P. Cossart, Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.108, issue.49, pp.19484-19491, 2011.
DOI : 10.1073/pnas.1112371108

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/nrmicro2934

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 : 10.1038/nature08080

G. Storz, J. Vogel, and K. Wassarman, Regulation by Small RNAs in Bacteria: Expanding Frontiers, Molecular Cell, vol.43, issue.6, pp.880-891, 2011.
DOI : 10.1016/j.molcel.2011.08.022

K. Makarova, D. Haft, R. Barrangou, S. Brouns, and E. Charpentier, Evolution and classification of the CRISPR???Cas systems, Nature Reviews Microbiology, vol.35, issue.6, pp.467-477, 2011.
DOI : 10.1038/nrmicro2577

V. Sangal, P. Fineran, and P. Hoskisson, Novel configurations of Type I and II CRISPR/Cas systems in Corynebacterium diphtheriae, Microbiology.Epub, 2013.

A. Bolotin, B. Quinquis, A. Sorokin, and S. Ehrlich, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology (Reading, Engl), vol.151, pp.2551-2561, 2005.

F. Mojica, C. Diez-villasenor, J. Garcia-martinez, and E. Soria, Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements, Journal of Molecular Evolution, vol.2, issue.2, pp.174-182, 2005.
DOI : 10.1007/s00239-004-0046-3

C. Pourcel, G. Salvignol, and G. Vergnaud, CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology (Reading, Engl), vol.151, pp.653-663, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01158317

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, and P. Boyaval, CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1712, 2007.
DOI : 10.1126/science.1138140

S. Brouns, M. Jore, M. Lundgren, E. Westra, and R. Slijkhuis, Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes, Science, vol.321, issue.5891, pp.960-964, 2008.
DOI : 10.1126/science.1159689

L. Marraffini and E. Sontheimer, CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA, Science, vol.322, issue.5909, pp.1843-1845, 2008.
DOI : 10.1126/science.1165771

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695655

R. Barrangou, CRISPR-Cas systems and RNA-guided interference, Wiley Interdisciplinary Reviews: RNA, vol.10, issue.3, pp.267-278, 2013.
DOI : 10.1002/wrna.1159

B. Wiedenheft, S. Sternberg, and J. Doudna, RNA-guided genetic silencing systems in bacteria and archaea, Nature, vol.466, issue.7385, pp.331-338, 2012.
DOI : 10.1038/nature10886

C. Kuenne, S. Voget, J. Pischimarov, S. Oehm, and A. Goesmann, Comparative Analysis of Plasmids in the Genus Listeria, PLoS ONE, vol.8, issue.9, p.12511, 2010.
DOI : 10.1371/journal.pone.0012511.s002

J. Dorscht, J. Klumpp, R. Bielmann, M. Schmelcher, and Y. Born, Comparative Genome Analysis of Listeria Bacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site, Journal of Bacteriology, vol.191, issue.23, pp.7206-7215, 2009.
DOI : 10.1128/JB.01041-09

C. Kuenne, A. Billion, M. Mraheil, A. Strittmatter, and R. Daniel, Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome, BMC Genomics, vol.14, issue.1, p.47, 2013.
DOI : 10.1186/1471-2164-13-384.:384-13

P. Glaser, L. Frangeul, C. Buchrieser, C. Rusniok, and A. Amend, Comparative genomics of Listeria species, Science, vol.294, pp.849-852, 2001.

K. Nelson, D. Fouts, E. Mongodin, J. Ravel, and R. Deboy, Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species, Nucleic Acids Research, vol.32, issue.8, pp.2386-2395, 2004.
DOI : 10.1093/nar/gkh562

T. Hain, R. Ghai, A. Billion, C. Kuenne, and C. Steinweg, Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes, BMC Genomics, vol.13, issue.1, p.144, 2012.
DOI : 10.1093/bioinformatics/btl466

URL : https://hal.archives-ouvertes.fr/pasteur-00724699

P. Mandin, F. Repoila, M. Vergassola, T. Geissmann, and P. Cossart, Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Research, vol.35, issue.3, pp.962-974, 2007.
DOI : 10.1093/nar/gkl1096

URL : https://hal.archives-ouvertes.fr/hal-00129258

C. Condon, Maturation and degradation of RNA in bacteria, Current Opinion in Microbiology, vol.10, issue.3, pp.271-278, 2007.
DOI : 10.1016/j.mib.2007.05.008

URL : https://hal.archives-ouvertes.fr/hal-00159548

M. Schmuki, D. Erne, M. Loessner, and J. Klumpp, Bacteriophage P70: Unique Morphology and Unrelatedness to Other Listeria Bacteriophages, Journal of Virology, vol.86, issue.23, pp.13099-13102, 2012.
DOI : 10.1128/JVI.02350-12

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497695

V. Kunin, R. Sorek, and P. Hugenholtz, Evolutionary conservation of sequence and secondary structures in CRISPR repeats, Genome Biology, vol.8, issue.4, p.61, 2007.
DOI : 10.1186/gb-2007-8-4-r61

C. Arraiano, J. Andrade, S. Domingues, I. Guinote, and M. Malecki, The critical role of RNA processing and degradation in the control of gene expression, FEMS Microbiology Reviews, vol.34, issue.5, pp.883-923, 2010.
DOI : 10.1111/j.1574-6976.2010.00242.x

D. Bhaya, M. Davison, and R. Barrangou, CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation, Annual Review of Genetics, vol.45, issue.1, pp.273-297, 2011.
DOI : 10.1146/annurev-genet-110410-132430

D. Bikard and L. Marraffini, Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages, Current Opinion in Immunology, vol.24, issue.1, pp.15-20, 2012.
DOI : 10.1016/j.coi.2011.10.005

C. Almendros, N. Guzman, C. Diez-villasenor, J. Garcia-martinez, and F. Mojica, Target Motifs Affecting Natural Immunity by a Constitutive CRISPR-Cas System in Escherichia coli, PLoS ONE, vol.14, issue.11, p.50797, 2012.
DOI : 10.1371/journal.pone.0050797.s005

E. Westra, D. Swarts, R. Staals, M. Jore, and S. Brouns, The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity, Annual Review of Genetics, vol.46, issue.1, pp.311-339, 2012.
DOI : 10.1146/annurev-genet-110711-155447

P. Fineran and E. Charpentier, Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information, Virology, vol.434, issue.2, pp.202-209, 2012.
DOI : 10.1016/j.virol.2012.10.003

E. Deltcheva, K. Chylinski, C. Sharma, K. Gonzales, and Y. Chao, CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, Nature, vol.25, issue.7340, pp.602-607, 2011.
DOI : 10.1038/nature09886

Y. Zhang, N. Heidrich, B. Ampattu, C. Gunderson, and H. Seifert, Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis, Molecular Cell, vol.50, issue.4, pp.488-503, 2013.
DOI : 10.1016/j.molcel.2013.05.001

G. Farrr, I. Oussenko, and D. Bechhhofer, Protection against 39-to-59 RNA Decay in Bacillus subtilis, J Bacteriol, vol.23, pp.1-9, 1999.

M. Lehnik-habrink, R. Lewis, U. Mä-der, and J. Stülke, RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases, Molecular Microbiology, vol.193, issue.6, pp.1005-1017, 2012.
DOI : 10.1111/j.1365-2958.2012.08072.x

P. Cardenas, B. Carrasco, H. Sanchez, G. Deikus, and D. Bechhofer, Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair, Nucleic Acids Research, vol.37, issue.12, pp.4157-4169, 2009.
DOI : 10.1093/nar/gkp314

P. Cardenas, T. Carzaniga, S. Zangrossi, F. Briani, and E. Garcia-tirado, Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins, Nucleic Acids Research, vol.39, issue.21, pp.9250-9261, 2011.
DOI : 10.1093/nar/gkr635

J. Andrade, V. Pobre, A. Matos, and C. Arraiano, The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq, RNA, vol.18, issue.4, pp.844-855, 2012.
DOI : 10.1261/rna.029413.111

D. Lay, N. Gottesman, and S. , Role of polynucleotide phosphorylase in sRNA function in Escherichia coli, RNA, vol.17, issue.6, pp.1172-1189, 2011.
DOI : 10.1261/rna.2531211

C. Kuo and H. Ochman, The Extinction Dynamics of Bacterial Pseudogenes, PLoS Genetics, vol.5, issue.8, p.1001050, 2010.
DOI : 10.1371/journal.pgen.1001050.s001

O. Wurtzel, N. Sesto, J. Mellin, I. Karunker, and S. Edelheit, Comparative transcriptomics of pathogenic and non-pathogenic Listeria species, Molecular Systems Biology, vol.270, p.583, 2012.
DOI : 10.1093/nar/gkm951

M. Zegans, J. Wagner, K. Cady, D. Murphy, and J. Hammond, Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa, Journal of Bacteriology, vol.191, issue.1, pp.210-219, 2009.
DOI : 10.1128/JB.00797-08

P. Viswanathan, K. Murphy, B. Julien, A. Garza, and L. Kroos, Regulation of dev, an Operon That Includes Genes Essential for Myxococcus xanthus Development and CRISPR-Associated Genes and Repeats, Journal of Bacteriology, vol.189, issue.10, pp.3738-3750, 2007.
DOI : 10.1128/JB.00187-07

T. Sampson, S. Saroj, A. Llewellyn, Y. Tzeng, and D. Weiss, A CRISPR/Cas system mediates bacterial innate immune evasion and virulence, Nature, vol.175, issue.7448, pp.254-257, 2013.
DOI : 10.1371/journal.pone.0013244

M. Roossinck, The good viruses: viral mutualistic symbioses, Nature Reviews Microbiology, vol.42, issue.2, pp.99-108, 2011.
DOI : 10.1038/nrmicro2491

E. Boyd and H. Brussow, Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved, Trends in Microbiology, vol.10, issue.11, pp.521-529, 2002.
DOI : 10.1016/S0966-842X(02)02459-9

L. Rabinovich, N. Sigal, I. Borovok, R. Nir-paz, and A. Herskovits, Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence, Cell, vol.150, issue.4, pp.792-802, 2012.
DOI : 10.1016/j.cell.2012.06.036

URL : http://doi.org/10.1016/j.cell.2012.06.036

M. Arnaud, A. Chastanet, and M. Debarbouille, New Vector for Efficient Allelic Replacement in Naturally Nontransformable, Low-GC-Content, Gram-Positive Bacteria, Applied and Environmental Microbiology, vol.70, issue.11, pp.6887-6891, 2004.
DOI : 10.1128/AEM.70.11.6887-6891.2004

D. Balestrino, M. Hamon, L. Dortet, M. Nahori, and J. Pizarro-cerda, Single-Cell Techniques Using Chromosomally Tagged Fluorescent Bacteria To Study Listeria monocytogenes Infection Processes, Applied and Environmental Microbiology, vol.76, issue.11, pp.3625-3636, 2010.
DOI : 10.1128/AEM.02612-09

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2876438

P. Lauer, M. Chow, M. Loessner, D. Portnoy, and R. Calendar, Construction, Characterization, and Use of Two Listeria monocytogenes Site-Specific Phage Integration Vectors, Journal of Bacteriology, vol.184, issue.15, pp.4177-4186, 2002.
DOI : 10.1128/JB.184.15.4177-4186.2002

J. Jestin, E. Dème, and A. Jacquier, Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron, The EMBO Journal, vol.16, issue.10, pp.2945-2954, 1997.
DOI : 10.1093/emboj/16.10.2945

N. Said, R. Rieder, R. Hurwitz, J. Deckert, and H. Urlaub, In vivo expression and purification of aptamer-tagged small RNA regulators, Nucleic Acids Research, vol.37, issue.20, p.133, 2009.
DOI : 10.1093/nar/gkp719

C. Chevalier, T. Geissmann, A. Helfer, and P. Romby, Probing mRNA Structure and sRNA???mRNA Interactions in Bacteria Using Enzymes and Lead(II), Methods Mol Biol, vol.540, pp.215-232, 2009.
DOI : 10.1007/978-1-59745-558-9_16

URL : https://hal.archives-ouvertes.fr/hal-00477293

L. Bobay, E. Rocha, and M. Touchon, The Adaptation of Temperate Bacteriophages to Their Host Genomes, Molecular Biology and Evolution, vol.30, issue.4, pp.737-757, 2013.
DOI : 10.1093/molbev/mss279

URL : https://hal.archives-ouvertes.fr/pasteur-01374945

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

URL : http://doi.org/10.1371/journal.pcbi.1002195

M. Touchon, C. Hoede, O. Tenaillon, V. Barbe, and S. Baeriswyl, 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

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

URL : http://doi.org/10.1093/nar/gkh340

H. Schmidt, K. Strimmer, M. Vingron, and A. Von-haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/18/3/502

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

C. Bland, T. Ramsey, F. Sabree, M. Lowe, and K. Brown, CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, vol.8, issue.1, p.209, 2007.
DOI : 10.1186/1471-2105-8-209