T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, p.8, 2006.

A. Boehm and J. Vogel, The csgD mRNA as a hub for signal integration via multiple small RNAs, Molecular microbiology, vol.84, pp.1-5, 2012.

V. Bordeau and B. Felden, 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 research, vol.42, pp.4682-4696, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-00941995

A. Bougdour, C. Lelong, G. , and J. , Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase, The Journal of biological chemistry, vol.279, pp.19540-19550, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00173294

S. Brantl, Regulatory mechanisms employed by cis-encoded antisense RNAs, Current opinion in microbiology, vol.10, pp.102-109, 2007.

A. Coornaert, C. Chiaruttini, M. Springer, and M. Guillier, Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB, PLoS genetics, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00823468

D. L. Court, J. Gan, Y. H. Liang, G. X. Shaw, J. E. Tropea et al., , 2013.

I. Rnase, Genetics and function; structure and mechanism, Annual review of genetics, vol.47, pp.405-431

N. De-lay, D. J. Schu, G. , and S. , Bacterial small RNA-based negative regulation: Hfq and its accomplices, The Journal of biological chemistry, vol.288, pp.7996-8003, 2013.

M. Doetsch, S. Stampfl, B. Furtig, M. Beich-frandsen, K. Saxena et al., Study of E. coli Hfq's RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents, Nucleic acids research, vol.41, pp.487-497, 2013.

T. Dong, M. G. Kirchhof, and H. E. Schellhorn, RpoS regulation of gene expression during exponential growth of Escherichia coli K12. Molecular genetics and genomics : MGG 279, pp.267-277, 2008.

T. Dong and H. E. Schellhorn, Control of RpoS in global gene expression of Escherichia coli in minimal media. Molecular genetics and genomics : MGG 281, pp.19-33, 2009.

T. Dong, R. Yu, and H. Schellhorn, Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli, Molecular microbiology, vol.79, pp.375-386, 2011.

C. Dorel, O. Vidal, C. Prigent-combaret, I. Vallet, L. et al., Involvement of the Cpx signal transduction pathway of E. coli in biofilm formation, FEMS microbiology letters, vol.178, pp.169-175, 1999.

E. M. Fozo, M. Kawano, F. Fontaine, Y. Kaya, K. S. Mendieta et al., Repression of small toxic protein synthesis by the Sib and OhsC small RNAs, Molecular microbiology, vol.70, pp.1076-1093, 2008.

K. S. Frohlich, K. Papenfort, A. A. Berger, and J. Vogel, A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD, Nucleic acids research, vol.40, pp.3623-3640, 2012.

K. S. Frohlich and J. Vogel, Activation of gene expression by small RNA, Current opinion in microbiology, vol.12, pp.674-682, 2009.

M. Guillier, G. , and S. , Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs, Molecular microbiology, vol.59, pp.231-247, 2006.

K. Han, K. S. Kim, G. Bak, H. Park, L. et al., Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family, Nucleic acids research, vol.38, pp.5851-5866, 2010.

C. A. Henderson, H. A. Vincent, A. Casamento, C. M. Stone, J. O. Phillips et al., Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS, Rna, vol.19, pp.1089-1104, 2013.

T. M. Henkin, Control of transcription termination in prokaryotes. Annual review of genetics, vol.30, pp.35-57, 1996.

A. Herbig and K. Nieselt, nocoRNAc: characterization of non-coding RNAs in prokaryotes, BMC bioinformatics, vol.12, p.40, 2011.

E. Holmqvist, J. Reimegard, M. Sterk, N. Grantcharova, U. Romling et al., Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis, The EMBO journal, vol.29, pp.1840-1850, 2010.

E. Holmqvist and J. Vogel, A small RNA serving both the Hfq and CsrA regulons, Genes & development, vol.27, pp.1073-1078, 2013.

A. Huttenhofer and J. Vogel, Experimental approaches to identify non-coding RNAs, Nucleic acids research, vol.34, pp.635-646, 2006.

A. Ishihama, Functionnal modulation of Escherichia coli RNA polymerase, Annual review of microbiology, vol.54, pp.499-518, 2000.

M. G. Jorgensen, J. S. Nielsen, A. Boysen, T. Franch, J. Moller-jensen et al., Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli, Molecular microbiology, vol.84, pp.36-50, 2012.

G. Jubelin, A. Vianney, C. Beloin, J. M. Ghigo, J. C. Lazzaroni et al., , 2005.

, CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli, Journal of bacteriology, vol.187, pp.2038-2049

A. S. Kraev, A simple system of cloning in phage M13 and DNA sequencing with terminators, 1988.

, Molekuliarnaia biologiia, vol.22, pp.1164-1197

M. Kroger, Compilation of DNA sequences of Escherichia coli, Nucleic acids research, vol.17, pp.283-309, 1989.

M. Kroger and R. Wahl, Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995), Nucleic acids research, vol.24, pp.29-31, 1996.

M. Kroger and R. Wahl, Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC (update 1996), Nucleic acids research, vol.25, pp.39-42, 1997.

M. Kroger and R. Wahl, Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC, Nucleic acids research, vol.26, pp.46-49, 1998.

S. Lacour, A. Kolb, and P. Landini, Nucleotides from-16 to-12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase, The Journal of biological chemistry, vol.278, pp.37160-37168, 2003.

Y. Y. Lee, C. S. Barker, P. Matsumura, and R. Belas, Refining the binding of the Escherichia coli flagellar master regulator, FlhD4C2, on a base-specific level, Journal of bacteriology, vol.193, pp.4057-4068, 2011.

C. Levi-meyrueis, V. Monteil, O. Sismeiro, M. A. Dillies, M. Monot et al., Expanding the RpoS/sigmaS-Network by RNA Sequencing and Identification of sigmaS-Controlled Small RNAs in Salmonella, PloS one, vol.9, p.96918, 2014.

S. Li, X. Dong, and Z. Su, Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling, BMC genomics, vol.14, p.520, 2013.

M. Y. Liu, The RNA Molecule CsrB Binds to the Global Regulatory Protein CsrA and Antagonizes Its Activity in Escherichia coli, Journal of Biological Chemistry, vol.272, pp.17502-17510, 1997.

M. Y. Liu, The Global Regulator CsrA of Escherichia coli Is a Specific mRNA-Binding Protein, Journal of bacteriology, vol.179, pp.4639-4642, 1997.

O. Lukjancenko, T. M. Wassenaar, and D. W. Ussery, Comparison of 61 sequenced Escherichia coli genomes, Microbial ecology, vol.60, pp.708-720, 2010.

A. Maciag, C. Peano, A. Pietrelli, T. Egli, G. De-bellis et al., In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identification of sigmaS-specific promoter sequence elements, Nucleic acids research, vol.39, pp.5338-5355, 2011.

C. A. Mccullen, J. N. Benhammou, N. Majdalani, G. , and S. , Mechanism of positive regulation by DsrA and RprA small noncoding RNAs: pairing increases translation and protects rpoS mRNA from degradation, Journal of bacteriology, vol.192, pp.5559-5571, 2010.

F. Mika, S. Busse, A. Possling, J. Berkholz, N. Tschowri et al., Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli, Molecular microbiology, vol.84, pp.51-65, 2012.

H. Ogasawara, K. Yamada, A. Kori, K. Yamamoto, and A. Ishihama, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors, Microbiology, vol.156, pp.2470-2483, 2010.

H. Ogasawara, K. Yamamoto, and A. Ishihama, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis, Journal of bacteriology, vol.193, pp.2587-2597, 2011.

J. A. Opdyke, E. M. Fozo, M. R. Hemm, and G. Storz, RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA, Journal of molecular biology, vol.406, pp.29-43, 2011.

K. Papenfort, M. Bouvier, F. Mika, C. M. Sharma, and J. Vogel, Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA, Proceedings of the National Academy of Sciences of the United States of America, vol.107, pp.20435-20440, 2010.

C. L. Patten, M. G. Kirchhof, M. R. Schertzberg, R. A. Morton, and H. E. Schellhorn, Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Molecular genetics and genomics : MGG 272, pp.580-591, 2004.

C. Pesavento, G. Becker, N. Sommerfeldt, A. Possling, N. Tschowri et al., Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli, Genes & development, vol.22, pp.2434-2446, 2008.

C. Prigent-combaret, E. Brombacher, O. Vidal, A. Ambert, P. Lejeune et al., Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene, Journal of bacteriology, vol.183, pp.7213-7223, 2001.

C. Prigent-combaret, G. Prensier, T. T. Le-thi, O. Vidal, P. Lejeune et al., Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid, Environmental microbiology, vol.2, pp.450-464, 2000.

B. Reichenbach, A. Maes, F. Kalamorz, E. Hajnsdorf, G. et al., The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli, Nucleic acids research, vol.36, pp.2570-2580, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00348797

S. M. Reshamwala and S. B. Noronha, Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis, Archives of microbiology, vol.193, pp.711-722, 2011.

R. Serra-moreno, S. Acosta, J. P. Hernalsteens, J. Jofre, and M. Muniesa, Use of the lambda Red recombinase system to produce recombinant prophages carrying antibiotic resistance genes, BMC molecular biology, vol.7, p.31, 2006.

U. K. Sharma, C. , and D. , Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity, FEMS microbiology reviews, vol.34, pp.646-657, 2010.

A. Shinhara, M. Matsui, K. Hiraoka, W. Nomura, R. Hirano et al., Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli, BMC genomics, vol.12, p.428, 2011.

I. J. Silva, A. D. Ortega, S. C. Viegas, . Garcia-del, F. Portillo et al., An RpoSdependent sRNA regulates the expression of a chaperone involved in protein folding, Rna, vol.19, pp.1253-1265, 2013.

D. D. Sledjeski, A. Gupta, G. , and S. , The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli, The EMBO journal, vol.15, pp.3993-4000, 1996.

T. Soper, M. P. Majdalani, N. Gottesman, S. Woodson, and S. A. , Positive regulation by small RNAs and the role of Hfq, PNAS, vol.107, pp.9602-9607, 2010.

R. Sorek, C. , and P. , Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity, Nature reviews Genetics, vol.11, pp.9-16, 2010.

J. Sridhar, N. Sambaturu, R. Sabarinathan, H. Y. Ou, Z. Deng et al., sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes, PloS one, vol.5, 2010.

L. C. Thomason, N. Costantino, and D. L. Court, E. coli genome manipulation by P1 transduction. Current protocols in molecular biology, vol.1, p.17, 2007.

M. K. Thomason, F. Fontaine, N. De-lay, and G. Storz, 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.

C. Toffano-nioche, Y. Luo, C. Kuchly, C. Wallon, D. Steinbach et al., Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline, Methods, vol.63, pp.60-65, 2013.

J. I. Tomizawa, Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA, Proceedings of the National Academy of Sciences of the United States of America, vol.78, pp.1421-1425, 1981.

O. Vidal, R. Longin, C. Prigent-combaret, C. Dorel, M. Hooreman et al., Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression, Journal of bacteriology, vol.180, pp.2442-2449, 1998.

R. Wahl, P. Rice, C. M. Rice, and M. Kroger, ECD-a totally integrated database of Escherichia coli K12, Nucleic acids research, vol.22, pp.3450-3455, 1994.

K. M. Wassarman, 6S RNA: a small RNA regulator of transcription, Current opinion in microbiology, vol.10, pp.164-168, 2007.

L. S. Waters and G. Storz, Regulatory RNAs in bacteria, Cell, vol.136, pp.615-628, 2009.

C. A. White-ziegler, S. Um, N. M. Perez, A. L. Berns, A. J. Malhowski et al., Low temperature (23 degrees C) increases expression of biofilm-, cold-shock-and RpoS-dependent genes in Escherichia coli K-12, Microbiology, vol.154, pp.148-166, 2008.

A. Zhang, K. M. Wassarman, C. Rosenow, B. C. Tjaden, G. Storz et al., Global analysis of small RNA and mRNA targets of Hfq, Molecular microbiology, vol.50, pp.1111-1124, 2003.

D. Zheng, C. Constantinidou, J. L. Hobman, and S. D. Minchin, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling, Nucleic acids research, vol.32, pp.5874-5893, 2004.