M. Albrecht, C. Sharma, R. Reinhardt, J. Vogel, and T. Rudel, Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome, Nucleic Acids Research, vol.76, issue.Suppl. 1, pp.868-77, 2010.
DOI : 10.1128/IAI.00102-08

S. Almagro-moreno, K. Pruss, and R. Taylor, Intestinal Colonization Dynamics of Vibrio cholerae, PLOS Pathogens, vol.49, issue.2, pp.1004787-1004790, 2015.
DOI : 10.1371/journal.ppat.1004787.g001

C. Archambaud, M. Nahori, G. Soubigou, C. Becavin, and L. Laval, Impact of lactobacilli on orally acquired listeriosis, Proceedings of the National Academy of Sciences, vol.19, issue.2, pp.16684-16693, 2012.
DOI : 10.1093/bioinformatics/19.2.185
URL : https://hal.archives-ouvertes.fr/hal-01003361

C. Archambaud, O. Sismeiro, J. Toedling, G. Soubigou, and C. Becavin, The Intestinal Microbiota Interferes with the microRNA Response upon Oral Listeria Infection, mBio, vol.4, issue.6, pp.707-720, 2013.
DOI : 10.1128/mBio.00707-13
URL : https://hal.archives-ouvertes.fr/hal-01350904

C. Arciola, D. Campoccia, P. Speziale, L. Montanaro, and J. Costerton, Biofilm formation in Staphylococcus implant infections. A review of molecular mechanisms and implications for biofilm-resistant materials, Biomaterials, vol.33, issue.26, pp.5967-82, 2012.
DOI : 10.1016/j.biomaterials.2012.05.031

K. Bandyra, N. Said, V. Pfeiffer, M. Gorna, J. Vogel et al., The Seed Region of a Small RNA Drives the Controlled Destruction of the Target mRNA by the Endoribonuclease RNase E, Molecular Cell, vol.47, issue.6, pp.943-53, 2012.
DOI : 10.1016/j.molcel.2012.07.015

L. Barquist and J. Vogel, Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies, Annual Review of Genetics, vol.49, issue.1, pp.367-94, 2015.
DOI : 10.1146/annurev-genet-112414-054804

C. Blenkiron, D. Simonov, A. Muthukaruppan, P. Tsai, and P. Dauros, Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA, PLOS ONE, vol.588, issue.15, pp.160440-160449, 2016.
DOI : 10.1371/journal.pone.0160440.s002
URL : https://doi.org/10.1371/journal.pone.0160440

S. Boisset, T. Geissmann, E. Huntzinger, P. Fechter, and N. Bendridi, Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism, Genes & Development, vol.21, issue.11, pp.1353-66, 2007.
DOI : 10.1101/gad.423507
URL : https://hal.archives-ouvertes.fr/hal-00167517

L. Bossi, A. Schwartz, B. Guillemardet, M. Boudvillain, and N. Figueroa-bossi, A role for Rho-dependent polarity in gene regulation by a noncoding small RNA, Genes & Development, vol.26, issue.16, pp.1864-73, 2012.
DOI : 10.1101/gad.195412.112
URL : https://hal.archives-ouvertes.fr/hal-00727260

D. Bronesky, Z. Wu, S. Marzi, P. Walter, and T. Geissmann, Staphylococcus aureus RNAIII and Its Regulon Link Quorum Sensing, Stress Responses, Metabolic Adaptation, and Regulation of Virulence Gene Expression, Annu Rev Microbiol, vol.12, 2016.

C. Buchrieser, C. Rusniok, F. Kunst, P. Cossart, P. Glaser et al., : clues for evolution and pathogenicity, FEMS Immunology & Medical Microbiology, vol.170, issue.3, pp.207-220, 2003.
DOI : 10.1073/pnas.95.8.4641

J. Burnett and J. Rossi, RNA-Based Therapeutics: Current Progress and Future Prospects, Chemistry & Biology, vol.19, issue.1, pp.60-71, 2012.
DOI : 10.1016/j.chembiol.2011.12.008
URL : https://doi.org/10.1016/j.chembiol.2011.12.008

I. Caldelari, Y. Chao, P. Romby, J. Vogel, S. Chabelskaya et al., RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med 3:a010298 15 Dual RNA regulatory control of a Staphylococcus aureus virulence factor, Nucleic Acids Res, vol.42, pp.4847-58, 2013.
DOI : 10.1101/cshperspect.a010298

Y. Chao, K. Papenfort, R. Reinhardt, C. Sharma, and J. Vogel, An atlas of Hfq-bound transcripts reveals 3??? UTRs as a genomic reservoir of regulatory small RNAs, The EMBO Journal, vol.155, issue.20, pp.4005-4024, 2012.
DOI : 10.1099/mic.0.023598-0

Y. Chao and J. Vogel, A 3??? UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response, Molecular Cell, vol.61, issue.3, pp.352-63, 2016.
DOI : 10.1016/j.molcel.2015.12.023

E. Charpentier, H. Richter, J. Van-der-oost, and M. White, Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity, FEMS Microbiology Reviews, vol.41, issue.3, pp.428-469, 2015.
DOI : 10.1042/BST20130129

C. Chevalier, S. Boisset, C. Romilly, B. Masquida, and P. Fechter, Staphylococcus aureus RNAIII Binds to Two Distant Regions of coa mRNA to Arrest Translation and Promote mRNA Degradation, PLoS Pathogens, vol.150, issue.3, 2010.
DOI : 10.1371/journal.ppat.1000809.s003
URL : https://hal.archives-ouvertes.fr/hal-00526396

P. Cossart, Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.22, issue.3, pp.19484-91, 2011.
DOI : 10.1016/j.smim.2010.02.002

S. Cramton, C. Gerke, N. Schnell, W. Nichols, and F. Gotz, The intercellular adhesion (ica) locus is present in Staphylococcus aureus and is required for biofilm formation, Infect Immun, vol.67, pp.5427-5460, 1999.

F. Crick, Central Dogma of Molecular Biology, Nature, vol.215, issue.5258, pp.561-564, 1970.
DOI : 10.1038/227561a0

D. Dar, M. Shamir, J. Mellin, M. Koutero, and N. Stern-ginossar, Term-seq reveals abundant riboregulation of antibiotics resistance in bacteria Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence, Science Cell, vol.352, issue.149, pp.358-70, 2012.

S. Debroy, M. Gebbie, R. A. Goodson, J. Cruz, and M. , A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator, Science, vol.75, issue.7, pp.937-977, 2014.
DOI : 10.1073/pnas.75.7.3479

M. Duval, P. Cossart, and A. Lebreton, Mammalian microRNAs and long noncoding RNAs in the hostbacterial pathogen crosstalk, Semin Cell Dev Biol, vol.27, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01350977

J. Fei, D. Singh, Q. Zhang, S. Park, and D. Balasubramanian, Determination of in vivo target search kinetics of regulatory noncoding RNA, Science, vol.14, issue.1, pp.1371-1375, 2015.
DOI : 10.1016/0263-7855(96)00018-5

K. Frohlich, K. Papenfort, A. Fekete, and J. Vogel, A small RNA activates CFA synthase by isoform-specific mRNA stabilization, The EMBO Journal, vol.6, issue.22, pp.2963-79, 2013.
DOI : 10.1038/nrmicro1839

K. Frohlich and J. Vogel, Activation of gene expression by small RNA, Current Opinion in Microbiology, vol.12, issue.6, pp.674-82, 2009.
DOI : 10.1016/j.mib.2009.09.009

J. Galan, Interactions with Host Cells: Type III Secretion at Work, Annual Review of Cell and Developmental Biology, vol.17, issue.1, pp.53-86, 2001.
DOI : 10.1146/annurev.cellbio.17.1.53

C. Garzoni and W. Kelley, Staphylococcus aureus: new evidence for intracellular persistence, Trends in Microbiology, vol.17, issue.2, pp.59-65, 2009.
DOI : 10.1016/j.tim.2008.11.005

E. Geisinger, R. Adhikari, J. R. Ross, H. Novick, and R. , Inhibition of rot translation by RNAIII, a key feature of agr function, Molecular Microbiology, vol.12, issue.4, pp.1038-1086, 2006.
DOI : 10.1128/JB.186.24.8407-8423.2004

H. Gong, G. Vu, Y. Bai, E. Chan, and R. Wu, A Salmonella small non-coding RNA facilitates bacterial invasion and intracellular replication by modulating the expression of virulence factors Bacterial small RNA regulators: versatile roles and rapidly evolving variations, PLoS Pathog Cold Spring Harb Perspect Biol, vol.7, issue.3, pp.1002120-1002154, 2011.

B. Hammer and B. Bassler, Quorum sensing controls biofilm formation in Vibrio cholerae, Molecular Microbiology, vol.99, issue.1, pp.101-105, 2003.
DOI : 10.1073/pnas.052694299
URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03688.x/pdf

J. Harris, R. Larocque, F. Qadri, E. Ryan, and S. Calderwood, Cholera, The Lancet, vol.379, issue.9835, pp.2466-76, 2012.
DOI : 10.1016/S0140-6736(12)60436-X

B. Howden, M. Beaume, P. Harrison, D. Hernandez, and J. Schrenzel, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.57, issue.8, pp.3864-74, 2013.
DOI : 10.1128/AAC.00263-13

E. Huntzinger, S. Boisset, C. Saveanu, Y. Benito, and T. Geissmann, Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression, The EMBO Journal, vol.11, issue.4, pp.824-859, 2005.
DOI : 10.1023/A:1020660230497
URL : https://hal.archives-ouvertes.fr/pasteur-01404709

L. Janzon and S. Arvidson, The role of the delta-lysin gene (hld) in the regulation of virulence genes by the accessory gene regulator (agr) in Staphylococcus aureus, EMBO J, vol.9, pp.1391-1400, 1990.

K. Jefferson, S. Cramton, F. Gotz, and G. Pier, Identification of a 5-nucleotide sequence that controls expression of the ica locus in Staphylococcus aureus and characterization of the DNA-binding properties of IcaR, Molecular Microbiology, vol.65, issue.4, pp.889-99, 2003.
DOI : 10.1093/infdis/147.2.236

J. Johansson, P. Mandin, A. Renzoni, C. Chiaruttini, M. Springer et al., An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes, Cell, vol.110, issue.5, pp.551-61, 2002.
DOI : 10.1016/S0092-8674(02)00905-4

H. Kawamoto, Y. Koide, T. Morita, and H. Aiba, Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq, Molecular Microbiology, vol.58, issue.4, pp.1013-1035, 2006.
DOI : 10.1046/j.1365-2958.2003.03734.x

M. Kawano, A. Reynolds, J. Miranda-rios, and G. Storz, 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.1040-50, 2005.
DOI : 10.1093/nar/gki256

T. Kim, G. Bak, J. Lee, and K. Kim, Systematic analysis of the role of bacterial Hfq-interacting sRNAs in the response to antibiotics, Journal of Antimicrobial Chemotherapy, vol.123, issue.8, pp.1659-68, 2015.
DOI : 10.1016/j.amjmed.2010.07.009

D. Larock, A. Chaudhary, and S. Miller, Salmonellae interactions with host processes, Nature Reviews Microbiology, vol.328, issue.4, pp.191-205, 2015.
DOI : 10.1126/science.1188658

I. Lasa, A. Toledo-arana, A. Dobin, M. Villanueva, and I. De-los-mozos, Genome-wide antisense transcription drives mRNA processing in bacteria, Proceedings of the National Academy of Sciences, vol.39, issue.7, pp.20172-20179, 2011.
DOI : 10.1093/nar/gkr012

A. Lebreton and P. Cossart, virulence gene expression, RNA Biology, vol.180, issue.5, p.0, 2016.
DOI : 10.1016/j.febslet.2014.05.051
URL : https://hal.archives-ouvertes.fr/hal-01350979

E. Lee, J. Choi, and E. Groisman, Control of a Salmonella virulence operon by proline-charged tRNAPro, Proceedings of the National Academy of Sciences, vol.266, issue.36, pp.3140-3145, 2014.
DOI : 10.1016/j.cell.2006.01.043

E. Lee and E. Groisman, Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA, Nature, vol.419, issue.7402, pp.271-276, 2012.
DOI : 10.1007/978-1-59745-033-1_4

E. Lee and E. Groisman, virulence operon, Molecular Microbiology, vol.84, issue.1, pp.212-236, 2012.
DOI : 10.1111/j.1365-2958.2012.08036.x

E. Lee, M. Pontes, and E. Groisman, A Bacterial Virulence Protein Promotes Pathogenicity by Inhibiting the Bacterium???s Own F1Fo ATP Synthase, Cell, vol.154, issue.1, pp.146-56, 2013.
DOI : 10.1016/j.cell.2013.06.004

J. Lee and E. Lee, Regulation and function of the Salmonella MgtC virulence protein, Journal of Microbiology, vol.5, issue.10, pp.667-72, 2015.
DOI : 10.1128/mBio.01485-14

S. Lee, D. Mitchell, A. Markley, M. Hensler, and D. Gonzalez, Discovery of a widely distributed toxin biosynthetic gene cluster, Proceedings of the National Academy of Sciences, vol.6, issue.5, pp.5879-84, 2008.
DOI : 10.1016/S1074-5521(99)80076-3

H. Liu, X. Wang, H. Wang, J. Wu, and J. Ren, Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans, Nature Communications, vol.161, issue.418, p.1073, 2012.
DOI : 10.1016/j.biocel.2009.04.023

S. Liu, A. Da-cunha, R. Rezende, R. Cialic, and Z. Wei, The Host Shapes the Gut Microbiota via Fecal MicroRNA, Cell Host & Microbe, vol.19, issue.1, pp.32-43, 2016.
DOI : 10.1016/j.chom.2015.12.005
URL : https://doi.org/10.1016/j.chom.2015.12.005

E. Loh, O. Dussurget, J. Gripenland, K. Vaitkevicius, and T. Tiensuu, A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes, Cell, vol.139, issue.4, pp.770-779, 2009.
DOI : 10.1016/j.cell.2009.08.046

N. Lopez-montero, E. Ramos-marques, C. Risco, G. Portillo, and F. , induces aggrephagy of host endomembranes in persistent infections, Autophagy, vol.12, issue.10, pp.1-16, 2016.
DOI : 10.1371/journal.pone.0026930

M. Lowden, K. Skorupski, M. Pellegrini, M. Chiorazzo, R. Taylor et al., Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes, Proceedings of the National Academy of Sciences, vol.59, issue.1, pp.2860-2865, 2010.
DOI : 10.1073/pnas.94.1.265

K. Lundin, O. Gissberg, and C. Smith, Oligonucleotide Therapies: The Past and the Present, Human Gene Therapy, vol.26, issue.8, pp.475-85, 2015.
DOI : 10.1089/hum.2015.070

A. Mandlik, J. Livny, W. Robins, J. Ritchie, J. Mekalanos et al., RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression, Cell Host & Microbe, vol.10, issue.2, pp.165-74, 2011.
DOI : 10.1016/j.chom.2011.07.007

J. Mellin and P. Cossart, Unexpected versatility in bacterial riboswitches, Trends in Genetics, vol.31, issue.3, pp.150-156, 2015.
DOI : 10.1016/j.tig.2015.01.005
URL : https://hal.archives-ouvertes.fr/pasteur-01145383

J. Mellin, M. Koutero, D. Dar, M. Nahori, R. Sorek et al., Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA, Science, vol.3, issue.12, pp.940-943, 2014.
DOI : 10.1101/cshperspect.a003798
URL : https://hal.archives-ouvertes.fr/pasteur-01120664

J. Mellin, T. Tiensuu, C. Becavin, E. Gouin, J. Johansson et al., A riboswitch-regulated antisense RNA in Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.109, issue.41, pp.13132-13139, 2013.
DOI : 10.1073/pnas.1212809109

E. Morfeldt, D. Taylor, A. Von-gabain, and S. Arvidson, Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII, EMBO J, vol.14, pp.4569-77, 1995.

G. Nechooshtan, M. Elgrably-weiss, and S. Altuvia, Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element, Nucleic Acids Research, vol.5, issue.1, pp.622-652, 2014.
DOI : 10.1017/S1355838299991033

R. Novick and E. Geisinger, Quorum Sensing in Staphylococci, Annual Review of Genetics, vol.42, issue.1, pp.541-64, 2008.
DOI : 10.1146/annurev.genet.42.110807.091640

R. Novick, H. Ross, S. Projan, J. Kornblum, B. Kreiswirth et al., Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule, EMBO J, vol.12, pp.3967-75, 1993.

G. Oliva, T. Sahr, and C. Buchrieser, Small RNAs, 5??? UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence, FEMS Microbiology Reviews, vol.22, issue.3, pp.331-380, 2015.
DOI : 10.1038/cr.2011.158
URL : https://hal.archives-ouvertes.fr/pasteur-01226492

A. Ortega, J. Quereda, M. Pucciarelli, G. Portillo, and F. , Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells, Frontiers in Cellular and Infection Microbiology, vol.89, issue.392, p.162, 2014.
DOI : 10.1111/mmi.12325

K. Papenfort, K. Forstner, J. Cong, C. Sharma, and B. Bassler, identifies the VqmR small RNA as a regulator of biofilm formation, Proceedings of the National Academy of Sciences, vol.4, issue.1, pp.766-75, 2015.
DOI : 10.1016/j.cell.2013.03.003

M. Pinel-marie, R. Brielle, and B. Felden, Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally, Cell Reports, vol.7, issue.2, pp.424-459, 2014.
DOI : 10.1016/j.celrep.2014.03.012
URL : https://hal.archives-ouvertes.fr/inserm-00976764

J. Pizarro-cerda, A. Kuhbacher, and P. Cossart, Entry of Listeria monocytogenes in Mammalian Epithelial Cells: An Updated View, Cold Spring Harbor Perspectives in Medicine, vol.2, issue.11, 2012.
DOI : 10.1101/cshperspect.a010009

J. Quereda, O. Dussurget, M. Nahori, A. Ghozlane, and S. Volant, strains alters the host intestinal microbiota to favor infection, Proceedings of the National Academy of Sciences, vol.57, issue.1, pp.5706-5717, 2016.
DOI : 10.1186/s13059-014-0550-8
URL : https://hal.archives-ouvertes.fr/hal-01533881

J. Quereda, G. Portillo, F. Pucciarelli, and M. , Listeria monocytogenes remodels the cell surface in the blood-stage, Environ Microbiol Rep, vol.75, 2016.

J. Quereda, A. Ortega, M. Pucciarelli, G. Portillo, and F. , The Listeria Small RNA Rli27 Regulates a Cell Wall Protein inside Eukaryotic Cells by Targeting a Long 5???-UTR Variant, PLoS Genetics, vol.11, issue.10, pp.1004765-76, 2014.
DOI : 10.1371/journal.pgen.1004765.s011

J. Quereda, J. Pizarro-cerda, D. Balestrino, A. Bobard, and A. Danckaert, ABSTRACT, Applied and Environmental Microbiology, vol.82, issue.1, pp.211-218, 2015.
DOI : 10.1128/AEM.02302-15

J. Quereda and M. Pucciarelli, Deletion of the membrane protein Lmo0412 increases the virulence of Listeria monocytogenes, Microbes and Infection, vol.16, issue.8, pp.623-655, 2014.
DOI : 10.1016/j.micinf.2014.07.002

D. Ribet and P. Cossart, How bacterial pathogens colonize their hosts and invade deeper tissues, Microbes and Infection, vol.17, issue.3, pp.173-83, 2015.
DOI : 10.1016/j.micinf.2015.01.004
URL : https://hal.archives-ouvertes.fr/pasteur-01115526

I. Ruiz-de-los-mozos, M. Vergara-irigaray, V. Segura, M. Villanueva, and N. Bitarte, Base Pairing Interaction between 5???- and 3???-UTRs Controls icaR mRNA Translation in Staphylococcus aureus, PLoS Genetics, vol.3, issue.12, pp.1004001-80, 2013.
DOI : 10.1371/journal.pgen.1004001.s010

S. Rutherford, J. Van-kessel, Y. Shao, and B. Bassler, AphA and LuxR/HapR reciprocally control quorum sensing in vibrios, Genes & Development, vol.25, issue.4, pp.397-408, 2011.
DOI : 10.1101/gad.2015011
URL : http://genesdev.cshlp.org/content/25/4/397.full.pdf

A. Saliba, A. Westermann, S. Gorski, and J. Vogel, Single-cell RNA-seq: advances and future challenges, Nucleic Acids Research, vol.30, issue.14, pp.8845-60, 2014.
DOI : 10.1038/nrmicro2852
URL : https://academic.oup.com/nar/article-pdf/42/14/8845/5248376/gku555.pdf

N. Sayed, A. Jousselin, and B. Felden, A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide, Nature Structural & Molecular Biology, vol.1, issue.1, pp.105-117, 2012.
DOI : 10.1038/nprot.2006.4
URL : https://hal.archives-ouvertes.fr/inserm-00696345

N. Sayed, S. Nonin-lecomte, S. Rety, and B. Felden, Apoptotic-like Membrane Peptide from a Toxin-Antitoxin Module, Journal of Biological Chemistry, vol.23, issue.52, pp.43454-63, 2012.
DOI : 10.1021/bi1005128
URL : https://hal.archives-ouvertes.fr/inserm-00762197

N. Sedlyarova, I. Shamovsky, B. Bharati, V. Epshtein, and J. Chen, sRNA-Mediated Control of Transcription Termination in E.??coli, Cell, vol.167, issue.1, pp.111-132, 2016.
DOI : 10.1016/j.cell.2016.09.004

N. Sesto, M. Touchon, J. Andrade, J. Kondo, and E. Rocha, A PNPase Dependent CRISPR System in Listeria, PLoS Genetics, vol.8, issue.1, pp.1004065-86, 2014.
DOI : 10.1371/journal.pgen.1004065.s013
URL : https://hal.archives-ouvertes.fr/pasteur-01145428

N. Sesto, O. Wurtzel, C. Archambaud, R. Sorek, and P. Cossart, The excludon: a new concept in bacterial antisense RNA-mediated gene regulation, Nature Reviews Microbiology, vol.6, issue.2, pp.75-82, 2013.
DOI : 10.1038/nrmicro1932

Y. Shao and B. Bassler, Quorum-sensing non-coding small RNAs use unique pairing regions to differentially control mRNA targets, Molecular Microbiology, vol.99, issue.3, pp.599-611, 2012.
DOI : 10.1073/pnas.052694299
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2011.07959.x/pdf

C. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, and S. Findeiss, The primary transcriptome of the major human pathogen Helicobacter pylori, Nature, vol.73, issue.7286, pp.250-255, 2010.
DOI : 10.1128/jb.179.15.4676-4683.1997

A. Silva and J. Benitez, Vibrio cholerae Biofilms and Cholera Pathogenesis, PLOS Neglected Tropical Diseases, vol.304, issue.5???6, pp.4330-91, 2016.
DOI : 10.1371/journal.pntd.0004330.t001
URL : https://doi.org/10.1371/journal.pntd.0004330

K. Skorupski and R. Taylor, A new level in the Vibrio cholerae ToxR virulence cascade: AphA is required for transcriptional activation of the tcpPH operon, Molecular Microbiology, vol.180, issue.3, pp.763-71, 1999.
DOI : 10.1016/S0378-1119(96)00495-7

A. Smirnov, K. Forstner, E. Holmqvist, A. Otto, and R. Gunster, Grad-seq guides the discovery of ProQ as a major small RNA-binding protein, Proceedings of the National Academy of Sciences, vol.181, issue.5, pp.11591-11597, 2016.
DOI : 10.1093/bioinformatics/btu533

E. Sonnleitner, N. Gonzalez, T. Sorger-domenigg, S. Heeb, and A. Richter, The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal, Molecular Microbiology, vol.31, issue.4, pp.868-85, 2011.
DOI : 10.1093/nar/gkg595

D. Srivastava, R. Harris, and C. Waters, in Vibrio cholerae, Journal of Bacteriology, vol.193, issue.22, pp.6331-6372, 2011.
DOI : 10.1128/JB.05167-11

G. Storz, J. Vogel, and K. Wassarman, Regulation by Small RNAs in Bacteria: Expanding Frontiers, Molecular Cell, vol.43, issue.6, pp.880-91, 2011.
DOI : 10.1016/j.molcel.2011.08.022

S. Svensson and C. Sharma, Small RNAs in Bacterial Virulence and Communication, Microbiol Spectr, vol.4, 2016.
DOI : 10.1128/microbiolspec.VMBF-0028-2015

P. Thiennimitr, S. Winter, M. Winter, M. Xavier, and V. Tolstikov, Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota, Proceedings of the National Academy of Sciences, vol.6, issue.8, pp.17480-17485, 2011.
DOI : 10.1371/journal.ppat.1001060

A. Toledo-arana, O. Dussurget, G. Nikitas, N. Sesto, and H. Guet-revillet, The Listeria transcriptional landscape from saprophytism to virulence, Nature, vol.99, issue.7249, pp.950-956, 2009.
DOI : 10.1016/S1438-4221(00)80086-7

K. Traber, E. Lee, S. Benson, R. Corrigan, and M. Cantera, agr function in clinical Staphylococcus aureus isolates, Microbiology, vol.187, issue.16, pp.2265-74, 2008.
DOI : 10.1128/JB.187.16.5585-5594.2005
URL : http://mic.microbiologyresearch.org/deliver/fulltext/micro/154/8/2265.pdf?itemId=/content/journal/micro/10.1099/mic.0.2007/011874-0&mimeType=pdf&isFastTrackArticle=

E. Wagner and P. Romby, Small RNAs in Bacteria and Archaea, Adv Genet, vol.90, pp.133-208, 2015.
DOI : 10.1016/bs.adgen.2015.05.001

K. Wassarman, 6S RNA: a regulator of transcription, Molecular Microbiology, vol.148, issue.6, pp.1425-1456, 2007.
DOI : 10.1038/nature04337

C. Waters, W. Lu, J. Rabinowitz, and B. Bassler, Quorum Sensing Controls Biofilm Formation in Vibrio cholerae through Modulation of Cyclic Di-GMP Levels and Repression of vpsT, Journal of Bacteriology, vol.190, issue.7, pp.2527-2563, 2008.
DOI : 10.1128/JB.01756-07

L. Waters and G. Storz, Regulatory RNAs in Bacteria, Cell, vol.136, issue.4, pp.615-643, 2009.
DOI : 10.1016/j.cell.2009.01.043
URL : https://doi.org/10.1016/j.cell.2009.01.043

A. Westermann, K. Forstner, F. Amman, L. Barquist, and Y. Chao, Dual RNA-seq unveils noncoding RNA functions in host???pathogen interactions, Nature, vol.10, issue.7587, pp.496-501, 2016.
DOI : 10.1261/rna.5248604

A. Westermann, S. Gorski, and J. Vogel, Dual RNA-seq of pathogen and host, Nature Reviews Microbiology, vol.316, issue.9, pp.618-648, 2012.
DOI : 10.1016/j.yexcr.2010.02.036

A. Wright, J. Nunez, and J. Doudna, Biology and Applications of CRISPR Systems: Harnessing Nature???s Toolbox for Genome Engineering, Cell, vol.164, issue.1-2, pp.29-44, 2016.
DOI : 10.1016/j.cell.2015.12.035

O. Wurtzel, D. Yoder-himes, K. Han, A. Dandekar, and S. Edelheit, The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature, PLoS Pathogens, vol.8, issue.9, p.1002945, 2012.
DOI : 10.1371/journal.ppat.1002945.s011

J. Yu and T. Schneiders, Tigecycline challenge triggers sRNA production in Salmonella enterica serovar Typhimurium, BMC Microbiology, vol.12, issue.1, p.195, 2012.
DOI : 10.1073/pnas.120163297
URL : https://bmcmicrobiol.biomedcentral.com/track/pdf/10.1186/1471-2180-12-195?site=bmcmicrobiol.biomedcentral.com

J. Zheng, O. Shin, D. Cameron, and J. Mekalanos, Quorum sensing and a global regulator TsrA control expression of type VI secretion and virulence in Vibrio cholerae, Proceedings of the National Academy of Sciences, vol.64, issue.6, pp.21128-21161, 2010.
DOI : 10.1128/IAI.68.11.6487-6492.2000

J. Zhu, M. Miller, R. Vance, M. Dziejman, B. Bassler et al., Quorum-sensing regulators control virulence gene expression in Vibrio cholerae, Proceedings of the National Academy of Sciences, vol.180, issue.19, pp.3129-3163, 2002.
DOI : 10.1016/S0378-1119(00)00117-7