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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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2
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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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3
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Mearls EB, Jackter J, Colquhoun JM, Farmer V, Matthews AJ, Murphy LS, Fenton C, Camp AH. Transcription and translation of the sigG gene is tuned for proper execution of the switch from early to late gene expression in the developing Bacillus subtilis spore. PLoS Genet 2018; 14:e1007350. [PMID: 29702640 PMCID: PMC5942855 DOI: 10.1371/journal.pgen.1007350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/09/2018] [Accepted: 04/03/2018] [Indexed: 12/01/2022] Open
Abstract
A cascade of alternative sigma factors directs developmental gene expression during spore formation by the bacterium Bacillus subtilis. As the spore develops, a tightly regulated switch occurs in which the early-acting sigma factor σF is replaced by the late-acting sigma factor σG. The gene encoding σG (sigG) is transcribed by σF and by σG itself in an autoregulatory loop; yet σG activity is not detected until σF-dependent gene expression is complete. This separation in σF and σG activities has been suggested to be due at least in part to a poorly understood intercellular checkpoint pathway that delays sigG expression by σF. Here we report the results of a careful examination of sigG expression during sporulation. Unexpectedly, our findings argue against the existence of a regulatory mechanism to delay sigG transcription by σF and instead support a model in which sigG is transcribed by σF with normal timing, but at levels that are very low. This low-level expression of sigG is the consequence of several intrinsic features of the sigG regulatory and coding sequence—promoter spacing, secondary structure potential of the mRNA, and start codon identity—that dampen its transcription and translation. Especially notable is the presence of a conserved hairpin in the 5’ leader sequence of the sigG mRNA that occludes the ribosome-binding site, reducing translation by up to 4-fold. Finally, we demonstrate that misexpression of sigG from regulatory and coding sequences lacking these features triggers premature σG activity in the forespore during sporulation, as well as inappropriate σG activity during vegetative growth. Altogether, these data indicate that transcription and translation of the sigG gene is tuned to prevent vegetative expression of σG and to ensure the precise timing of the switch from σF to σG in the developing spore. Global changes in gene expression occur during normal cellular growth and development, as well as during cancer cell transformation and bacterial pathogenesis. In this study we have investigated the molecular mechanisms that drive the switch from early to late developmental gene expression during spore formation by the model bacterium Bacillus subtilis. At early times, gene expression in the developing spore is directed by the transcription factor σF; at later times σF is replaced by σG. An important, yet poorly understood aspect of this σF-to-σG transition is how σG activation is delayed until the early, σF-directed phase of gene expression is complete. Here we have carefully examined expression of the gene encoding σG, sigG, and found that its transcription and translation are ordinarily dampened by several features of its regulatory and coding sequences. Moreover, we have found that this “tuning” of sigG expression is required for proper timing of the switch to σG. These results reframe our understanding of how sigG is regulated during B. subtilis sporulation and, more broadly, advance our understanding of how global changes in gene expression can be precisely executed at the molecular/genetic level.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/physiology
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Inverted Repeat Sequences
- Models, Genetic
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sigma Factor/biosynthesis
- Sigma Factor/genetics
- Signal Transduction
- Spores, Bacterial/genetics
- Spores, Bacterial/physiology
- Transcription, Genetic
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Affiliation(s)
- Elizabeth B. Mearls
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Jacquelin Jackter
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Veronica Farmer
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Allison J. Matthews
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Laura S. Murphy
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Colleen Fenton
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
- * E-mail:
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Martínez-Lumbreras S, Alfano C, Evans NJ, Collins KM, Flanagan KA, Atkinson RA, Krysztofinska EM, Vydyanath A, Jackter J, Fixon-Owoo S, Camp AH, Isaacson RL. Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB. Structure 2018; 26:640-648.e5. [PMID: 29526435 PMCID: PMC5890618 DOI: 10.1016/j.str.2018.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/17/2017] [Accepted: 02/06/2018] [Indexed: 11/23/2022]
Abstract
Global changes in bacterial gene expression can be orchestrated by the coordinated activation/deactivation of alternative sigma (σ) factor subunits of RNA polymerase. Sigma factors themselves are regulated in myriad ways, including via anti-sigma factors. Here, we have determined the solution structure of anti-sigma factor CsfB, responsible for inhibition of two alternative sigma factors, σG and σE, during spore formation by Bacillus subtilis. CsfB assembles into a symmetrical homodimer, with each monomer bound to a single Zn2+ ion via a treble-clef zinc finger fold. Directed mutagenesis indicates that dimer formation is critical for CsfB-mediated inhibition of both σG and σE, and we have characterized these interactions in vitro. This work represents an advance in our understanding of how CsfB mediates inhibition of two alternative sigma factors to drive developmental gene expression in a bacterium.
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MESH Headings
- Amino Acid Sequence
- Bacillus subtilis/chemistry
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Binding Sites
- Cations, Divalent
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Multimerization
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sigma Factor/antagonists & inhibitors
- Sigma Factor/chemistry
- Sigma Factor/genetics
- Sigma Factor/metabolism
- Spores, Bacterial/chemistry
- Spores, Bacterial/genetics
- Spores, Bacterial/metabolism
- Zinc/chemistry
- Zinc/metabolism
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Affiliation(s)
| | - Caterina Alfano
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy
| | - Nicola J Evans
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katherine M Collins
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Kelly A Flanagan
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - R Andrew Atkinson
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Ewelina M Krysztofinska
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Anupama Vydyanath
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Jacquelin Jackter
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Sarah Fixon-Owoo
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Amy H Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
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A Membrane-Embedded Amino Acid Couples the SpoIIQ Channel Protein to Anti-Sigma Factor Transcriptional Repression during Bacillus subtilis Sporulation. J Bacteriol 2016; 198:1451-63. [PMID: 26929302 DOI: 10.1128/jb.00958-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/22/2016] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED SpoIIQ is an essential component of a channel connecting the developing forespore to the adjacent mother cell during Bacillus subtilis sporulation. This channel is generally required for late gene expression in the forespore, including that directed by the late-acting sigma factor σ(G) Here, we present evidence that SpoIIQ also participates in a previously unknown gene regulatory circuit that specifically represses expression of the gene encoding the anti-sigma factor CsfB, a potent inhibitor of σ(G) The csfB gene is ordinarily transcribed in the forespore only by the early-acting sigma factor σ(F) However, in a mutant lacking the highly conserved SpoIIQ transmembrane amino acid Tyr-28, csfB was also aberrantly transcribed later by σ(G), the very target of CsfB inhibition. This regulation of csfB by SpoIIQ Tyr-28 is specific, given that the expression of other σ(F)-dependent genes was unaffected. Moreover, we identified a conserved element within the csfB promoter region that is both necessary and sufficient for SpoIIQ Tyr-28-mediated inhibition. These results indicate that SpoIIQ is a bifunctional protein that not only generally promotes σ(G)activity in the forespore as a channel component but also specifically maximizes σ(G)activity as part of a gene regulatory circuit that represses σ(G)-dependent expression of its own inhibitor, CsfB. Finally, we demonstrate that SpoIIQ Tyr-28 is required for the proper localization and stability of the SpoIIE phosphatase, raising the possibility that these two multifunctional proteins cooperate to fine-tune developmental gene expression in the forespore at late times. IMPORTANCE Cellular development is orchestrated by gene regulatory networks that activate or repress developmental genes at the right time and place. Late gene expression in the developing Bacillus subtilis spore is directed by the alternative sigma factor σ(G) The activity of σ(G)requires a channel apparatus through which the adjacent mother cell provides substrates that generally support gene expression. Here we report that the channel protein SpoIIQ also specifically maximizes σ(G)activity as part of a previously unknown regulatory circuit that prevents σ(G)from activating transcription of the gene encoding its own inhibitor, the anti-sigma factor CsfB. The discovery of this regulatory circuit significantly expands our understanding of the gene regulatory network controlling late gene expression in the developing B. subtilis spore.
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Dual-specificity anti-sigma factor reinforces control of cell-type specific gene expression in Bacillus subtilis. PLoS Genet 2015; 11:e1005104. [PMID: 25835496 PMCID: PMC4383634 DOI: 10.1371/journal.pgen.1005104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gene expression during spore development in Bacillus subtilis is controlled by cell type-specific RNA polymerase sigma factors. σFand σE control early stages of development in the forespore and the mother cell, respectively. When, at an intermediate stage in development, the mother cell engulfs the forespore, σF is replaced by σG and σE is replaced by σK. The anti-sigma factor CsfB is produced under the control of σF and binds to and inhibits the auto-regulatory σG, but not σF. A position in region 2.1, occupied by an asparagine in σG and by a glutamate in οF, is sufficient for CsfB discrimination of the two sigmas, and allows it to delay the early to late switch in forespore gene expression. We now show that following engulfment completion, csfB is switched on in the mother cell under the control of σK and that CsfB binds to and inhibits σE but not σK, possibly to facilitate the switch from early to late gene expression. We show that a position in region 2.3 occupied by a conserved asparagine in σE and by a conserved glutamate in σK suffices for discrimination by CsfB. We also show that CsfB prevents activation of σG in the mother cell and the premature σG-dependent activation of σK. Thus, CsfB establishes negative feedback loops that curtail the activity of σE and prevent the ectopic activation of σG in the mother cell. The capacity of CsfB to directly block σE activity may also explain how CsfB plays a role as one of the several mechanisms that prevent σE activation in the forespore. Thus the capacity of CsfB to differentiate between the highly similar σF/σG and σE/σK pairs allows it to rinforce the cell-type specificity of these sigma factors and the transition from early to late development in B. subtilis, and possibly in all sporeformers that encode a CsfB orthologue. Precise temporal and cell-type specific regulation of gene expression is required for development of differentiated cells even in simple organisms. Endospore development by the bacterium Bacillus subtilis involves only two types of differentiated cells, a forespore that develops into the endospore, and a mother cell that nurtures the developing endospore. During development temporal and cell-type specific regulation of gene expression is controlled by transcription factors called sigma factors (σ). An anti-sigma factor known as CsfB binds to σG to prevent its premature activity in the forespore. We found that CsfB is also expressed in the mother cell where it blocks ectopic activity of σG, and blocks the activity σE to allow σK to take over control of gene expression during the final stages of development. Our finding that CsfB directly blocks σE activity also explains how CsfB plays a role in preventing ectopic activity of σE in the forespore. Remarkably, each of the major roles of CsfB, (i.e., control of ectopic σG and σE activities, and the temporal limitation of σE activity) is also accomplished by redundant regulatory processes. This redundancy reinforces control of key regulatory steps to insure reliability and stability of the developmental process.
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7
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Saujet L, Pereira FC, Serrano M, Soutourina O, Monot M, Shelyakin PV, Gelfand MS, Dupuy B, Henriques AO, Martin-Verstraete I. Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile. PLoS Genet 2013; 9:e1003756. [PMID: 24098137 PMCID: PMC3789822 DOI: 10.1371/journal.pgen.1003756] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/12/2013] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile, a Gram positive, anaerobic, spore-forming bacterium is an emergent pathogen and the most common cause of nosocomial diarrhea. Although transmission of C. difficile is mediated by contamination of the gut by spores, the regulatory cascade controlling spore formation remains poorly characterized. During Bacillus subtilis sporulation, a cascade of four sigma factors, σ(F) and σ(G) in the forespore and σ(E) and σ(K) in the mother cell governs compartment-specific gene expression. In this work, we combined genome wide transcriptional analyses and promoter mapping to define the C. difficile σ(F), σ(E), σ(G) and σ(K) regulons. We identified about 225 genes under the control of these sigma factors: 25 in the σ(F) regulon, 97 σ(E)-dependent genes, 50 σ(G)-governed genes and 56 genes under σ(K) control. A significant fraction of genes in each regulon is of unknown function but new candidates for spore coat proteins could be proposed as being synthesized under σ(E) or σ(K) control and detected in a previously published spore proteome. SpoIIID of C. difficile also plays a pivotal role in the mother cell line of expression repressing the transcription of many members of the σ(E) regulon and activating sigK expression. Global analysis of developmental gene expression under the control of these sigma factors revealed deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We showed that the expression of the σ(E) regulon in the mother cell was not strictly under the control of σ(F) despite the fact that the forespore product SpoIIR was required for the processing of pro-σ(E). In addition, the σ(K) regulon was not controlled by σ(G) in C. difficile in agreement with the lack of pro-σ(K) processing. This work is one key step to obtain new insights about the diversity and evolution of the sporulation process among Firmicutes.
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Affiliation(s)
- Laure Saujet
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Fátima C. Pereira
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Monica Serrano
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Pavel V. Shelyakin
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny per, 19, Moscow, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny per, 19, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Biengineering and Bioinformatics, Vorobievy Gory 1-73, Moscow, Russia
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Adriano O. Henriques
- Microbial Development Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
- * E-mail:
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Global analysis of the sporulation pathway of Clostridium difficile. PLoS Genet 2013; 9:e1003660. [PMID: 23950727 PMCID: PMC3738446 DOI: 10.1371/journal.pgen.1003660] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/28/2013] [Indexed: 12/19/2022] Open
Abstract
The Gram-positive, spore-forming pathogen Clostridium difficile is the leading definable cause of healthcare-associated diarrhea worldwide. C. difficile infections are difficult to treat because of their frequent recurrence, which can cause life-threatening complications such as pseudomembranous colitis. The spores of C. difficile are responsible for these high rates of recurrence, since they are the major transmissive form of the organism and resistant to antibiotics and many disinfectants. Despite the importance of spores to the pathogenesis of C. difficile, little is known about their composition or formation. Based on studies in Bacillus subtilis and other Clostridium spp., the sigma factors σ(F), σ(E), σ(G), and σ(K) are predicted to control the transcription of genes required for sporulation, although their specific functions vary depending on the organism. In order to determine the roles of σ(F), σ(E), σ(G), and σ(K) in regulating C. difficile sporulation, we generated loss-of-function mutations in genes encoding these sporulation sigma factors and performed RNA-Sequencing to identify specific sigma factor-dependent genes. This analysis identified 224 genes whose expression was collectively activated by sporulation sigma factors: 183 were σ(F)-dependent, 169 were σ(E)-dependent, 34 were σ(G)-dependent, and 31 were σ(K)-dependent. In contrast with B. subtilis, C. difficile σ(E) was dispensable for σ(G) activation, σ(G) was dispensable for σ(K) activation, and σ(F) was required for post-translationally activating σ(G). Collectively, these results provide the first genome-wide transcriptional analysis of genes induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes.
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Serrano M, Real G, Santos J, Carneiro J, Moran CP, Henriques AO. A negative feedback loop that limits the ectopic activation of a cell type-specific sporulation sigma factor of Bacillus subtilis. PLoS Genet 2011; 7:e1002220. [PMID: 21935351 PMCID: PMC3174212 DOI: 10.1371/journal.pgen.1002220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 06/18/2011] [Indexed: 11/18/2022] Open
Abstract
Two highly similar RNA polymerase sigma subunits, σF and σG, govern the early and late phases of forespore-specific gene expression during spore differentiation in Bacillus subtilis. σF drives synthesis of σG but the latter only becomes active once engulfment of the forespore by the mother cell is completed, its levels rising quickly due to a positive feedback loop. The mechanisms that prevent premature or ectopic activation of σG while discriminating between σF and σG in the forespore are not fully comprehended. Here, we report that the substitution of an asparagine by a glutamic acid at position 45 of σG (N45E) strongly reduced binding by a previously characterized anti-sigma factor, CsfB (also known as Gin), in vitro, and increased the activity of σG in vivo. The N45E mutation caused the appearance of a sub-population of pre-divisional cells with strong activity of σG. CsfB is normally produced in the forespore, under σF control, but sigGN45E mutant cells also expressed csfB and did so in a σG-dependent manner, autonomously from σF. Thus, a negative feedback loop involving CsfB counteracts the positive feedback loop resulting from ectopic σG activity. N45 is invariant in the homologous position of σG orthologues, whereas its functional equivalent in σF proteins, E39, is highly conserved. While CsfB does not bind to wild-type σF, a E39N substitution in σF resulted in efficient binding of CsfB to σF. Moreover, under certain conditions, the E39N alteration strongly restrains the activity of σF in vivo, in a csfB-dependent manner, and the efficiency of sporulation. Therefore, a single amino residue, N45/E39, is sufficient for the ability of CsfB to discriminate between the two forespore-specific sigma factors in B. subtilis. Positive auto-regulation of a transcriptional activator during cell differentiation or development often allows the rapid and robust deployment of cell- and stage-specific genes and the routing of the differentiating cell down a specific path. Positive auto-regulation however, raises the potential for inappropriate activity of the transcription factor. Here we unravel the role of a previously characterized anti-sigma factor, CsfB, in a negative feedback loop that prevents ectopic expression of the sporulation-specific sigma factor σG of Bacillus subtilis. σG is activated in the forespore, one of the two chambers of the developing cell, at an intermediate stage in spore development. Once active, a positive feedback loop allows the rapid accumulation of σG. Synthesis of both σG and CsfB is under the control of the early forespore regulator σF, and CsfB may help prevent the premature activity of σG in the forespore. However, CsfB is also produced under σG control in non-sporulating cells, setting a negative feedback loop that we show limits its ectopic activation. We further show that an asparagine residue conserved among σG orthologues is critical for binding and inhibition by CsfB, whereas the exclusion of asparagine from the homologous position in σF confers immunity to CsfB.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gonçalo Real
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Joana Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Charles P. Moran
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Adriano O. Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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Inactivation of σF in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division and abolishes σE and σG protein expression but does not block solvent formation. J Bacteriol 2011; 193:2429-40. [PMID: 21421765 DOI: 10.1128/jb.00088-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum is both a model organism for the understanding of sporulation in solventogenic clostridia and its relationship to solvent formation and an industrial organism for anaerobic acetone-butanol-ethanol (ABE) fermentation. How solvent production is coupled to endospore formation--both stationary-phase events--remains incompletely understood at the molecular level. Specifically, it is unclear how sporulation-specific sigma factors affect solvent formation. Here the sigF gene in C. acetobutylicum was successfully disrupted and silenced. Not only σ(F) but also the sigma factors σ(E) and σ(G) were not detected in the sigF mutant (FKO1), and differentiation was stopped prior to asymmetric division. Since plasmid expression of the spoIIA operon (spoIIAA-spoIIAB-sigF) failed to complement FKO1, the operon was integrated into the FKO1 chromosome to generate strain FKO1-C. In FKO1-C, σ(F) expression was restored along with sporulation and σ(E) and σ(G) protein expression. Quantitative reverse transcription-PCR (RT-PCR) analysis of a select set of genes (csfB, gpr, spoIIP, sigG, lonB, and spoIIR) that could be controlled by σ(F), based on the Bacillus subtilis model, indicated that sigG may be under the control of σ(F), but spoIIR, an important activator of σ(E) in B. subtilis, is not, and neither are the rest of the genes investigated. FKO1 produced solvents at a level similar to that of the parent strain, but solvent levels were dependent on the physiological state of the inoculum. Finally, the complementation strain FKO1-C is the first reported instance of purposeful integration of multiple functional genes into a clostridial chromosome--here, the C. acetobutylicum chromosome--with the aim of altering cell metabolism and differentiation.
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A small protein required for the switch from {sigma}F to {sigma}G during sporulation in Bacillus subtilis. J Bacteriol 2010; 193:116-24. [PMID: 21037003 DOI: 10.1128/jb.00949-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cascade of alternative sigma factors governs the program of developmental gene expression during sporulation in Bacillus subtilis. Little is known, however, about how the early-acting sigma factors are inactivated and replaced by the later-acting factors. Here we identify a small protein, Fin (formerly known as YabK), that is required for efficient switching from σ(F)- to σ(G)-directed gene expression in the forespore compartment of the developing sporangium. The fin gene, which is conserved among Bacillus species and species of related genera, is transcribed in the forespore under the control of both σ(F) and σ(G). Cells mutant for fin are unable to fully deactivate σ(F) and, conversely, are unable to fully activate σ(G). Consistent with their deficiency in σ(G)-directed gene expression, fin cells are arrested in large numbers following the engulfment stage of sporulation, ultimately forming 50-fold fewer heat-resistant spores than the wild type. Based in part on the similarity of Fin to the anti-σ(G) factor CsfB (also called Gin), we speculate that Fin is an anti-σ(F) factor which, by disabling σ(F), promotes the switch to late developmental gene expression in the forespore.
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