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Furuya K, Kiyoshi K, Punjuy C, Yoshida N, Maruyama R, Yasuda T, Watanabe K, Kadokura T, Nakayama S. Effect of spo0A, sigE, sigG, and sigK disruption on butanol production and spore formation in Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564). J Biosci Bioeng 2023; 136:198-204. [PMID: 37487916 DOI: 10.1016/j.jbiosc.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
Clostridium saccharoperbutylacetonicum strain N1-4 (ATCC13564) is a butanol-producing strain suitable for application to butanol production from cellulosic materials by co-culture with cellulolytic and thermophilic species, such as Hungateiclostridium thermocellum (synonym: Clostridium thermocellum). The optimal temperature for butanol production by strain N1-4 is 30 °C, and the strain is sensitive to a high culture temperature of 37 °C. Given that spore formation is observed at high frequency when strain N1-4 is cultivated at 37 °C, we assumed in a previous study that the initiation of sporulation is related to a decrease in butanol production. Therefore, to investigate the relationship between butanol production and spore formation, we generated strain N1-4 isolates in which genes related to spore formation were disrupted. The sporulation-related gene disruptants of spo0A, sigE, sigG, and sigK lost the ability to produce heat-resistant spores, irrespective of the culture temperature. Among the gene disruptants produced, only the spo0A disruptant lost butanol-producing ability when cultivated at 30 °C. Interestingly, the sigE disruptant maintained butanol productivity similar to that observed at 30 °C, even when cultivated at 37 °C. In addition, the sigE disruptant successfully produced butanol from Avicel cellulose by co-culture with H. thermocellum at a fermentation temperature of 37 °C.
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Affiliation(s)
- Kazuhiko Furuya
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Keiji Kiyoshi
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Chaophaya Punjuy
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Naoto Yoshida
- Department of Biochemistry and Applied Bioscience, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Risa Maruyama
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tatsuki Yasuda
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kota Watanabe
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Toshimori Kadokura
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shunichi Nakayama
- Department of Fermentation Science and Technology, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
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2
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DiCandia MA, Edwards AN, Jones JB, Swaim GL, Mills BD, McBride SM. Identification of functional Spo0A residues critical for sporulation in Clostridioides difficile. J Mol Biol 2022; 434:167641. [PMID: 35597553 DOI: 10.1016/j.jmb.2022.167641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/26/2022] [Accepted: 05/15/2022] [Indexed: 10/18/2022]
Abstract
Clostridioides difficile is an anaerobic, Gram-positive pathogen that is responsible for C. difficile infection (CDI). To survive in the environment and spread to new hosts, C. difficile must form metabolically dormant spores. The formation of spores requires activation of the transcription factor Spo0A, which is the master regulator of sporulation in all endospore-forming bacteria. Though the sporulation initiation pathway has been delineated in the Bacilli, including the model spore-former Bacillus subtilis, the direct regulators of Spo0A in C. difficile remain undefined. C. difficile Spo0A shares highly conserved protein interaction regions with the B. subtilis sporulation proteins Spo0F and Spo0A, although many of the interacting factors present in B. subtilis are not encoded in C. difficile. To determine if comparable Spo0A residues are important for C. difficile sporulation initiation, site-directed mutagenesis was performed at conserved receiver domain residues and the effects on sporulation were examined. Mutation of residues important for homodimerization and interaction with positive and negative regulators of B. subtilis Spo0A and Spo0F impacted C. difficile Spo0A function. The data also demonstrated that mutation of many additional conserved residues altered C. difficile Spo0A activity, even when the corresponding Bacillus interacting proteins are not apparent in the C. difficile genome. Finally, the conserved aspartate residue at position 56 of C. difficile Spo0A was determined to be the phosphorylation site that is necessary for Spo0A activation. The finding that Spo0A interacting motifs maintain functionality suggests that C. difficile Spo0A interacts with yet unidentified proteins that regulate its activity and control spore formation.
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Affiliation(s)
- Michael A DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Joshua B Jones
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Grace L Swaim
- Department of Neuroscience and Cell Biology, Yale University Graduate School of Arts and Sciences, New Haven, CT, USA
| | - Brooke D Mills
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA.
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3
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Malik AA, Bouskill NJ. Drought impacts on microbial trait distribution and feedback to soil carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ashish A. Malik
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
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Genomics and Proteomics Analyses Revealed Novel Candidate Pesticidal Proteins in a Lepidopteran-Toxic Bacillus thuringiensis Strain. Toxins (Basel) 2020; 12:toxins12110673. [PMID: 33114565 PMCID: PMC7693509 DOI: 10.3390/toxins12110673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 11/17/2022] Open
Abstract
Discovery and identification of novel insecticidal proteins in Bacillus thuringiensis (Bt) strains are of crucial importance for efficient biological control of pests and better management of insect resistance. In this study, the Bt strain KhF, toxic for Plodia interpunctella and Grapholita molesta larvae, underwent genomics and proteomics analyses to achieve a better understanding of the bases of its pathogenicity. The whole-genome sequencing results revealed that the KhF strain contained nine coding sequences with homologies to Bt insecticidal genes. The lepidopteran toxic mixture of spores and crystals of this Bt strain was subjected to liquid chromatography and tandem mass spectrometry (LC-MS/MS) to assess the protein composition. The results of the proteomic analyses, combined with the toxin gene sequences, revealed that two of the main components of the crystals were two new candidate pesticidal proteins, named KhFA and KhFB. These proteins showed a similarity lower than 36% to the other known Bt toxins. The phylogenetic analysis showed that the KhFA and KhFB grouped with the newly denominated Xpp and Mpp (former ETX/Mtx) pesticidal protein groups, respectively. Altogether, this study has led to the discovery of two novel candidate pesticidal toxins in the lepidopteran toxic KhF strain.
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Ramos-Silva P, Serrano M, Henriques AO. From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. Mol Biol Evol 2020; 36:2714-2736. [PMID: 31350897 PMCID: PMC6878958 DOI: 10.1093/molbev/msz175] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.
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Affiliation(s)
- Paula Ramos-Silva
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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6
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Shen A, Edwards AN, Sarker MR, Paredes-Sabja D. Sporulation and Germination in Clostridial Pathogens. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0017-2018. [PMID: 31858953 PMCID: PMC6927485 DOI: 10.1128/microbiolspec.gpp3-0017-2018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
As obligate anaerobes, clostridial pathogens depend on their metabolically dormant, oxygen-tolerant spore form to transmit disease. However, the molecular mechanisms by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly understood. While sporulation and germination have been well characterized in Bacillus subtilis and Bacillus anthracis, striking differences in the regulation of these processes have been observed between the bacilli and the clostridia, with even some conserved proteins exhibiting differences in their requirements and functions. Here, we review our current understanding of how clostridial pathogens, specifically Clostridium perfringens, Clostridium botulinum, and Clostridioides difficile, induce sporulation in response to environmental cues, assemble resistant spores, and germinate metabolically dormant spores in response to environmental cues. We also discuss the direct relationship between toxin production and spore formation in these pathogens.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University Medical School, Boston, MA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Mahfuzur R Sarker
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Daniel Paredes-Sabja
- Department of Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biolo gicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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Zhu G, Wang S, Wang C, Zhou L, Zhao S, Li Y, Li F, Jetten MSM, Lu Y, Schwark L. Resuscitation of anammox bacteria after >10,000 years of dormancy. THE ISME JOURNAL 2019; 13:1098-1109. [PMID: 30504897 PMCID: PMC6461854 DOI: 10.1038/s41396-018-0316-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/03/2018] [Accepted: 11/17/2018] [Indexed: 11/09/2022]
Abstract
Water is essential for life on Earth, and an important medium for microbial energy and metabolism. Dormancy is a state of low metabolic activity upon unfavorable conditions. Many microorganisms can switch to a metabolically inactive state after water shortage, and recover once the environmental conditions become favorable again. Here, we resuscitated dormant anammox bacteria from dry terrestrial ecosystems after a resting period of >10 ka by addition of water without any other substrates. Isotopic-tracer analysis showed that water induced nitrate reduction yielding sufficient nitrite as substrate and energy for activating anammox bacteria. Subsequently, dissimilatory nitrate reduction to ammonium (DNRA) provided the substrate ammonium for anammox bacteria. The ammonium and nitrite formed were used to produce dinitrogen gas. High throughput sequencing and network analysis identified Brocadia as the dominant anammox species and a Jettenia species seemed to connect the other community members. Under global climate change, increasing precipitation and soil moisture may revive dormant anammox bacteria in arid soils and thereby impact global nitrogen and carbon cycles.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Cheng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liguang Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixiao Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Sciences and Technology, Guangzhou, 510650, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Yonglong Lu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, D-24098, Kiel, Germany.
- WA-OIGC, Department of Chemistry, Curtin University, Perth, Australia.
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8
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Feng ZV, Miller BR, Linn TG, Pho T, Hoang KNL, Hang MN, Mitchell SL, Hernandez RT, Carlson EE, Hamers RJ. Biological impact of nanoscale lithium intercalating complex metal oxides to model bacterium B. subtilis. ENVIRONMENTAL SCIENCE. NANO 2019; 6:305-314. [PMID: 31572614 PMCID: PMC6768416 DOI: 10.1039/c8en00995c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The wide applications of lithium intercalating complex metal oxides in energy storage devices call for a better understanding of their environmental impact at the end of their life cycle. In this study, we examine the biological impact of a panel of nanoscale lithium nickel manganese cobalt oxides (Li x Ni y Mn z Co1-y-z O2, 0 < x, y, z < 1, abbreviated to NMCs) to a model Gram-positive bacterium, Bacillus subtilis, in terms of cellular respiration and growth. A highly sensitive single-cell gel electrophoresis method is also applied for the first time to understand the genotoxicity of these nanomaterials to bacterial cells. Results from these assays indicate that the free Ni and Co ions released from the incongruent dissolution of the NMC material in B. subtilis growth medium induced both hindered growth and cellular respiration. More remarkably, the DNA damage induced by the combination of the two ions in solution is comparable to that induced by the NMC material, which suggests that the free Ni and Co ions are responsible for the toxicity observed. A material redesign by enriching Mn is also presented. The combined approaches of evaluating their impact on bacterial growth, respiration, and DNA damage at a single-cell level, as well as other phenotypical changes allows us to probe the nanomaterials and bacterial cells from a mechanistic prospective, and provides a useful means to an understanding of bacterial response to new potential environmental stressors.
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Affiliation(s)
- Z. Vivian Feng
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Blake R. Miller
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Taylor G. Linn
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | - Thomas Pho
- Chemistry Department, Augsburg University, Minneapolis, MN 55454, USA
| | | | - Mimi N. Hang
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | | | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J. Hamers
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
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9
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Davidson P, Eutsey R, Redler B, Hiller NL, Laub MT, Durand D. Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes. PLoS Genet 2018; 14:e1007470. [PMID: 30212463 PMCID: PMC6136694 DOI: 10.1371/journal.pgen.1007470] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
The evolution of signal transduction pathways is constrained by the requirements of signal fidelity, yet flexibility is necessary to allow pathway remodeling in response to environmental challenges. A detailed understanding of how flexibility and constraint shape bacterial two component signaling systems is emerging, but how new signal transduction architectures arise remains unclear. Here, we investigate pathway remodeling using the Firmicute sporulation initiation (Spo0) pathway as a model. The present-day Spo0 pathways in Bacilli and Clostridia share common ancestry, but possess different architectures. In Clostridium acetobutylicum, sensor kinases directly phosphorylate Spo0A, the master regulator of sporulation. In Bacillus subtilis, Spo0A is activated via a four-protein phosphorelay. The current view favors an ancestral direct phosphorylation architecture, with the phosphorelay emerging in the Bacillar lineage. Our results reject this hypothesis. Our analysis of 84 broadly distributed Firmicute genomes predicts phosphorelays in numerous Clostridia, contrary to the expectation that the Spo0 phosphorelay is unique to Bacilli. Our experimental verification of a functional Spo0 phosphorelay encoded by Desulfotomaculum acetoxidans (Class Clostridia) further supports functional phosphorelays in Clostridia, which strongly suggests that the ancestral Spo0 pathway was a phosphorelay. Cross complementation assays between Bacillar and Clostridial phosphorelays demonstrate conservation of interaction specificity since their divergence over 2.7 BYA. Further, the distribution of direct phosphorylation Spo0 pathways is patchy, suggesting multiple, independent instances of remodeling from phosphorelay to direct phosphorylation. We provide evidence that these transitions are likely the result of changes in sporulation kinase specificity or acquisition of a sensor kinase with specificity for Spo0A, which is remarkably conserved in both architectures. We conclude that flexible encoding of interaction specificity, a phenotype that is only intermittently essential, and the recruitment of kinases to recognize novel environmental signals resulted in a consistent and repeated pattern of remodeling of the Spo0 pathway. Survival in a changing world requires signal transduction circuitry that can evolve to sense and respond to new environmental challenges. The Firmicute sporulation initiation (Spo0) pathway is a compelling example of a pathway with a circuit diagram that has changed over the course of evolution. In Clostridium acetobutylicum, a sensor kinase directly activates the master regulator of sporulation, Spo0A. In Bacillus subtilis, Spo0A is activated indirectly via a four-protein phosphorelay. These early observations suggested that the ancestral Spo0A was directly phosphorylated by a kinase in the earliest spore-former and that the Spo0 phosphorelay arose later in Bacilli via gain of additional proteins and interactions. Our analysis, based on a much larger set of genomes, surprisingly reveals phosphorelays, not only in Bacilli, but in many Clostridia. These findings support a model wherein sporulation was initiated by a Spo0 phosphorelay in the ancestral spore-former and the direct phosphorylation Spo0 pathways, which are observed in distinct sets of Clostridial taxa, are the result of convergent, reductive evolution. Further, our evidence suggests that these remodeling events were mediated by changes in kinase specificity, implicating flexible pathway remodeling, potentially combined with the recruitment of kinases, in Spo0 pathway evolution.
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Affiliation(s)
- Philip Davidson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Brendan Redler
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania, United States of America
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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10
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García García T, Ventroux M, Derouiche A, Bidnenko V, Correia Santos S, Henry C, Mijakovic I, Noirot-Gros MF, Poncet S. Phosphorylation of the Bacillus subtilis Replication Controller YabA Plays a Role in Regulation of Sporulation and Biofilm Formation. Front Microbiol 2018; 9:486. [PMID: 29619013 PMCID: PMC5871692 DOI: 10.3389/fmicb.2018.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis cells can adopt different life-styles in response to various environmental cues, including planktonic cells during vegetative growth, sessile cells during biofilm formation and sporulation. While switching life-styles, bacteria must coordinate the progression of their cell cycle with their physiological status. Our current understanding of the regulatory pathways controlling the decision-making processes and triggering developmental switches highlights a key role of protein phosphorylation. The regulatory mechanisms that integrate the bacterial chromosome replication status with sporulation involve checkpoint proteins that target the replication initiator DnaA or the kinase phosphorelay controlling the master regulator Spo0A. B. subtilis YabA is known to interact with DnaA to prevent over-initiation of replication during vegetative growth. Here, we report that YabA is phosphorylated by YabT, a Ser/Thr kinase expressed during sporulation and biofilm formation. The phosphorylation of YabA has no effect on replication initiation control but hyper-phosphorylation of YabA leads to an increase in sporulation efficiency and a strong inhibition of biofilm formation. We also provide evidence that YabA phosphorylation affects the level of Spo0A-P in cells. These results indicate that YabA is a multifunctional protein with a dual role in regulating replication initiation and life-style switching, thereby providing a potential mechanism for cross-talk and coordination of cellular processes during adaptation to environmental change.
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Affiliation(s)
| | - Magali Ventroux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sara Correia Santos
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | | | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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11
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Das S, Majumder S, Mathur C, Kingston JJ. Molecular characterization and phylogenetic analysis of Clostridium perfringens from animals and their environments by cpn60 UT sequencing analysis. INFECTION GENETICS AND EVOLUTION 2018; 58:209-217. [DOI: 10.1016/j.meegid.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 01/17/2023]
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12
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Gorr TA. Hypometabolism as the ultimate defence in stress response: how the comparative approach helps understanding of medically relevant questions. Acta Physiol (Oxf) 2017; 219:409-440. [PMID: 27364602 DOI: 10.1111/apha.12747] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/28/2016] [Accepted: 06/28/2016] [Indexed: 12/22/2022]
Abstract
First conceptualized from breath-hold diving mammals, later recognized as the ultimate cell autonomous survival strategy in anoxia-tolerant vertebrates and burrowing or hibernating rodents, hypometabolism is typically recruited by resilient organisms to withstand and recover from otherwise life-threatening hazards. Through the coordinated down-regulation of biosynthetic, proliferative and electrogenic expenditures at times when little ATP can be generated, a metabolism turned 'down to the pilot light' allows the re-balancing of energy demand with supply at a greatly suppressed level in response to noxious exogenous stimuli or seasonal endogenous cues. A unifying hallmark of stress-tolerant organisms, the adaptation effectively prevents lethal depletion of ATP, thus delineating a marked contrast with susceptible species. Along with disengaged macromolecular syntheses, attenuated transmembrane ion shuttling and PO2 -conforming respiration rates, the metabolic slowdown in tolerant species usually culminates in a non-cycling, quiescent phenotype. However, such a reprogramming also occurs in leading human pathophysiologies. Ranging from microbial infections through ischaemia-driven infarcts to solid malignancies, cells involved in these disorders may again invoke hypometabolism to endure conditions non-permissive for growth. At the same time, their reduced activities underlie the frequent development of a general resistance to therapeutic interventions. On the other hand, a controlled induction of hypometabolic and/or hypothermic states by pharmacological means has recently stimulated intense research aimed at improved organ preservation and patient survival in situations requiring acutely administered critical care. The current review article therefore presents an up-to-date survey of concepts and applications of a coordinated and reversibly down-regulated metabolic rate as the ultimate defence in stress responses.
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Affiliation(s)
- T. A. Gorr
- Institute of Veterinary Physiology; Vetsuisse Faculty; University of Zurich; Zurich Switzerland
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Kermgard E, Yang Z, Michel AM, Simari R, Wong J, Ibba M, Lazazzera BA. Quality Control by Isoleucyl-tRNA Synthetase of Bacillus subtilis Is Required for Efficient Sporulation. Sci Rep 2017; 7:41763. [PMID: 28139725 PMCID: PMC5282499 DOI: 10.1038/srep41763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 11/11/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an aminoacyl-tRNA synthetase whose essential function is to aminoacylate tRNAIle with isoleucine. Like some other aminoacyl-tRNA synthetases, IleRS can mischarge tRNAIle and correct this misacylation through a separate post-transfer editing function. To explore the biological significance of this editing function, we created a ileS(T233P) mutant of Bacillus subtilis that allows tRNAIle mischarging while retaining wild-type Ile-tRNAIle synthesis activity. As seen in other species defective for aminoacylation quality control, the growth rate of the ileS(T233P) strain was not significantly different from wild-type. When the ileS(T233P) strain was assessed for its ability to promote distinct phenotypes in response to starvation, the ileS(T233P) strain was observed to exhibit a significant defect in formation of environmentally resistant spores. The sporulation defect ranged from 3-fold to 30-fold and was due to a delay in activation of early sporulation genes. The loss of aminoacylation quality control in the ileS(T233P) strain resulted in the inability to compete with a wild-type strain under selective conditions that required sporulation. These data show that the quality control function of IleRS is required in B. subtilis for efficient sporulation and suggests that editing by aminoacyl-tRNA synthetases may be important for survival under starvation/nutrient limitation conditions.
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Affiliation(s)
- Elizabeth Kermgard
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Zhou Yang
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Annika-Marisa Michel
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Technische Universität Braunschweig, Institut of Microbiology, Braunschweig, Germany
| | - Rachel Simari
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA
| | - Jacqueline Wong
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Michael Ibba
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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14
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Updates on the sporulation process in Clostridium species. Res Microbiol 2015; 166:225-35. [DOI: 10.1016/j.resmic.2014.12.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 12/19/2022]
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Abstract
Since the first application of high hydrostatic pressure (HHP) for food preservation more than 100 years ago, a wealth of knowledge has been gained on molecular mechanisms underlying the HHP-mediated destruction of microorganisms. However, one observation made back then is still valid, i.e. that HHP alone is not sufficient for the complete inactivation of bacterial endospores. To achieve "commercial sterility" of low-acid foods, i.e. inactivation of spores capable of growing in a specific product under typical storage conditions, a combination of HHP with other hurdles is required (most effectively with heat (HPT)). Although HPT processes are not yet industrially applied, continuous technical progress and increasing consumer demand for minimally processed, additive-free food with long shelf life, makes HPT sterilization a promising alternative to thermal processing.In recent years, considerable progress has been made in understanding the response of spores of the model organism B. subtilis to HPT treatments and detailed insights into some basic mechanisms in Clostridium species shed new light on differences in the HPT-mediated inactivation of Bacillus and Clostridium spores. In this chapter, current knowledge on sporulation and germination processes, which presents the basis for understanding development and loss of the extreme resistance properties of spores, is summarized highlighting commonalities and differences between Bacillus and Clostridium species. In this context, the effect of HPT treatments on spores, inactivation mechanism and kinetics, the role of population heterogeneity, and influence factors on the results of inactivation studies are discussed.
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Affiliation(s)
- Christian A Lenz
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, 85354, Freising, Germany
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16
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Abstract
ABSTRACT
Clostridia are Gram-positive, anaerobic, endospore-forming bacteria, incapable of dissimilatory sulfate reduction. Comprising approximately 180 species, the genus
Clostridium
is one of the largest bacterial genera. Physiology is mostly devoted to acid production. Numerous pathways are known, such as the homoacetate fermentation by acetogens, the propionate fermentation by
Clostridium propionicum
, and the butyrate/butanol fermentation by
C. acetobutylicum
, a well-known solvent producer. Clostridia degrade sugars, alcohols, amino acids, purines, pyrimidines, and polymers such as starch and cellulose. Energy conservation can be performed by substrate-level phosphorylation as well as by the generation of ion gradients. Endospore formation resembles the mechanism elucidated in
Bacillus
. Morphology, contents, and properties of spores are very similar to bacilli endospores. Sporulating clostridia usually form swollen mother cells and accumulate the storage substance granulose. However, clostridial sporulation differs by not employing the so-called phosphorelay. Initiation starts by direct phosphorylation of the master regulator Spo0A. The cascade of sporulation-specific sigma factors is again identical to what is known from
Bacillus
. The onset of sporulation is coupled in some species to either solvent (acetone, butanol) or toxin (e.g.,
C. perfringens
enterotoxin) formation. The germination of spores is often induced by various amino acids, often in combination with phosphate and sodium ions. In medical applications,
C. butyricum
spores are used as a
C. difficile
prophylaxis and as treatment against diarrhea. Recombinant spores are currently under investigation and testing as antitumor agents, because they germinate only in hypoxic tissues (i.e., tumor tissue), allowing precise targeting and direct killing of tumor cells.
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Barketi-Klai A, Monot M, Hoys S, Lambert-Bordes S, Kuehne SA, Minton N, Collignon A, Dupuy B, Kansau I. The flagellin FliC of Clostridium difficile is responsible for pleiotropic gene regulation during in vivo infection. PLoS One 2014; 9:e96876. [PMID: 24841151 PMCID: PMC4026244 DOI: 10.1371/journal.pone.0096876] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/12/2014] [Indexed: 01/09/2023] Open
Abstract
Clostridium difficile is the main agent responsible for hospital acquired antibiotic associated diarrhoea. In recent years, epidemic strains have emerged causing more severe infections. Whilst C. difficile has two major virulence factors, toxins TcdA and TcdB, it is generally accepted that other virulence components of the bacterium contribute to disease. Previously, it has been suggested that flagella expression from pathogenic bacteria might be implicated in virulence. In a recent study, we observed an increased mortality in a gnotobiotic mouse model when animals were colonized with an isogenic fliC mutant constructed in the PCR-ribotype 027 (B1/NAP1) strain R20291, while animals survived when colonized by the parental strain or after colonization by other high-toxin-producing C. difficile strains. To understand the reasons for this increased virulence, we compared the global gene expression profiles between the fliC-R20291 mutant and its parental strain using an in vitro and in vivo transcriptomic approach. The latter made use of the gnotobiotic mouse model. Interestingly, in the fliC mutant, we observed considerable up-regulation of genes involved in mobility, membrane transport systems (PTS, ABC transporters), carbon metabolism, known virulence factors and sporulation. A smaller but significant up-regulation of genes involved in cell growth, fermentation, metabolism, stress and antibiotic resistance was also apparent. All of these genes may be associated with the increased virulence of the fliC-R20921 mutant. We confirmed that the fliC mutation is solely responsible for the observed changes in gene expression in the mutant strain since expression profiles were restored to that of the wild-type strain in the fliC-complemented strain. Thus, the absence of FliC is directly or indirectly involved in the high mortality observed in the fliC mutant infected animals. Therefore, we provide the first evidence that when the major structural component of the flagellum is neutralized, deregulation of gene expression can occur during infection.
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Affiliation(s)
- Amira Barketi-Klai
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Sandra Hoys
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
| | | | - Sarah A. Kuehne
- Clostridia Research Group, Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nigel Minton
- Clostridia Research Group, Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Anne Collignon
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Imad Kansau
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
- * E-mail:
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Donald RGK, Flint M, Kalyan N, Johnson E, Witko SE, Kotash C, Zhao P, Megati S, Yurgelonis I, Lee PK, Matsuka YV, Severina E, Deatly A, Sidhu M, Jansen KU, Minton NP, Anderson AS. A novel approach to generate a recombinant toxoid vaccine against Clostridium difficile. MICROBIOLOGY-SGM 2013; 159:1254-1266. [PMID: 23629868 PMCID: PMC3749728 DOI: 10.1099/mic.0.066712-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Clostridium difficile toxins A and B are primarily responsible for symptoms of C. difficile associated disease and are prime targets for vaccine development. We describe a plasmid-based system for the production of genetically modified toxins in a non-sporulating strain of C. difficile that lacks the toxin genes tcdA and tcdB. TcdA and TcdB mutations targeting established glucosyltransferase cytotoxicity determinants were introduced into recombinant plasmids and episomally expressed toxin mutants purified from C. difficile transformants. TcdA and TcdB mutants lacking glucosyltransferase and autoproteolytic processing activities were ~10 000-fold less toxic to cultured human IMR-90 cells than corresponding recombinant or native toxins. However, both mutants retained residual cytotoxicity that could be prevented by preincubating the antigens with specific antibodies or by formalin treatment. Such non-toxic formalin-treated mutant antigens were immunogenic and protective in a hamster model of infection. The remaining toxicity of untreated TcdA and TcdB mutant antigens was associated with cellular swelling, a phenotype consistent with pore-induced membrane leakage. TcdB substitution mutations previously shown to block vesicular pore formation and toxin translocation substantially reduced residual toxicity. We discuss the implications of these results for the development of a C. difficile toxoid vaccine.
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Affiliation(s)
| | - Mike Flint
- Centers for Disease Control, 1600 Clifton Rd, Atlanta, GA 30333, USA
| | | | - Erik Johnson
- Pfizer Vaccine Research, Pearl River, NY 10654, USA
| | | | | | - Ping Zhao
- Pfizer Vaccine Research, Pearl River, NY 10654, USA
| | | | | | | | | | | | - Anne Deatly
- Pfizer Vaccine Research, Pearl River, NY 10654, USA
| | - Mini Sidhu
- Pfizer Vaccine Research, Pearl River, NY 10654, USA
| | | | - Nigel P. Minton
- Clostridia Research Group, NIHR Biomedical Research Unit in GI Disease, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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19
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Kumar A, Singh TR. A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:33-9. [PMID: 24432140 DOI: 10.1007/s11693-013-9105-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/21/2013] [Accepted: 02/21/2013] [Indexed: 11/26/2022]
Abstract
Quorum sensing (QS) is a process which allows a population of bacteria to coordinately regulate gene expression of their entire community. Bacillus subtilis is a soil organism which uses QS to alternate between competence for DNA uptake and sporulation. We propose a model to describe the components involved in QS and to analyze reaction species involved in the regulation of QS machinery. We targeted only those QS phenotypes for which the genetic organization and molecular characterization of the components are fully elucidated. We have analyzed simulations for concentration of different species involved in competence as well as sporulation pathways at diverse time period using quantitative methods. It was observed that there is possibility of achieving different measurement from reactions taken place between species by applying irreversible Michaelis-Menten kinetic law. We obtain variation in measurement on changing parameters such as concentrations ranging from 0.3 to 50 μM in stepwise manner by setting end time in the range of 0.1-100 ms. Additionally we observe covariance between different reaction species involved in QS by fluctuating their quantities in real-time simulations. Our model mimics correctly the phenotype for competence and virulence. We concluded that time factor play major role to determine rate kinetics of diverse reaction species as compared to their concentrations and support the hypothesis of getting genetic stability while colonies are in synchronization.
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Affiliation(s)
- Ashwani Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, 173234 HP India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, 173234 HP India
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20
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Bassi D, Cappa F, Cocconcelli PS. Array-based transcriptional analysis of Clostridium sporogenes UC9000 during germination, cell outgrowth and vegetative life. Food Microbiol 2012; 33:11-23. [PMID: 23122496 DOI: 10.1016/j.fm.2012.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/04/2012] [Accepted: 08/05/2012] [Indexed: 01/22/2023]
Abstract
The members of the genus Clostridium, including the spore-forming anaerobic bacteria, have a complex and strictly regulated life cycle, but very little is known about the genetic pathways involved in the different stages of their life cycle. Clostridium sporogenes, a Gram-positive bacterium usually involved in food spoilage and frequently isolated from late blowing cheese, is genetically indistinguishable from the proteolytic Clostridium botulinum. As the non-neurotoxic counterpart, it is often used as an exemplar for the toxic subtypes. In this work, we performed a microscopic study combined with a custom array-based analysis of the C. sporogenes cycle, from dormant spores to the early stationary phase. We identified a total of 211 transcripts in spores, validating the hypothesis that mRNAs are abundant in spores and the pattern of mRNA expression is strikingly different from that present in growing cells. The spore transcripts included genes responsible for different life-sustaining functions, suggesting there was transcript entrapment or basic poly-functional gene activation for future steps. In addition, 3 h after the beginning of the germination process, 20% of the total up-regulated genes were temporally expressed in germinating spores. The vegetative condition appeared to be more active in terms of gene transcription and protein synthesis than the spore, and genes coding for germination and sporulation factors seemed to be expressed at this point. These results suggest that spores are not silent entities, and a broader knowledge of the genetic pathways involved in the Clostridium life cycle could provide a better understanding of pathogenic clostridia types.
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Affiliation(s)
- Daniela Bassi
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza/Via Milano 24, 26100 Cremona, Italy.
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21
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Involvement of Clostridium botulinum ATCC 3502 sigma factor K in early-stage sporulation. Appl Environ Microbiol 2012; 78:4590-6. [PMID: 22544236 DOI: 10.1128/aem.00304-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A key survival mechanism of Clostridium botulinum, the notorious neurotoxic food pathogen, is the ability to form heat-resistant spores. While the genetic mechanisms of sporulation are well understood in the model organism Bacillus subtilis, nothing is known about these mechanisms in C. botulinum. Using the ClosTron gene-knockout tool, sigK, encoding late-stage (stage IV) sporulation sigma factor K in B. subtilis, was disrupted in C. botulinum ATCC 3502 to produce two different mutants with distinct insertion sites and orientations. Both mutants were unable to form spores, and their elongated cell morphology suggested that the sporulation pathway was blocked at an early stage. In contrast, sigK-complemented mutants sporulated successfully. Quantitative real-time PCR analysis of sigK in the parent strain revealed expression at the late log growth phase in the parent strain. Analysis of spo0A, encoding the sporulation master switch, in the sigK mutant and the parent showed significantly reduced relative levels of spo0A expression in the sigK mutant compared to the parent strain. Similarly, sigF showed significantly lower relative transcription levels in the sigK mutant than the parent strain, suggesting that the sporulation pathway was blocked in the sigK mutant at an early stage. We conclude that σ(K) is essential for early-stage sporulation in C. botulinum ATCC 3502, rather than being involved in late-stage sporulation, as reported for the sporulation model organism B. subtilis. Understanding the sporulation mechanism of C. botulinum provides keys to control the public health risks that the spores of this dangerous pathogen cause through foods.
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22
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23
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24
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Steiner E, Dago AE, Young DI, Heap JT, Minton NP, Hoch JA, Young M. Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum. Mol Microbiol 2011; 80:641-54. [PMID: 21401736 DOI: 10.1111/j.1365-2958.2011.07608.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phosphorylated Spo0A transcription factor controls the initiation of endospore formation in Clostridium acetobutylicum, but genes encoding key phosphorelay components, Spo0F and Spo0B, are missing in the genome. We hypothesized that the five orphan histidine kinases of C. acetobutylicum interact directly with Spo0A to control its phosphorylation state. Sequential targeted gene disruption and gene expression profiling provided evidence for two pathways for Spo0A activation, one dependent on a histidine kinase encoded by cac0323, the other on both histidine kinases encoded by cac0903 and cac3319. Purified Cac0903 and Cac3319 kinases autophosphorylated and transferred phosphoryl groups to Spo0A in vitro, confirming their role in Spo0A activation in vivo. A cac0437 mutant hyper-sporulated, suggesting that Cac0437 is a modulator that prevents sporulation and maintains cellular Spo0A∼P homeostasis during growth. Accordingly, Cac0437 has apparently lost the ability to autophosphorylate in vitro; instead it catalyses the ATP-dependent dephosphorylation of Spo0A∼P releasing inorganic phosphate. Direct phosphorylation of Spo0A by histidine kinases and dephosphorylation by kinase-like proteins may be a common feature of the clostridia that may represent the ancestral state before the great oxygen event some 2.4 billion years ago, after which additional phosphorelay proteins were recruited in the evolutionary lineage that led to the bacilli.
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Affiliation(s)
- Elisabeth Steiner
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion SY23 3DD, UK
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25
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Abstract
Bacteria can exist in metabolically inactive states that allow them to survive conditions that are not conducive for growth. Such dormant cells may sense when conditions have improved and re-initiate growth, lest they be outcompeted by their neighbours. Growing bacteria turn over and release large quantities of their cell walls into the environment. Drawing from recent work on the germination of Bacillus subtilis spores, we propose that many microorganisms exit dormancy in response to cell wall muropeptides.
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26
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Singh B, Ghosh J, Islam NM, Dasgupta S, Kirsebom LA. Growth, cell division and sporulation in mycobacteria. Antonie van Leeuwenhoek 2010; 98:165-77. [PMID: 20437098 PMCID: PMC2906719 DOI: 10.1007/s10482-010-9446-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 04/13/2010] [Indexed: 01/25/2023]
Abstract
Bacteria have the ability to adapt to different growth conditions and to survive in various environments. They have also the capacity to enter into dormant states and some bacteria form spores when exposed to stresses such as starvation and oxygen deprivation. Sporulation has been demonstrated in a number of different bacteria but Mycobacterium spp. have been considered to be non-sporulating bacteria. We recently provided evidence that Mycobacterium marinum and likely also Mycobacterium bovis bacillus Calmette–Guérin can form spores. Mycobacterial spores were detected in old cultures and our findings suggest that sporulation might be an adaptation of lifestyle for mycobacteria under stress. Here we will discuss our current understanding of growth, cell division, and sporulation in mycobacteria.
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Affiliation(s)
- Bhupender Singh
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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27
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Dodatko T, Akoachere M, Jimenez N, Alvarez Z, Abel-Santos E. Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores. MICROBIOLOGY-SGM 2009; 156:1244-1255. [PMID: 20035009 DOI: 10.1099/mic.0.030270-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus cereus 569 spores germinate either with inosine as a sole germinant or with a combination of nucleosides and L-alanine. Whereas the inosine-only germination pathway requires the presence of two different germination receptors (GerI and GerQ) to be activated, the nucleoside/alanine germination pathway only needs one of the two receptors. To differentiate how nucleoside recognition varies between the inosine-only germination pathway and the nucleoside/alanine germination pathway, we tested 61 purine analogues as agonists and antagonists of the two pathways in wild-type, DeltagerI and DeltagerQ spores. The structure-activity relationships of germination agonists and antagonists suggest that the inosine-only germination pathway is restricted to recognize a single germinant (inosine), but can be inhibited in predictable patterns by structurally distinct purine nucleosides. B. cereus spores encoding GerI as the only nucleoside receptor (DeltagerQ mutant) showed a germination inhibition profile similar to wild-type spores treated with inosine only. Thus, GerI seems to have a well-organized binding site that recognizes inosine and inhibitors through specific substrate-protein interactions. Structure-activity analysis also showed that the nucleoside/alanine germination pathway is more promiscuous toward purine nucleoside agonists, and is only inhibited by hydrophobic analogues. B. cereus spores encoding GerQ as the only nucleoside receptor (DeltagerI mutant) behaved like wild-type spores treated with inosine and L-alanine. Thus, the GerQ receptor seems to recognize substrates in a more flexible binding site through non-specific interactions. We propose that the GerI receptor is responsible for germinant detection in the inosine-only germination pathway. On the other hand, supplementing inosine with l-alanine allows bypassing of the GerI receptor to activate the more flexible GerQ receptor.
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Affiliation(s)
- Tetyana Dodatko
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Monique Akoachere
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Nadia Jimenez
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Zadkiel Alvarez
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Ernesto Abel-Santos
- Department of Chemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
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Characterization of the sporulation initiation pathway of Clostridium difficile and its role in toxin production. J Bacteriol 2009; 191:7296-305. [PMID: 19783633 DOI: 10.1128/jb.00882-09] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clostridium difficile is responsible for significant mortality and morbidity in the hospitalized elderly. C. difficile spores are infectious and are a major factor contributing to nosocomial transmission. The Spo0A response regulator is the master regulator for sporulation initiation and can influence many other cellular processes. Using the ClosTron gene knockout system, we inactivated genes encoding Spo0A and a putative sporulation-associated sensor histidine kinase in C. difficile. Inactivation of spo0A resulted in an asporogeneous phenotype, whereas inactivation of the kinase reduced C. difficile sporulation capacity by 3.5-fold, suggesting that this kinase also has a role in sporulation initiation. Furthermore, inactivation of either spo0A or the kinase resulted in a marked defect in C. difficile toxin production. Therefore, Spo0A and the signaling pathway that modulates its activity appear to be involved in regulation of toxin synthesis in C. difficile. In addition, Spo0A was directly phosphorylated by a putative sporulation-associated kinase, supporting the hypothesis that sporulation initiation in C. difficile is controlled by a two-component signal transduction system rather than a multicomponent phosphorelay. The implications of these findings for C. difficile sporulation, virulence, and transmission are discussed.
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The effect of calcium on the transcriptome of sporulating B. subtilis cells. Int J Food Microbiol 2009; 133:234-42. [PMID: 19552981 DOI: 10.1016/j.ijfoodmicro.2009.05.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 05/08/2009] [Accepted: 05/11/2009] [Indexed: 11/21/2022]
Abstract
Bacterial spores formed in the presence of high concentrations of minerals are a major problem in the food industry because of their extreme heat resistance. In order to enhance our insight in the molecular mechanisms underlying this phenomenon we have performed a detailed time-resolved analysis of the genome-wide transcriptome pattern of Bacillus subtilis sporulated both in the absence and presence of high calcium concentrations. The data was analysed in two ways. First, we determined the influence of the presence of high calcium levels during sporulation on the expression of gene groups as defined in Subtilist and KEGG pathways database. Second, we assessed the differential expression at the level of individual genes. When analysing groups and pathways, we found that those annotated as being involved in sporulation were significantly affected. Also, groups and pathways involved in flagella formation and biofilm matrix production were affected by the presence of calcium in the sporulation medium. When we analysed the behaviour of individual genes we found 305 genes influenced by calcium, including all known spore coat polysaccharide biosynthesis genes (10 induced and 1 repressed). A number of the calcium affected genes were also involved in biofilm formation. Minimal overlap with other stress outputs like sigma B activation and weak acid stress response was noted. Those genes that did overlap were unique to that combination which corroborates the notion that the cells sense these conditions differently.
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30
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Whitworth DE, Cock PJA. Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 2009; 37:459-66. [DOI: 10.1007/s00726-009-0259-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 02/02/2009] [Indexed: 01/22/2023]
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31
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Dubey GP, Narayan A, Mattoo AR, Singh GP, Kurupati RK, Zaman MS, Aggarwal A, Baweja RB, Basu-Modak S, Singh Y. Comparative genomic study of spo0E family genes and elucidation of the role of Spo0E in Bacillus anthracis. Arch Microbiol 2008; 191:241-53. [DOI: 10.1007/s00203-008-0446-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 09/05/2008] [Accepted: 11/03/2008] [Indexed: 11/30/2022]
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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: 11] [Impact Index Per Article: 0.7] [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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Galperin MY, Nikolskaya AN. Identification of sensory and signal-transducing domains in two-component signaling systems. Methods Enzymol 2007; 422:47-74. [PMID: 17628134 PMCID: PMC4445681 DOI: 10.1016/s0076-6879(06)22003-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The availability of complete genome sequences of diverse bacteria and archaea makes comparative sequence analysis a powerful tool for analyzing signal transduction systems encoded in these genomes. However, most signal transduction proteins consist of two or more individual protein domains, which significantly complicates their functional annotation and makes automated annotation of these proteins in the course of large-scale genome sequencing projects particularly unreliable. This chapter describes certain common-sense protocols for sequence analysis of two-component histidine kinases and response regulators, as well as other components of the prokaryotic signal transduction machinery: Ser/Thr/Tyr protein kinases and protein phosphatases, adenylate and diguanylate cyclases, and c-di-GMP phosphodiesterases. These protocols rely on publicly available computational tools and databases and can be utilized by anyone with Internet access.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Galperin MY. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 2006; 188:4169-82. [PMID: 16740923 PMCID: PMC1482966 DOI: 10.1128/jb.01887-05] [Citation(s) in RCA: 374] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 03/28/2006] [Indexed: 11/20/2022] Open
Abstract
CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (approximately 14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Paredes CJ, Alsaker KV, Papoutsakis ET. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol 2005; 3:969-78. [PMID: 16261177 DOI: 10.1038/nrmicro1288] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Clostridia are anaerobic, endospore-forming prokaryotes that include strains of importance to human and animal health and physiology, cellulose degradation, solvent production and bioremediation. Their differentiation and related developmental programmes are not well understood at the molecular level. Recent genome sequencing and transcriptional-profiling studies have offered a glimpse of their inner workings and indicate that a better understanding of the orchestration of the molecular events that underlie their unique physiology, capabilities and diversity will pay major dividends.
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Affiliation(s)
- Carlos J Paredes
- Department of Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
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