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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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Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. J Bacteriol 2011; 193:5420-30. [PMID: 21821775 DOI: 10.1128/jb.05309-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus cereus group of bacteria is a group of closely related species that are of medical and economic relevance, including B. anthracis, B. cereus, and B. thuringiensis. Bacteria from the Bacillus cereus group encode three large, highly conserved genes of unknown function (named crdA, crdB, and crdC) that are composed of 16 to 35 copies of a repeated domain of 132 amino acids at the protein level. Bioinformatic analysis revealed that there is a phylogenetic bias in the genomic distribution of these genes and that strains harboring all three large genes mainly belong to cluster III of the B. cereus group phylogenetic tree. The evolutionary history of the three large genes implicates gain, loss, duplication, internal deletion, and lateral transfer. Furthermore, we show that the transcription of previously identified antisense open reading frames in crdB is simultaneously regulated with its host gene throughout the life cycle in vitro, with the highest expression being at the onset of sporulation. In B. anthracis, different combinations of double- and triple-knockout mutants of the three large genes displayed slower and less efficient sporulation processes than the parental strain. Altogether, the functional studies suggest an involvement of these three large genes in the sporulation process.
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Zimmer M, Scherer S, Loessner MJ. Genomic analysis of Clostridium perfringens bacteriophage phi3626, which integrates into guaA and possibly affects sporulation. J Bacteriol 2002; 184:4359-68. [PMID: 12142405 PMCID: PMC135250 DOI: 10.1128/jb.184.16.4359-4368.2002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2002] [Accepted: 05/17/2002] [Indexed: 11/20/2022] Open
Abstract
Two temperate viruses, phi3626 and phi8533, have been isolated from lysogenic Clostridium perfringens strains. Phage phi3626 was chosen for detailed analysis and was inspected by electron microscopy, protein profiling, and host range determination. For the first time, the nucleotide sequence of a bacteriophage infecting Clostridium species was determined. The virus belongs to the Siphoviridae family of the tailed phages, the order Caudovirales. Its genome consists of a linear double-stranded DNA molecule of 33,507 nucleotides, with invariable 3'-protruding cohesive ends of nine residues. Fifty open reading frames were identified, which are organized in three major life cycle-specific gene clusters. The genes required for lytic development show an opposite orientation and arrangement compared to the lysogeny control region. A function could be assigned to 19 gene products, based upon bioinformatic analyses, N-terminal amino acid sequencing, or experimental evidence. These include DNA-packaging proteins, structural components, a dual lysis system, a putative lysogeny switch, and proteins that are involved in replication, recombination, and modification of phage DNA. The presence of genes encoding a putative sigma factor related to sporulation-dependent sigma factors and a putative sporulation-dependent transcription regulator suggests a possible interaction of phi3626 with onset of sporulation in C. perfringens. We found that the phi3626 attachment site attP lies in a noncoding region immediately downstream of int. Integration of the viral genome occurs into the bacterial attachment site attB, which is located within the 3' end of a guaA homologue. This essential housekeeping gene is functionally independent of the integration status, due to reconstitution of its terminal codons by phage sequence.
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Affiliation(s)
- Markus Zimmer
- Institut für Mikrobiologie, FML Weihenstephan, Technische Universität München, D-85350 Freising, Germany
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Komano T, Takabe S, Sakai H. Transcription of the insecticidal crystal protein genes of Bacillus thuringiensis. BIOTECHNOLOGY ANNUAL REVIEW 2000; 5:131-54. [PMID: 10874999 DOI: 10.1016/s1387-2656(00)05034-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Production of a large amount of insecticidal crystal proteins encoded on large plasmids is largely dependent upon the mother cell, Bacillus thuringiensis (B. thuringiensis, also Bt), specific transcription systems attributable to sporulation. In the middle stages of sporulation, cry4A is most actively transcribed from the promoter cry4A-P1. The proximal transcriptional start point of cry4A, which is under the control of the promoter P1, is used in Bacillus subtilis (B. subtilis) in the middle stage of sporulation. The nucleotide sequence that determines the cry4A-P1 promoter is homologous to the consensus sequence for the promoter of sigma E-specific genes in B. subtilis, and to those promoters of the insecticidal protein genes that are efficiently transcribed in vitro with the RNA polymerase E sigma 35 isolated from B. thuringiensis. The sigma factor sigma 35 of B. thuringiensis is highly homologous and functionally equivalent to sigma E of B. subtilis. These results suggest that the cry4A transcription from P1 is under the control of sigma E in B. subtilis, and under the control of sigma 35 in B. thuringiensis.
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Affiliation(s)
- T Komano
- Department of Genetic Engineering, Faculty of Biology-oriented Science and Technology, Kinki University, Wakayama, Japan.
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Yoshisue H, Ihara K, Nishimoto T, Sakai H, Komano T. Expression of the genes for insecticidal crystal proteins in Bacillus thuringiensis: cryIVA, not cryIVB, is transcribed by RNA polymerase containing sigma H and that containing sigma E. FEMS Microbiol Lett 1995; 127:65-72. [PMID: 7737485 DOI: 10.1111/j.1574-6968.1995.tb07451.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
To investigate the mechanism of transcriptional regulation of cryIVA and cryIVB, encoding 130-kDa dipteran-active crystal proteins, in Bacillus thuringiensis subsp. israelensis, we introduced each gene into several sporulation mutants of Bacillus subtilis. A spoIIG mutation, the wild-type gene of which encodes sigma E precursor, completely blocked the cryIVB transcription. In contrast, low but detectable transcription of cryIVA was observed in the spoIIG mutant. In the wild-type B. subtilis, no transcription of cryIVB was detected before T2 (2 h after the onset of stationary phase), while the cryIVA transcription started at the late exponential phase at low levels. Furthermore, in a wild-type strain of B. thuringiensis subsp. israelensis, transcription of cryIVA began earlier than that of genes encoding other crystal components, cryIVB and cytA. A consensus sequence recognized by an RNA polymerase containing sigma H of B. subtilis was found upstream of the transcription start point of cryIVA, which overlapped with that recognized by sigma E.
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Affiliation(s)
- H Yoshisue
- Department of Agricultural Chemistry, Faculty of Agriculture, Kyoto University, Japan
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