L. Deakin, C. S. Fagan, R. Dawson, L. Pickard, and D. , Gene Is a Persistence and Transmission Factor, Infection and Immunity, vol.80, issue.8, pp.2704-2711, 2012.
DOI : 10.1128/IAI.00147-12

T. Lawley, C. S. Deakin, L. Goulding, D. Yen, and J. , Use of Purified Clostridium difficile Spores To Facilitate Evaluation of Health Care Disinfection Regimens, Applied and Environmental Microbiology, vol.76, issue.20, pp.6895-6900, 2010.
DOI : 10.1128/AEM.00718-10

M. Sarker and D. Paredes-sabja, infection: germination and colonization, Future Microbiology, vol.7, issue.8, pp.933-943, 2012.
DOI : 10.2217/fmb.12.64

J. Sorg and A. Sonenshein, Bile Salts and Glycine as Cogerminants for Clostridium difficile Spores, Journal of Bacteriology, vol.190, issue.7, pp.2505-2512, 2008.
DOI : 10.1128/JB.01765-07

D. Hilbert and P. Piggot, Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation, Microbiology and Molecular Biology Reviews, vol.68, issue.2, pp.234-262, 2004.
DOI : 10.1128/MMBR.68.2.234-262.2004

D. Higgins and J. Dworkin, sporulation, FEMS Microbiology Reviews, vol.36, issue.1, pp.131-148, 2012.
DOI : 10.1111/j.1574-6976.2011.00310.x

V. Molle, M. Fujita, S. Jensen, P. Eichenberger, and J. Gonzalez-pastor, The Spo0A regulon of Bacillus subtilis, Molecular Microbiology, vol.10, issue.5, pp.1683-1701, 2003.
DOI : 10.1046/j.1365-2958.2003.03818.x

URL : https://hal.archives-ouvertes.fr/hal-00314423

L. Steil, M. Serrano, A. Henriques, and U. Volker, Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis, Microbiology, vol.151, issue.2, pp.399-420, 2005.
DOI : 10.1099/mic.0.27493-0

S. Wang, B. Setlow, E. Conlon, J. Lyon, and D. Imamura, The Forespore Line of Gene Expression in Bacillus subtilis, Journal of Molecular Biology, vol.358, issue.1, pp.16-37, 2006.
DOI : 10.1016/j.jmb.2006.01.059

J. Londono-vallejo and P. Stragier, Cell-cell signaling pathway activating a developmental transcription factor in Bacillus subtilis., Genes & Development, vol.9, issue.4, pp.503-508, 1995.
DOI : 10.1101/gad.9.4.503

P. Eichenberger, S. Jensen, E. Conlon, C. Van-ooij, and J. Silvaggi, The ??E Regulon and the Identification of Additional Sporulation Genes in Bacillus subtilis, Journal of Molecular Biology, vol.327, issue.5, pp.945-972, 2003.
DOI : 10.1016/S0022-2836(03)00205-5

A. Feucht, L. Evans, and J. Errington, Identification of sporulation genes by genome-wide analysis of the ??E regulon of Bacillus subtilis, Microbiology, vol.149, issue.10, pp.3023-3034, 2003.
DOI : 10.1099/mic.0.26413-0

P. Eichenberger, M. Fujita, S. Jensen, E. Conlon, and D. Rudner, The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis, PLoS Biology, vol.212, issue.10, p.328, 2004.
DOI : 10.1371/journal.pbio.0020328.st004

A. Abecassis, M. Serrano, R. Alves, L. Quintais, and J. Pereira-leal, A Genomic Signature and the Identification of New Sporulation Genes, Journal of Bacteriology, vol.195, issue.9, pp.2101-2115, 2013.
DOI : 10.1128/JB.02110-12

M. De-hoon, P. Eichenberger, and D. Vitkup, Hierarchical Evolution of the Bacterial Sporulation Network, Current Biology, vol.20, issue.17, pp.735-745, 2010.
DOI : 10.1016/j.cub.2010.06.031

M. Galperin, S. Mekhedov, P. Puigbo, S. Smirnov, and Y. Wolf, : towards the minimal set of sporulation-specific genes, Environmental Microbiology, vol.187, issue.11, pp.2870-2890, 2012.
DOI : 10.1111/j.1462-2920.2012.02841.x

C. Paredes, K. Alsaker, and E. Papoutsakis, A comparative genomic view of clostridial sporulation and physiology, Nature Reviews Microbiology, vol.177, issue.12, pp.969-978, 2005.
DOI : 10.1038/nrmicro1288

F. Pereira, L. Saujet, A. Tomé, M. Serrano, and M. Monot, The Spore Differentiation Pathway in the Enteric Pathogen Clostridium difficile, PLoS Genetics, vol.60, issue.1, p.1003782, 2013.
DOI : 10.1371/journal.pgen.1003782.s013

URL : https://hal.archives-ouvertes.fr/pasteur-01370787

P. Stragier, A gene odyssey: exploring the genomes of endospore-forming bacteria Bacillus subtilis: from cells to genes and from genes to cells, 2002.

K. Harry, R. Zhou, L. Kroos, and S. Melville, Sporulation and Enterotoxin (CPE) Synthesis Are Controlled by the Sporulation-Specific Sigma Factors SigE and SigK in Clostridium perfringens, Journal of Bacteriology, vol.191, issue.8, pp.2728-2742, 2009.
DOI : 10.1128/JB.01839-08

S. Jones, B. Tracy, S. Gaida, and E. Papoutsakis, Inactivation of ??F in Clostridium acetobutylicum ATCC 824 Blocks Sporulation Prior to Asymmetric Division and Abolishes ??E and ??G Protein Expression but Does Not Block Solvent Formation, Journal of Bacteriology, vol.193, issue.10, pp.2429-2440, 2011.
DOI : 10.1128/JB.00088-11

J. Li and B. Mcclane, Evaluating the Involvement of Alternative Sigma Factors SigF and SigG in Clostridium perfringens Sporulation and Enterotoxin Synthesis, Infection and Immunity, vol.78, issue.10, pp.4286-4293, 2010.
DOI : 10.1128/IAI.00528-10

B. Tracy, S. Jones, and E. Papoutsakis, Inactivation of ??E and ??G in Clostridium acetobutylicum Illuminates Their Roles in Clostridial-Cell-Form Biogenesis, Granulose Synthesis, Solventogenesis, and Spore Morphogenesis, Journal of Bacteriology, vol.193, issue.6, pp.1414-1426, 2011.
DOI : 10.1128/JB.01380-10

J. Haraldsen and A. Sonenshein, Efficient sporulation in Clostridium difficile requires disruption of the ??K gene, Molecular Microbiology, vol.181, issue.Suppl., pp.811-821, 2003.
DOI : 10.1046/j.1365-2958.2003.03471.x

S. Jones, C. Paredes, B. Tracy, N. Cheng, and R. Sillers, The transcriptional program underlying the physiology of clostridial sporulation, Genome Biology, vol.9, issue.7, 2008.
DOI : 10.1186/gb-2008-9-7-r114

L. Saujet, M. Monot, B. Dupuy, O. Soutourina, and I. Martin-verstraete, The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile, Journal of Bacteriology, vol.193, issue.13, pp.3186-3196, 2011.
DOI : 10.1128/JB.00272-11

URL : https://hal.archives-ouvertes.fr/pasteur-01370840

S. Underwood, S. Guan, V. Vijayasubhash, S. Baines, and L. Graham, Characterization of the Sporulation Initiation Pathway of Clostridium difficile and Its Role in Toxin Production, Journal of Bacteriology, vol.191, issue.23, pp.7296-7305, 2009.
DOI : 10.1128/JB.00882-09

E. Steiner, A. Dago, D. Young, J. Heap, and N. Minton, Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum, Molecular Microbiology, vol.31, issue.3, pp.641-654, 2011.
DOI : 10.1111/j.1365-2958.2011.07608.x

K. Rosenbusch, D. Bakker, E. Kuijper, and W. Smits, C. difficile 630??erm Spo0A Regulates Sporulation, but Does Not Contribute to Toxin Production, by Direct High-Affinity Binding to Target DNA, PLoS ONE, vol.180, issue.8, p.48608, 2012.
DOI : 10.1371/journal.pone.0048608.s003

O. Soutourina, M. Monot, P. Boudry, L. Saujet, and C. Pichon, Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile, PLoS Genetics, vol.39, issue.1, p.1003493, 2013.
DOI : 10.1371/journal.pgen.1003493.s014

URL : https://hal.archives-ouvertes.fr/pasteur-01370770

K. Tatti, M. Shuler, C. Moran, and J. , Sequence-specific Interactions Between Promoter DNA and the RNA Polymerase Sigma Factor E, Journal of Molecular Biology, vol.253, issue.1, pp.8-16, 1995.
DOI : 10.1006/jmbi.1995.0531

Y. Zhao and S. Melville, Identification and characterization of sporulationdependent promoters upstream of the enterotoxin gene (cpe) of Clostridium perfringens, J Bacteriol, vol.180, pp.136-142, 1998.

P. Eichenberger, P. Fawcett, and R. Losick, A three-protein inhibitor of polar septation during sporulation in Bacillus subtilis, Molecular Microbiology, vol.39, issue.5, pp.1147-1162, 2001.
DOI : 10.1046/j.1365-2958.2001.02660.x

C. Morlot, T. Uehara, K. Marquis, T. Bernhardt, and D. Rudner, A highly coordinated cell wall degradation machine governs spore morphogenesis in Bacillus subtilis, Genes & Development, vol.24, issue.4, pp.411-422, 2010.
DOI : 10.1101/gad.1878110

A. Camp and R. Losick, involves a protein with similarity to a component of type III secretion channels, Molecular Microbiology, vol.12, issue.Suppl. 1, pp.402-417, 2008.
DOI : 10.1111/j.1365-2958.2008.06289.x

J. Meisner, T. Maehigashi, I. Andre, C. Dunham, C. Moran et al., Structure of the basal components of a bacterial transporter, Proceedings of the National Academy of Sciences, vol.109, issue.14, pp.5446-5451, 2012.
DOI : 10.1073/pnas.1120113109

T. Lawley, N. Croucher, L. Yu, C. S. Sebaihia, and M. , Proteomic and Genomic Characterization of Highly Infectious Clostridium difficile 630 Spores, Journal of Bacteriology, vol.191, issue.17, pp.5377-5386, 2009.
DOI : 10.1128/JB.00597-09

E. Putman, A. Nock, T. Lawley, and A. Shen, SpoIVA and SipL are Clostridium difficile spore morphogenic proteins, J Bacteriol, vol.195, pp.1214-1225, 2013.

P. Permpoonpattana, E. Tolls, R. Nadem, S. Tan, and A. Brisson, Surface Layers of Clostridium difficile Endospores, Journal of Bacteriology, vol.193, issue.23, pp.6461-6470, 2011.
DOI : 10.1128/JB.05182-11

M. Gilmore, D. Bandyopadhyay, A. Dean, S. Linnstaedt, and D. P. , Production of Muramic ??-Lactam in Bacillus subtilis Spore Peptidoglycan, Journal of Bacteriology, vol.186, issue.1, pp.80-89, 2004.
DOI : 10.1128/JB.186.1.80-89.2004

D. Paredes-sabja, N. Sarker, B. Setlow, P. Setlow, and M. Sarker, Roles of DacB and Spm Proteins in Clostridium perfringens Spore Resistance to Moist Heat, Chemicals, and UV Radiation, Applied and Environmental Microbiology, vol.74, issue.12, pp.3730-3738, 2008.
DOI : 10.1128/AEM.00169-08

M. Figueiredo, S. Lobo, J. Carita, L. Nobre, and L. Saraiva, Bacterioferritin protects the anaerobe Desulfovibrio vulgaris Hildenborough against oxygen, Anaerobe, vol.18, issue.4, pp.454-458, 2012.
DOI : 10.1016/j.anaerobe.2012.06.001

C. Adams, B. Eckenroth, E. Putnam, S. Doublie, and A. Shen, Structural and Functional Analysis of the CspB Protease Required for Clostridium Spore Germination, PLoS Pathogens, vol.16, issue.2, p.1003165, 2013.
DOI : 10.1371/journal.ppat.1003165.s008

S. Cartman and N. Minton, A mariner-Based Transposon System for In Vivo Random Mutagenesis of Clostridium difficile, Applied and Environmental Microbiology, vol.76, issue.4, pp.1103-1109, 2010.
DOI : 10.1128/AEM.02525-09

D. Paredes-sabja, P. Setlow, and M. Sarker, Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved, Trends in Microbiology, vol.19, issue.2, pp.85-94, 2011.
DOI : 10.1016/j.tim.2010.10.004

M. Francis, C. Allen, R. Shrestha, and J. Sorg, Bile Acid Recognition by the Clostridium difficile Germinant Receptor, CspC, Is Important for Establishing Infection, PLoS Pathogens, vol.48, issue.5, p.1003356, 2013.
DOI : 10.1371/journal.ppat.1003356.s003

F. Chen, L. Shen, M. Tsai, and K. Chak, The IspA protease???s involvement in the regulation of the sporulation process of Bacillus thuringiensis is revealed by proteomic analysis, Biochemical and Biophysical Research Communications, vol.312, issue.3, pp.708-715, 2003.
DOI : 10.1016/j.bbrc.2003.10.155

F. Rothenbacher, M. Suzuki, J. Hurley, T. Montville, and T. Kirn, Clostridium difficile MazF Toxin Exhibits Selective, Not Global, mRNA Cleavage, Journal of Bacteriology, vol.194, issue.13, pp.3464-3474, 2012.
DOI : 10.1128/JB.00217-12

E. Adler, I. Barak, and P. Stragier, Bacillus subtilis Locus Encoding a Killer Protein and Its Antidote, Journal of Bacteriology, vol.183, issue.12, pp.3574-3581, 2001.
DOI : 10.1128/JB.183.12.3574-3581.2001

F. Tovar-rojo, M. Chander, B. Setlow, and P. Setlow, The Products of the spoVA Operon Are Involved in Dipicolinic Acid Uptake into Developing Spores of Bacillus subtilis, Journal of Bacteriology, vol.184, issue.2, pp.584-587, 2002.
DOI : 10.1128/JB.184.2.584-587.2002

P. Permpoonpattana, J. Phetcharaburanin, A. Mikelsone, M. Dembek, and S. Tan, Functional Characterization of Clostridium difficile Spore Coat Proteins, Journal of Bacteriology, vol.195, issue.7, pp.1492-1503, 2013.
DOI : 10.1128/JB.02104-12

D. Burns, J. Heap, and N. Minton, Clostridium difficile spore germination: an update, Research in Microbiology, vol.161, issue.9, pp.730-734, 2010.
DOI : 10.1016/j.resmic.2010.09.007

Y. Xiao, C. Francke, T. Abee, and M. Wells-bennik, Clostridial spore germination versus bacilli: Genome mining and current insights, Food Microbiology, vol.28, issue.2, pp.266-274, 2011.
DOI : 10.1016/j.fm.2010.03.016

A. Henriques, C. Moran, and J. , Structure, Assembly, and Function of the Spore Surface Layers, Annual Review of Microbiology, vol.61, issue.1, pp.555-588, 2007.
DOI : 10.1146/annurev.micro.61.080706.093224

C. Steichen, J. Kearney, C. Turnbough, and J. , Non-uniform assembly of the Bacillus anthracis exosporium and a bottle cap model for spore germination and outgrowth, Molecular Microbiology, vol.69, issue.2, pp.359-367, 2007.
DOI : 10.1111/j.1365-2958.2007.05658.x

F. Nugroho, H. Yamamoto, Y. Kobayashi, and J. Sekiguchi, Characterization of a new sigma-K-dependent peptidoglycan hydrolase gene that plays a role in Bacillus subtilis mother cell lysis, J Bacteriol, vol.181, pp.6230-6237, 1999.

D. Burns, J. Heap, and N. Minton, SleC Is Essential for Germination of Clostridium difficile Spores in Nutrient-Rich Medium Supplemented with the Bile Salt Taurocholate, Journal of Bacteriology, vol.192, issue.3, pp.657-664, 2010.
DOI : 10.1128/JB.01209-09

K. Gerdes, S. Christensen, and A. Lobner-olesen, Prokaryotic toxin???antitoxin stress response loci, Nature Reviews Microbiology, vol.269, issue.5, pp.371-382, 2005.
DOI : 10.1016/S0092-8674(03)01034-1

L. Harris, N. Welker, and E. Papoutsakis, Northern, Morphological, and Fermentation Analysis of spo0A Inactivation and Overexpression in Clostridium acetobutylicum ATCC 824, Journal of Bacteriology, vol.184, issue.13, pp.3586-3597, 2002.
DOI : 10.1128/JB.184.13.3586-3597.2002

L. Rhayat, S. Duperrier, R. Carballido-lopez, O. Pellegrini, and P. Stragier, Genetic Dissection of an Inhibitor of the Sporulation Sigma Factor ??G, Journal of Molecular Biology, vol.390, issue.5, pp.835-844, 2009.
DOI : 10.1016/j.jmb.2009.05.073

M. Serrano, G. Real, J. Santos, J. Carneiro, C. Moran et al., A Negative Feedback Loop That Limits the Ectopic Activation of a Cell Type???Specific Sporulation Sigma Factor of Bacillus subtilis, PLoS Genetics, vol.55, issue.9, p.1002220, 2011.
DOI : 10.1371/journal.pgen.1002220.s009

I. Bagyan, J. Hobot, and S. Cutting, A compartmentalized regulator of developmental gene expression in Bacillus subtilis., Journal of Bacteriology, vol.178, issue.15, pp.4500-4507, 1996.
DOI : 10.1128/jb.178.15.4500-4507.1996

A. Ramirez-peralta, K. Stewart, S. Thomas, B. Setlow, and Z. Chen, Effects of the SpoVT Regulatory Protein on the Germination and Germination Protein Levels of Spores of Bacillus subtilis, Journal of Bacteriology, vol.194, issue.13, pp.3417-3425, 2012.
DOI : 10.1128/JB.00504-12

G. Cangiano, A. Mazzone, L. Baccigalupi, R. Isticato, and P. Eichenberger, Direct and Indirect Control of Late Sporulation Genes by GerR of Bacillus subtilis, Journal of Bacteriology, vol.192, issue.13, pp.3406-3413, 2010.
DOI : 10.1128/JB.00329-10

P. Himes, S. Mcbryant, and L. Kroos, Two Regions of Bacillus subtilis Transcription Factor SpoIIID Allow a Monomer To Bind DNA, Journal of Bacteriology, vol.192, issue.6, pp.1596-1606, 2010.
DOI : 10.1128/JB.01506-09

B. Kunkel, R. Losick, and P. Stragier, The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene., Genes & Development, vol.4, issue.4, pp.525-535, 1990.
DOI : 10.1101/gad.4.4.525

J. Errington, Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis, Microbiol Rev, vol.57, pp.1-33, 1993.

H. Yoshisue, K. Ihara, T. Nishimoto, H. Sakai, and T. Komano, Cloning and characterization of a Bacillus thuringiensis homolog of the spoIIID gene from Bacillus subtilis, Gene, vol.154, issue.1, pp.23-29, 1995.
DOI : 10.1016/0378-1119(94)00822-A

V. Oke and R. Losick, Multilevel regulation of the sporulation transcription factor sigma K in Bacillus subtilis., Journal of Bacteriology, vol.175, issue.22, pp.7341-7347, 1993.
DOI : 10.1128/jb.175.22.7341-7347.1993

D. Kirk, E. Dahlsten, Z. Zhang, H. Korkeala, and M. Lindstrom, Involvement of Clostridium botulinum ATCC 3502 Sigma Factor K in Early-Stage Sporulation, Applied and Environmental Microbiology, vol.78, issue.13, pp.4590-4606, 2012.
DOI : 10.1128/AEM.00304-12

P. Fawcett, P. Eichenberger, R. Losick, and P. Youngman, The transcriptional profile of early to middle sporulation in Bacillus subtilis, Proceedings of the National Academy of Sciences, vol.97, issue.14, pp.8063-8068, 2000.
DOI : 10.1073/pnas.140209597

R. Jonas and W. Haldenwang, Influence of spo mutations on sigma E synthesis in Bacillus subtilis., Journal of Bacteriology, vol.171, issue.9, pp.5226-5228, 1989.
DOI : 10.1128/jb.171.9.5226-5228.1989

M. Karow, P. Glaser, and P. Piggot, Identification of a gene, spoIIR, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in Bacillus subtilis., Proceedings of the National Academy of Sciences, vol.92, issue.6, pp.2012-2016, 1995.
DOI : 10.1073/pnas.92.6.2012

A. Eldar, V. Chary, P. Xenopoulos, M. Fontes, and O. Loson, Partial penetrance facilitates developmental evolution in bacteria, Nature, vol.190, pp.510-514, 2009.
DOI : 10.1038/nature08150

L. Zhang, M. Higgins, P. Piggot, and M. Karow, Analysis of the role of prespore gene expression in the compartmentalization of mother cell-specific gene expression during sporulation of Bacillus subtilis., Journal of Bacteriology, vol.178, issue.10, pp.2813-2817, 1996.
DOI : 10.1128/jb.178.10.2813-2817.1996

C. Guillot, C. Moran, and J. , Essential Internal Promoter in the spoIIIA Locus of Bacillus subtilis, Journal of Bacteriology, vol.189, issue.20, pp.7181-7189, 2007.
DOI : 10.1128/JB.00915-07

S. Cutting, V. Oke, A. Driks, R. Losick, and S. Lu, A forespore checkpoint for mother cell gene expression during development in B. subtilis, Cell, vol.62, issue.2, pp.239-250, 1990.
DOI : 10.1016/0092-8674(90)90362-I

B. Traag, A. Pugliese, J. Eisen, and R. Losick, Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis, Journal of Bacteriology, vol.195, issue.2, pp.253-260, 2013.
DOI : 10.1128/JB.01778-12

J. Dworkin and R. Losick, Developmental Commitment in a Bacterium, Cell, vol.121, issue.3, pp.401-409, 2005.
DOI : 10.1016/j.cell.2005.02.032

X. Jiang, A. Rubio, S. Chiba, and K. Pogliano, Engulfment-regulated proteolysis of SpoIIQ: evidence that dual checkpoints control ??K activity, Molecular Microbiology, vol.101, issue.1, pp.102-115, 2005.
DOI : 10.1111/j.1365-2958.2005.04811.x

V. Oke, M. Shchepetov, and S. Cutting, SpoIVB has two distinct functions during spore formation in Bacillus subtilis, Molecular Microbiology, vol.23, issue.2, pp.223-230, 1997.
DOI : 10.1046/j.1365-2958.1997.2091573.x

Y. Wang, X. Li, Y. Mao, and H. Blaschek, Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq, BMC Genomics, vol.13, issue.1, p.102, 2012.
DOI : 10.1186/1471-2164-13-102

K. Wilson, M. Kennedy, and F. Fekety, Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile, J Clin Microbiol, vol.15, pp.443-446, 1982.

J. Heap, O. Pennington, S. Cartman, G. Carter, and N. Minton, The ClosTron: A universal gene knock-out system for the genus Clostridium, Journal of Microbiological Methods, vol.70, issue.3, pp.452-464, 2007.
DOI : 10.1016/j.mimet.2007.05.021

H. Hussain, A. Roberts, and P. Mullany, Generation of an erythromycin-sensitive derivative of Clostridium difficile strain 630 (630??erm) and demonstration that the conjugative transposon Tn916??E enters the genome of this strain at multiple sites, Journal of Medical Microbiology, vol.54, issue.2, pp.137-141, 2005.
DOI : 10.1099/jmm.0.45790-0

J. Heap, O. Pennington, S. Cartman, and N. Minton, A modular system for Clostridium shuttle plasmids, Journal of Microbiological Methods, vol.78, issue.1, pp.79-85, 2009.
DOI : 10.1016/j.mimet.2009.05.004

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.25, 2009.
DOI : 10.1186/gb-2009-10-3-r25

H. Li, B. Handsaker, A. Wysoker, T. Fennell, and J. Ruan, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

K. Livak and T. Schmittgen, Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2???????CT Method, Methods, vol.25, issue.4, pp.402-408, 2001.
DOI : 10.1006/meth.2001.1262

G. Smyth and T. Speed, Normalization of cDNA microarray data, Methods, vol.31, issue.4, pp.265-273, 2003.
DOI : 10.1016/S1046-2023(03)00155-5

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J Roy Statist Soc, pp.289-300, 1995.

A. Mironov, N. Vinokurova, and M. Gelfand, GenomeExplorer: software for analysis of complete bacterial genomes, Mol Biol (Mosk), vol.34, pp.253-262, 2000.

N. Sierro, Y. Makita, M. De-hoon, and K. Nakai, DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information, Nucleic Acids Research, vol.36, issue.Database, pp.93-96, 2008.
DOI : 10.1093/nar/gkm910

M. Serrano, R. Zilhao, R. E. Ozin, A. Moran, and C. Jr, A Bacillus subtilis secreted protein with a role in endospore coat assembly and function, J Bacteriol, vol.181, pp.3632-3643, 1999.