Multiple Sigma Subunits and the Partitioning of Bacterial Transcription Space, Annual Review of Microbiology, vol.57, issue.1, pp.441-466, 2003. ,
DOI : 10.1146/annurev.micro.57.030502.090913
Regulation of Alternative Sigma Factor Use, Annual Review of Microbiology, vol.65, issue.1, pp.37-55, 2011. ,
DOI : 10.1146/annurev.micro.112408.134219
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective, Annual Review of Microbiology, vol.68, issue.1, pp.357-376, 2014. ,
DOI : 10.1146/annurev-micro-092412-155737
The general stress response in Gram-negative bacteria Bacterial Stress Responses, pp.251-289, 2011. ,
Elucidating the function of the RpoS regulon, Future Microbiology, vol.9, issue.4, pp.497-507, 2014. ,
DOI : 10.2217/fmb.14.9
: role, regulation and mechanisms of promoter recognition, Environmental Microbiology Reports, vol.17, issue.1, pp.1-13, 2014. ,
DOI : 10.1111/1758-2229.12112
Crl Activates Transcription Initiation of RpoS-Regulated Genes Involved in the Multicellular Behavior of Salmonella enterica Serovar Typhimurium, Journal of Bacteriology, vol.188, issue.11, pp.3983-3994, 2006. ,
DOI : 10.1128/JB.00033-06
Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae, Cellular and Molecular Life Sciences, vol.62, issue.11, pp.1234-1246, 2005. ,
DOI : 10.1007/s00018-005-4557-x
Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12, Molecular Genetics and Genomics, vol.181, issue.5, pp.580-591, 2004. ,
DOI : 10.1007/s00438-004-1089-2
rpoS Mutations and Loss of General Stress Resistance in Escherichia coli Populations as a Consequence of Conflict between Competing Stress Responses, Journal of Bacteriology, vol.184, issue.3, pp.806-811, 2002. ,
DOI : 10.1128/JB.184.3.806-811.2002
Expanding the RpoS/??S-Network by RNA Sequencing and Identification of ??S-Controlled Small RNAs in Salmonella, PLoS ONE, vol.191, issue.5, p.96918, 2014. ,
DOI : 10.1371/journal.pone.0096918.s007
Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli, Molecular Microbiology, vol.38, issue.2, pp.375-386, 2011. ,
DOI : 10.1111/j.1365-2958.2010.07449.x
Maintaining a healthy SPANC balance through regulatory and mutational adaptation, Molecular Microbiology, vol.176, issue.1, pp.1-8, 2005. ,
DOI : 10.1111/j.1365-2958.2005.04649.x
Microbial competition: Escherichia coli mutants that take over stationary phase cultures, Science, vol.259, issue.5102, pp.1757-1760, 1993. ,
DOI : 10.1126/science.7681219
Physiological Effects of Crl in Salmonella Are Modulated by ??S Level and Promoter Specificity, Journal of Bacteriology, vol.189, issue.8, pp.2976-2987, 2007. ,
DOI : 10.1128/JB.01919-06
Crl Binds to Domain 2 of ??S and Confers a Competitive Advantage on a Natural rpoS Mutant of Salmonella enterica Serovar Typhi, Journal of Bacteriology, vol.192, issue.24, pp.6401-6410, 2010. ,
DOI : 10.1128/JB.00801-10
URL : https://hal.archives-ouvertes.fr/pasteur-01414252
Negative regulation by RpoS: a case of sigma factor competition, Molecular Microbiology, vol.174, issue.4, pp.1039-1051, 1998. ,
DOI : 10.1046/j.1365-2958.1998.00990.x
Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition?, Molecular Microbiology, vol.95, issue.4, pp.855-862, 2004. ,
DOI : 10.1111/j.1365-2958.2004.04342.x
Regulation of sigma factor competition by the alarmone ppGpp, Genes & Development, vol.16, issue.10, pp.1260-1270, 2002. ,
DOI : 10.1101/gad.227902
The Role of the Alarmone (p)ppGpp in ??N Competition for Core RNA Polymerase, Journal of Biological Chemistry, vol.278, issue.3, pp.1494-1503, 2003. ,
DOI : 10.1074/jbc.M209268200
Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence, Nucleic Acids Research, vol.36, issue.6, pp.1913-1927, 2008. ,
DOI : 10.1093/nar/gkn050
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD, Nucleic Acids Research, vol.40, issue.8, pp.3623-3640, 2012. ,
DOI : 10.1093/nar/gkr1156
An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding, RNA, vol.19, issue.9, pp.1253-1265, 2013. ,
DOI : 10.1261/rna.039537.113
Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: ??S-Dependent Genes, Promoters, and Sigma Factor Selectivity, Journal of Bacteriology, vol.187, issue.5, pp.1591-1603, 2005. ,
DOI : 10.1128/JB.187.5.1591-1603.2005
In vitro transcription profiling of the ??S subunit of bacterial RNA polymerase: re-definition of the ??S regulon and identification of ??S-specific promoter sequence elements, Nucleic Acids Research, vol.39, issue.13, pp.5338-5355, 2011. ,
DOI : 10.1093/nar/gkr129
promoter, Molecular Microbiology, vol.400, issue.6, pp.1366-1377, 2008. ,
DOI : 10.1111/j.1365-2958.2008.06253.x
Dual regulation of mucoidy in Pseudomonas aeruginosa and sigma factor antagonism, Molecular Microbiology, vol.177, issue.2, pp.341-351, 2000. ,
DOI : 10.1074/jbc.271.51.32707
Osmo-Regulation of Bacterial Transcription via Poised RNA Polymerase, Molecular Cell, vol.14, issue.2, pp.153-162, 2004. ,
DOI : 10.1016/S1097-2765(04)00202-3
Post-initiation control by the initiation factor sigma, Molecular Microbiology, vol.68, issue.1, pp.1-3, 2008. ,
DOI : 10.1073/pnas.0708432105
??70-dependent Transcription Pausing in Escherichia coli, Journal of Molecular Biology, vol.412, issue.5, pp.782-792, 2011. ,
DOI : 10.1016/j.jmb.2011.02.011
The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting, Molecular Cell, vol.24, issue.5, pp.747-757, 2006. ,
DOI : 10.1016/j.molcel.2006.10.030
Potent Transcriptional Interference by Pausing of RNA Polymerases over a Downstream Promoter, Molecular Cell, vol.34, issue.5, pp.545-555, 2009. ,
DOI : 10.1016/j.molcel.2009.04.018
Direct and indirect effects in the regulation of overlapping promoters, Nucleic Acids Research, vol.39, issue.16, pp.6879-6885, 2011. ,
DOI : 10.1093/nar/gkr390
Transcriptional occlusion caused by overlapping promoters, Proceedings of the National Academy of Sciences, vol.111, issue.4, pp.1557-1561, 2014. ,
DOI : 10.1073/pnas.1323413111
Extensive functional overlap between ?? factors in Escherichia coli, Nature Structural & Molecular Biology, vol.179, issue.9, pp.806-814, 2006. ,
DOI : 10.1016/S0092-8674(01)00461-5
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states, BMC Biology, vol.12, issue.1, 2014. ,
DOI : 10.1093/nar/gks1201
Phage P22-mutants with increased or decreased transduction abilities, MGG Molecular & General Genetics, vol.15, issue.1, pp.75-88, 1972. ,
DOI : 10.1007/BF00270447
[2] Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium, Methods Enzymol, vol.204, pp.18-43, 1991. ,
DOI : 10.1016/0076-6879(91)04004-8
Molecular cloning: A Laboratory Manual, 1989. ,
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.6640-6645, 2000. ,
DOI : 10.1073/pnas.120163297
Rapid Oligonucleotide-Based Recombineering of the Chromosome of Salmonella enterica, Applied and Environmental Microbiology, vol.75, issue.6, pp.1575-1580, 2009. ,
DOI : 10.1128/AEM.02509-08
Positive selection for loss of tetracycline resistance, J. Bacteriol, vol.143, pp.926-933, 1980. ,
Identification of RpoS (sigma S)-Regulated Genes in Salmonella enterica Serovar Typhimurium, Journal of Bacteriology, vol.182, issue.20, pp.5749-5756, 2000. ,
DOI : 10.1128/JB.182.20.5749-5756.2000
Construction of targeted single copy lac fusions using ?? Red and FLP-mediated site-specific recombination in bacteria, Gene, vol.290, issue.1-2, pp.153-161, 2002. ,
DOI : 10.1016/S0378-1119(02)00551-6
Analysis of relative gene expression data using real-time quantitative PCR and the 2 ?CT method, pp.402-408, 2001. ,
) regulon, Molecular Microbiology, vol.63, issue.1, pp.149-160, 1996. ,
DOI : 10.1016/0264-410X(92)90392-W
Alteration in the electrophoretic mobility of OmpC due to variations in the ammonium persulfate concentration in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Electrophoresis, vol.58, issue.6, pp.448-450, 1991. ,
DOI : 10.1002/elps.1150120615
Binding of the Unorthodox Transcription Activator, Crl, to the Components of the Transcription Machinery, Journal of Biological Chemistry, vol.283, issue.48, pp.33455-33464, 2008. ,
DOI : 10.1074/jbc.M807380200
Experiments in Molecular Genetics, 1972. ,
The sigma70 family of sigma factors, Genome Biology, vol.4, issue.1, p.203, 2003. ,
DOI : 10.1186/gb-2003-4-1-203
Advances in bacterial promoter recognition and its control by factors that do not bind DNA, Nature Reviews Microbiology, vol.118, issue.7, pp.507-519, 2008. ,
DOI : 10.1038/nrmicro1912
subunit of RNA polymerase, Molecular Microbiology, vol.8, issue.5, pp.1296-1306, 2007. ,
DOI : 10.1128/JB.187.5.1591-1603.2005
Promoter Use by ??38 (rpoS) RNA Polymerase: AMINO ACID CLUSTERS FOR DNA BINDING AND ISOMERIZATION, Journal of Biological Chemistry, vol.277, issue.49, pp.47420-47427, 2002. ,
DOI : 10.1074/jbc.M208363200
Sigma38 (rpoS) RNA Polymerase Promoter Engagement via -10 Region Nucleotides, Journal of Biological Chemistry, vol.276, issue.32, pp.30064-30071, 2001. ,
DOI : 10.1074/jbc.M102886200
Open Complex Formation In Vitro by ??38 (rpoS) RNA Polymerase: Roles for Region 2 Amino Acids, Journal of Molecular Biology, vol.329, issue.5, pp.941-948, 2003. ,
DOI : 10.1016/S0022-2836(03)00369-3
Structural Basis of Transcription Initiation, Science, vol.338, issue.6110, pp.1076-1080, 2012. ,
DOI : 10.1126/science.1227786
[57] Sequencing end-labeled DNA with base-specific chemical cleavages, Methods Enzymol, vol.65, pp.499-560, 1980. ,
DOI : 10.1016/S0076-6879(80)65059-9
Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of ??s activity and levels, The EMBO Journal, vol.15, issue.6, pp.1569-1578, 2007. ,
DOI : 10.1038/sj.emboj.7601629
Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?, mBio, vol.2, issue.4, pp.1000034-1000045, 1128. ,
DOI : 10.1128/mBio.00034-11
The porin OmpD from nontyphoidal Salmonella is a key target for a protective B1b cell antibody response, Proceedings of the National Academy of Sciences, vol.106, issue.24, pp.9803-9808, 2009. ,
DOI : 10.1073/pnas.0812431106
The Primary Transcriptome of Salmonella enterica Serovar Typhimurium and Its Dependence on ppGpp during Late Stationary Phase, PLoS ONE, vol.25, issue.3, p.92690, 2014. ,
DOI : 10.1371/journal.pone.0092690.s014
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium, Proceedings of the National Academy of Sciences, vol.109, issue.20, pp.1277-1286, 2012. ,
DOI : 10.1073/pnas.1201061109
Molecular call and response: The physiology of bacterial small RNAs, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1809, issue.10, pp.1809-525, 2011. ,
DOI : 10.1016/j.bbagrm.2011.07.013
A Proximal Promoter Element Required for Positive Transcriptional Control by Guanosine Tetraphosphate and DksA Protein during the Stringent Response, Journal of Biological Chemistry, vol.288, issue.29, pp.21055-21064, 2013. ,
DOI : 10.1074/jbc.M113.479998
Effects of Combination of Different -10 Hexamers and Downstream Sequences on Stationary-Phase-Specific Sigma Factor sigma S-Dependent Transcription in Pseudomonas putida, Journal of Bacteriology, vol.182, issue.23, pp.6707-6713, 2000. ,
DOI : 10.1128/JB.182.23.6707-6713.2000
The transition from transcriptional initiation to elongation, Current Opinion in Genetics & Development, vol.18, issue.2, pp.130-136, 2008. ,
DOI : 10.1016/j.gde.2007.12.008