Two-component signaling circuit structure and properties, Curr. Opin. Microbiol, vol.13, pp.184-189, 2010. ,
Porin regulon of Escherichia coli, Two-Component Signal Transduction, 1995. ,
From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli, Mol. Microbiol, vol.20, pp.911-917, 1996. ,
Structure/function relationships in OmpR and other winged-helix transcription factors, Curr. Opin. Microbiol, vol.5, pp.135-141, 2002. ,
The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes, J. Bacteriol, vol.186, pp.4019-4024, 2004. ,
Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR, 1995. ,
, J. Bacteriol, vol.177, pp.4696-4702
Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors, Microbiology, vol.156, pp.2470-2483, 2010. ,
Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes, FEMS Microbiol. Lett, vol.186, pp.257-262, 2000. ,
BolA is a transcriptional switch that turns off motility and turns on biofilm development, mBio, vol.6, 2015. ,
, Nucleic Acids Research, vol.44, issue.20, p.9665, 2016.
Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response, PLoS Genet, vol.10, p.1004215, 2014. ,
A systems biology approach sheds new light on Escherichia coli acid resistance, Nucleic Acids Res, vol.39, pp.7512-7528, 2011. ,
Expression of micF involved in porin synthesis in Escherichia coli: two distinct cis-acting elements respectively regulate micF expression positively and negatively, FEMS Microbiol. Lett, vol.67, pp.39-44, 1991. ,
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli, J. Bacteriol, vol.186, pp.6689-6697, 2004. ,
Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, Mol. Microbiol, vol.59, pp.231-247, 2006. ,
Regulation by small RNAs in bacteria: expanding frontiers, Mol. Cell, vol.43, pp.880-891, 2011. ,
Bacterial small RNA-based negative regulation: Hfq and its accomplices, J. Biol. Chem, vol.288, pp.7996-8003, 2013. ,
Hfq and its constellation of RNA, Nat. Rev. Microbiol, vol.9, pp.578-589, 2011. ,
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis, EMBO J, vol.29, pp.1840-1850, 2010. ,
Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli, Mol. Microbiol, vol.84, pp.36-50, 2012. ,
A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli, Mol. Microbiol, vol.84, pp.17-35, 2012. ,
A complex network of small non-coding RNAs regulate motility in Escherichia coli, 2012. ,
, Mol. Microbiol, vol.86, pp.524-538
Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli, Mol. Microbiol, vol.84, pp.51-65, 2012. ,
A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA), 1984. ,
, Proc. Natl. Acad. Sci. U.S.A, vol.81, 1966.
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation, Nat. Struct. Mol. Biol, vol.16, pp.840-846, 2009. ,
Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, Mol. Microbiol, vol.59, pp.231-247, 2006. ,
The 5 end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic Acids Res, vol.36, pp.6781-6794, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00374118
Base pairing small RNAs and their roles in global regulatory networks, FEMS Microbiol. Rev, vol.34, pp.866-882, 2010. ,
Stress and environmental regulation of gene expression and adaptation in bacteria, pp.371-382, 2016. ,
The base-pairing RNA Spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli, Mol. Cell, vol.41, pp.286-297, 2011. ,
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.4772-4781, 2015. ,
, Nucleic Acids Research, vol.44, issue.20, 2016.
Amino acids important for DNA recognition by the response regulator OmpR, J. Biol. Chem, vol.283, pp.8664-8677, 2008. ,
Salmonella enterica response regulator SsrB relieves H-NS silencing by displacing H-NS bound in polymerization mode and directly activates transcription, J. Biol. Chem, vol.286, pp.1895-1902, 2011. ,
Analysis of RNA polymerase-promoter complex formation, Methods, vol.47, pp.13-24, 2009. ,
Comprehensive analysis of OmpR phosphorylation, dimerization, and DNA binding supports a canonical model for activation, J. Mol. Biol, vol.425, pp.1612-1626, 2013. ,
A Short Course in Bacterial Genetics, 1992. ,
E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo, EMBO J, vol.9, pp.3733-3742, 1990. ,
URL : https://hal.archives-ouvertes.fr/in2p3-00008924
EnvZ-OmpR interaction and osmoregulation in Escherichia coli, J. Biol. Chem, vol.277, pp.24155-24161, 2002. ,
Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system, Mol. Microbiol, vol.54, pp.1076-1089, 2004. ,
Mutations that alter the kinase and phosphatase activities of the two-component sensor EnvZ, J. Bacteriol, vol.180, pp.4538-4546, 1998. ,
Genetics and biochemistry of the peptidoglycan-associated proteins b and c of Escherichia coli K12, Mol. Gen. Genet, vol.169, pp.137-146, 1979. ,
The ompB locus and the regulation of the major outer membrane porin proteins of Escherichia coli K12, J. Mol. Biol, vol.146, pp.23-43, 1981. ,
Labelfree kinase profiling using phosphate affinity polyacrylamide gel electrophoresis, Mol. Cell Proteomics, vol.6, pp.356-366, 2007. ,
Genetic analysis of the switch that controls porin gene expression in Escherichia coli K-12, J. Mol. Biol, vol.210, pp.281-292, 1989. ,
A single amino acid substitution in the C terminus of OmpR alters DNA recognition and phosphorylation, J. Mol. Biol, vol.299, pp.1257-1270, 2000. ,
Evidence for the physiological importance of the phosphotransfer between the two regulatory components, EnvZ and OmpR, in osmoregulation in Escherichia coli, J. Biol. Chem, vol.264, pp.14090-14094, 1989. ,
Interaction of OmpR, a positive regulator, with the osmoregulated ompC and ompF genes of Escherichia coli. Studies with wild-type and mutant OmpR proteins, J. Biol. Chem, vol.263, pp.1008-1012, 1988. ,
Transcriptional regulation of Escherichia coli K-12 major outer membrane protein 1b, J. Bacteriol, vol.140, pp.342-350, 1979. ,
Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system, Proc. Natl. Acad. Sci. U.S.A, vol.100, pp.691-696, 2003. ,
Evolving a robust signal transduction pathway from weak cross-talk, Mol. Syst. Biol, vol.6, p.452, 2010. ,
Function of conserved histidine-243 in phosphatase activity of EnvZ, the sensor for porin osmoregulation in Escherichia coli, J. Bacteriol, vol.179, pp.3729-3735, 1997. ,
MicF: An antisense RNA gene involved in response of Escherichia coli to global stress factors, J. Mol. Biol, vol.313, pp.1-12, 2001. ,
OmpR regulation of the uropathogenic Escherichia colifimB gene in an acidic/high osmolality environment, Microbiology, vol.159, pp.316-327, 2013. ,
The inner membrane histidine kinase EnvZ senses osmolality via helixcoil transitions in the cytoplasm, EMBO J, vol.31, pp.2648-2659, 2012. ,
Cytoplasmic sensing by the inner membrane histidine kinase EnvZ, Progr. Biophys. Mol. Biol, vol.118, pp.119-129, 2015. ,
Integration host factor binds specifically to multiple sites in the ompB promoter of Escherichia coli and inhibits transcription, J. Bacteriol, vol.173, pp.5800-5807, 1991. ,
Positive and negative control of ompB transcription in Escherichia coli by cyclic AMP and the cyclic AMP receptor protein, J. Bacteriol, vol.174, pp.664-670, 1992. ,
Input output robustness in simple bacterial signaling systems, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.19931-19935, 2007. ,
The phosphorylation state of the DegU response regulator acts as a molecular switch allowing either degradative enzyme synthesis or expression of genetic competence in Bacillus subtilis, J. Biol. Chem, vol.267, pp.14509-14514, 1992. ,
Salmonella biofilm development depends on the phosphorylation status of RcsB, J. Bacteriol, vol.194, pp.3708-3722, 2012. ,
Rewiring two-component signal transduction with small RNAs, Curr. Opin. Microbiol, vol.15, pp.132-139, 2012. ,
Expanding control in bacteria: interplay between small RNAs and transcriptional regulators to control gene expression, Curr. Opin. Microbille, vol.16, pp.125-132, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00823497
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA, Mol. Microbiol, vol.84, pp.428-445, 2012. ,
A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp, Mol. Microbiol, vol.84, pp.414-427, 2012. ,
AphA and LuxR/HapR reciprocally control quorum sensing in vibrios, Genes Dev, vol.25, pp.397-408, 2011. ,
A negative feedback loop involving small RNAs accelerates Vibrio cholerae's transition out of quorum-sensing mode, Genes Dev, vol.22, pp.226-238, 2008. ,
A small-RNA-mediated negative feedback loop controls quorum-sensing dynamics in Vibrio harveyi, Mol. Microbiol, vol.70, pp.896-907, 2008. ,
Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response, Mol. Cell, vol.37, pp.567-579, 2010. ,
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions, Nature, vol.529, pp.496-501, 2016. ,
Introduction to Systems Biology: Design Principles of Biological Circuits, 2006. ,
Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment, J. Biol. Chem, vol.260, pp.10563-10568, 1985. ,
Signal-dependent binding of the response regulators PhoP and PmrA to their target promoters in vivo, J. Biol. Chem, vol.280, pp.4089-4094, 2005. ,
An efficient recombination system for chromosome engineering in Escherichia coli, Proc. Natl. Acad. Sci. USA, vol.97, pp.5978-5983, 2000. ,
Minilambda: a tractable system for chromosome and BAC engineering, Gene, vol.315, pp.63-69, 2003. ,
Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection, J. Bact, vol.192, pp.59-67, 2010. ,
Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, 2006. ,
, Mol. Microbiol, vol.59, pp.231-247
, , 1979.
, , 1981.
Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response, PLoS Genet, vol.10, p.1004215, 2014. ,
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic acids research, vol.36, pp.6781-6794, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00374118
A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system, Mol. Microbiol, vol.72, pp.551-565, 2009. ,
, , 1990.
, J. Bacteriol, vol.140, pp.342-350, 1979.
, J. Mol. Biol, vol.146, pp.23-43, 1981.
, Mol. Microbiol, vol.54, pp.1076-1089, 2004.
, Mol. Microbiol, vol.59, pp.231-247, 2006.
, PLoS Genet, vol.9, p.1003156, 2013.
, PLoS Genet, vol.10, p.1004215, 2014.
, EMBO J, vol.9, pp.3733-3742, 1990.
, Nucleic acids research, vol.36, pp.6781-6794, 2008.
, Studying the effect of an sRNA on a target using reporter gene fusions
, 71 3.1. Synthesis, labeling and detection of RNA molecules for in vitro studies, vitro study of translation initiation: the toeprinting assay
, Nat. Rev. Microbiol, vol.12, pp.647-653, 2014.
The noncoding RNA revolution-trashing old rules to forge new ones, Cell, vol.157, pp.77-94, 2014. ,
Small RNAs in bacteria and archaea: who they are, what they do, and how they do it, Adv. Genet, vol.90, pp.133-208, 2015. ,
MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein, Genes Dev, vol.28, pp.1620-1634, 2014. ,
, An atlas of Hfq-bound transcripts reveals 3
, UTRs as a genomic reservoir of regulatory small RNAs, EMBO J, vol.31, pp.4005-4019, 2012.
A 3 0 UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response, Mol. Cell, vol.61, pp.352-363, 2016. ,
, A, vol.3
Protection against deleterious nitrogen compounds: role of sigmaS-dependent small RNAs encoded adjacent to sdiA, Nucleic Acids Res, vol.44, pp.6935-6948, 2016. ,
Riboswitches as versatile gene control elements, Curr. Opin. Struct. Biol, vol.15, pp.342-348, 2005. ,
Regulatory RNAs in bacteria, Cell, vol.136, pp.615-628, 2009. ,
Global Mapping of Small RNA-Target Interactions in Bacteria, Mol. Cell, vol.63, pp.884-897, 2016. ,
Two-level inhibition of galK expression by Spot42: degradation of mRNA mK2 and enhanced transcription termination before the galK gene, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.7581-7586, 2015. ,
sRNA-Mediated Control of Transcription Termination in E. coli, Cell, vol.167, pp.111-121, 2016. ,
Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target, Genes Dev, vol.23, pp.2004-2015, 2009. ,
Role of polynucleotide phosphorylase in sRNA function in Escherichia coli, RNA, vol.17, pp.1172-1189, 2011. ,
Bistable expression of CsgD in biofilm development of Salmonella enterica serovar typhimurium, J. Bacteriol, vol.192, pp.456-466, 2010. ,
Translational control and target recognition by Escherichia coli small RNAs in vivo, Nucleic Acids Res, vol.35, pp.1018-1037, 2007. ,
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA, Mol. Microbiol, vol.84, pp.428-445, 2012. ,
The 5 0 end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic Acids Res, vol.36, pp.6781-6794, 2008. ,
Evidence for an autonomous 5 0 target recognition domain in an Hfq-associated small RNA, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.20435-20440, 2010. ,
, Small RNA binding to, vol.5
, mRNA coding region inhibits translational initiation, Mol. Cell, vol.32, pp.827-837, 2008.
Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed, Proc. Natl. Acad. Sci. U.S.A, vol.92, pp.12250-12254, 1995. ,
Lost in translation: the influence of ribosomes on bacterial mRNA decay, Genes Dev, vol.19, pp.2526-2533, 2005. ,
Killer and protective ribosomes, Prog. Mol. Biol. Transl. Sci, vol.85, pp.423-466, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00373983
Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.4858-4863, 2006. ,
Implications of membrane localization of target mRNA in the action of a small RNA: mechanism of posttranscriptional regulation of glucose transporter in Escherichia coli, Genes Dev, vol.19, pp.328-338, 2005. ,
Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage, Genes Dev, vol.25, pp.385-396, 2011. ,
Identification of bacterial sRNA regulatory targets using ribosome profiling, Nucleic Acids Res, vol.43, pp.10308-10320, 2015. ,
Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression, EMBO J, vol.24, pp.824-835, 2005. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01404709
Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis, Cell, vol.153, pp.426-437, 2013. ,
Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5 0 leader sequence ,
, , vol.77, pp.1416-1428, 2010.
Regulatory RNAs and target mRNA decay in prokaryotes, Biochim. Biophys. Acta, vol.2013, pp.742-747, 1829. ,
SRNA and mRNA turnover in Gram-positive bacteria, FEMS Microbiol. Rev, vol.39, pp.316-330, 2015. ,
Hfq and its constellation of RNA, Nat. Rev. Microbiol, vol.9, pp.578-589, 2011. ,
Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli, Mol. Microbiol, vol.65, pp.1518-1533, 2007. ,
Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA, Genes Dev, vol.27, pp.552-564, 2013. ,
In vivo expression and purification of aptamer-tagged small RNA regulators, Nucleic Acids Res, vol.37, p.133, 2009. ,
Grad-seq guides the discovery of ProQ as a major small RNA binding protein, Proc. Natl. Acad. Sci. U.S.A, 2016. ,
Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets, J. Mol. Biol, vol.425, pp.3678-3697, 2013. ,
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo, EMBO J, vol.35, pp.991-1011, 2016. ,
Silencing of natural transformation by an RNA chaperone and a multitarget small RNA, Proc. Natl. Acad. Sci. U.S.A, vol.113, pp.8813-8818, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01911308
Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq, Genes Dev, vol.26, pp.726-739, 2012. ,
Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB, PLoS Genet, vol.9, p.1003156, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00823468
Cloning and expression of the gene for bacteriophage T7 RNA polymerase, Proc. Natl. Acad. Sci. U.S.A, vol.81, pp.2035-2039, 1984. ,
A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes, Proc. Natl. Acad. Sci. U.S.A, vol.82, pp.1074-1078, 1985. ,
RNA template-directed RNA synthesis by T7 RNA polymerase, Proc. Natl. Acad. Sci. U.S.A, vol.91, pp.6972-6976, 1994. ,
Affinity purification of in vitro transcribed RNA with homogeneous ends using a 3 0 -ARiBo tag, Methods Enzymol, vol.549, pp.49-84, 2014. ,
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli, J. Bacteriol, vol.186, pp.6689-6697, 2004. ,
, Methods, vol.117, pp.67-76, 2017.
A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus, PLoS Pathog, vol.10, p.1003979, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00965591
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis, EMBO J, vol.29, pp.1840-1850, 2010. ,
A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus, Nucleic Acids Res, vol.42, pp.4892-4905, 2014. ,
URL : https://hal.archives-ouvertes.fr/inserm-00951043
Chemical probes for higher-order structure in RNA, Proc. Natl. Acad. Sci. U.S.A, vol.77, pp.4679-4682, 1980. ,
The reaction of guanine derivatives with 1,2-dicarbonyl compounds, Biochemistry, vol.5, pp.2799-2807, 1966. ,
On the reaction of guanine with glyoxal, pyruvaldehyde, and kethoxal, and the structure of the acylguanines. A new synthesis of N2-alkylguanines, Biochemistry, vol.8, pp.238-245, 1969. ,
Functional modification of 16S ribosomal RNA by kethoxal, Proc. Natl. Acad. Sci. U.S.A, vol.69, pp.3115-3118, 1972. ,
The reversible chemical modification of uracil, thymine, and guanine nucleotides and the modification of the action of ribonuclease on ribonucleic acid, Biochemistry, vol.6, pp.3632-3639, 1967. ,
Lead(II) as a probe for investigating RNA structure in vivo, RNA, vol.8, pp.534-541, 2002. ,
RNA structure analysis at single nucleotide resolution by selective 2 0 -hydroxyl acylation and primer extension (SHAPE), J. Am. Chem. Soc, vol.127, pp.4223-4231, 2005. ,
Metal ion-based RNA cleavage as a structural probe, Methods Enzymol, vol.468, pp.91-106, 2009. ,
RNA SHAPE analysis in living cells, Nat. Chem. Biol, vol.9, pp.18-20, 2013. ,
In-line probing analysis of riboswitches, Methods Mol. Biol, vol.419, pp.53-67, 2008. ,
Probing RNA structure and RNA-ligand complexes with chemical probes, Methods Enzymol, vol.318, pp.3-21, 2000. ,
Structural probing of RNA thermosensors, Methods Mol. Biol, vol.540, pp.233-245, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00410629
Probing the structure of RNAs in solution, Nucleic Acids Res, vol.15, pp.9109-9128, 1987. ,
Advances in RNA structure analysis by chemical probing, Curr. Opin. Struct. Biol, vol.20, pp.295-304, 2010. ,
In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA, Nucleic Acids Res, vol.35, pp.4331-4346, 2007. ,
Structural model of an mRNA in complex with the bacterial chaperone Hfq, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.17134-17139, 2014. ,
Curli synthesis and biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA chaperone, Nucleic Acids Res, vol.42, pp.4682-4696, 2014. ,
URL : https://hal.archives-ouvertes.fr/inserm-00941995
Computational analysis of RNA structures with chemical probing data, Methods, vol.79, pp.60-66, 2015. ,
Exploring RNA structural codes with SHAPE chemistry, Acc. Chem. Res, vol.44, pp.1280-1291, 2011. ,
Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), Methods, vol.103, pp.34-48, 2016. ,
Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function, PLoS Genet, vol.11, p.1005613, 2015. ,
Temperatureresponsive in vitro RNA structurome of Yersinia pseudotuberculosis, Proc. Natl. Acad. Sci. U.S.A, vol.113, pp.7237-7242, 2016. ,
Extension inhibition analysis of translation initiation complexes, Methods Enzymol, vol.164, pp.419-425, 1988. ,
Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria, Methods Mol. Biol, vol.540, pp.247-263, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00391772
DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription, Proc. Natl. Acad. Sci. U.S.A, vol.95, pp.12462-12467, 1998. ,
Regulation and mode of action of the second small RNA activator of RpoS translation, RprA, Mol. Microbiol, vol.46, pp.813-826, 2002. ,
Translational efficiency of rpoS mRNA from Borrelia burgdorferi: effects of the length and sequence of the mRNA leader region, Biochem. Biophys. Res. Commun, vol.433, pp.73-78, 2013. ,
An antisense RNA inhibits translation by competing with standby ribosomes, Mol. Cell, vol.26, pp.381-392, 2007. ,
Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding, EMBO J, vol.26, pp.965-975, 2007. ,
Cell-free translation reconstituted with purified components, Nat. Biotechnol, vol.19, pp.751-755, 2001. ,
The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E, Mol. Cell, vol.47, pp.943-953, 2012. ,
The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes, RNA, vol.22, pp.360-372, 2016. ,
The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide, Curr. Biol, vol.14, pp.2271-2276, 2004. ,
Footprinting mRNA-ribosome complexes with chemical probes, EMBO J, vol.13, pp.3892-3901, 1994. ,
Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA, EMBO J, vol.29, pp.3094-3107, 2010. ,
Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation, J Bacteriol, vol.192, pp.5559-5571, 2010. ,
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles, Mol. Microbiol, vol.70, pp.100-111, 2008. ,
Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation, PLoS Pathog, vol.6, p.1000809, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00526396
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation, Nat. Struct. Mol. Biol, vol.16, pp.840-846, 2009. ,
Bugging of the intestinal mucosa, N Engl J Med, vol.357, issue.7, pp.708-710, 2007. ,
An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli, Proc Natl Acad Sci U S A, vol.82, issue.17, pp.5724-5727, 1985. ,
Protection against Escherichia coli-induced urinary tract infections with hybridoma antibodies directed against type 1 fimbriae or complementary Dmannose receptors, Infect Immun, vol.48, issue.3, pp.625-628, 1985. ,
Regulation of the Escherichia coli ydhY-T operon in the presence of alternative electron acceptors, 2017. ,
Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites, Nucleic Acids Res, vol.35, issue.9, pp.3016-3031, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00161974
Network motifs: theory and experimental approaches, Nat Rev Genet, vol.8, issue.6, pp.450-461, 2007. ,
Switching on and off with RNA, Proc Natl Acad Sci U S A, vol.97, issue.18, pp.9824-9826, 2000. ,
A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator, Cell, vol.90, issue.1, pp.43-53, 1997. ,
The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding, EMBO J, vol.17, issue.20, pp.6069-6075, 1998. ,
Incidence of pathogenic bacteria from mesenteric lymph nodes and ileal serosa during Crohn's disease surgery, Br J Surg, vol.71, issue.8, pp.623-625, 1984. ,
The isolation and characterization of RNA coded by the micF gene in Escherichia coli, Nucleic Acids Res, vol.15, issue.5, pp.2089-2101, 1987. ,
RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq, Proc Natl Acad Sci U S A, vol.109, issue.12, pp.4621-4626, 2012. ,
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli, Curr Biol, vol.11, issue.12, pp.941-950, 2001. ,
The critical role of RNA processing and degradation in the control of gene expression, FEMS Microbiol Rev, vol.34, issue.5, pp.883-923, 2010. ,
The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand, Cell, vol.109, issue.2, pp.193-203, 2002. ,
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, vol.2, p.8, 2006. ,
The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli, Proc Natl Acad Sci U S A, vol.88, issue.1, pp.1-5, 1991. ,
Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli, Sci Rep, vol.5, p.15287, 2015. ,
CsrA inhibits translation initiation of Escherichia coli hfq by binding to a single site overlapping the Shine-Dalgarno sequence, J Bacteriol, vol.189, issue.15, pp.5472-5481, 2007. ,
CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli, Mol Microbiol, vol.44, issue.6, pp.1599-1610, 2002. ,
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution, Science, vol.289, issue.5481, pp.905-920, 2000. ,
The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E, Mol Cell, vol.47, issue.6, pp.943-953, 2012. ,
Comprehensive analysis of OmpR phosphorylation, dimerization, and DNA binding supports a canonical model for activation, J Mol Biol, vol.425, issue.10, pp.1612-1626, 2013. ,
Autoregulation of RNase III operon by mRNA processing, EMBO J, vol.8, issue.11, pp.3401-3407, 1989. ,
Regulatory and functional co-operation of flagella and type 1 pili in adhesive and invasive abilities of AIEC strain LF82 isolated from a patient with Crohn's disease, Mol Microbiol, vol.48, issue.3, pp.781-794, 2003. ,
Involvement of lipoprotein NlpI in the virulence of adherent invasive Escherichia coli strain LF82 isolated from a patient with Crohn's disease, Infect Immun, vol.72, issue.5, pp.2484-2493, 2004. ,
CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease, J Clin Invest, vol.117, issue.6, pp.1566-1574, 2007. ,
Two-component signal transduction as a target for microbial antiinfective therapy, Antimicrob Agents Chemother, vol.42, issue.7, pp.1529-1536, 1998. ,
Quantitative analysis of ribosome binding sites in E.coli, Nucleic Acids Res, vol.22, issue.7, pp.1287-1295, 1994. ,
Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system, Proc Natl Acad Sci U S A, vol.100, issue.2, pp.691-696, 2003. ,
Molecular characterization of two-component systems of Helicobacter pylori, J Bacteriol, vol.182, issue.8, pp.2068-2076, 2000. ,
Base pairing small RNAs and their roles in global regulatory networks, FEMS Microbiol Rev, vol.34, issue.5, pp.866-882, 2010. ,
The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli, Mol Cell, vol.41, issue.3, pp.286-297, 2011. ,
Insertion of transposon Tn5 into a structural gene of the membrane-bound nitrate reductase of Thiosphaera pantotropha results in anaerobic overexpression of periplasmic nitrate reductase activity, J Gen Microbiol, vol.139, issue.12, pp.3205-3214, 1993. ,
Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12, Genetics, vol.125, issue.4, pp.691-702, 1990. ,
The two-component regulatory system ompR-envZ controls the virulence of Shigella flexneri, J Bacteriol, vol.172, issue.11, pp.6274-6281, 1990. ,
The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival, EMBO J, vol.16, issue.17, pp.5376-5385, 1997. ,
Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators, Mol Microbiol, vol.16, issue.3, pp.521-534, 1995. ,
Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli, Mol Microbiol, vol.6, issue.23, pp.3595-3602, 1992. ,
Curli synthesis and biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA chaperone, Nucleic Acids Res, vol.42, issue.7, pp.4682-4696, 2014. ,
URL : https://hal.archives-ouvertes.fr/inserm-00941995
Type 1 pili-mediated adherence of Escherichia coli strain LF82 isolated from Crohn's disease is involved in bacterial invasion of intestinal epithelial cells, Mol Microbiol, vol.39, issue.5, pp.1272-1284, 2001. ,
Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease, Infect Immun, vol.67, issue.9, pp.4499-4509, 1999. ,
Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile, J Bacteriol, vol.196, issue.18, pp.3234-3248, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01370761
Terminator still moving forward: expanding roles for Rho factor, Curr Opin Microbiol, vol.16, issue.2, pp.118-124, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00840158
Fresh layers of RNA-mediated regulation in Gram-positive bacteria, Curr Opin Microbiol, vol.30, pp.30-35, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01412635
A tale of two mRNA degradation pathways mediated by RNase E, Mol Microbiol, vol.82, issue.6, pp.1305-1310, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00666936
Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates, 1996. ,
Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them, J Biomol Struct Dyn, vol.3, issue.4, pp.705-723, 1986. ,
Fine-structure mapping and identification of two regulators of capsule synthesis in Escherichia coli K-12, J Bacteriol, vol.170, issue.6, pp.2599-2611, 1988. ,
Replication of Crohn's disease-associated AIEC within macrophages is dependent on TNF-alpha secretion, Lab Invest, vol.92, issue.3, pp.411-419, 2012. ,
The Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 replicates in mature phagolysosomes within J774 macrophages, Cell Microbiol, vol.8, issue.3, pp.471-484, 2006. ,
Unexpected properties of sRNA promoters allow feedback control via regulation of a two-component system, Nucleic Acids Res, vol.44, issue.20, pp.9650-9666, 2016. ,
Local and global regulation of transcription initiation in bacteria, Nat Rev Microbiol, vol.14, issue.10, pp.638-650, 2016. ,
Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly, Mol Microbiol, vol.37, issue.5, pp.1258-1269, 2000. ,
Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter, Mol Microbiol, vol.53, issue.1, pp.203-215, 2004. ,
Global analysis of extracytoplasmic stress signaling in Escherichia coli, PLoS Genet, vol.5, issue.9, p.1000651, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00418796
DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes, Nucleic Acids Res, vol.37, issue.5, p.37, 2009. ,
The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues, Mol Microbiol, vol.50, issue.5, pp.1493-1505, 2003. ,
EnvZ-OmpR interaction and osmoregulation in Escherichia coli, J Biol Chem, vol.277, issue.27, pp.24155-24161, 2002. ,
Spontaneous subunit exchange and biochemical evidence for transautophosphorylation in a dimer of Escherichia coli histidine kinase (EnvZ), J Mol Biol, vol.329, issue.3, pp.495-503, 2003. ,
Evolution of two-component signal transduction systems, Annu Rev Microbiol, vol.66, pp.325-347, 2012. ,
The NarX and NarQ sensor-transmitter proteins of Escherichia coli each require two conserved histidines for nitrate-dependent signal transduction to NarL, J Bacteriol, vol.177, issue.9, pp.2416-2424, 1995. ,
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs, EMBO J, vol.31, issue.20, pp.4005-4019, 2012. ,
A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response, Mol Cell, vol.61, issue.3, pp.352-363, 2016. ,
Role of diet in the development of inflammatory bowel disease, Inflamm Bowel Dis, vol.16, issue.1, pp.137-151, 2010. ,
A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Res, vol.28, issue.22, p.97, 2000. ,
The physiological stimulus for the BarA sensor kinase, J Bacteriol, vol.192, issue.7, pp.2009-2012, 2010. ,
Determination of the optimal aligned spacing between the ShineDalgarno sequence and the translation initiation codon of Escherichia coli mRNAs, Nucleic Acids Res, vol.22, issue.23, pp.4953-4957, 1994. ,
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli, J Bacteriol, vol.186, issue.20, pp.6689-6697, 2004. ,
Contribution of the intestinal microbiota to human health: from birth to 100 years of age, Curr Top Microbiol Immunol, vol.358, pp.323-346, 2013. ,
An important role for RNase R in mRNA decay, Mol Cell, vol.17, issue.2, pp.313-318, 2005. ,
The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R, J Biol Chem, vol.273, issue.23, pp.14077-14080, 1998. ,
Structural analysis of ligand stimulation of the histidine kinase NarX, Structure, vol.17, issue.2, pp.190-201, 2009. ,
Identification and characterization of narQ, a second nitrate sensor for nitrate-dependent gene regulation in Escherichia coli, Mol Microbiol, vol.6, issue.14, pp.1913-1923, 1992. ,
Locked-on' and 'locked-off' signal transduction mutations in the periplasmic domain of the Escherichia coli NarQ and NarX sensors affect nitrate-and nitrite-dependent regulation by NarL and NarP, Mol Microbiol, vol.24, issue.5, pp.1049-1060, 1997. ,
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli, Proc Natl Acad Sci U S A, vol.105, issue.49, pp.19462-19467, 2008. ,
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts, Genome Res, vol.18, issue.6, pp.900-910, 2008. ,
Detecting envelope stress by monitoring beta-barrel assembly, Cell, vol.159, issue.7, pp.1652-1664, 2014. ,
DOI : 10.1016/j.cell.2014.11.045
URL : https://doi.org/10.1016/j.cell.2014.11.045
Identification of the regulatory sequence of anaerobically expressed locus aeg-46.5, J Bacteriol, vol.175, issue.4, pp.1165-1172, 1993. ,
One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution, Proc Natl Acad Sci U S A, vol.86, issue.7, pp.2172-2175, 1989. ,
Mechanism of mRNA destabilization by the glmS ribozyme, Genes Dev, vol.21, issue.24, pp.3356-3368, 2007. ,
The phylogenetic distribution of bacterial ribonucleases, Nucleic Acids Res, vol.30, issue.24, pp.5339-5346, 2002. ,
A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth, J Biol Chem, vol.281, issue.8, pp.4802-4815, 2006. ,
Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors, J Bacteriol, vol.179, issue.20, pp.6525-6530, 1997. ,
Post-transcriptional control of the Escherichia coli PhoQPhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB, PLoS Genet, vol.9, issue.1, p.1003156, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00823468
Post-transcriptional control of the Escherichia coli PhoQPhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB, PLoS Genet, vol.9, issue.1, p.1003156, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00823468
MicA sRNA links the PhoP regulon to cell envelope stress, Mol Microbiol, vol.76, issue.2, pp.467-479, 2010. ,
DOI : 10.1111/j.1365-2958.2010.07115.x
URL : https://hal.archives-ouvertes.fr/hal-00512637
Oxygen, nitrate, and molybdenum regulation of dmsABC gene expression in Escherichia coli, J Bacteriol, vol.171, issue.7, pp.3817-3823, 1989. ,
RNase III: Genetics and function; structure and mechanism, Annu Rev Genet, vol.47, pp.405-431, 2013. ,
DOI : 10.1146/annurev-genet-110711-155618
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311387
Mini-lambda: a tractable system for chromosome and BAC engineering, Gene, vol.315, pp.63-69, 2003. ,
DOI : 10.1016/s0378-1119(03)00728-5
Regulation of the flavorubredoxin nitric oxide reductase gene in Escherichia coli: nitrate repression, nitrite induction, and possible post-transcription control, FEMS Microbiol Lett, vol.218, issue.2, pp.385-393, 2003. ,
The phosphorylation state of the DegU response regulator acts as a molecular switch allowing either degradative enzyme synthesis or expression of genetic competence in Bacillus subtilis, J Biol Chem, vol.267, issue.20, pp.14509-14514, 1992. ,
Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease, Gastroenterology, vol.115, issue.6, pp.1405-1413, 1998. ,
Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site, J Mol Biol, vol.251, issue.1, pp.15-29, 1995. ,
Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement, Mol Microbiol, vol.25, issue.3, pp.583-595, 1997. ,
SigmaE is an essential sigma factor in Escherichia coli, J Bacteriol, vol.179, issue.21, pp.6862-6864, 1997. ,
The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior, J Bacteriol, vol.191, issue.2, pp.461-476, 2009. ,
A complex network of small non-coding RNAs regulate motility in Escherichia coli, Mol Microbiol, vol.86, issue.3, pp.524-538, 2012. ,
The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal, Nature, vol.451, issue.7176, pp.355-358, 2008. ,
Identification of a phosphorylation site and functional analysis of conserved aspartic acid residues of OmpR, a transcriptional activator for ompF and ompC in Escherichia coli, Mol Microbiol, vol.10, issue.5, pp.1037-1047, 1993. ,
MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors, J Mol Biol, vol.313, issue.1, pp.1-12, 2001. ,
To approximately P or Not to approximately P? Non-canonical activation by two-component response regulators, Mol Microbiol, vol.103, issue.2, pp.203-213, 2017. ,
The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing, 2016. ,
Characterization of porin and ompR mutants of a virulent strain of Salmonella typhimurium: ompR mutants are attenuated in vivo, Infect Immun, vol.57, issue.7, pp.2136-2140, 1989. ,
Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli, J Biol Chem, vol.281, issue.18, pp.12253-12259, 2006. ,
BolA is a transcriptional switch that turns off motility and turns on biofilm development, MBio, vol.6, issue.1, pp.2352-02314, 2015. ,
Killer and protective ribosomes, Prog Mol Biol Transl Sci, vol.85, pp.423-466, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00373983
Reprogramming of anaerobic metabolism by the FnrS small RNA, Mol Microbiol, vol.75, issue.5, pp.1215-1231, 2010. ,
Histidine kinases: diversity of domain organization, Mol Microbiol, vol.34, issue.4, pp.633-640, 1999. ,
B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli, Proc Natl Acad Sci U S A, vol.104, issue.47, pp.18712-18717, 2007. ,
Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli, J Bacteriol, vol.178, issue.5, pp.1248-1257, 1996. ,
Analysis of the ferric citrate transport gene promoter of Escherichia coli, J Bacteriol, vol.185, issue.7, pp.2387-2391, 2003. ,
Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing, J Mol Biol, vol.212, issue.3, pp.461-471, 1990. ,
Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target, Genes Dev, vol.23, issue.17, pp.2004-2015, 2009. ,
The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase, J Bacteriol, vol.189, issue.12, pp.4410-4417, 2007. ,
Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli, Proc Natl Acad Sci U S A, vol.86, issue.16, pp.6052-6056, 1989. ,
The target spectrum of SdsR small RNA in Salmonella, Nucleic Acids Res, vol.44, issue.21, pp.10406-10422, 2016. ,
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD, Nucleic Acids Res, vol.40, issue.8, pp.3623-3640, 2012. ,
A small RNA activates CFA synthase by isoform-specific mRNA stabilization, EMBO J, vol.32, issue.22, pp.2963-2979, 2013. ,
Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence, Cell, vol.84, issue.1, pp.165-174, 1996. ,
The roles of SsrA-SsrB and OmpR-EnvZ in the regulation of genes encoding the Salmonella typhimurium SPI-2 type III secretion system, Microbiology, vol.149, pp.2385-2396, 2003. ,
cis-antisense RNA, another level of gene regulation in bacteria, Microbiol Mol Biol Rev, vol.75, issue.2, pp.286-300, 2011. ,
Amplification of signaling activity of the arc two-component system of Escherichia coli by anaerobic metabolites. An in vitro study with different protein modules, J Biol Chem, vol.274, issue.50, pp.35950-35954, 1999. ,
ArcA regulator of Gamma-Proteobacteria: Identification of the Binding Signal and Description of the Regulon, Biophysics, vol.48, issue.1, pp.21-25, 2003. ,
MzrA: a novel modulator of the EnvZ/OmpR two-component regulon, Mol Microbiol, vol.72, issue.6, pp.1408-1422, 2009. ,
Complex regulation of csgD promoter activity by global regulatory proteins, Mol Microbiol, vol.49, issue.3, pp.639-654, 2003. ,
The treatment-naive microbiome in new-onset Crohn's disease, Cell Host Microbe, vol.15, issue.3, pp.382-392, 2014. ,
Oligoribonuclease is an essential component of the mRNA decay pathway, Proc Natl Acad Sci U S A, vol.96, issue.8, pp.4372-4377, 1999. ,
Adherent invasive Escherichia coli strains from patients with Crohn's disease survive and replicate within macrophages without inducing host cell death, Infect Immun, vol.69, issue.9, pp.5529-5537, 2001. ,
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon, Proc Natl Acad Sci U S A, vol.108, issue.31, pp.12875-12880, 2011. ,
Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system, J Bacteriol, vol.187, issue.14, pp.4890-4899, 2005. ,
The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes, J Bacteriol, vol.186, issue.12, pp.4019-4024, 2004. ,
Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli, J Bacteriol, vol.180, issue.24, pp.6586-6596, 1998. ,
Bacterial small RNA regulators: versatile roles and rapidly evolving variations, Cold Spring Harb Perspect Biol, vol.3, issue.12, 2011. ,
The CpxQ sRNA Negatively Regulates Skp To Prevent Mistargeting of beta-Barrel Outer Membrane Proteins into the Cytoplasmic Membrane, MBio, vol.7, issue.2, pp.312-00316, 2016. ,
Bistable expression of CsgD in biofilm development of Salmonella enterica serovar typhimurium, J Bacteriol, vol.192, issue.2, pp.456-466, 2010. ,
Ribosomes and translation, Annu Rev Biochem, vol.66, pp.679-716, 1997. ,
Thinking quantitatively about transcriptional regulation, Nat Rev Mol Cell Biol, vol.6, issue.3, pp.221-232, 2005. ,
Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, Mol. Microbiol, vol.59, issue.1, pp.231-247, 2006. ,
Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, Mol Microbiol, vol.59, issue.1, pp.231-247, 2006. ,
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic Acids Res, vol.36, issue.21, pp.6781-6794, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00374118
The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator, Nucleic Acids Res, vol.36, issue.21, pp.6781-6794, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00374118
Modulating the outer membrane with small RNAs, Genes Dev, vol.20, issue.17, pp.2338-2348, 2006. ,
MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein, Genes Dev, vol.28, issue.14, pp.1620-1634, 2014. ,
Mechanism of transmembrane signaling by sensor histidine kinases, Science, vol.356, issue.6342, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01526454
beta-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity, Nat Commun, vol.4, p.1610, 2013. ,
A competition mechanism regulates the translation of the Escherichia coli operon encoding ribosomal proteins L35 and L20, J Mol Biol, vol.375, issue.3, pp.612-625, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00311009
Transcriptional regulation of Escherichia coli K-12 major outer membrane protein 1b, J. Bacteriol, vol.140, issue.2, pp.342-350, 1979. ,
The ompB locus and the regulation of the major outer membrane porin proteins of Escherichia coli K12, J. Mol. Biol, vol.146, issue.1, pp.23-43, 1981. ,
The ompB locus and the regulation of the major outer membrane porin proteins of Escherichia coli K12, J Mol Biol, vol.146, issue.1, pp.23-43, 1981. ,
Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes, J Biol Chem, vol.255, issue.20, pp.9564-9570, 1980. ,
Protection against deleterious nitrogen compounds: role of sigmaS-dependent small RNAs encoded adjacent to sdiA, Nucleic Acids Res, vol.44, issue.14, pp.6935-6948, 2016. ,
Analysis of E. coli promoter sequences, Nucleic Acids Res, vol.15, issue.5, pp.2343-2361, 1987. ,
Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli, J Biol Chem, vol.270, issue.45, pp.26849-26856, 1995. ,
Transcriptional regulation of the moe (molybdate metabolism) operon of Escherichia coli, Arch Microbiol, vol.175, issue.3, pp.178-188, 2001. ,
The extracytoplasmic stress factor, sigmaE, is required to maintain cell envelope integrity in Escherichia coli, PLoS One, vol.3, issue.2, p.1573, 2008. ,
Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites, J Mol Biol, vol.281, issue.5, pp.857-870, 1998. ,
In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA, Nucleic Acids Res, vol.35, issue.13, pp.4331-4346, 2007. ,
Dynamics of intracellular bacterial replication at the single cell level, Proc Natl Acad Sci U S A, vol.107, issue.8, pp.3746-3751, 2010. ,
Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli, Mol Gen Genet, vol.240, issue.3, pp.339-347, 1993. ,
Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection, J. Bact, vol.192, issue.1, pp.59-67, 2010. ,
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis, EMBO J, vol.29, issue.11, pp.1840-1850, 2010. ,
A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp, Mol Microbiol, vol.84, issue.3, pp.414-427, 2012. ,
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo, EMBO J, vol.35, issue.9, pp.991-1011, 2016. ,
Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS, Mol Microbiol, vol.40, issue.1, pp.20-36, 2001. ,
Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism, J Biol Chem, vol.282, issue.28, pp.20667-20675, 2007. ,
Mutations that alter the kinase and phosphatase activities of the two-component sensor EnvZ, J Bacteriol, vol.180, issue.17, pp.4538-4546, 1998. ,
Function of conserved histidine-243 in phosphatase activity of EnvZ, the sensor for porin osmoregulation in Escherichia coli, J Bacteriol, vol.179, issue.11, pp.3729-3735, 1997. ,
Identification of the bases in the ompF regulatory region, which interact with the transcription factor OmpR, J Mol Biol, vol.262, issue.5, pp.615-628, 1996. ,
A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene, J Bacteriol, vol.176, issue.5, pp.1309-1315, 1994. ,
Positive and negative control of ompB transcription in Escherichia coli by cyclic AMP and the cyclic AMP receptor protein, J Bacteriol, vol.174, issue.3, pp.664-670, 1992. ,
Messenger RNA degradation in bacterial cells, Annu Rev Genet, vol.48, pp.537-559, 2014. ,
DOI : 10.1146/annurev-genet-120213-092340
URL : http://europepmc.org/articles/pmc4431577?pdf=render
Footprinting mRNA-ribosome complexes with chemical probes, EMBO J, vol.13, issue.16, pp.3892-3901, 1994. ,
Sensor-response regulator interactions in a cross-regulated signal transduction network, Microbiology, vol.161, issue.7, pp.1504-1515, 2015. ,
DOI : 10.1099/mic.0.000092
URL : http://mic.microbiologyresearch.org/deliver/fulltext/micro/161/7/1504_mic000092.pdf?itemId=/content/journal/micro/10.1099/mic.0.000092&mimeType=pdf&isFastTrackArticle=
EnvZ, a transmembrane environmental sensor of Escherichia coli K-12, is phosphorylated in vitro, J Bacteriol, vol.170, issue.12, pp.5971-5973, 1988. ,
Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli, J Bacteriol, vol.196, issue.15, pp.2718-2727, 2014. ,
The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli, Proc Natl Acad Sci U S A, vol.84, issue.11, pp.3901-3905, 1987. ,
arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways, Proc Natl Acad Sci U S A, vol.85, issue.6, pp.1888-1892, 1988. ,
Adaptation of Escherichia coli to redox environments by gene expression, Mol Microbiol, vol.9, issue.1, pp.9-15, 1993. ,
Genetic regulatory mechanisms in the synthesis of proteins, J Mol Biol, vol.3, pp.318-356, 1961. ,
Mechanistic study of base-pairing small regulatory RNAs in bacteria, Methods, vol.117, pp.67-76, 2017. ,
RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity, Genes Dev, vol.9, issue.1, pp.84-96, 1995. ,
Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1, J Mol Biol, vol.232, issue.2, pp.484-492, 1993. ,
Down-regulation of outer membrane proteins by noncoding RNAs: unraveling the cAMP-CRP-and sigmaE-dependent CyaR-ompX regulatory case, J Mol Biol, vol.383, issue.1, pp.1-9, 2008. ,
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease, Nature, vol.491, issue.7422, pp.119-124, 2012. ,
K+ stimulates specifically the autokinase activity of purified and reconstituted EnvZ of Escherichia coli, J Biol Chem, vol.276, issue.44, pp.40896-40902, 2001. ,
Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP, J Bacteriol, vol.177, issue.13, pp.3647-3655, 1995. ,
Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli, Mol Microbiol, vol.65, issue.6, pp.1518-1533, 2007. ,
Identification of a second gene involved in global regulation of fumarate reductase and other nitrate-controlled genes for anaerobic respiration in Escherichia coli, J Bacteriol, vol.171, issue.7, pp.3810-3816, 1989. ,
Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray, Inflamm Bowel Dis, vol.16, issue.12, pp.2034-2042, 2010. ,
Pathogenic Escherichia coli, Nat Rev Microbiol, vol.2, issue.2, pp.123-140, 2004. ,
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor, BMC Bioinformatics, vol.16, p.297, 2015. ,
Gene activation by the Escherichia coli positive regulator OmpR: a mutational study of the DNA-binding domain of OmpR, Mol Gen Genet, vol.248, issue.4, pp.399-406, 1995. ,
Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq, Mol Microbiol, vol.61, issue.4, pp.1013-1022, 2006. ,
Mechanisms of ribosome rescue in bacteria, Nat Rev Microbiol, vol.13, issue.5, pp.285-297, 2015. ,
Structure/function relationships in OmpR and other winged-helix transcription factors, Curr Opin Microbiol, vol.5, issue.2, pp.135-141, 2002. ,
EcoCyc: fusing model organism databases with systems biology, Nucleic Acids Res, vol.41, pp.605-612, 2013. ,
The RNase E of Escherichia coli is a membrane-binding protein, Mol Microbiol, vol.70, issue.4, pp.799-813, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00356021
Oxygen sensing by the global regulator, FNR: the role of the ironsulfur cluster, FEMS Microbiol Rev, vol.22, issue.5, pp.341-352, 1998. ,
Chemotaxis-like regulatory systems: unique roles in diverse bacteria, Annu Rev Microbiol, vol.63, pp.45-59, 2009. ,
Transcriptional regulation by cAMP and its receptor protein, Annu Rev Biochem, vol.62, pp.749-795, 1993. ,
Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site, Nat Struct Biol, vol.4, issue.1, pp.28-31, 1997. ,
Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element, Mol Microbiol, vol.72, issue.4, pp.830-843, 2009. ,
Bacterial outer membrane vesicles and the host-pathogen interaction, Genes Dev, vol.19, issue.22, pp.2645-2655, 2005. ,
mRNA Decay. Escherichia coli and Salmonella. F. C. Neidhardt, vol.1, pp.849-860, 1996. ,
Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase, J Biol Chem, vol.278, issue.39, pp.37160-37168, 2003. ,
DOI : 10.1074/jbc.m305281200
URL : http://www.jbc.org/content/278/39/37160.full.pdf
Selected loss of tolerance evidenced by Crohn's diseaseassociated immune responses to auto-and microbial antigens, Gastroenterology, vol.123, issue.3, pp.689-699, 2002. ,
Salmonella biofilm development depends on the phosphorylation status of RcsB, J Bacteriol, vol.194, issue.14, pp.3708-3722, 2012. ,
Specificity in two-component signal transduction pathways, Annu Rev Genet, vol.41, pp.121-145, 2007. ,
DOI : 10.1146/annurev.genet.41.042007.170548
Riboregulation by DsrA RNA: trans-actions for global economy, Mol Microbiol, vol.38, issue.4, pp.667-672, 2000. ,
The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli, J Bacteriol, vol.186, issue.18, pp.6179-6185, 2004. ,
Signal-dependent phosphorylation of the membrane-bound NarX two-component sensor-transmitter protein of Escherichia coli: nitrate elicits a superior anion ligand response compared to nitrite, J Bacteriol, vol.181, issue.17, pp.5309-5316, 1999. ,
OmpR regulates the two-component system SsrA-ssrB in Salmonella pathogenicity island 2, J Bacteriol, vol.182, issue.3, pp.771-781, 2000. ,
Re-examination of the role of the periplasmic domain of EnvZ in sensing of osmolarity signals in Escherichia coli, Mol Microbiol, vol.22, issue.3, pp.405-413, 1996. ,
Prediction of rho-independent transcriptional terminators in Escherichia coli, Nucleic Acids Res, vol.29, issue.17, pp.3583-3594, 2001. ,
Expanding the RpoS/sigmaS-network by RNA sequencing and identification of sigmaS-controlled small RNAs in Salmonella, PLoS One, vol.9, issue.5, p.96918, 2014. ,
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources, Cell, vol.157, issue.3, pp.624-635, 2014. ,
Activation of yeaR-yoaG operon transcription by the nitrateresponsive regulator NarL is independent of oxygen-responsive regulator Fnr in Escherichia coli K-12, J Bacteriol, vol.189, issue.21, pp.7539-7548, 2007. ,
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA, Proc Natl Acad Sci U S A, vol.106, issue.46, pp.19292-19297, 2009. ,
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts, Nucleic Acids Res, vol.38, issue.11, pp.3794-3808, 2010. ,
Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters, J Bacteriol, vol.178, issue.21, pp.6238-6249, 1996. ,
Ribonuclease E is a 5'-end-dependent endonuclease, Nature, vol.395, issue.6703, pp.720-723, 1998. ,
RNase E: at the interface of bacterial RNA processing and decay, Nat Rev Microbiol, vol.11, issue.1, pp.45-57, 2013. ,
Evidence for multiple OmpR-binding sites in the upstream activation sequence of the ompC promoter in Escherichia coli: a single OmpR-binding site is capable of activating the promoter, J Bacteriol, vol.172, issue.1, pp.501-503, 1990. ,
Activation of the osmoregulated ompC gene by the OmpR protein in Escherichia coli: a study involving synthetic OmpR-binding sequences, J Biochem, vol.110, issue.3, pp.324-327, 1991. ,
The role of smoking in Crohn's disease as defined by clinical variables, Dig Dis Sci, vol.52, issue.11, pp.2897-2903, 2007. ,
Regulation of RpoS by a novel small RNA: the characterization of RprA, Mol Microbiol, vol.39, issue.5, pp.1382-1394, 2001. ,
DsrA RNA regulates translation of RpoS message by an antiantisense mechanism, independent of its action as an antisilencer of transcription, Proc Natl Acad Sci U S A, vol.95, issue.21, pp.12462-12467, 1998. ,
The Rcs phosphorelay: a complex signal transduction system, Annu Rev Microbiol, vol.59, pp.379-405, 2005. ,
Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli, J Bacteriol, vol.187, pp.6770-6778, 2005. ,
Regulation and mode of action of the second small RNA activator of RpoS translation, RprA, Mol Microbiol, vol.46, issue.3, pp.813-826, 2002. ,
Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression, Antioxid Redox Signal, vol.8, issue.5-6, pp.781-795, 2006. ,
A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system, Mol. Microbiol, vol.72, issue.3, pp.551-565, 2009. ,
Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA, EMBO J, vol.29, issue.18, pp.3094-3107, 2010. ,
DOI : 10.1038/emboj.2010.179
URL : http://emboj.embopress.org/content/29/18/3094.full.pdf
Expanding control in bacteria: interplay between small RNAs and transcriptional regulators to control gene expression, Curr Opin Microbiol, vol.16, issue.2, pp.125-132, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00823497
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Res, vol.35, issue.3, pp.962-974, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00129258
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions, Nucleic Acids Res, 2017. ,
Control of membrane lipid fluidity by molecular thermosensors, J Bacteriol, vol.186, issue.20, pp.6681-6688, 2004. ,
DOI : 10.1128/jb.186.20.6681-6688.2004
URL : https://jb.asm.org/content/186/20/6681.full.pdf
Primary and secondary modes of DNA recognition by the NarL two-component response regulator, Biochemistry, vol.44, issue.44, pp.14538-14552, 2005. ,
Identifying global regulators in transcriptional regulatory networks in bacteria, Curr Opin Microbiol, vol.6, issue.5, pp.482-489, 2003. ,
The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor, Structure, vol.5, issue.1, pp.109-124, 1997. ,
Stimulus perception in bacterial signal-transducing histidine kinases, Microbiol Mol Biol Rev, vol.70, issue.4, pp.910-938, 2006. ,
DOI : 10.1128/mmbr.00020-06
URL : https://mmbr.asm.org/content/70/4/910.full.pdf
Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli, Genes Dev, vol.17, pp.2374-2383, 2003. ,
A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli, Proc Natl Acad Sci U S A, vol.99, issue.7, pp.4620-4625, 2002. ,
Effect of RyhB small RNA on global iron use in Escherichia coli, J Bacteriol, vol.187, issue.20, pp.6962-6971, 2005. ,
5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA, Cell, vol.129, issue.4, pp.681-692, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00159472
Tuning of the porin expression under anaerobic growth conditions by his-to-Asp cross-phosphorelay through both the EnvZ-osmosensor and ArcBanaerosensor in Escherichia coli, Genes Cells, vol.5, issue.7, pp.555-569, 2000. ,
EnvZ-independent phosphotransfer signaling pathway of the OmpR-mediated osmoregulatory expression of OmpC and OmpF in Escherichia coli, Biosci Biotechnol Biochem, vol.63, issue.2, pp.408-414, 1999. ,
Escherichia coli RNase III (rnc) autoregulation occurs independently of rnc gene translation, Mol Microbiol, vol.26, issue.5, pp.1125-1135, 1997. ,
DOI : 10.1046/j.1365-2958.1997.6652007.x
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.1997.6652007.x
The linker region plays an important role in the interdomain communication of the response regulator OmpR, J Biol Chem, vol.277, issue.36, pp.32714-32721, 2002. ,
mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo, J Mol Biol, vol.221, issue.1, pp.81-95, 1991. ,
Adherent-invasive Escherichia coli isolated from Crohn's disease patients induce granulomas in vitro, Cell Microbiol, vol.9, issue.5, pp.1252-1261, 2007. ,
Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS, J Bacteriol, vol.181, issue.24, pp.7571-7579, 1999. ,
In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N), Mol Microbiol, vol.10, issue.5, pp.903-909, 1993. ,
Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli, Mol Microbiol, vol.84, issue.1, pp.51-65, 2012. ,
Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli, RNA Biol, vol.11, issue.5, pp.494-507, 2014. ,
Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli, J Bacteriol, vol.185, issue.13, pp.3696-3702, 2003. ,
Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82, PLoS One, vol.5, issue.9, 2010. ,
Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli, DNA Res, vol.4, issue.2, pp.161-168, 1997. ,
A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA), Proc Natl Acad Sci U S A, vol.81, issue.7, pp.1966-1970, 1984. ,
Functional characterization of bacterial sRNAs using a network biology approach, Proc Natl Acad Sci U S A, vol.108, issue.37, pp.15522-15527, 2011. ,
Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs, RNA, vol.9, issue.11, pp.1308-1314, 2003. ,
Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon, Genes Dev, vol.16, issue.13, pp.1696-1706, 2002. ,
Highlighting new phylogenetic specificities of Crohn's disease microbiota, Inflamm Bowel Dis, vol.17, issue.1, pp.185-192, 2011. ,
A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides, Mol Microbiol, vol.74, issue.6, pp.1314-1330, 2009. ,
Competition among Hfq-binding small RNAs in Escherichia coli, Mol Microbiol, vol.82, issue.6, pp.1545-1562, 2011. ,
The regulation of microcin B, C and J operons, Biochimie, vol.84, issue.5-6, pp.521-529, 2002. ,
RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria, Genes Dev, vol.25, issue.4, pp.294-298, 2011. ,
RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs, Genes Dev, vol.19, issue.18, pp.2176-2186, 2005. ,
Transcriptional induction of the conserved alternative sigma factor RpoS in Escherichia coli is dependent on BarA, a probable two-component regulator, Bioinformatics, vol.37, issue.2, pp.4187-4189, 2000. ,
Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function, RNA Biol, vol.10, issue.4, pp.636-651, 2013. ,
Chemical composition of Escherichia coli. Escherichia coli and Salmonella, Cellular And Molecular Biology. F. C. Neidhardt, vol.2, pp.13-16, 1996. ,
The structural basis of ribosome activity in peptide bond synthesis, Science, vol.289, issue.5481, pp.920-930, 2000. ,
Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC, Proc Natl Acad Sci U S A, vol.83, issue.20, pp.7850-7854, 1986. ,
High-resolution structure of the Escherichia coli ribosome, Nat Struct Mol Biol, vol.22, issue.4, pp.336-341, 2015. ,
Asymmetric cross-regulation between the nitrate-responsive NarX-NarL and NarQ-NarP two-component regulatory systems from Escherichia coli K-12, Mol Microbiol, vol.75, issue.2, pp.394-412, 2010. ,
Interaction of a transcriptional activator, OmpR, with reciprocally osmoregulated genes, ompF and ompC, of Escherichia coli, J Biol Chem, vol.261, issue.36, pp.17113-17119, 1986. ,
Quorum sensing in staphylococci, Annu Rev Genet, vol.42, pp.541-564, 2008. ,
Transcription termination and anti-termination in E. coli, Genes Cells, vol.7, issue.8, pp.755-768, 2002. ,
Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade, J Bacteriol, vol.189, issue.13, pp.4791-4799, 2007. ,
Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli, Microbiology, vol.158, pp.1482-1492, 2012. ,
RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA, J Mol Biol, vol.406, issue.1, pp.29-43, 2011. ,
GadY, a small-RNA regulator of acid response genes in Escherichia coli, J Bacteriol, vol.186, issue.20, pp.6698-6705, 2004. ,
Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12, Mol Microbiol, vol.46, issue.1, pp.281-291, 2002. ,
Regulation of alternative sigma factor use, Annu Rev Microbiol, vol.65, pp.37-55, 2011. ,
PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action, Proc Natl Acad Sci U S A, vol.108, issue.32, pp.13059-13064, 2011. ,
Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria, Arch Microbiol, vol.154, issue.4, pp.349-354, 1990. ,
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella, Proc Natl Acad Sci U S A, vol.112, issue.34, pp.4772-4781, 2015. ,
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay, Mol Microbiol, vol.62, issue.6, pp.1674-1688, 2006. ,
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA, Mol Microbiol, vol.74, issue.1, pp.139-158, 2009. ,
Mutational analysis of the linker region of EnvZ, an osmosensor in Escherichia coli, J Bacteriol, vol.179, issue.13, pp.4382-4390, 1997. ,
Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome, Eur J Biochem, vol.191, issue.2, pp.315-323, 1990. ,
Characterization of the Escherichia coli sigma(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis, Sci Rep, vol.5, p.10469, 2015. ,
The ArcB sensor kinase of Escherichia coli autophosphorylates by an intramolecular reaction, J Bacteriol, vol.192, issue.6, pp.1735-1739, 2010. ,
LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli, J Bacteriol, vol.188, issue.9, pp.3175-3181, 2006. ,
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation, Nat Struct Mol Biol, vol.16, issue.8, pp.840-846, 2009. ,
Pathogenic agents in inflammatory bowel diseases, Curr Opin Gastroenterol, vol.24, issue.4, pp.440-447, 2008. ,
Translational autocontrol of the Escherichia coli ribosomal protein S15, J Mol Biol, vol.211, issue.2, pp.407-414, 1990. ,
Nitrate reduction in the periplasm of gram-negative bacteria, Adv Microb Physiol, vol.45, pp.51-112, 2001. ,
From acids to osmZ: multiple factors influence synthesis of the OmpF and OmpC porins in Escherichia coli, Mol Microbiol, vol.20, issue.5, pp.911-917, 1996. ,
Identification of base pairs important for OmpR-DNA interaction, Mol Microbiol, vol.17, issue.3, pp.565-573, 1995. ,
DOI : 10.1111/j.1365-2958.1995.mmi_17030565.x
Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage, Genes Dev, vol.25, issue.4, pp.385-396, 2011. ,
DOI : 10.1101/gad.2001711
URL : http://genesdev.cshlp.org/content/25/4/385.full.pdf
Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene, J Bacteriol, vol.183, issue.24, pp.7213-7223, 2001. ,
Developmental pathway for biofilm formation in curliproducing Escherichia coli strains: role of flagella, curli and colanic acid, Environ Microbiol, vol.2, issue.4, pp.450-464, 2000. ,
Photoregulation in prokaryotes, Curr Opin Microbiol, vol.11, issue.2, pp.168-178, 2008. ,
DOI : 10.1016/j.mib.2008.02.014
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, issue.7285, pp.59-65, 2010. ,
DOI : 10.1038/nature08821
URL : https://hal.archives-ouvertes.fr/cea-00908974
Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response, PLoS Genet, vol.10, issue.3, p.1004215, 2014. ,
Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response, PLoS Genet, vol.10, issue.3, p.1004215, 2014. ,
Either of two functionally redundant sensor proteins, NarX and NarQ, is sufficient for nitrate regulation in Escherichia coli K-12, Proc Natl Acad Sci, vol.89, issue.18, pp.8419-8423, 1992. ,
Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate-and nitrite-regulated gene expression in Escherichia coli K-12, J Bacteriol, vol.175, issue.11, pp.3259-3268, 1993. ,
Simultaneous Gene Transcription and Translation in Bacteria, Nature Education, vol.1, issue.1, 2008. ,
The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript, Mol Microbiol, vol.78, issue.6, pp.1332-1347, 2010. ,
The second RNA chaperone, Hfq2, is also required for survival under stress and full virulence of Burkholderia cenocepacia J2315, J Bacteriol, vol.193, issue.7, pp.1515-1526, 2011. ,
Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control, Mol Microbiol, vol.58, issue.5, pp.1421-1429, 2005. ,
Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation, Mol Microbiol, vol.32, issue.4, pp.765-775, 1999. ,
OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment, Microbiology, vol.159, issue.2, pp.316-327, 2013. ,
Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm, Mol Microbiol, vol.48, issue.4, pp.855-861, 2003. ,
New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system, FEMS Microbiol Lett, vol.225, issue.1, pp.1-7, 2003. ,
Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli, Microbiology, vol.145, pp.2903-2912, 1999. ,
Molecular call and response: the physiology of bacterial small RNAs, Biochim Biophys Acta, vol.1809, issue.10, pp.525-531, 2011. ,
How to find RNA thermometers, Front Cell Infect Microbiol, vol.4, p.132, 2014. ,
Computational identification of noncoding RNAs in E. coli by comparative genomics, Curr Biol, vol.11, issue.17, pp.1369-1373, 2001. ,
Gene expression control by selective RNA processing and stabilization in bacteria, FEMS Microbiol Lett, vol.344, issue.2, pp.104-113, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00848172
Lack of interchangeability of Hfq-like proteins, Biochimie, vol.94, issue.7, pp.1554-1559, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00704468
Strong decrease in invasive ability and outer membrane vesicle release in Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 with the yfgL gene deleted, J Bacteriol, vol.187, issue.7, pp.2286-2296, 2005. ,
OmpC and the sigma(E) regulatory pathway are involved in adhesion and invasion of the Crohn's disease-associated Escherichia coli strain LF82, Mol Microbiol, vol.63, issue.6, pp.1684-1700, 2007. ,
Translational Control in Prokaryotes, Translational Control in Biology and, pp.803-827, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00261368
Fonction de nouveaux ARN non codant dans la régulation de l'expression des gènes de Staphylococcus aureus : adaptation à l'environnement et virulence, 2012. ,
E. coli Fis protein activates ribosomal RNA transcription in vitro and in vivo, EMBO J, vol.9, pp.3733-3742, 1990. ,
URL : https://hal.archives-ouvertes.fr/in2p3-00008924
E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo, EMBO J, vol.9, issue.11, pp.3733-3742, 1990. ,
URL : https://hal.archives-ouvertes.fr/in2p3-00008924
Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli, J Bacteriol, vol.187, issue.18, pp.6317-6323, 2005. ,
EnvZ controls the concentration of phosphorylated OmpR to mediate osmoregulation of the porin genes, J Mol Biol, vol.222, issue.3, pp.567-580, 1991. ,
Mutations that affect separate functions of OmpR the phosphorylated regulator of porin transcription in Escherichia coli, J Mol Biol, vol.231, issue.2, pp.261-273, 1993. ,
Bacterial DNA within granulomas of patients with Crohn's disease--detection by laser capture microdissection and PCR, Am J Gastroenterol, vol.99, issue.8, pp.1539-1543, 2004. ,
Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR, J Biol Chem, vol.278, issue.32, pp.29837-29855, 2003. ,
Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis, Wiley Interdiscip Rev RNA, vol.3, issue.1, pp.26-36, 2012. ,
Genetic locus (ompB) affecting a major outer-membrane protein in Escherichia coli K-12, J Bacteriol, vol.132, issue.1, pp.23-27, 1977. ,
Microbial influences in inflammatory bowel diseases, Gastroenterology, vol.134, issue.2, pp.577-594, 2008. ,
DOI : 10.1053/j.gastro.2007.11.059
Structural basis for RNA 3'-end recognition by Hfq, Proc Natl Acad Sci U S A, vol.108, issue.32, pp.13065-13070, 2011. ,
DOI : 10.1073/pnas.1103420108
URL : https://www.pnas.org/content/pnas/108/32/13065.full.pdf
Revisiting regulation of potassium homeostasis in Escherichia coli: the connection to phosphate limitation, 2017. ,
Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition, EMBO J, vol.34, issue.20, pp.2557-2573, 2015. ,
DOI : 10.15252/embj.201591569
URL : http://emboj.embopress.org/content/34/20/2557.full.pdf
Crohn's disease, Lancet, vol.359, issue.9300, pp.62-69, 2002. ,
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites, Genes Dev, vol.21, issue.21, pp.2804-2817, 2007. ,
Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA, Mol Microbiol, vol.81, issue.5, pp.1144-1165, 2011. ,
Regulation of gene expression by small non-coding RNAs: a quantitative view, Mol Syst Biol, vol.3, p.138, 2007. ,
Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR, J Bacteriol, vol.177, issue.16, pp.4696-4702, 1995. ,
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites, Proc Natl Acad Sci U S A, vol.71, issue.4, pp.1342-1346, 1974. ,
A role for the RNA chaperone Hfq in controlling adherentinvasive Escherichia coli colonization and virulence, PLoS One, vol.6, issue.1, p.16387, 2011. ,
Cross-talk suppression between the CpxA-CpxR and EnvZOmpR two-component systems in E. coli, Mol Microbiol, vol.70, issue.2, pp.494-506, 2008. ,
Evolving a robust signal transduction pathway from weak cross-talk, Mol Syst Biol, vol.6, p.452, 2010. ,
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq, PLoS Genet, vol.4, issue.8, p.1000163, 2008. ,
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium, Mol Microbiol, vol.63, issue.1, pp.193-217, 2007. ,
Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes, RNA Biol, vol.6, issue.3, pp.266-275, 2009. ,
Rewiring the specificity of two-component signal transduction systems, Cell, vol.133, issue.6, pp.1043-1054, 2008. ,
Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis, PLoS Biol, vol.3, issue.10, p.334, 2005. ,
Genetic analysis of the switch that controls porin gene expression in Escherichia coli K-12, J Mol Biol, vol.210, issue.2, pp.281-292, 1989. ,
A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli, Proc Natl Acad Sci U S A, vol.92, issue.6, pp.2003-2007, 1995. ,
Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal, RNA Biol, vol.7, issue.1, pp.104-110, 2010. ,
CRISPR-mediated adaptive immune systems in bacteria and archaea, Annu Rev Biochem, vol.82, pp.237-266, 2013. ,
FNR and its role in oxygen-regulated gene expression in Escherichia coli, FEMS Microbiol Rev, vol.6, issue.4, pp.399-428, 1990. ,
Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters, Biochem J, vol.420, issue.2, pp.249-257, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00479159
Nitrate respiration in relation to facultative metabolism in enterobacteria, Microbiol Rev, vol.52, issue.2, pp.190-232, 1988. ,
Biochemical Society Special Lecture. Nitrate-and nitrite-responsive sensors NarX and NarQ of proteobacteria, Biochem Soc Trans, vol.31, pp.1-10, 2003. ,
Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12, J Bacteriol, vol.185, pp.5862-5870, 2003. ,
Identification and expression of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12, J Bacteriol, vol.170, issue.4, pp.1589-1597, 1988. ,
A systems biology approach sheds new light on Escherichia coli acid resistance, Nucleic Acids Res, vol.39, issue.17, pp.7512-7528, 2011. ,
Two-component signal transduction, Annu Rev Biochem, vol.69, pp.183-215, 2000. ,
Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E, Genes Dev, vol.20, issue.18, pp.2605-2617, 2006. ,
Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli, J Bacteriol, vol.184, issue.18, pp.5130-5140, 2002. ,
Repression of in vitro transcription of the Escherichia coli fnr and nar X genes by FNR protein, FEBS Lett, vol.340, issue.1-2, pp.59-64, 1994. ,
Bacterial translocation in patients with Crohn's disease undergoing surgery, Dis Colon Rectum, vol.45, issue.12, pp.1665-1671, 2002. ,
NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ, Nature, vol.396, issue.6706, pp.88-92, 1998. ,
Escherichia coli-host macrophage interactions in the pathogenesis of inflammatory bowel disease, World J Gastroenterol, vol.20, issue.27, pp.8751-8763, 2014. ,
Isolation and characterization of mutations altering expression of the major outer membrane porin proteins using the local anaesthetic procaine, J Mol Biol, vol.166, issue.3, pp.273-282, 1983. ,
Pathways leading from BarA/SirA to motility and virulence gene expression in Salmonella, J Bacteriol, vol.185, issue.24, pp.7257-7265, 2003. ,
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli, J Bacteriol, vol.197, issue.1, pp.18-28, 2015. ,
A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli, Mol Microbiol, vol.84, issue.1, pp.17-35, 2012. ,
Bacterial antisense RNAs: how many are there, and what are they doing?, Annu Rev Genet, vol.44, pp.167-188, 2010. ,
SigmaE regulates and is regulated by a small RNA in Escherichia coli, J Bacteriol, vol.189, issue.11, pp.4243-4256, 2007. ,
Transmembrane signal transduction and osmoregulation in Escherichia coli. Functional importance of the periplasmic domain of the membrane-located protein kinase, EnvZ, J Biol Chem, vol.266, issue.11, pp.6780-6785, 1991. ,
Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA, Proc Natl Acad Sci U S A, vol.78, issue.3, pp.1421-1425, 1981. ,
Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ, Nat Struct Biol, vol.6, issue.8, pp.729-734, 1999. ,
GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites, Mol Microbiol, vol.70, issue.4, pp.965-982, 2008. ,
Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12, Mol Microbiol, vol.13, issue.1, pp.35-49, 1994. ,
Integration host factor binds specifically to multiple sites in the ompB promoter of Escherichia coli and inhibits transcription, J Bacteriol, vol.173, issue.18, pp.5800-5807, 1991. ,
Nitrite and nitrate regulation at the promoters of two Escherichia coli operons encoding nitrite reductase: identification of common target heptamers for both NarP-and NarL-dependent regulation, Mol Microbiol, vol.13, issue.6, pp.1045-1055, 1994. ,
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA, Genes Dev, vol.19, pp.2355-2366, 2005. ,
Sigma E controls biogenesis of the antisense RNA MicA, Nucleic Acids Res, vol.35, issue.4, pp.1279-1288, 2007. ,
The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins, Cell, vol.88, issue.2, pp.187-196, 1997. ,
The MiST2 database: a comprehensive genomics resource on microbial signal transduction, Nucleic Acids Res, vol.38, pp.401-407, 2010. ,
Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors, Biochim Biophys Acta, vol.1320, issue.3, pp.217-234, 1997. ,
A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis, J Mol Biol, vol.373, issue.3, pp.521-528, 2007. ,
The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli, Mol Microbiol, vol.37, issue.4, pp.856-868, 2000. ,
Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate, Science, vol.245, issue.4923, pp.1246-1249, 1989. ,
Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system, Mol Microbiol, vol.54, issue.4, pp.1076-1089, 2004. ,
Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system, Mol. Microbiol, vol.54, pp.1076-1089, 2004. ,
Translational autocontrol of the Escherichia coli hfq RNA chaperone gene, RNA, vol.11, issue.6, pp.976-984, 2005. ,
Dissection du mécanisme de terminaison/antiterminaison au niveau du terminateur du phage lambda : application à l'étude des complexes ARN-protéines in vivo, 2004. ,
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis, Proc Natl Acad Sci U S A, vol.106, issue.4, pp.1063-1068, 2009. ,
In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape, Biochemistry, vol.42, issue.13, pp.3798-3811, 2003. ,
The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide, Curr Biol, vol.14, issue.24, pp.2271-2276, 2004. ,
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria, Nucleic Acids Res, vol.31, issue.22, pp.6435-6443, 2003. ,
The Cpx envelope stress response regulates and is regulated by small noncoding RNAs, J Bacteriol, vol.196, issue.24, pp.4229-4238, 2014. ,
Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs, Genes Dev, vol.26, issue.13, pp.1498-1507, 2012. ,
Interdomain linkers of homologous response regulators determine their mechanism of action, J Bacteriol, vol.185, issue.1, pp.317-324, 2003. ,
The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite, J Bacteriol, vol.182, issue.20, pp.5813-5822, 2000. ,
Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP, J Bacteriol, vol.185, issue.17, pp.5076-5085, 2003. ,
The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite, J Bacteriol, vol.181, issue.17, pp.5303-5308, 1999. ,
The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm, EMBO J, vol.31, issue.11, pp.2648-2659, 2012. ,
CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli, Mol Microbiol, vol.56, issue.6, pp.1648-1663, 2005. ,
Sigma 32-dependent promoter activity in vivo: sequence determinants of the groE promoter, J Bacteriol, vol.185, pp.5800-5806, 2003. ,
Identification of novel small RNAs using comparative genomics and microarrays, Genes Dev, vol.15, issue.13, pp.1637-1651, 2001. ,
Regulatory RNAs in bacteria, Cell, vol.136, issue.4, pp.615-628, 2009. ,
Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli, Mol Microbiol, vol.62, issue.4, pp.1014-1034, 2006. ,
Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli, Mol Microbiol, vol.40, issue.1, pp.245-256, 2001. ,
Discrimination between structurally related ligands nitrate and nitrite controls autokinase activity of the NarX transmembrane signal transducer of Escherichia coli K-12, Mol Microbiol, vol.26, issue.5, pp.911-925, 1997. ,
The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding, Cell Mol Life Sci, vol.64, issue.1, pp.3-16, 2007. ,
Control of gene expression by a natural metabolite-responsive ribozyme, Nature, vol.428, issue.6980, pp.281-286, 2004. ,
Comparative genomics boosts target prediction for bacterial small RNAs, Proc Natl Acad Sci U S A, vol.110, issue.37, pp.3487-3496, 2013. ,
Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors, Mol Microbiol, vol.27, issue.2, pp.493-505, 1998. ,
Osmoregulation of gene expression. I. DNA sequence of the ompR gene of the ompB operon of Escherichia coli and characterization of its gene product, J Biol Chem, vol.257, issue.22, pp.13685-13691, 1982. ,
Transcriptional Regulation of the Outer Membrane Porin Gene ompW Reveals its Physiological Role during the Transition from the Aerobic to the Anaerobic Lifestyle of Escherichia coli, Front Microbiol, vol.7, p.799, 2016. ,
Activation and repression at the Escherichia coli ynfEFGHI operon promoter, J Bacteriol, vol.191, issue.9, pp.3172-3176, 2009. ,
Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli, J Biol Chem, vol.280, issue.2, pp.1448-1456, 2005. ,
Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes, FEMS Microbiol Lett, vol.186, issue.2, pp.257-262, 2000. ,
Translation enhancing ACA motifs and their silencing by a bacterial small regulatory RNA, PLoS Genet, vol.10, issue.1, p.1004026, 2014. ,
Attenuation in the control of expression of bacterial operons, Nature, vol.289, issue.5800, pp.751-758, 1981. ,
Cross talk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system, Genes Cells, vol.20, issue.7, pp.601-612, 2015. ,
An efficient recombination system for chromosome engineering in Escherichia coli, Proc. Natl. Acad. Sci. USA, vol.97, issue.11, pp.5978-5983, 2000. ,
Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli, Prog Nucleic Acid Res Mol Biol, vol.47, pp.331-370, 1994. ,
Mutations in interaction surfaces differentially impact E. coli Hfq association with small RNAs and their mRNA targets, J Mol Biol, vol.425, pp.3678-3697, 2013. ,
Global analysis of small RNA and mRNA targets of Hfq, Mol Microbiol, vol.50, issue.4, pp.1111-1124, 2003. ,
Phosphatase activity of histidine kinase EnvZ without kinase catalytic domain, Proc Natl Acad Sci U S A, vol.97, issue.14, pp.7808-7813, 2000. ,
DOI : 10.1073/pnas.97.14.7808
URL : http://www.pnas.org/content/97/14/7808.full.pdf
Hfq variant with altered RNA binding functions, Nucleic Acids Res, vol.34, issue.2, pp.709-720, 2006. ,
DOI : 10.1093/nar/gkj464
URL : https://hal.archives-ouvertes.fr/hal-00090174
Mechanism of activation of catabolite-sensitive genes: a positive control system, Proc Natl Acad Sci U S A, vol.66, issue.1, pp.104-110, 1970. ,
Chemosensory pathways, motility and development in Myxococcus xanthus, Nat Rev Microbiol, vol.5, issue.11, pp.862-872, 2007. ,
DOI : 10.1038/nrmicro1770