. Results In this work, we employed RNA-Seq in a genome-wide determination of mRNA half-lives in the Gram-positive bacterium Bacillus cereus. By utilizing a newly developed normalization protocol, RNA-Seq was used successfully to determine global mRNA decay rates at the single nucleotide level. The analysis revealed positional degradation patterns, with mRNAs being degraded from both ends of the molecule, indicating that both 5' to 3' and 3' to 5' directions of RNA decay are present in B. cereus. Other operons showed segmental degradation patterns where specific ORFs within polycistrons were degraded at variable rates, underlining the importance of RNA processing in gene regulation. We determined the half-lives for more than 2,700 ORFs in B. cereus ATCC 10987, ranging from less than one minute to more than fifteen minutes, and showed that mRNA decay rate correlates globally with mRNA expression level, GC content, and functional class of the ORF. Conclusions To our knowledge, this study presents the first global analysis of mRNA decay in a bacterium at single nucleotide resolution. We provide a proof of principle for using RNA-Seq in bacterial mRNA decay analysis, revealing RNA processing patterns at the single nucleotide level.
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Affiliation(s)
- Simen M Kristoffersen
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, PB 1068 Blindern, 0316 Oslo, Norway
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Abee T, Wels M, de Been M, den Besten H. From transcriptional landscapes to the identification of biomarkers for robustness. Microb Cell Fact 2011; 10 Suppl 1:S9. [PMID: 21995521 PMCID: PMC3231935 DOI: 10.1186/1475-2859-10-s1-s9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ability of microorganisms to adapt to changing environments and gain cell robustness, challenges the prediction of their history-dependent behaviour. Using our model organism Bacillus cereus, a notorious Gram-positive food spoilage and pathogenic spore-forming bacterium, a strategy will be described that allows for identification of biomarkers for robustness. First an overview will be presented of its two-component systems that generally include a transmembrane sensor histidine kinase and its cognate response regulator, allowing rapid and robust responses to fluctuations in the environment. The role of the multisensor hybrid kinase RsbK and the PP2C-type phosphatase RsbY system in activation of the general stress sigma factor σB is highlighted. An extensive comparative analysis of transcriptional landscapes derived from B. cereus exposed to mild stress conditions such as heat, acid, salt and oxidative stress, revealed that, amongst others σB regulated genes were induced in most conditions tested. The information derived from the transcriptome data was subsequently implemented in a framework for identifying and selecting cellular biomarkers at their mRNA, protein and/or activity level, for mild stressinduced microbial robustness towards lethal stresses. Exposure of unstressed and mild stress-adapted cells to subsequent lethal stress conditions (heat, acid and oxidative stress) allowed for quantification of the robustness advantage provided by mild stress pretreatment using the plate-count method. The induction levels of the selected candidate-biomarkers, σB protein, catalase activity and transcripts of certain proteases upon mild stress treatment, were significantly correlated to mild stress-induced enhanced robustness towards lethal thermal, oxidative and acid stresses, and were therefore suitable to predict these adaptive traits. Cellular biomarkers that are quantitatively correlated to adaptive behavior will facilitate our ability to predict the impact of adaptive behavior on cell robustness and will allow to control and/or exploit these adaptive traits. Extrapolation to other species and genera is discussed such as avenues towards mechanism-based design of microbial fitness and robustness.
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Affiliation(s)
- Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
| | - Michiel Wels
- TI Food and Nutrition, Wageningen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Mark de Been
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Heidy den Besten
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
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27
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Ceuppens S, Rajkovic A, Heyndrickx M, Tsilia V, Van De Wiele T, Boon N, Uyttendaele M. Regulation of toxin production by Bacillus cereus and its food safety implications. Crit Rev Microbiol 2011; 37:188-213. [PMID: 21417966 DOI: 10.3109/1040841x.2011.558832] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Toxin expression is of utmost importance for the food-borne pathogen B. cereus, both in food poisoning and non-gastrointestinal host infections as well as in interbacterial competition. Therefore it is no surprise that the toxin gene expression is tightly regulated by various internal and environmental signals. An overview of the current knowledge regarding emetic and diarrheal toxin transcription and expression is presented in this review. The food safety aspects and management tools such as temperature control, food preservatives and modified atmosphere packaging are discussed specifically for B. cereus emetic and diarrheal toxin production.
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Affiliation(s)
- Siele Ceuppens
- Ghent University, Faculty of Bioscience Engineering, Laboratory of Food Microbiology and Food Preservation, Ghent, Belgium
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28
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Kang CC, Chuang YJ, Tung KC, Chao CC, Tang CY, Peng SC, Wong DSH. A genetic algorithm-based Boolean delay model of intracellular signal transduction in inflammation. BMC Bioinformatics 2011; 12 Suppl 1:S17. [PMID: 21342546 PMCID: PMC3044271 DOI: 10.1186/1471-2105-12-s1-s17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Signal transduction is the major mechanism through which cells transmit external stimuli to evoke intracellular biochemical responses. Understanding relationship between external stimuli and corresponding cellular responses, as well as the subsequent effects on downstream genes, is a major challenge in systems biology. Thus, a systematic approach to integrate experimental data and qualitative knowledge to identify the physiological consequences of environmental stimuli is needed. Results In present study, we employed a genetic algorithm-based Boolean model to represent NF-κB signaling pathway. We were able to capture feedback and crosstalk characteristics to enhance our understanding on the acute and chronic inflammatory response. Key network components affecting the response dynamics were identified. Conclusions We designed an effective algorithm to elucidate the process of immune response using comprehensive knowledge about network structure and limited experimental data on dynamic responses. This approach can potentially be implemented for large-scale analysis on cellular processes and organism behaviors.
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Affiliation(s)
- Chu Chun Kang
- Department of Computer Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC.
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29
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de Been M, Francke C, Siezen RJ, Abee T. Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases. MICROBIOLOGY-SGM 2010; 157:3-12. [PMID: 21051490 DOI: 10.1099/mic.0.045740-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor σ(B) is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated σ(B) activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.
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Affiliation(s)
- Mark de Been
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, Veterinary Microbiology and Epidemiology, University of Helsinki, Helsinki, Finland.,TI Food and Nutrition (TIFN), Wageningen, The Netherlands.,Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands.,Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Christof Francke
- TI Food and Nutrition (TIFN), Wageningen, The Netherlands.,Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Roland J Siezen
- NIZO food research BV, Ede, The Netherlands.,TI Food and Nutrition (TIFN), Wageningen, The Netherlands.,Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Tjakko Abee
- TI Food and Nutrition (TIFN), Wageningen, The Netherlands.,Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
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Carlin F, Brillard J, Broussolle V, Clavel T, Duport C, Jobin M, Guinebretière MH, Auger S, Sorokine A, Nguyen-Thé C. Adaptation of Bacillus cereus, an ubiquitous worldwide-distributed foodborne pathogen, to a changing environment. Food Res Int 2010. [DOI: 10.1016/j.foodres.2009.10.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Analysis of developmental gene conservation in the Actinomycetales using DNA/DNA microarray comparisons. Antonie van Leeuwenhoek 2010; 99:159-77. [DOI: 10.1007/s10482-010-9473-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 06/11/2010] [Indexed: 01/21/2023]
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van Melis CCJ, Nierop Groot MN, Tempelaars MH, Moezelaar R, Abee T. Characterization of germination and outgrowth of sorbic acid-stressed Bacillus cereus ATCC 14579 spores: phenotype and transcriptome analysis. Food Microbiol 2010; 28:275-83. [PMID: 21315984 DOI: 10.1016/j.fm.2010.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/01/2010] [Accepted: 04/10/2010] [Indexed: 11/15/2022]
Abstract
Sorbic acid (SA) is widely used as a preservative, but the effect of SA on spore germination and outgrowth has gained limited attention up to now. Therefore, the effect of sorbic acid on germination of spores of Bacillus cereus strain ATCC 14579 was analyzed both at phenotype and transcriptome level. Spore germination and outgrowth were assessed at pH 5.5 without and with 0.75, 1.5 and 3.0 mM (final concentrations) undissociated sorbic acid (HSA). This resulted in distinct HSA concentration-dependent phenotypes, varying from reduced germination and outgrowth rates to complete blockage of germination at 3.0 mM HSA. The phenotypes reflecting different stages in the germination process could be confirmed using flow cytometry and could be recognized at transcriptome level by distinct expression profiles. In the absence and presence of 0.75 and 1.5 mM HSA, similar cellular ATP levels were found up to the initial stage of outgrowth, suggesting that HSA-induced inhibition of outgrowth is not caused by depletion of ATP. Transcriptome analysis revealed the presence of a limited number of transcripts in dormant spores, outgrowth related expression, and genes specifically associated with sorbic acid stress, including alterations in cell envelope and multidrug resistance. The potential role of these HSA-stress associated genes in spore outgrowth is discussed.
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Affiliation(s)
- C C J van Melis
- Top Institute Food and Nutrition, Wageningen, The Netherlands.
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33
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Identification and classification of a two-component system based on domain structures in bacteria and differences in domain structure between Gram-positive and Gram-negative bacteria. Biosci Biotechnol Biochem 2010; 74:716-20. [PMID: 20378989 DOI: 10.1271/bbb.90746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genome sequencing has revealed many pairs of proteins termed two-component systems (TCSs) in bacteria. Each pair consists of a sensor or histidine kinase (HK) and an effector or response regulator (RR). The HK is usually a membrane-spanning protein that senses specific environmental parameters and communicates this information to the cytoplasmic RR protein through phosphotransfer reactions to cope with a variety of environmental stresses, including osmotic pressure, nitrogen lack, phosphoric acid lack, and the presence of oxygen. Furthermore, some proteins have been identified as hybrid kinases composed of HK and RR. We identified the domain structures of 360 bacteria and 43 archaea by domain search against the PFAM database using HMMER. We then classified 8,573 HK, 10,807 RR, and 2,477 hybrid kinases. In addition, we identified specific domains among phylogenic clusters based on differences in domain structure of TCS genes applying the Signal-to-Noise ratio.
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Identification of Bacillus cereus genes specifically expressed during growth at low temperatures. Appl Environ Microbiol 2010; 76:2562-73. [PMID: 20190083 DOI: 10.1128/aem.02348-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The mechanisms involved in the ability of Bacillus cereus to multiply at low temperatures were investigated. It was assumed that many genes involved in cold acclimation would be upregulated at low temperatures. Recombinase-based in vivo expression technology (IVET) was adapted to the detection of the transient activation of B. cereus promoters during growth at 10 degrees C. Four independent screenings of a promoter library from type strain ATCC 14579 were performed, and 17 clones were isolated. They corresponded to 17 promoter regions that displayed reproducibly elevated expression at 10 degrees C relative to expression at 30 degrees C. This analysis revealed several genes that may be important for B. cereus to grow successfully under the restrictive conditions of cold habitats. Among them, a locus corresponding to open reading frames BC5402 to BC5398, harboring a lipase-encoding gene and a putative transcriptional regulator, was identified three times. While a mutation in the putative regulator-encoding gene did not cause any particular phenotype, a mutant deficient in the lipase-encoding gene showed reduced growth abilities at low temperatures compared with the parental strain. The mutant did not change its fatty acid profiles in the same way as the wild type when grown at 12 degrees C instead of 37 degrees C. This study demonstrates the feasibility of a promoter trap strategy for identifying cold-induced genes. It outlines a first picture of the different processes involved in B. cereus cold acclimation.
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de Been M, Tempelaars MH, van Schaik W, Moezelaar R, Siezen RJ, Abee T. A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus. Environ Microbiol 2009; 12:730-45. [PMID: 19958380 DOI: 10.1111/j.1462-2920.2009.02116.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor sigma(B) is activated by the RR RsbY. Here we present strong indications that the PP2C-type phosphatase RsbY receives its input from the multi-sensor hybrid kinase BC1008 (renamed RsbK). Genome analyses revealed that, across bacilli, rsbY and rsbK are located in a conserved gene cluster. A B. cereus rsbK deletion strain was shown to be incapable of inducing sigma(B) upon stress conditions and was impaired in its heat adaptive response. Comparison of the wild-type and rsbK mutant transcriptomes upon heat shock revealed that RsbK was primarily involved in the activation of the sigma(B)-mediated stress response. Truncation of the RsbK RR receiver domain demonstrated the importance of this domain for sigma(B) induction upon stress. The domain architecture of RsbK suggests that in the B. cereus group and in other bacilli, environmental and intracellular stress signalling routes are combined into one single protein. This strategy is markedly different from the sigma(B) activation pathway in other low-GC Gram-positives.
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Affiliation(s)
- Mark de Been
- TI Food and Nutrition (TIFN), Wageningen, the Netherlands.
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37
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Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Méjean V, Whitworth DE. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics 2009; 10:315. [PMID: 19604365 PMCID: PMC2716373 DOI: 10.1186/1471-2164-10-315] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 07/15/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/metagenomes. Two-component system (TCS) signal transduction pathways are the dominant mechanisms by which micro-organisms sense and respond to external as well as internal environmental changes. These systems respond to a wide range of stimuli by triggering diverse physiological adjustments, including alterations in gene expression, enzymatic reactions, or protein-protein interactions. DESCRIPTION We present P2CS (Prokaryotic 2-Component Systems), an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely sequenced prokaryotic genomes and 39 metagenomes. P2CS provides detailed annotation of each TCS gene including family classification, sequence features, functional domains, as well as genomic context visualization. To bypass the generic problem of gene underestimation during genome annotation, we also constituted and searched an ORFeome, which improves the recovery of TCS proteins compared to searches on the equivalent proteomes. CONCLUSION P2CS has been developed for computational analysis of the modular TCSs of prokaryotic genomes and metagenomes. It provides a complete overview of information on TCSs, including predicted candidate proteins and probable proteins, which need further curation/validation. The database can be browsed and queried with a user-friendly web interface at http://www.p2cs.org/.
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Affiliation(s)
- Mohamed Barakat
- CEA, DSV, IBEB, LEMiRE, CNRS, Université Aix-Marseille II, CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France.
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ResDE-dependent regulation of enterotoxin gene expression in Bacillus cereus: evidence for multiple modes of binding for ResD and interaction with Fnr. J Bacteriol 2009; 191:4419-26. [PMID: 19395489 DOI: 10.1128/jb.00321-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the food-borne pathogen Bacillus cereus F4430/73, the production of major virulence factors hemolysin BL (Hbl) and nonhemolytic enterotoxin (Nhe) is regulated through complex mechanisms. The two-component regulatory system ResDE is involved in the activation of hbl and nhe transcription. Here, the response regulator ResD and the sensor kinase ResE were overexpressed and purified, and autophosphorylation of ResE and transphosphorylation of ResD by ResE were demonstrated in vitro. ResD is mainly monomeric in solution, regardless of its phosphorylation state. ResD was shown to interact directly with promoter regions (p) of the enterotoxin regulator genes resDE, fnr, and plcR and the enterotoxin structural genes nhe and hbl, but with different affinities. Binding of ResD to pplcR, pnhe, and phbl was not dependent on the ResD phosphorylation status. In contrast, ResD phosphorylation significantly increased interactions between ResD and presDE and pfnr. Taken together, these results showed that phosphorylation of ResD results in a different target expression pattern. Furthermore, ResD and the redox activator Fnr were found to physically interact and simultaneously bind their target DNAs. We propose that unphosphorylated ResD acts as an antiactivator of Fnr, while phosphorylated ResD acts as a coactivator of Fnr. Finally, our findings represent the first molecular evidence of the role of ResDE as a sentinel system capable of sensing redox changes and coordinating a response that modulates B. cereus virulence.
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Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. Amino Acids 2009; 37:443-58. [PMID: 19198978 DOI: 10.1007/s00726-009-0241-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 01/12/2009] [Indexed: 02/07/2023]
Abstract
Adaptive signal transduction within microbial cells involves a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile two-component systems (TCS), arisen early in bacterial evolution. In Escherichia coli, cross-talk between the AtoS histidine kinase and the AtoC response regulator, forming the AtoSC TCS, through His --> Asp phosphotransfer, activates AtoC directly to induce atoDAEB operon expression, thus modulating diverse fundamental cellular processes such as short-chain fatty acid catabolism, poly-(R)-3-hydroxybutyrate biosynthesis and chemotaxis. Among the inducers hitherto identified, acetoacetate is the classical activator. The AtoSC TCS functional modulation by polyamines, histamine and Ca(2+), as well as the role of AtoC as transcriptional regulator, add new promising perspectives in the physiological significance and potential pharmacological exploitation of this TCS in cell proliferation, bacteria-host interactions, chemotaxis, and adaptation.
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40
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Two-component signal transduction systems in Streptomyces and related organisms studied using DNA comparative microarray analysis. Antonie Van Leeuwenhoek 2009; 95:189-206. [PMID: 19151927 DOI: 10.1007/s10482-008-9302-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 12/18/2008] [Indexed: 10/21/2022]
Abstract
Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare 14 Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis.
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Mattoo AR, Arora A, Maiti S, Singh Y. Identification, characterization and activation mechanism of a tyrosine kinase of Bacillus anthracis. FEBS J 2008; 275:6237-47. [PMID: 19016839 DOI: 10.1111/j.1742-4658.2008.06748.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacillus subtilis has three active tyrosine kinases, PtkA, PtkB and McsB, which play an important role in the physiology of the bacterium. Genome sequence analysis and biochemical experiments indicated that the ortholog of McsB, BAS0080, is the only active tyrosine kinase present in Bacillus anthracis. The autophosphorylation of McsB of B. anthracis was enhanced in the presence of an activator protein McsA (BAS0079), a property similar to that reported for B. subtilis. However, the process of enhanced phosphorylation of McsB in the presence of McsA remains elusive. To understand the activation mechanism of McsB, we carried out spectroscopic and calorimetric experiments with McsB and McsA. The spectroscopic results suggest that the binding affinity of Mg-ATP for McsB increased by one order from 10(3) to 10(4) in the presence of McsA. The calorimetric experiments revealed that the interaction between McsB and McsA is endothermic in nature, with unfavourable positive enthalpy (DeltaH) and favourable entropy (DeltaS) changes leading to an overall favourable free energy change (DeltaG). Kinetics of binding of both ATP and McsA with McsB showed low association rates (k(a)) and fast dissociation rates (k(d)). These results suggest that enhanced phosphorylation of McsB in the presence of McsA is due to increased affinity of ATP for McsB.
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Affiliation(s)
- Abid R Mattoo
- Institute of Genomics and Integrative Biology, Delhi, India
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Brillard J, Susanna K, Michaud C, Dargaignaratz C, Gohar M, Nielsen-Leroux C, Ramarao N, Kolstø AB, Nguyen-the C, Lereclus D, Broussolle V. The YvfTU two-component system is involved in plcR expression in Bacillus cereus. BMC Microbiol 2008; 8:183. [PMID: 18925929 PMCID: PMC2588459 DOI: 10.1186/1471-2180-8-183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 10/16/2008] [Indexed: 11/30/2022] Open
Abstract
Background Most extracellular virulence factors produced by Bacillus cereus are regulated by the pleiotropic transcriptional activator PlcR. Among strains belonging to the B. cereus group, the plcR gene is always located in the vicinity of genes encoding the YvfTU two-component system. The putative role of YvfTU in the expression of the PlcR regulon was therefore investigated. Results Expression of the plcR gene was monitored using a transcriptional fusion with a lacZ reporter gene in a yvfTU mutant and in its B. cereus ATCC 14579 parental strain. Two hours after the onset of the stationary phase, a stage at which the PlcR regulon is highly expressed, the plcR expression in the yvfTU mutant was only 50% of that of its parental strain. In addition to the reduced plcR expression in the yvfTU mutant, a few members of the PlcR regulon showed a differential expression, as revealed by transcriptomic and proteomic analyses. The virulence of the yvfTU mutant in a Galleria mellonella insect model was slightly lower than that of the parental strain. Conclusion The YvfTU two-component system is not required for the expression of most of the virulence factors belonging to the PlcR regulon. However, YvfTU is involved in expression of plcR, a major regulator of virulence in B. cereus.
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Affiliation(s)
- Julien Brillard
- UMR408, Sécurité et Qualité des Produits d'Origine Végétale, INRA, Université d'Avignon, F-84000 Avignon, France.
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de Been M, Bart MJ, Abee T, Siezen RJ, Francke C. The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives. Environ Microbiol 2008; 10:2796-809. [PMID: 18662309 DOI: 10.1111/j.1462-2920.2008.01700.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In bacteria, environmental challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). A phylogenetic footprinting/shadowing approach was designed and used to identify many novel RR-specific operators for species of the Bacillus cereus group and related Gram-positives. Analysis of the operator sequences revealed characteristic traits for each RR subfamily. For instance, operators related to the largest subfamily (OmpR) typically consisted of direct repeats (e.g. TTAAGA-N5-TTAAGA), whereas operators related to the second largest family (NarL) consisted of inverted repeats (e.g. ATGACA-N2-TGTCAT). This difference indicates a fundamentally different organization of the bound RR dimers between the two subfamilies. Moreover, the identification of the specific operator motifs allowed relating several RRs to a minimal regulon and thereby to a characteristic transcriptional response. Mostly, these regulons comprised genes encoding transport systems, suggesting a direct coupling of stimulus perception to the transport of target compounds. New biological roles could be attributed to various TCSs, including roles in cytochrome c biogenesis (HssRS), transport of carbohydrates, peptides and/or amino acids (YkoGH, LytSR), and resistance to toxic ions (LiaSR), antimicrobial peptides (BceRS) and beta-lactam antibiotics (BacRS, YcbLM). As more and more bacterial genome sequences are becoming available, the use of comparative analyses such as the approach applied in this study will further increase our knowledge of bacterial signal transduction mechanisms and provide directions for the assessment of their role in bacterial performance and survival strategies.
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Affiliation(s)
- Mark de Been
- TI Food and Nutrition (TIFN), Wageningen, the Netherlands.
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Mattoo AR, Saif Zaman M, Dubey GP, Arora A, Narayan A, Jailkhani N, Rathore K, Maiti S, Singh Y. Spo0B of Bacillus anthracis - a protein with pleiotropic functions. FEBS J 2008; 275:739-52. [PMID: 18190531 DOI: 10.1111/j.1742-4658.2007.06240.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spo0B is an important component of the phosphorelay signal transduction pathway, the pathway involved in the initiation of sporulation in Bacillus subtilis. Bioinformatic, phylogenetic and biochemical studies showed that Spo0B of Bacillus anthracis has evolved from citrate/malate kinases. During the course of evolution, Spo0B has retained the characteristic histidine kinase boxes H, N, F, G(1) and G(2), and has acquired nucleotide-binding domains, Walker A and Walker B, of ATPases. Owing to the presence of these domains, autophosphorylation and ATPase activity was observed in Spo0B of B. anthracis. Mutational studies showed that among the six histidine residues, His13 of the H-box is involved in the autophosphorylation activity of Spo0B, whereas Lys33 of the Walker A domain is associated with the ATPase activity of the protein. Thermodynamic and binding studies of the binding of Mg-ATP to Spo0B using isothermal titration calorimetry (ITC) suggested that the binding is driven by favorable entropy changes and that the reaction is exothermic, with an apparent dissociation constant (K(d)) equal to 0.02 mm. The value of the dissociation constant (K(d) = 0.05 mm) determined by the intrinsic fluorescence of trytophan of Spo0B was similar to that obtained by ITC studies. The purified Spo0B of B. anthracis also showed nucleoside diphosphate kinase-like activity of phosphate transfer from nucleoside triphosphate to nucleoside diphosphate. This is the first evidence for Spo0B of B. anthracis as an enzyme with histidine kinase and ATPase activities, which may have important roles to play in sporulation and pathogenesis.
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Affiliation(s)
- Abid R Mattoo
- Allergy and Infectious Diseases, Institute of Genomics and Integrative Biology, Delhi, India
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Lavín JL, Kiil K, Resano O, Ussery DW, Oguiza JA. Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae. BMC Genomics 2007; 8:397. [PMID: 17971244 PMCID: PMC2222644 DOI: 10.1186/1471-2164-8-397] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 10/31/2007] [Indexed: 11/26/2022] Open
Abstract
Background Pseudomonas syringae is a widespread bacterial plant pathogen, and strains of P. syringae may be assigned to different pathovars based on host specificity among different plant species. The genomes of P. syringae pv. syringae (Psy) B728a, pv. tomato (Pto) DC3000 and pv. phaseolicola (Pph) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR). P. syringae requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions. Results Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes of Psy B728a, Pto DC3000 and Pph 1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed important differences in TCS proteins among the three P. syringae pathovars. Conclusion In this article we present a thorough analysis of the identification and distribution of TCS proteins among the sequenced genomes of P. syringae. We have identified differences in TCS proteins among the three P. syringae pathovars that may contribute to their diverse host ranges and association with plant hosts. The identification and analysis of the repertoire of TCS proteins in the genomes of P. syringae pathovars constitute a basis for future functional genomic studies of the signal transduction pathways in this important bacterial phytopathogen.
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Affiliation(s)
- José L Lavín
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain.
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