Regulatory RNAs in Bacteria, Cell, vol.136, issue.4, pp.615-628, 2009. ,
DOI : 10.1016/j.cell.2009.01.043
Proteins that interact with bacterial small RNA regulators, FEMS Microbiology Reviews, vol.31, issue.5, pp.614-625, 2007. ,
DOI : 10.1111/j.1574-6976.2007.00079.x
URL : https://hal.archives-ouvertes.fr/inserm-00712150
Emerging views on tmRNA-mediated protein tagging and ribosome rescue, Molecular Microbiology, vol.2, issue.4, pp.879-885, 2001. ,
DOI : 10.1126/science.1060089
URL : https://hal.archives-ouvertes.fr/inserm-00718190
Regulatory mechanisms employed by cis-encoded antisense RNAs, Current Opinion in Microbiology, vol.10, issue.2, pp.102-109, 2007. ,
DOI : 10.1016/j.mib.2007.03.012
Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains, Proc. Natl Acad, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00713114
A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome, Molecular Microbiology, vol.27, issue.5, pp.1174-1191, 2007. ,
DOI : 10.1128/JB.188.1.124-131.2006
The role of RNAs in the regulation of virulence-gene expression, Current Opinion in Microbiology, vol.9, issue.2, pp.229-236, 2006. ,
DOI : 10.1016/j.mib.2006.02.005
URL : https://hal.archives-ouvertes.fr/hal-00094433
The Listeria transcriptional landscape from saprophytism to virulence, Nature, vol.99, issue.7249, pp.950-956, 2009. ,
DOI : 10.1038/nature08080
The primary transcriptome of the major human pathogen Helicobacter pylori, Nature, vol.73, issue.7286, pp.250-255, 2010. ,
DOI : 10.1038/nature08756
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts, Nucleic Acids Research, vol.38, issue.11, pp.3794-3808, 2010. ,
DOI : 10.1093/nar/gkq032
Bacterial Antisense RNAs: How Many Are There, and What Are They Doing?, Annual Review of Genetics, vol.44, issue.1, pp.167-188, 2010. ,
DOI : 10.1146/annurev-genet-102209-163523
An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin, Molecular Microbiology, vol.3, issue.3, pp.738-754, 2007. ,
DOI : 10.1074/jbc.M502050200
An internal antisense RNA regulates expression of the photosynthesis gene isiA, Proc. Natl. Acad. Sci. USA, pp.7054-7058, 2008. ,
Small RNA gene identification and mRNA target predictions in bacteria, Bioinformatics, vol.24, issue.24, pp.2807-2813, 2008. ,
DOI : 10.1093/bioinformatics/btn560
URL : https://hal.archives-ouvertes.fr/inserm-00706679
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli, Current Biology, vol.11, issue.12, pp.941-950, 2001. ,
DOI : 10.1016/S0960-9822(01)00270-6
Computational identification of noncoding RNAs in E. coli by comparative genomics, Current Biology, vol.11, issue.17, pp.1369-1373, 2001. ,
DOI : 10.1016/S0960-9822(01)00401-8
Intergenic sequence inspector: searching and identifying bacterial RNAs, Bioinformatics, vol.19, issue.13, pp.1707-1709, 2003. ,
DOI : 10.1093/bioinformatics/btg235
URL : https://hal.archives-ouvertes.fr/inserm-00714226
Identification of cyanobacterial non-coding RNAs by comparative genome analysis, Genome Biology, vol.6, issue.9, p.73, 2005. ,
DOI : 10.1186/gb-2005-6-9-r73
sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes, Nucleic Acids Research, vol.33, issue.13, pp.4096-4105, 2005. ,
DOI : 10.1093/nar/gki715
A computational approach to identify genes for functional RNAs in genomic sequences, Nucleic Acids Research, vol.29, issue.19, pp.3928-3938, 2001. ,
DOI : 10.1093/nar/29.19.3928
Searching for RNA genes using base-composition statistics, Nucleic Acids Research, vol.30, issue.9, pp.2076-2082, 2002. ,
DOI : 10.1093/nar/30.9.2076
Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming, Nucleic Acids Research, vol.33, issue.10, pp.3263-3270, 2005. ,
DOI : 10.1093/nar/gki644
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model, Gene, vol.372, pp.171-181, 2006. ,
DOI : 10.1016/j.gene.2005.12.034
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes, Bioinformatics, vol.22, issue.21, pp.2590-2596, 2006. ,
DOI : 10.1093/bioinformatics/btl441
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change, BMC Bioinformatics, vol.7, issue.1, pp.173-203, 2006. ,
DOI : 10.1186/1471-2105-7-173
RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Research, vol.29, issue.22, pp.4724-4735, 2001. ,
DOI : 10.1093/nar/29.22.4724
Prediction of rho-independent transcriptional terminators in Escherichia coli, Nucleic Acids Research, vol.29, issue.17, pp.3583-3594, 2001. ,
DOI : 10.1093/nar/29.17.3583
MELTING, computing the melting temperature of nucleic acid duplex, Bioinformatics, vol.17, issue.12, pp.1226-1227, 2001. ,
DOI : 10.1093/bioinformatics/17.12.1226
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake, Genome Biology, vol.8, issue.2, p.22, 2007. ,
DOI : 10.1186/gb-2007-8-2-r22
afa-8 Gene Cluster Is Carried by a Pathogenicity Island Inserted into the tRNAPhe of Human and Bovine Pathogenic Escherichia coli Isolates, Infection and Immunity, vol.69, issue.2, pp.937-948, 2001. ,
DOI : 10.1128/IAI.69.2.937-948.2001
Cloning of the chromosomal determinants encoding haemolysin production and mannose resistant haemagglutination in Escherichia coli, J. Bacteriol, vol.152, pp.1241-1247, 1982. ,
Demonstration of regulatory cross-talk between P fimbriae and type 1 fimbriae in uropathogenic Escherichia coli, Microbiology, vol.152, issue.4, pp.1143-1153, 2006. ,
DOI : 10.1099/mic.0.28677-0
Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease, Molecular Microbiology, vol.181, issue.6, pp.1499-1513, 2002. ,
DOI : 10.1046/j.1365-2958.2002.03126.x
Translational control and target recognition by Escherichia coli small RNAs in vivo, Nucleic Acids Research, vol.35, issue.3, pp.1018-1037, 2007. ,
DOI : 10.1093/nar/gkl1040
Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant, Gene, vol.158, issue.1, pp.9-14, 1995. ,
DOI : 10.1016/0378-1119(95)00193-A
A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Research, vol.28, issue.22, p.97, 2000. ,
DOI : 10.1093/nar/28.22.e97
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements, Nucleic Acids Research, vol.25, issue.6, pp.1203-1210, 1997. ,
DOI : 10.1093/nar/25.6.1203
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. USA, pp.6640-6645, 2000. ,
DOI : 10.1073/pnas.120163297
A Small Bacterial RNA Regulates a Putative ABC Transporter, Journal of Biological Chemistry, vol.280, issue.9, pp.7901-7908, 2005. ,
DOI : 10.1074/jbc.M413071200
URL : https://hal.archives-ouvertes.fr/hal-00196808
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, pp.402-408, 2001. ,
AL511 requires flagellum to enter renal collecting duct cells, Cellular Microbiology, vol.8, issue.4, pp.616-628, 2009. ,
DOI : 10.1111/j.1462-5822.2008.01278.x
Biofilm Formation in a Hydrodynamic Environment by Novel FimH Variants and Ramifications for Virulence, Infection and Immunity, vol.69, issue.3, pp.1322-1328, 2001. ,
DOI : 10.1128/IAI.69.3.1322-1328.2001
Flexible Sequence Similarity Searching with the FASTA3 Program Package, Methods Mol. Biol, vol.132, pp.185-219, 2000. ,
DOI : 10.1385/1-59259-192-2:185
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999. ,
DOI : 10.1006/jmbi.1999.2700
Improved microbial gene identification with GLIMMER, Nucleic Acids Research, vol.27, issue.23, pp.4636-4641, 1999. ,
DOI : 10.1093/nar/27.23.4636
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays, Nucleic Acids Research, vol.30, issue.17, pp.3732-3738, 2002. ,
DOI : 10.1093/nar/gkf505
Genome-wide detection of novel regulatory, 2011. ,
Cartography of Methicillin-Resistant S. aureus Transcripts: Detection, Orientation and Temporal Expression during Growth Phase and Stress Conditions, PLoS ONE, vol.191, issue.5, p.10725, 2010. ,
DOI : 10.1371/journal.pone.0010725.s005
URL : https://hal.archives-ouvertes.fr/hal-00526375
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009. ,
DOI : 10.1371/journal.pgen.1000344.s016
URL : https://hal.archives-ouvertes.fr/hal-00390293
Pathogenic Escherichia coli, Nature Reviews Microbiology, vol.63, issue.2, pp.123-140, 2004. ,
DOI : 10.1128/IAI.69.1.315-324.2001
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach, Proc. Natl. Acad. Sci. USA, pp.5977-5982, 2006. ,
DOI : 10.1073/pnas.0600938103
Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536, Molecular Microbiology, vol.64, issue.3, pp.584-595, 2006. ,
DOI : 10.1073/pnas.252529799
depends on type 1 pili, Cellular Microbiology, vol.93, issue.Suppl. 1A, pp.2230-2241, 2007. ,
DOI : 10.1111/j.1462-5822.2007.00952.x
biofilm formation: roles of flagella, motility, chemotaxis and type I pili, Molecular Microbiology, vol.86, issue.2, pp.285-293, 1998. ,
DOI : 10.1046/j.1365-2958.1998.01061.x
MicroReview: Envelope stress responses and Gram-negative bacterial pathogenesis, Molecular Microbiology, vol.64, issue.5, pp.1119-1128, 2005. ,
DOI : 10.1111/j.1365-2958.2005.04625.x
Impact of the RNA Chaperone Hfq on the Fitness and Virulence Potential of Uropathogenic Escherichia coli, Infection and Immunity, vol.76, issue.7, pp.3019-3026, 2008. ,
DOI : 10.1128/IAI.00022-08
Invasive Group B Streptococcal Infections in Infants, France, Emerging Infectious Diseases, vol.14, issue.10, pp.1647-1649, 2008. ,
DOI : 10.3201/eid1410.080185
URL : https://hal.archives-ouvertes.fr/hal-00307826
Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus, BMC Genomics, vol.11, issue.1, p.661, 2010. ,
DOI : 10.1186/1471-2164-11-661
Identification of Group B Streptococcal Sip Protein, Which Elicits Cross-Protective Immunity, Infection and Immunity, vol.68, issue.10, pp.5610-5618, 2000. ,
DOI : 10.1128/IAI.68.10.5610-5618.2000
Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli, PLoS ONE, vol.4, p.7526, 2009. ,
Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi, Nucleic Acids Research, vol.38, issue.17, pp.5893-5908, 2010. ,
DOI : 10.1093/nar/gkq281
Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule, EMBO J, vol.12, pp.3967-3975, 1993. ,
A Staphylococcus aureus Small RNA Is Required for Bacterial Virulence and Regulates the Expression of an Immune-Evasion Molecule, PLoS Pathogens, vol.164, issue.6, p.1000927, 2010. ,
DOI : 10.1371/journal.ppat.1000927.s009
URL : https://hal.archives-ouvertes.fr/inserm-00697384
Global epithelial cell transcriptional responses reveal Streptococcus pyogenes Fas regulator activity association with bacterial aggressiveness, Cellular Microbiology, vol.16, issue.9, pp.1237-1250, 2005. ,
DOI : 10.1111/j.1462-5822.2005.00548.x
An antisense RNA that governs the expression kinetics of a multifunctional virulence gene, Molecular Microbiology, vol.102, issue.4, pp.1020-1033, 2010. ,
DOI : 10.1111/j.1365-2958.2010.07161.x
Small RNAs promote mRNA stability to activate the synthesis of virulence factors, Molecular Microbiology, vol.278, issue.3, pp.1327-1331, 2010. ,
DOI : 10.1111/j.1365-2958.2010.07428.x
Identification of the genes directly controlled by the response regulator CiaR in Streptococcus pneumoniae: five out of 15 promoters drive expression of small non-coding RNAs, Molecular Microbiology, vol.174, issue.1, pp.110-126, 2007. ,
DOI : 10.1093/nar/gkg595
A Genome-Wide Analysis of Small Regulatory RNAs in the Human Pathogen Group A Streptococcus, PLoS ONE, vol.186, issue.11, p.7668, 2009. ,
DOI : 10.1371/journal.pone.0007668.s005
The 4.5 S RNA gene of Escherichia coli is essential for cell growth, Journal of Molecular Biology, vol.178, issue.3, pp.533-550, 1984. ,
DOI : 10.1016/0022-2836(84)90237-7
URL : https://hal.archives-ouvertes.fr/in2p3-01025397
Sequence of 6S RNA of E. coli, Nature New Biology, vol.229, issue.5, pp.147-149, 1971. ,
DOI : 10.1038/newbio229147a0
Mechanism for the autogenous control of the crp operon: transcriptional inhibition by a divergent RNA transcript., Proc. Natl. Acad. Sci. USA, pp.5000-5004, 1986. ,
DOI : 10.1073/pnas.83.14.5000
The RNA Molecule CsrB Binds to the Global Regulatory Protein CsrA and Antagonizes Its Activity in Escherichia coli, Journal of Biological Chemistry, vol.272, issue.28, pp.17502-17510, 1997. ,
DOI : 10.1074/jbc.272.28.17502
Identification of novel small RNAs using comparative genomics and microarrays, Genes & Development, vol.15, issue.13, pp.1637-1651, 2001. ,
DOI : 10.1101/gad.901001
Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules, Molecular Microbiology, vol.13, issue.5, pp.615-620, 1992. ,
DOI : 10.1016/0092-8674(85)90290-9
A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli., Proc. Natl. Acad. Sci. USA, 1995. ,
DOI : 10.1073/pnas.92.6.2003
A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome, Biosystems, vol.65, issue.2-3, pp.157-177, 2002. ,
DOI : 10.1016/S0303-2647(02)00013-8
Noncoding RNA gene detection using comparative sequence analysis, BMC Bioinformatics, vol.2, pp.1-19, 2001. ,
Transcription of the sulA-ompA region of Escherichia Coli during the SOS response and the role of an antisense RNA molecule, Molecular Microbiology, vol.133, issue.6, pp.715-722, 1989. ,
DOI : 10.1038/312075a0
The Small RNA IstR Inhibits Synthesis of an SOS-Induced Toxic Peptide, Current Biology, vol.14, issue.24, pp.2271-2276, 2004. ,
DOI : 10.1016/j.cub.2004.12.003
A small RNA that complements mutants in the RNA processing enzyme ribonuclease P, Journal of Molecular Biology, vol.162, issue.3, pp.515-533, 1982. ,
DOI : 10.1016/0022-2836(82)90386-2
A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA)., Proc. Natl. Acad. Sci, 1966. ,
DOI : 10.1073/pnas.81.7.1966
fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex11Edited by M. Gottesman, Journal of Molecular Biology, vol.300, issue.5, pp.1101-1112, 2000. ,
DOI : 10.1006/jmbi.2000.3942
Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli, Molecular Microbiology, vol.37, issue.2, pp.333-349, 2002. ,
DOI : 10.1006/jmbi.2000.3667
Regulation of RpoS by a novel small RNA: the characterization of RprA, Molecular Microbiology, vol.95, issue.5, pp.1382-1394, 2001. ,
DOI : 10.1111/j.1365-2958.2001.02329.x
Down-regulation of Porins by a Small RNA Bypasses the Essentiality of the Regulated Intramembrane Proteolysis Protease RseP in Escherichia coli, Journal of Biological Chemistry, vol.281, issue.18, pp.12253-12256, 2006. ,
DOI : 10.1074/jbc.M600819200
Global analysis of small RNA and mRNA targets of Hfq, Molecular Microbiology, vol.9, issue.4, pp.1111-1124, 2003. ,
DOI : 10.1046/j.1365-2958.2003.03734.x
Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli, Nucleic Acids Research, vol.33, issue.3, pp.1040-1050, 2005. ,
DOI : 10.1093/nar/gki256
DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA., Journal of Bacteriology, vol.170, issue.5, pp.2083-2088, 1988. ,
DOI : 10.1128/jb.170.5.2083-2088.1988
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria, Nucleic Acids Research, vol.31, issue.22, pp.6435-6443, 2003. ,
DOI : 10.1093/nar/gkg867
Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA, Science, vol.271, issue.5251, pp.990-993, 1996. ,
DOI : 10.1126/science.271.5251.990
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation, Nucleic Acids Research, vol.37, issue.21, pp.7239-7257, 2009. ,
DOI : 10.1093/nar/gkp668
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles, Genome Research, vol.19, issue.6, pp.1084-1092, 2009. ,
DOI : 10.1101/gr.089714.108
URL : https://hal.archives-ouvertes.fr/hal-00529723
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism, Nucleic Acids Research, vol.38, issue.19, pp.6620-6636, 2010. ,
DOI : 10.1093/nar/gkq462
URL : https://hal.archives-ouvertes.fr/hal-00538925
Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype, Journal of Molecular Medicine, vol.42, issue.6, 2010. ,
DOI : 10.1007/s00109-010-0597-2