An updated evolutionary classification of CRISPR-Cas systems, Nat Rev Microbiol, vol.13, pp.722-736, 2015. ,
Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J Bacteriol, vol.169, pp.5429-5462, 1987. ,
Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, vol.151, pp.2551-2561, 2005. ,
Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, J Mol Evol, vol.60, pp.174-182, 2005. ,
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, vol.151, pp.653-663, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01158317
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.80, pp.1709-1712, 2007. ,
CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science (80-), vol.322, pp.1843-1845, 2008. ,
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, vol.468, pp.67-71, 2010. ,
CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection, Cell Host Microbe, vol.12, pp.177-186, 2012. ,
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194414
CRISPRDetect: A flexible algorithm to define CRISPR arrays, BMC Genomics, vol.17, p.356, 2016. ,
Diversity and evolution of class 2 CRISPR-Cas systems, Nat Rev Microbiol, vol.15, pp.169-182, 2017. ,
Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system, Proc Natl Acad Sci U S A, vol.30, pp.16359-16364, 2011. ,
Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation, Nat Struct Mol Biol, vol.21, pp.771-777, 2014. ,
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity, Science (80-), vol.337, pp.816-822, 2012. ,
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System, Cell, vol.163, pp.759-771, 2015. ,
, Discovery and Functional Characterization Mol Cell, vol.61, pp.797-808, 2015.
CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea, Nat Rev Genet, vol.11, pp.181-190, 2010. ,
Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering, Cell, vol.164, pp.29-44, 2016. ,
RNA-guided genetic silencing systems in bacteria and archaea, Doudna J a, vol.482, pp.331-338, 2012. ,
Structural basis for CRISPR RNA-guided DNA recognition by Cascade, Nat Struct Mol Biol, vol.18, pp.529-536, 2011. ,
CRISPR-based adaptive and heritable immunity in prokaryotes, Trends Biochem Sci, vol.17, pp.401-407, 2009. ,
The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages, J Bacteriol, vol.194, pp.5728-5738, 2012. ,
CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli, RNA Biol, vol.10, pp.792-802, 2013. ,
Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms, Mol Microbiol, vol.91, pp.505-510, 2012. ,
Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process, Nucleic Acids Res, vol.42, pp.2483-2492, 2014. ,
Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation, Nucleic Acids Res, vol.42, pp.7226-7235, 2014. ,
High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli, RNA Biol, vol.10, pp.716-741, 2013. ,
Pervasive generation of oppositely oriented spacers during CRISPR adaptation, Nucleic Acids Res, vol.42, pp.5907-5916, 2014. ,
Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer, Nucleic Acids Res, vol.42, pp.8516-8526, 2014. ,
Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens, Nucleic Acids Res, vol.43, pp.8913-8923, 2015. ,
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli, Nucleic Acids Res, 2012. ,
DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array, Proc Natl Acad Sci U S A, vol.110, pp.14396-401, 2013. ,
Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, vol.151, pp.2551-2561, 2005. ,
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, pp.1709-1721, 2007. ,
An updated evolutionary classification of CRISPR Cas systems, Nat. Rev. Microbiol, vol.13, pp.722-736, 2015. ,
A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems, PLoS One, vol.9, p.110726, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
Diversity and evolution of class 2 CRISPR Cas systems, Nat. Rev. Microbiol, 2017. ,
Classification and evolution of type II CRISPR-Cas systems, Nucleic Acids Res, vol.42, pp.6091-6105, 2014. ,
DOI : 10.1093/nar/gku241
URL : https://academic.oup.com/nar/article-pdf/42/10/6091/17423023/gku241.pdf
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, Nature, vol.471, pp.602-607, 2011. ,
DOI : 10.1038/nature09886
URL : http://europepmc.org/articles/pmc3070239?pdf=render
Double-strand DNA end-binding and sliding of the toroidal CRISPRassociated protein Csn2, Nucleic Acids Res, vol.41, pp.6347-6359, 2013. ,
The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae, J. Struct. Biol, vol.178, pp.350-362, 2012. ,
Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR-mediated bacterial immunity, Proteins Struct. Funct. Bioinforma, vol.80, pp.2573-2582, 2012. ,
Cas9 specifies functional viral targets during CRISPR Cas adaptation, Nature, vol.519, pp.199-202, 2015. ,
DOI : 10.1038/nature14245
URL : http://europepmc.org/articles/pmc4385744?pdf=render
Cas9 function and host genome sampling in Type II-A CRISPR -Cas adaptation, Genes Dev, vol.29, pp.356-361, 2015. ,
DOI : 10.1101/gad.257550.114
URL : http://genesdev.cshlp.org/content/29/4/356.full.pdf
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, vol.337, pp.816-837, 2012. ,
DOI : 10.1126/science.1225829
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286148
The Streptococcus thermophilus CRISPR / Cas system provides immunity in Escherichia coli, Nucleic Acids Res, vol.39, pp.9275-9282, 2011. ,
DOI : 10.1093/nar/gkr606
URL : https://academic.oup.com/nar/article-pdf/39/21/9275/16778730/gkr606.pdf
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.2579-86, 2012. ,
DOI : 10.1073/pnas.1208507109
URL : http://www.pnas.org/content/109/39/E2579.full.pdf
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus, J. Bacteriol, vol.190, pp.1390-1400, 2008. ,
Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, vol.155, pp.733-740, 2009. ,
Consequences of Cas9 cleavage in the chromosome of Escherichia coli, Nucleic Acids Res, vol.44, pp.4243-4251, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01967442
Bacterial DNA repair by non-homologous end joining ,
Nucleotide Sequence and Functional Map of pC194, a Plasmid That Specifies Inducible Chloramphenicol Resistance, J. Bacteriol, vol.150, pp.815-825, 1982. ,
Post-transcriptional regulation of chloramphenicol acetyl transferase, J. Bacteriol, vol.158, pp.543-550, 1984. ,
Functional origin of replication of pT181 plasmid DNA is contained within a 168-base-pair segment, Proc. Natl. Acad. Sci. U. S. A, vol.79, pp.4580-4584, 1982. ,
Systematic function analysis of Bacillus subtilis genes, Res. Microbiol, vol.151, pp.129-134, 2000. ,
Gene cloning in lactic streptococci, Netherlands Milk Dairy J, vol.40, pp.141-154, 1986. ,
Expression of the Arp protein, a member of the M protein family, is not sufficient to inhibit phagocytosis of Streptococcus pyogenes, Infect. Immun, vol.63, pp.345-348, 1995. ,
Novel Cassette-Based Shuttle Vector System for Gram-Positive Bacteria Novel Cassette-Based Shuttle Vector System for Gram-Positive Bacteria, Appl. Environ. Microbiol, vol.70, pp.6076-6085, 2004. ,
Cas9 specifies functional viral targets during CRISPR-Cas adaptation, Nature, vol.519, pp.199-202, 2015. ,
DOI : 10.1038/nature14245
URL : http://europepmc.org/articles/pmc4385744?pdf=render
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, vol.4, pp.633-637, 2014. ,
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems, PloS one, vol.9, issue.10, p.110726, 2014. ,
C2c2 is a singlecomponent programmable RNA-guided RNA-targeting CRISPR effector, Science, vol.353, issue.6299, p.5573, 2016. ,
Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection, Journal of Molecular Biology, vol.395, issue.2, pp.270-281, 2010. ,
Early steps of double-strand break repair in Bacillus subtilis, DNA Repair, vol.12, issue.3, pp.162-176, 2013. ,
Intracellular signaling in CRISPR-Cas defense, Science, vol.357, issue.6351, pp.550-551, 2017. ,
Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization, Molecular Microbiology, vol.69, issue.4, pp.994-1007, 2008. ,
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease, Nature, vol.513, issue.7519, pp.569-573, 2014. ,
Using, FEMS Microbiology Ecology, vol.77, issue.1, pp.120-133, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02008681
Virus population dynamics and acquired virus resistance in natural microbial communities, Science, vol.320, issue.5879, pp.1047-1050, 2008. ,
The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends, Genes and Development, vol.22, issue.4, pp.512-527, 2008. ,
Evolutionary Analysis of CRISPRs in Archaea : An Evidence for Horizontal, Journal of Proteomics & Bioinformatics, vol.9, 2014. ,
Prokaryotic homologs of the eukaryotic DNAend-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system, Genome Research, vol.11, issue.8, pp.1365-1374, 2001. ,
Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system, Nucleic Acids Research, vol.42, issue.12, pp.7884-93, 2014. ,
Double-strand DNA endbinding and sliding of the toroidal CRISPR-associated protein Csn2, Nucleic Acids Research, vol.41, issue.12, pp.6347-6359, 2013. ,
Double-strand break repair in bacteria: A view from Bacillus subtilis, FEMS Microbiology Reviews, vol.35, issue.6, pp.1055-1081, 2011. ,
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair, Molecular microbiology, vol.79, issue.2, pp.484-502, 2011. ,
, The roles of CRISPR Cas systems in adaptive immunity and beyond, vol.32, pp.36-41, 2015.
Applications of CRISPR technologies in research and beyond, Nature Biotechnology, vol.34, issue.9, pp.933-941, 2016. ,
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.315, issue.5819, pp.1709-1721, 2007. ,
A decade of discovery: CRISPR functions and applications, Nature Microbiology, vol.2, 2017. ,
, Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains, vol.9, p.108353, 2014.
Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic Acids Research, vol.44, issue.21, pp.10367-10376, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01384627
Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa, pp.1-13, 2015. ,
Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNATarget Cleavage Activity in Cmr4, Molecular Cell, vol.56, issue.1, pp.43-54, 2014. ,
Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis, Biology direct, vol.9, issue.1, p.13, 2014. ,
Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome, Environmental Microbiology, vol.14, issue.1, pp.207-227, 2012. ,
Microbial Evolutionary Genomics, and Synthetic Biology Group, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems, bioRxiv, 2017. ,
The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5, Proceedings of the National Academy of Sciences of the United States of America, vol.94, issue.13, pp.6706-6717, 1997. ,
Using CRISPR-Cas systems as antimicrobials, Current Opinion in Microbiology, vol.37, pp.155-160, 2017. ,
DOI : 10.1016/j.mib.2017.08.005
URL : https://hal.archives-ouvertes.fr/pasteur-01911231
Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, Nature biotechnology, vol.32, issue.11, pp.1146-1150, 2014. ,
DOI : 10.1038/nbt.3043
URL : https://hal.archives-ouvertes.fr/hal-01103559
CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection, Cell host & microbe, vol.12, issue.2, pp.177-86, 2012. ,
DOI : 10.1016/j.chom.2012.06.003
URL : https://doi.org/10.1016/j.chom.2012.06.003
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
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-8-209
Two Distinct DNA Binding Modes Guide Dual Roles of a CRISPR-Cas Protein Complex, Molecular Cell, vol.58, issue.1, pp.60-70, 2015. ,
Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, vol.151, issue.8, pp.2551-2561, 2005. ,
Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system, Nature, vol.493, issue.7432, pp.429-461, 2013. ,
DOI : 10.1038/nature11723
URL : http://europepmc.org/articles/pmc4931913?pdf=render
Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins, Nature, vol.526, issue.7571, pp.136-139, 2015. ,
DOI : 10.1038/nature15254
URL : http://europepmc.org/articles/pmc4935067?pdf=render
The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs, Annual Review of Virology, vol.4, 2017. ,
Making ends meet: repairing breaks in bacterial DNA by non-homologous end-joining, PLoS genetics, vol.2, issue.2, p.8, 2006. ,
DOI : 10.1371/journal.pgen.0020008
URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.0020008&type=printable
Deciphering and shaping bacterial diversity through CRISPR, Current Opinion in Microbiology, vol.31, pp.101-108, 2016. ,
Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, vol.321, issue.5891, pp.960-964, 2008. ,
Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9, mBio, vol.6, issue.32, pp.1-9, 2015. ,
DOI : 10.1128/mbio.00648-15
URL : https://mbio.asm.org/content/6/3/e00648-15.full.pdf
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defense systems, Nature Communications, vol.7, p.10613, 2016. ,
New CRISPR-Cas systems from uncultivated microbes, Nature, vol.542, issue.7640, pp.237-241, 2016. ,
Non-identity-mediated CRISPRbacteriophage interaction mediated via the Csy and Cas3 proteins, Journal of Bacteriology, vol.193, issue.14, pp.3433-3445, 2011. ,
Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes, Genes & development, vol.22, issue.24, pp.3489-96, 2008. ,
HMM-CAS: a web tool for the identification and domain annotations of Cas proteins, IEEE/ACM Transactions on Computational Biology and Bioinformatics, p.5963, 2017. ,
Comparative network clustering of direct repeats (DRs) and cas genes confirms the possibility of the BIBLIOGRAPHY horizontal transfer of CRISPR locus among bacteria, Molecular Phylogenetics and Evolution, vol.56, issue.3, pp.878-887, 2010. ,
An end-joining repair mechanism in Escherichia coli, Proceedings of the National Academy of Sciences of the United States of America, vol.107, pp.2141-2147, 2010. ,
, CRISPR-Induced Distributed Immunity in Microbial Populations, vol.9, p.101710, 2014.
Multiscale model of crispr-induced coevolutionary dynamics: Diversification at the interface of Lamarck and Darwin, Evolution, vol.66, issue.7, pp.2015-2029, 2012. ,
Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex, Cell, vol.169, issue.1, pp.47-57, 2017. ,
Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases, Nature Biotechnology, vol.32, issue.11, pp.1141-1145, 2014. ,
Multiplex genome engineering using CRISPR/Cas systems, Science, vol.339, issue.6121, pp.819-842, 2013. ,
Motoring along with the bacterial RecA protein, Nature Reviews Molecular Cell Biology, vol.8, issue.2, pp.127-138, 2007. ,
, Regulation of Bacterial RecA Protein Function, Critical Reviews in Biochemistry and Molecular Biology, vol.42, pp.41-63, 2007.
Phylogenetic ubiquity and shuffling of the bacterial RecBCD and AddAB recombination complexes, Journal of bacteriology, vol.191, issue.16, pp.5076-84, 2009. ,
Consequences of Cas9 cleavage in the chromosome of Escherichia coli, Nucleic Acids Research, vol.44, issue.9, pp.4243-4251, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01967442
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system, Nature communications, vol.3, 0945. ,
Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma Gallisepticum, vol.8, 2012. ,
Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine, Science, vol.306, issue.5696, pp.683-685, 2004. ,
CRISPR RNA maturation by transencoded small RNA and host factor RNase III, Nature, vol.471, issue.7340, pp.602-607, 2011. ,
Philippe Horvath, and Sylvain Moineau, Phage response to CRISPR-encoded resistance in Streptococcus thermophilus, Journal of Bacteriology, vol.190, issue.4, pp.1390-1400, 2008. ,
CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli, RNA biology, vol.10, issue.5, pp.792-802, 2013. ,
RecBCD enzyme and the repair of double-stranded DNA breaks, Microbiology and molecular biology reviews : MMBR 72, pp.642-71, 2008. ,
Structural basis of CRISPR SpyCas9 inhibition by an anti-CRISPR protein, Nature, vol.546, issue.7658, pp.436-439, 2017. ,
A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, 2017. ,
A constant rate of spontaneous mutation in DNA-based microbes, Proceedings of the National Academy of Sciences of the United States of America, vol.88, pp.7160-7164, 1991. ,
CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance, Nature communications, vol.4, 2013. ,
DOI : 10.1038/ncomms3087
URL : https://www.nature.com/articles/ncomms3087.pdf
Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, vol.538, issue.7624, pp.270-273, 2016. ,
Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998. ,
PILER-CR: fast and accurate identification of CRISPR repeats, BMC bioinformatics, vol.8, p.18, 2007. ,
The Escherichia coli CRISPR system protects from ? lysogenization, lysogens, and prophage induction, Journal of Bacteriology, vol.192, issue.23, pp.6291-6294, 2010. ,
DOI : 10.1128/jb.00644-10
URL : https://jb.asm.org/content/192/23/6291.full.pdf
A phylogenomic study of DNA repair genes, proteins, and processes, vol.435, 1999. ,
The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae, Journal of Structural Biology, vol.178, issue.3, pp.350-362, 2012. ,
Virus-host and CRISPR dynamics in archaea-dominated hypersaline Lake tyrrell, Archaea, vol.370871, 2013. ,
Evolutionary causes and consequences of diversified CRISPR immune profiles in natural populations, Biochemical Society transactions, vol.41, issue.6, pp.1431-1437, 2013. ,
Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms, Molecular Microbiology, vol.85, issue.6, pp.1044-1056, 2012. ,
RNA-activated DNA cleavage by the Type III-B CRISPR Cas effector complex, Genes and Development, vol.30, issue.4, pp.460-470, 2016. ,
DOI : 10.1101/gad.273722.115
URL : http://genesdev.cshlp.org/content/30/4/460.full.pdf
Phylogenies and the Comparative Method, The American Naturalist, vol.125, issue.1, pp.1-15, 1985. ,
DOI : 10.1086/284325
Prospects for building large timetrees using molecular data with incomplete gene coverage among species, Molecular Biology and Evolution, vol.31, issue.9, pp.2542-2550, 2014. ,
DOI : 10.1093/molbev/msu200
URL : https://academic.oup.com/mbe/article-pdf/31/9/2542/9596013/msu200.pdf
Degenerate target sites mediate rapid primed CRISPR adaptation, Proceedings of the National Academy of Sciences of the United States of America, vol.111, pp.1629-1667, 2014. ,
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA, Nature, pp.1-19, 2016. ,
Crystal structure of Muts2 endonuclease domain and the mechanism of homologous recombination suppression, Journal of Biological Chemistry, vol.283, issue.48, pp.33417-33427, 2008. ,
Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system, Biochimie, vol.118, pp.322-332, 2015. ,
, Current Biology, vol.17, issue.11, pp.395-397, 2007.
CRISPR Content Correlates with the Pathogenic Potential of Escherichia coli, Plos One, vol.10, issue.7, p.131935, 2015. ,
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, vol.468, issue.7320, pp.67-71, 2010. ,
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proceedings of the National Academy of Sciences of the United States of America, vol.109, pp.2579-86, 2012. ,
, CRISPRdigger: detecting CRISPRs with better direct repeat annotations, vol.6, p.32942, 2016.
The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes, Journal of molecular evolution, vol.62, issue.6, pp.718-747, 2006. ,
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs, BMC genomics, vol.15, issue.1, p.202, 2014. ,
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, vol.514, issue.7524, pp.633-637, 2014. ,
Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C, Nature Structural & Molecular Biology, vol.12, issue.4, pp.304-312, 2005. ,
No evidence of inhibition of horizontal gene transfer by CRISPR Cas on evolutionary timescales, The ISME Journal, vol.9, issue.9, pp.2021-2027, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01464867
Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array, Cell Reports, vol.16, issue.11, pp.2811-2818, 2016. ,
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic acids research, vol.35, pp.52-59, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194414
The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae, mBio, vol.4, issue.2, pp.74-87, 2013. ,
Nuclease activity of Legionella pneumophila Cas2 promotes intracellular infection of amoebal host cells, Infection and Immunity, vol.83, issue.3, pp.1008-1018, 2015. ,
Characterization of the multiple CRISPR loci on Streptomyces linear plasmid pSHK1, Acta Biochimica et Biophysica Sinica, vol.43, issue.8, pp.630-639, 2011. ,
Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways, Molecular Microbiology, vol.79, issue.2, pp.316-330, 2011. ,
Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus, pp.1-6, 2012. ,
Targeted Bacterial Immunity Buffers Phage Diversity, Journal of Virology, vol.85, issue.20, pp.10554-10560, 2011. ,
Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens, Current opinion in microbiology, vol.17, pp.82-90, 2014. ,
Structural basis for promiscuous PAM recognition in type IE Cascade from E. coli, Nature, vol.530, issue.7591, pp.499-503, 2016. ,
Heterogeneous diversity of spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), Physical Review Letters, vol.105, issue.12, p.128102, 2010. ,
Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes, PLoS ONE, vol.4, issue.1, p.4169, 2009. ,
Viral biogeography revealed by signatures in Sulfolobus islandicus genomes, Environmental Microbiology, vol.11, issue.2, pp.457-466, 2009. ,
Cas9 specifies functional viral targets during CRISPR Cas adaptation, Nature, vol.519, issue.7542, pp.199-202, 2015. ,
Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response, Molecular Cell, vol.65, issue.1, pp.168-175, 2016. ,
Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay, Journal of Bacteriology, vol.198, issue.22, pp.458-474, 2016. ,
Friendly Fire: Biological Functions and Consequences of Chromosomal-Targeting by CRISPR-Cas Systems, Journal of Bacteriology, vol.198, issue.10, pp.1481-1486, 2016. ,
The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications, Nucleic Acids Research, vol.43, issue.16, pp.1-12, 2015. ,
Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein, Frontiers in microbiology, vol.5, 2014. ,
An enrichment of CRISPR and other defense-related features in marine spongeassociated microbial metagenomes, Frontiers in M, vol.7, 2016. ,
Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies, Proceedings of the Royal Society B: Biological Sciences, vol.283, 2016. ,
Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system, Proceedings of the National Academy of Sciences of the United States of America, vol.114, pp.131-135, 2016. ,
The effect of Mycobacterium tuberculosis CRISPR-associated Cas2 (Rv2816c) on stress response genes expression, morphology and macrophage survival of Mycobacterium smegmatis, Infection, Genetics and Evolution, vol.40, pp.295-301, 2015. ,
An anti-CRISPR from a virulent streptococcal phage inhibits Streptococcus pyogenes Cas9, Nature Microbiology Epub, 2017. ,
Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages, Nature Communications, vol.5, issue.4399, 2014. ,
Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context, Journal of bacteriology, vol.195, issue.17, pp.3834-3878, 2013. ,
Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, Journal of bacteriology, vol.169, issue.12, pp.5429-5462, 1987. ,
Different genome stability proteins underpin primed and naïve adaptation in E. coli CRISPR-Cas immunity, Nucleic Acids Research, vol.43, issue.22, pp.10821-10851, 2015. ,
Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli, Science, vol.345, issue.6203, pp.1479-84, 2014. ,
CRISPR-Cas: Adapting to change, Science, vol.356, issue.6333, p.5056, 2017. ,
Identification of a Novel Family of Sequence Repeats among Prokaryotes, OMICS: A Journal of Integrative Biology, vol.6, issue.1, pp.23-33, 2002. ,
Identification of genes that are associated with DNA repeats in prokaryotes, Molecular Microbiology, vol.43, issue.6, pp.1565-1575, 2002. ,
RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nature biotechnology, issue.3, pp.233-242, 2013. ,
Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids, PLoS genetics, vol.9, issue.9, 2013. ,
Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity, Cell, vol.164, issue.4, pp.710-721, 2016. ,
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, vol.337, issue.6096, pp.816-837, 2012. ,
Structures of Cas9 endonucleases reveal RNA-mediated conformational activation, Science, vol.343, issue.6176, p.1247997, 2014. ,
Structural basis for CRISPR RNA-guided DNA recognition by Cascade, Nature Structural & Molecular Biology, vol.18, issue.5, pp.529-536, 2011. ,
An evolutionary link between natural transformation and crispr adaptive immunity, mBio, vol.3, issue.5, pp.1-7, 2012. ,
DOI : 10.1128/mbio.00309-12
URL : https://mbio.asm.org/content/3/5/e00309-12.full.pdf
Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System, Structure, vol.24, issue.1, pp.70-79, 2015. ,
ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs, Journal of Bacteriology, vol.198, issue.5, pp.797-807, 2015. ,
?eslovas Venclovas, Gintautas Tamulaitis, and Virginijus Siksnys, A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems, Science, vol.357, issue.6351, pp.605-609, 2017. ,
, CRISPR-Cas Adaptive Immunity and the Three Rs, vol.37, 2017.
Crystal structure of streptococcus pyogenes Csn2 reveals calcium-dependent conformational changes in its tertiary and quaternary structure, PLoS ONE, vol.7, issue.3, p.33401, 2012. ,
Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nature Reviews Genetics, vol.16, issue.3, pp.184-92, 2014. ,
Diversity, classification and evolution of CRISPR-Cas systems, Current Opinion in Microbiology, vol.37, pp.67-78, 2017. ,
Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery, Current Opinion in Microbiology, vol.38, pp.36-43, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977358
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC biology, vol.12, issue.1, p.36, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01001796
Recent mobility of casposons, self-synthesizing transposons at the origin of the CRISPR-Cas immunity, Genome Biology and Evolution, vol.8, issue.2, pp.375-386, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01443928
Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation, Molecular Cell, vol.63, issue.5, pp.852-864, 2016. ,
The contribution of genetic recombination to CRISPR array evolution, Genome Biology and Evolution, vol.7, issue.7, pp.1925-1939, 2015. ,
The Heroes of CRISPR, Cell, vol.164, issue.1-2, pp.18-28, 2015. ,
Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPRmediated bacterial immunity, Proteins: Structure, Function and Bioinformatics, vol.80, issue.11, pp.2573-2582, 2012. ,
, Toroidal structure and DNA cleavage by the CRISPR-associated, vol.135, pp.17476-17487, 2013.
DOI : 10.1021/ja408729b
URL : http://europepmc.org/articles/pmc3889865?pdf=render
Udi Qimron, and Rotem Sorek, CRISPR adaptation biases explain preference for acquisition of foreign DNA, Nature, vol.520, issue.7548, pp.505-510, 2015. ,
Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process, Nucleic Acids Research, vol.42, issue.4, pp.2483-2492, 2014. ,
Imipenem represses CRISPR-Cas interference of DNA acquisition through H-NS stimulation in Klebsiella pneumoniae, Scientific reports, vol.6, p.31644, 2016. ,
Wenfang Peng, Yunxiang Liang, Qunxin She, and Nan Peng, Coupling transcriptional activation of CRISPR Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus, Nucleic Acids Research, vol.45, issue.15, pp.8978-8992, 2017. ,
Dissociation of synthetic Holliday junctions by E. coli RecG protein, The EMBO journal, vol.12, issue.1, pp.17-22, 1993. ,
Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow, Frontiers in Microbiology, vol.7, pp.1-13, 2016. ,
The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome, Molecular Microbiology, vol.85, issue.6, pp.1057-1071, 2012. ,
A novel link between Campylobacter jejuni bacteriophage defence, virulence and GuillainBarré syndrome, European Journal of Clinical Microbiology and Infectious Diseases, vol.32, issue.2, pp.207-226, 2013. ,
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs, BioMed Research International Epub, 2016. ,
Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus, RNA, vol.21, issue.6, pp.1147-58, 2015. ,
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis, Nucleic Acids Research, vol.30, issue.2, pp.482-496, 2002. ,
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biology direct, p.1, 2006. ,
,
An updated evolutionary classification of CRISPR Cas systems, Nature Reviews Microbiology, vol.13, issue.11, pp.722-736, 2015. ,
The basic building blocks and evolution of CRISPR-Cas systems, Biochemical Society transactions, vol.41, issue.6, pp.1392-400, 2013. ,
SnapShot: Class 1 CRISPR-Cas Systems, Cell, vol.168, issue.5, 2017. ,
DOI : 10.1016/j.cell.2017.02.018
, SnapShot: Class 2 CRISPR-Cas Systems, Cell, vol.168, issue.1-2, 2017.
Cas9 as a versatile tool for engineering biology, Nature methods, vol.10, issue.10, pp.957-63, 2013. ,
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Research, vol.35, issue.3, pp.962-974, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00129258
Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls, BMC Systems Biology, vol.10, issue.S1, p.5, 2016. ,
CRISPR-Cas immunity in prokaryotes, Nature, vol.526, issue.7571, pp.55-61, 2015. ,
DOI : 10.1038/nature15386
CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA, Science, vol.322, issue.5909, pp.1843-1845, 2008. ,
Self versus non-self discrimination during CRISPR RNA-directed immunity, Nature, vol.463, issue.7280, pp.568-71, 2010. ,
Bacillus subtilis SbcC protein plays an important role in DNA inter-strand crosslink repair, BMC molecular biology, vol.7, p.20, 2006. ,
Diversity of immune strategies explained by adaptation to pathogen statistics, Proceedings of the National Academy of Sciences, vol.113, issue.31, pp.8630-8635, 2015. ,
CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration, Molecular Cell, vol.64, issue.3, pp.616-623, 2016. ,
The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi, Journal of Bacteriology, vol.193, issue.10, pp.2396-2407, 2011. ,
, Homologous Recombinatio Enzymes and Pathways, EcoSal Plus, vol.5, issue.1, 2012.
Holding a grudge, RNA Biology, vol.10, issue.5, pp.900-906, 2013. ,
DOI : 10.4161/rna.23929
URL : http://europepmc.org/articles/pmc3737347?pdf=render
Mobile CRISPR/Cas-Mediated Bacteriophage Resistance in Lactococcus lactis, PLoS ONE, vol.7, issue.12, p.51663, 2012. ,
DOI : 10.1371/journal.pone.0051663
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051663&type=printable
The human gut virome : Inter-individual variation and dynamic response to diet, Genome research, vol.21, issue.10, pp.1616-1625, 2011. ,
DOI : 10.1101/gr.122705.111
URL : http://genome.cshlp.org/content/21/10/1616.full.pdf
CRISPR Cas systems exploit viral DNA injection to establish and maintain adaptive immunity, Nature, vol.544, issue.7648, pp.101-104, 2017. ,
DOI : 10.1038/nature21719
URL : http://europepmc.org/articles/pmc5540373?pdf=render
Role of DNA repair by nonhomologous-end joining in Bacillus subtilis spore resistance to extreme dryness, mono-and polychromatic UV, and ionizing radiation, Journal of Bacteriology, vol.189, issue.8, pp.3306-3311, 2007. ,
Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems, Science, vol.353, issue.6299, p.5147, 2016. ,
Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, Journal of Molecular Evolution, vol.60, issue.2, pp.174-182, 2005. ,
Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning, Molecular Microbiology, vol.17, issue.1, pp.85-93, 1995. ,
Host diversity limits the evolution of parasite local adaptation, Molecular Ecology, vol.26, issue.7, pp.1756-1763, 2017. ,
Next Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit, Trends in Biotechnology, vol.34, issue.7, pp.575-587, 2016. ,
Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target, Science, vol.345, issue.6203, pp.1479-84, 2014. ,
Cas5d protein processes Pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg crispr-cas system, Structure, vol.20, issue.9, pp.1574-1584, 2012. ,
Proteomic Profiling of ClpXP Substrates after DNA Damage Reveals Extensive Instability within SOS Regulon, Molecular Cell, vol.22, issue.2, pp.193-204, 2006. ,
Type III CRISPR-Cas systems generate cyclic oligoadenylate 200 BIBLIOGRAPHY second messengers to activate Csm6 RNases, Nature, vol.548, issue.7669, pp.543-548, 2017. ,
Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases, Nucleic Acids Research, vol.42, issue.2, pp.1341-1353, 2014. ,
Crystal structure of Cas9 in complex with guide RNA and target DNA, Cell, vol.156, issue.5, pp.935-949, 2014. ,
CRISPR Immunological Memory Requires a Host Factor for Specificity, Molecular Cell, vol.62, issue.6, pp.824-833, 2016. ,
Foreign DNA capture during CRISPRCas adaptive immunity, Nature, vol.527, issue.7579, pp.535-538, 2015. ,
Integrase mediated spacer acquisition during CRISPR Cas adaptive immunity, Nature, vol.519, issue.7542, pp.193-198, 2015. ,
CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri, Nucleic Acids Research, vol.42, issue.17, pp.1-11, 2014. ,
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic acids research, vol.42, issue.16, pp.10618-10632, 2014. ,
Regulation of genetic flux between bacteria by restriction modification systems, Proceedings of the National Academy of Sciences of the United States of America, vol.113, issue.20, pp.5658-5663, 2016. ,
Strong bias in the bacterial CRISPR elements that confer immunity to phage, Nature communications, vol.4, p.1430, 2013. ,
CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus, mBio, vol.6, issue.2, pp.1-9, 2015. ,
Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters, Proceedings of the Royal Society B: Biological Sciences, vol.255, issue.1342, pp.37-45, 1994. ,
Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible Jump Markov Chain Monte Carlo, The American Naturalist, vol.167, issue.6, pp.808-825, 2013. ,
Multidrug-Resistant Enterococci Lack CRISPR cas, mBio, vol.1, issue.4, pp.1-10, 2010. ,
NHEJ enzymes LigD and Ku participate in stationary-phase mutagenesis in Pseudomonas putida, DNA Repair, vol.31, pp.11-18, 2015. ,
Fineran, Regulation of the type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference, Nucleic Acids Research, vol.43, issue.12, pp.6038-6048, 2015. ,
, Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems, vol.64, pp.1-7, 2016.
Regulation of CRISPRCas adaptive immune systems, Current Opinion in Microbiology, vol.37, pp.1-7, 2017. ,
, Naturally Occurring Off-Switches for CRISPR-Cas9, vol.167, pp.1829-1838, 2016.
,
A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of pseudomonas aeruginosa, mBio, vol.5, issue.2, pp.1-7, 2014. ,
Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species, Nature Microbiology, vol.1, issue.8, p.16085, 2016. ,
Differential distribution of Type II CRISPR-Cas systems in agricultural and non-agricultural Campylobacter coli and Campylobacter jejuni shared environments, Genome Biology and Evolution, vol.7, issue.9, pp.2663-2679, 2015. ,
Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli, Molecular Microbiology, vol.79, issue.3, pp.584-599, 2011. ,
Recruitment of CRISPR-Cas systems by Tn7-like transposons, Proceedings of the National Academy of Sciences of the United States of, America, vol.114, issue.35, pp.7358-7366, 2017. ,
Non homologous end-joining in bacteria: a microbial perspective, Annual review of microbiology, pp.259-282, 2007. ,
Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase, Journal of Molecular Biology, vol.366, issue.2, pp.391-405, 2007. ,
NHEJ protects mycobacteria in stationary phase against the harmful effects of desiccation, DNA Repair, vol.6, pp.1271-1276, 2007. ,
Lennart Randau, and Reinhard Hensel, Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax, Journal of Bacteriology, vol.194, issue.10, pp.2491-2500, 2012. ,
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies, Microbiology, vol.151, issue.3, pp.653-663, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-01158317
Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009. ,
Massive activation of archaeal defense genes during viral infection, Journal of virology, vol.87, issue.15, pp.8419-8447, 2013. ,
Essential Structural and Functional Roles of the Cmr4 Subunit in RNA Cleavage by the Cmr CRISPR-Cas Complex, Cell Reports, vol.9, issue.5, pp.1610-1618, 2014. ,
Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen, Cellular Microbiology, vol.18, issue.10, pp.1319-1338, 2016. ,
I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope, Current Opinion in Infectious Diseases, vol.28, issue.3, pp.267-274, 2015. ,
Inhibition of CRISPR-Cas9 with Bacteriophage Proteins, Cell, vol.168, issue.1-2, pp.150-158, 2016. ,
Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System Article Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System, Cell, vol.163, issue.4, pp.1-12, 2015. ,
Diverse CRISPRs evolving in human microbiomes, PLoS Genetics, vol.8, issue.6, 2012. ,
Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer, Nucleic Acids Research, vol.42, issue.13, pp.8516-8526, 2014. ,
Comparative and evolutionary analysis of the bacterial homologous recombination systems, PLoS genetics, vol.1, issue.2, p.15, 2005. ,
Type I CRISPR-Cas targets endogenous genes and regulates virulence to evade mammalian host immunity, Cell Research, vol.26, issue.12, pp.1273-1287, 2016. ,
Structure of the CRISPR interference complex CSM reveals key similarities with cascade, Molecular Cell, vol.52, issue.1, pp.124-134, 2013. ,
Virginijus Siksnys, and Ralf Seidel, Directional R-loop formation by the CRISPR-cas surveillance complex cascade provides efficient off-target site rejection, Cell Reports, vol.10, issue.9, pp.1534-1543, 2015. ,
RecFOR and RecOR as distinct RecA loading pathways, Journal of Biological Chemistry, vol.284, issue.5, pp.3264-3272, 2009. ,
Co-transcriptional DNA and RNA cleavage during type III CRISPR-cas immunity, Cell, vol.161, issue.5, pp.1164-1174, 2015. ,
A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion, Proceedings of the National Academy of Sciences of the United States of America, vol.111, issue.30, pp.11163-11168, 2014. ,
A CRISPR/Cas system mediates bacterial innate immune evasion and virulence, Nature, vol.497, issue.7448, pp.254-261, 2013. ,
CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein, PLoS ONE, vol.8, issue.2, p.56470, 2013. ,
A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity, Nature, vol.494, issue.7438, pp.489-91, 2013. ,
CRISPR-based screening of genomic island excision events in bacteria, Proceedings of the National Academy of Sciences of the United States of America, vol.112, issue.26, 2015. ,
, Stan J J Brouns
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence, Proceedings of the National Academy of Sciences of the United States of America, vol.108, pp.10098-103, 2011. ,
Role of the Streptococcus mutans CRISPR-Cas systems in immunity and cell physiology, Journal of Bacteriology, vol.197, issue.4, pp.749-761, 2015. ,
CRISPRs: Molecular Signatures Used for Pathogen Subtyping, Applied and Environmental Microbiology, vol.80, issue.2, pp.430-439, 2014. ,
DOI : 10.1128/aem.02790-13
URL : https://aem.asm.org/content/80/2/430.full.pdf
Disabling Cas9 by an anti-CRISPR DNA mimic, Science Advances, vol.3, issue.7, p.1701620, 2017. ,
DOI : 10.1126/sciadv.1701620
URL : http://advances.sciencemag.org/content/advances/3/7/e1701620.full.pdf
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems, Molecular Cell, vol.60, issue.3, pp.1-13, 2015. ,
DOI : 10.1016/j.molcel.2015.10.008
URL : https://doi.org/10.1016/j.molcel.2015.10.008
Pervasive generation of oppositely oriented spacers during CRISPR adaptation, Nucleic Acids Research, vol.42, issue.9, pp.5907-5916, 2014. ,
,
,
Diversity and evolution of class 2 CRISPR Cas systems, Nature Reviews Microbiology, 2017. ,
The CRISPR spacer space is dominated by sequences from the species-specific mobilome, mBio, vol.8, issue.5, pp.1-18, 2017. ,
Bacterial DNA repair by nonhomologous end joining, Nature Reviews Microbiology, vol.5, issue.11, pp.852-61, 2007. ,
DOI : 10.1038/nrmicro1768
Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems, Andrew Z Fire, and Antonio 206 BIBLIOGRAPHY Sánchez-Amat, issue.6, p.27601, 2017. ,
DOI : 10.7554/elife.27601
URL : https://doi.org/10.7554/elife.27601
, On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires, 2017.
Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptaseCas1 fusion protein, Science, vol.351, issue.6276, p.4234, 2016. ,
Why are the genomes of endosymbiotic bacteria so stable?, Trends in Genetics, vol.19, issue.4, pp.172-176, 2003. ,
AdnAB : a new DSB-resecting motor nuclease from mycobacteria, Genes & development, vol.23, issue.12, pp.1423-1437, 2009. ,
Inhibition of CRISPR-Cas systems by mobile genetic elements, Current Opinion in Microbiology, vol.37, pp.120-127, 2017. ,
DOI : 10.1016/j.mib.2017.06.003
URL : http://europepmc.org/articles/pmc5737815?pdf=render
, Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01370770
, Homologous Recombination by the RecBCD and RecF Pathways ., Homologous Recombination by the RecBCD and RecF Pathways, 2004.
Structure of an RNA Silencing Complex of the CRISPR-Cas Immune System, Molecular Cell, vol.52, issue.1, pp.146-152, 2013. ,
, , p.207
Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus, Molecular Cell, vol.52, issue.1, pp.135-145, 2013. ,
RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus, Molecular Cell, vol.56, issue.4, pp.518-530, 2014. ,
Interference dominates and amplifies spacer acquisition in a native CRISPR-Cas system, Nature Communications, vol.23, pp.127-135, 2016. ,
Self-Targeting by CRISPR : Gene regulation or autoimmunity?, Trends in genetics : TIG 26, pp.335-340, 2010. ,
Or Sagy, and Rotem Sorek, CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome, Genome Research, vol.22, issue.10, pp.1985-1994, 2012. ,
Conformational control of DNA target cleavage by CRISPRCas9, Nature, vol.527, issue.7576, pp.110-113, 2015. ,
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9, Nature, vol.507, issue.7490, pp.62-67, 2014. ,
Phage mutations in response to CRISPR diversification in a bacterial population, Environmental Microbiology, vol.15, issue.2, pp.463-470, 2013. ,
, Metagenomic reconstructions of bacterial CRISPR loci constrain population histories, vol.10, pp.1-13, 2015.
CRISPR interference directs strand specific spacer acquisition, PloS one, vol.7, issue.4, p.35888, 2012. ,
Nature and intensity of selection pressure on CRISPR-associated genes, Journal of bacteriology 194, pp.1216-1241, 2012. ,
Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning, Science, vol.348, issue.6234, pp.581-585, 2015. ,
Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of Shiga toxin-producing Escherichia coli, Applied and Environmental Microbiology, vol.80, issue.4, pp.1411-1420, 2014. ,
Genetic and lifehistory traits associated with the distribution of prophages in bacteria, The ISME Journal, vol.10, issue.11, pp.2744-2754, 2016. ,
CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection, Journal of bacteriology, vol.193, issue.10, pp.2460-2467, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374943
Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements, Microbiology, vol.158, pp.2997-3004, 2012. ,
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PloS one, vol.5, issue.6, p.11126, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374940
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses, Environmental Microbiology, vol.10, issue.1, pp.200-207, 2008. ,
Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus, Proceedings. Biological sciences, vol.282, 2015. ,
Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli, Nucleic Acids Research, vol.43, issue.17, pp.8381-8391, 2015. ,
, Evolutionary Ecology of Prokaryotic Immune Mechanisms, Microbiology and Molecular Biology Reviews, vol.80, issue.3, pp.745-763, 2016.
The diversity-generating benefits of a prokaryotic adaptive immune system, Nature, vol.532, issue.7599, pp.385-388, 2016. ,
NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes, Molecular Microbiology, vol.93, issue.5, pp.1026-1042, 2014. ,
Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands, PLoS Genetics, vol.9, issue.4, p.1003454, 2013. ,
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. ,
and Ekaterina Semenova, Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery, Nucleic acids research, vol.43, issue.22, pp.1-13, 2015. ,
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems, Cell, vol.163, issue.4, pp.840-853, 2015. ,
A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses, Cell Research, vol.26, issue.10, pp.1165-1168, 2016. ,
DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica, Nucleic Acids Research, vol.44, issue.9, pp.4266-4277, 2016. ,
Structural basis of Cas3 inhibition by the bacteriophage protein AcrF3, Nature Structural & Molecular Biology, vol.23, issue.9, pp.868-871, 2016. ,
Modified Bases in Bacteriophage DNAs, Annual Review of Microbiology, vol.34, issue.1, pp.137-158, 1980. ,
Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus, Nucleic acids research, vol.43, issue.3, pp.1749-58, 2015. ,
,
Persisting viral sequences shape microbial CRISPR-based immunity, PLoS Computational Biology, vol.8, issue.4, 2012. ,
Viral diversity threshold for adaptive immunity in prokaryotes, mBio, vol.3, issue.6, pp.1-10, 2012. ,
Is having more than one CRISPR array adaptive ?, 2017. ,
A family of DNA repair ligases in bacteria?, FEBS Letters, vol.505, issue.2, pp.340-342, 2001. ,
Identification of a DNA nonhomologous end-joining complex in bacteria, Science, vol.297, issue.5587, pp.1686-1689, 2002. ,
, CRISPR-Cas systems: beyond adaptive immunity, vol.12, pp.317-343, 2014.
, Annual Review of Ecology, Evolution, and Systematics, vol.47, issue.1, pp.307-331, 2016.
,
H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO, Molecular Microbiology, vol.77, issue.6, pp.1380-1393, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00560024
Mike Boots, and Angus Buckling, Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense, Current Biology, vol.25, issue.8, pp.1043-1049, 2015. ,
Branch migration of three-strand recombination intermediates by RecG, a possible pathway for securing exchanges initiated by 3'-tailed duplex DNA, The EMBO journal, vol.14, issue.14, pp.3302-3310, 1995. ,
Structures of the RNA-guided surveillance complex from a bacterial immune system, Nature, vol.477, issue.7365, pp.486-489, 2011. ,
Bacterial DNA repair: recent insights into the mechanism of RecBCD, Nature Reviews Microbiology, vol.11, issue.1, pp.9-13, 2013. ,
Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation, Extremophiles, vol.11, issue.1, pp.19-29, 2007. ,
Protecting genome integrity during CRISPR immune adaptation, Nature Structural & Molecular Biology, vol.23, issue.10, 2016. ,
Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System, Cell, vol.170, issue.1, pp.48-60, 2017. ,
DOI : 10.1016/j.cell.2017.06.012
URL : http://europepmc.org/articles/pmc5841471?pdf=render
CRISPR interference and priming varies with individual spacer sequences, Nucleic acids research, vol.43, issue.22, pp.10831-10847, 2015. ,
DOI : 10.1093/nar/gkv1259
URL : https://academic.oup.com/nar/article-pdf/43/22/10831/16662225/gkv1259.pdf
Conformational Control of Cascade Interference and Priming Activities in CRISPR Immunity, Molecular Cell, vol.64, issue.4, pp.826-834, 2016. ,
, Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA, vol.165, issue.4, pp.949-962, 2016.
Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR, Shaofu Qiu, and Hongbin Song, vol.12, pp.1109-1129, 2015. ,
Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9, Molecular Cell, vol.67, issue.1, pp.117-127, 2017. ,
Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system, Nucleic Acids Research, vol.45, issue.1, pp.367-381, 2017. ,
High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, Proceedings of the National Academy of Sciences of the United States of America, vol.108, issue.50, pp.20136-20141, 2011. ,
Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in streptococcus thermophilus, PLoS ONE, vol.7, issue.5, p.38077, 2012. ,
Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa, Journal of Bacteriology, vol.91, issue.1, pp.210-219, 2009. ,
A split-Cas9 architecture for inducible genome editing and transcription modulation, Nature Biotechnology, vol.33, issue.2, pp.139-142, 2015. ,
DOI : 10.1038/nbt.3149
URL : http://europepmc.org/articles/pmc4503468?pdf=render
The CRISPR Associated Protein Cas4 Is a 5' to 3' DNA Exonuclease with an Iron-Sulfur Cluster, PLoS ONE, vol.7, issue.10, p.47232, 2012. ,
, Structure and Mechanism of the CMR Complex for CRISPRMediated Antiviral Immunity, vol.45, pp.303-313, 2012.
Expanding the catalog of cas genes with metagenomes, Nucleic Acids Research, vol.42, issue.4, pp.2448-2459, 2014. ,
5" min_mandatory_genes_required="2" min_genes_required="3"> #Present in other CRISPR-Cas systems <gene name="cas1_TypeI-II-III" presence="accessory" system_ref="CAS"/> <gene name="cas1_I_II_III_V_maka" presence="accessory" system_ref="CAS"/> <gene name="cas2_TypeI-II-III" presence="accessory" system_ref="CAS"/> <gene name="cas2_I_II_III_V_maka" presence="accessory" system_ref="CAS"/> <gene name="cas1_TypeIA" presence="accessory" system_ref="CAS-TypeIA"/> <gene name="cas1_TypeIC" presence="accessory" system_ref="CAS-TypeIC"/> <gene name= ,
csm2_IIID_maka_1" presence="mandatory"/> <gene name="csx10_IIID_maka_4" presence="mandatory"/> <gene name="csm3_IIID_maka_5" presence="mandatory"/> <gene name="csm3_IIID_maka_6" presence="mandatory"/> #Often associated with TypeIIID <gene name="csm3_IIIAD_maka_1" presence="mandatory" exchangeable="1"> <homologs> <gene name= ,
CAS-TypeIA"/> <gene name="cas4_TypeI-II" presence="accessory" system_ref="CAS"/> #Distinguishing from other Types <gene name="cas9_TypeII" presence="forbidden" system_ref="CAS-TypeIIC"/> <gene name="cas9_TypeIIB" presence="forbidden" system_ref="CAS-TypeIIB"/> #Other subtypes III sometimes associated with TypeIIIB <gene name="cas10_TypeIIIA" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name="cas10_III_maka_5" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name="csm3_TypeIIIA" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name="csm2_IIIA_maka_7" presence="accessory" system_ref="CAS-TypeIIIA"/>/> <gene name="csm4_TypeIIIA" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name="csm5_TypeIIIA" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name="csm6_TypeIIIA" presence="accessory" system_ref="CAS-TypeIIIA"/> <gene name= ,
5" min_mandatory_genes_required="2" min_genes_required="3"> #Present in all CRISPR-Cas systems <gene name="cas2_TypeI-II-III" presence="accessory" system_ref="CAS"/> <gene name= ,
CAS-TypeIIC"/> <gene name="cas9_TypeIIB" presence="forbidden" system_ref="CAS-TypeIIB"/> <gene name="cas10_TypeIIIA" presence="forbidden" system_ref="CAS-TypeIIIA"/> <gene name="cas10_TypeIIIB" presence="forbidden" system_ref="CAS-TypeIIIB"/> </system> ############################### Type VI <system inter_gene_max_space="5" min_mandatory_genes_required="1" min_genes_required="1"> <gene name="cas13a" presence="mandatory" loner="1"/> <gene name="cas13b1" presence="mandatory" loner="1"/> <gene name="cas13b2" presence="mandatory" loner="1"/> <gene name="cas13c" presence="mandatory" loner="1"/> <gene name="cas2_TypeI-II-III" presence="accessory" system_ref="CAS"/> <gene name="cas2_I_II_III_V_maka" presence="accessory" system_ref="CAS"/> <gene name="cas1_I_II_III_V_maka" presence="accessory" system_ref="CAS"/> <gene name="cas1_TypeI-II-III" presence="accessory" system_ref="CAS"/> "5" min_mandatory_genes_required="2" min_genes_required="3"> <gene name="cas1_TypeI-II ,
MacSyFinder: A program to Mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS One, vol.9, p.110726, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses, 2008. ,
Why bacteriophage encode exotoxins and other virulence factors, Evol Bioinform Online, vol.1, pp.97-110, 2005. ,
Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli, J Bacteriol, vol.177, pp.6791-6797, 1995. ,
Studies on lysogenesis. III. Superinfection of lysogenic Shigella dysenteriae with temperate mutants of the carried phage, J Bacteriol, vol.67, pp.696-707, 1954. ,
The adaptation of temperate bacteriophages to their host genomes, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374945
, Mol Biol Evol, vol.30, pp.737-751
Prophage contribution to bacterial population dynamics, J Bacteriol, vol.185, pp.6467-6471, 2003. ,
Restitution of r-and K-selection as a model of density-dependent natural selection, Annu Rev Ecol Syst, vol.15, pp.427-447, 1984. ,
Modulation of chemical composition and other parameters of the cell by growth rate, Escherichia Coli and Salmonella: Cellular and Molecular Biology, pp.1553-1569, 1996. ,
The Proteobacteria, bergey's manual of systematic bacteriology, vol.XXVI, p.304, 2005. ,
Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion, Microbiol Mol Biol Rev, vol.68, pp.560-602, 2004. ,
Phage as agents of lateral gene transfer, Curr Opin Microbiol, vol.6, pp.4-5, 2003. ,
, Prophage genomics. Microbiol Mol Biol Rev, vol.67, pp.238-276, 2003.
Prophages and bacterial genomics: what have we learned so far?, Mol Microbiol, vol.49, pp.277-300, 2003. ,
Seasonal variation in cell volume of epilimnetic bacteria, Microb Ecol, vol.16, pp.155-163, 1988. ,
Seasonal abundance of lysogenic bacteria in a subtropical estuary, Appl Environ Microbiol, vol.64, pp.2308-2312, 1998. ,
The impact of long-distance horizontal gene transfer on prokaryotic genome size, Proc Natl Acad Sci, vol.106, pp.21748-21753, 2009. ,
Applied Regression Analysis, 1998. ,
Accelerated profile HMM searches, PLoS Comput Biol, vol.7, p.1002195, 2011. ,
The Pfam protein families database, Nucleic Acids Res, vol.36, pp.281-288, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-01294685
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Res, vol.34, pp.5839-5851, 2006. ,
Marine viruses and their biogeochemical and ecological effects, Nature, vol.399, pp.541-548, 1999. ,
A non-hyperthermophylic common ancestor to extant life forms, Science, vol.283, pp.220-221, 1999. ,
Temperate bacterial viruses as double-edged swords in bacterial warfare, PLoS One, vol.8, p.59043, 2013. ,
Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA, Appl Environ Microbiol, vol.74, pp.495-502, 2008. ,
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, vol.514, pp.633-637, 2014. ,
The evolution of life history trade-offs in viruses, Curr Opin Virol, vol.8, pp.79-84, 2014. ,
No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales, ISME J, vol.9, pp.2021-2027, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01464867
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res, vol.35, pp.52-57, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00194414
Mycobacteriophages: genes and genomes, Annu Rev Microbiol, vol.64, pp.331-356, 2010. ,
The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness, Annu Rev Genet, vol.14, pp.399-445, 1980. ,
Bacteriophage host range and bacterial resistance, Adv Appl Microbiol, vol.70, pp.217-248, 2010. ,
Gene transfer by transduction in the marine environment, Appl Environ Microbiol, vol.64, pp.2780-2787, 1998. ,
Oligotrophs versus copiotrophs, Bioessays, vol.23, pp.657-661, 2001. ,
DOI : 10.1002/bies.1091
Lysogenization by bacteriophage lambda. I. Multiple infection and the lysogenic response, Mol Gen Genet, vol.122, pp.183-195, 1973. ,
DOI : 10.1016/s0300-9084(75)80274-4
Bacteriophage resistance mechanisms, Nat Rev Microbiol, vol.8, pp.317-327, 2010. ,
DOI : 10.1038/nrmicro2315
Studies on lysogenization in Escherichia coli, Cold Spring Harb Symp Quant Biol, vol.18, pp.7-8, 1953. ,
DOI : 10.1101/sqb.1953.018.01.015
, Lysogeny. Bacteriol Rev, vol.17, pp.269-337, 1953.
Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons, Environ Microbiol, vol.15, pp.2463-2475, 2013. ,
Effect of nutrient addition and environmental factors on prophage induction in natural populations of marine synechococcus species, 2005. ,
, Appl Environ Microbiol, vol.71, pp.842-850
Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages, Mol Microbiol, vol.43, pp.0-9, 2002. ,
PHACTS, a computational approach to classifying the lifestyle of phages, Bioinformatics, vol.28, pp.614-618, 2012. ,
Transcription termination controls prophage maintenance in Escherichia coli genomes, Proc Natl Acad Sci, vol.110, pp.1-4, 2013. ,
DOI : 10.1073/pnas.1303400110
URL : https://hal.archives-ouvertes.fr/hal-00874882
Bacterial growth rate and marine virus-host dynamics, Microb Ecol, vol.40, pp.114-124, 2000. ,
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome, Nature, vol.499, pp.219-222, 2013. ,
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res, vol.42, pp.10618-10631, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374960
APE: analyses of phylogenetics and evolution in R596 language, Bioinformatics, vol.20, pp.289-290, 2004. ,
Q and A: What is a pathogen? A question that begs the point, BMC Biol, vol.10, p.6, 2012. ,
Resources drive trade-off between viral lifestyles in the plankton: evidence from freshwater microbial microcosms, Environ Microbiol, vol.12, pp.467-479, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00527101
Genetic Switch: Phage Lambda and Higher Organisms, 1992. ,
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes, Elife, vol.4, pp.1-20, 2015. ,
DOI : 10.7554/elife.08490
URL : https://doi.org/10.7554/elife.08490
Temperature dependent bacteriophages of a tropical bacterial pathogen, Front Microbiol, vol.5, pp.5-9, 2014. ,
Mobility of plasmids, Microbiol Mol Biol Rev, vol.74, pp.434-452, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374958
The proof and measurement of association between two things, Am J Psychol, vol.15, pp.7-9, 1904. ,
Determination of cell fate selection during phage lambda infection, Proc Natl Acad Sci, vol.105, pp.20705-20710, 2008. ,
The evolution of life history traits: a critique of the theory and a review of the data, Annu Rev Ecol Syst, vol.8, pp.145-171, 1977. ,
The population biology of bacterial viruses: why be temperate?, Theor Popul Biol, vol.26, pp.93-117, 1984. ,
, , 1981.
, Appl Environ Microbiol, vol.41, pp.518-527
CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection, J Bacteriol, vol.193, pp.2460-2467, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374943
Causes of insertion sequences abundance in prokaryotic genomes, Mol Biol Evol, vol.24, pp.969-981, 2007. ,
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PLoS ONE, vol.5, p.11126, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374940
The systemic imprint of growth and its uses in ecological (meta)genomics, PLoS Genet, vol.6, p.1000808, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00488678
Investment in rapid growth shapes the evolutionary rates of essential proteins, Proc Natl Acad Sci, vol.108, pp.20030-20035, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00655553
Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling, PLoS One, vol.6, p.23126, 2011. ,
Bacteriophage control of bacterial virulence, Infect Immun, vol.70, pp.3985-3993, 2002. ,
Phage regulatory circuits and virulence gene expression, Curr Opin Microbiol, vol.8, pp.459-465, 2005. ,
Cryptic prophages help bacteria cope with adverse environments, Nat Commun, vol.1, p.147, 2010. ,
Ecology of prokaryotic viruses, FEMS Microbiol Rev, vol.28, pp.127-181, 2004. ,
CRISPR-Cas systems: beyond adaptive immunity, Nat Rev Microbiol, vol.12, pp.317-326, 2014. ,
Individual comparisons by ranking methods, Biometrics Bull, vol.1, pp.80-83, 1945. ,
Viruses and nutrient cycles in the sea viruses play critical roles in the structure and function of aquatic food webs, Bioscience, vol.49, pp.7-8, 1999. ,
Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl Environ Microbiol, vol.68, pp.4307-4314, 2002. ,
Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited, Microbiol Mol Biol Rev, vol.74, pp.42-57, 2010. ,
The existence of a second STK, known as Stk2, present in only some isolates of S. aureus, was noted in a few studies, but its function remained mysterious, PLoS Comput Biol, vol.3, 2005. ,
, EOP of phage phiNM1 on RN4220 S. aureus cells in the presence of the wild-type Stk2 protein (pDB31) or various mutants: K152Q (pDB81), D243A (pDB82), and T275A (pDB83)
, Growth curve of S. aureus RN4220 carrying control plasmid pC194 or pDB31 (pC194Ustk2)
, PFUs and colony-forming units (CFUs) recovered after infection of RN4220 cells carrying stk2 or not. Cells were grown to OD = 0.2 and incubated with phiNM1 for 2 hr. Cells were then plated on TSA to measure CFUs, and the filtered supernatant was spotted on a top agar lawn of RN4220 cells to measure PFUs. Upon infection with phiNM1 and in the presence of stk2
, PFUs and CFUs recovered after induction with mitomycin C (MMC) of growing RN4220 carrying a phiNM1 lysogenic phage or not, in the presence or absence of stk2. Upon induction, cells carrying a lysogenic phage are killed regardless of the presence of stk2, but the production of phage is inhibited in the presence of stk2. Note that PFUs are recovered even in the absence of MMC due to the spontaneous induction of the phage. See also Figure S1. Error bars represent the SD of three replicates, Cell Host & Microbe, vol.20, p.475, 2016.
, Induction of Candidate Activators of Stk2 S. aureus strains were grown in triplicate overnight at 37 C, diluted 1:100 in TSB, and incubated at 37 C with shaking. When cultures reached OD 600 z 0.2, aTc was added at a final concentration of 0.5 mg/mL. All the strains were grown in parallel without aTc as a control. After 1.5 hr of incubation in the presence or absence of aTc, the samples were serially diluted and 5 mL was spotted in TSA with appropriate antibiotics to count viable bacteria, Prophage Induction S. aureus strains (RN4220, RN4220::phiNM1, RN4220::phiNM1/pC194, and RN4220::phiNM1/pDB31were also centrifuged to recover the supernatant and measure the phage titer, vol.2, pp.50-54
Prophages of Staphylococcus aureus Newman and their contribution to virulence, Mol. Microbiol, vol.62, pp.1035-1047, 2006. ,
Modulation of cell wall structure and antimicrobial susceptibility by a Staphylococcus aureus eukaryote-like serine/threonine kinase and phosphatase, Infect. Immun, vol.77, pp.1406-1416, 2009. ,
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics, Nat. Protoc, vol.4, pp.484-494, 2009. ,
Phage abortive infection in lactococci: variations on a theme, Curr. Opin. Microbiol, vol.8, pp.473-479, 2005. ,
Activation of PKR/eIF2a signaling cascade is associated with dihydrotestosterone-induced cell cycle arrest and apoptosis in human liver cells, J. Cell. Biochem, vol.113, pp.1800-1808, 2012. ,
, Cell Host & Microbe, vol.20, pp.471-481, 2016.
First complete genome sequence of two Staphylococcus epidermidis bacteriophages, J. Bacteriol, vol.189, pp.2086-2100, 2007. ,
, , 2009.
Phosphorylation of the virulence regulator SarA modulates its ability to bind DNA in Staphylococcus aureus, FEMS Microbiol. Lett, vol.306, pp.30-36, 2010. ,
Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus, 2009. ,
, J. Bacteriol, vol.191, pp.4056-4069
Chemical properties and separation of phosphoamino acids by thin-layer chromatography and/or electrophoresis, Methods Enzymol, vol.201, pp.10-21, 1991. ,
URL : https://hal.archives-ouvertes.fr/hal-00313233
HMMER web server: interactive sequence similarity searching, Nucleic Acids Res, vol.39, pp.29-37, 2011. ,
, , 2011.
, , 1996.
, Non-detergent sulphobetaines: a new class of molecules that facilitate in vitro protein renaturation, Fold. Des, vol.1, pp.21-27
Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature, vol.514, pp.633-637, 2014. ,
, , 2015.
Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system, J. Bacteriol, vol.196, pp.310-317, 2014. ,
Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance, 1982. ,
, J. Bacteriol, vol.150, pp.815-825
Nucleotide sequence and functional map of pE194, a plasmid that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibodies, J. Bacteriol, vol.150, pp.804-814, 1982. ,
DNA methyltransferase, protein kinase and ATPase activity, Virology, vol.477, pp.100-109, 2015. ,
, , 2004.
The conformational plasticity of protein kinases, Cell, vol.109, pp.275-282, 2002. ,
, , 2013.
, Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids, PLoS Genet, vol.9, 1003844.
Central roles of NLRs and inflammasomes in viral infection, Nat. Rev. Immunol, vol.10, pp.688-698, 2010. ,
Protein Ser/Thr/Tyr phosphorylation in the Archaea, 2014. ,
, J. Biol. Chem, vol.289, pp.9480-9487
Bacteriophage resistance mechanisms, Nat. Rev. Microbiol, vol.8, pp.317-327, 2010. ,
, , 2005.
Genomics of staphylococcal Twort-like phagespotential therapeutics of the post-antibiotic era, Adv. Virus Res, vol.83, pp.143-216, 2012. ,
Several enzymes of the central metabolism are phosphorylated in Staphylococcus aureus, FEMS Microbiol. Lett, vol.272, pp.35-42, 2007. ,
Renaturation of Escherichia coli tryptophanase after exposure to 8 M urea. Evidence for the existence of nucleation centers, Eur. J. Biochem, vol.47, pp.409-415, 1974. ,
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems, 2011. ,
, J. Bacteriol, vol.193, pp.6039-6056
CD-Search: protein domain annotations on the fly, Nucleic Acids Res, vol.32, pp.327-331, 2004. ,
Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon, Cell, vol.62, pp.379-390, 1990. ,
Characterization of the phosphorylation sites of Mycobacterium tuberculosis serine/threonine protein kinases, PknA, PknD, PknE, and PknH by mass spectrometry, Proteomics, vol.6, pp.3754-3766, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00314725
Whole-genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that affect not only virulence factors but also the fitness of the strain, J. Bacteriol, vol.193, pp.2332-2335, 2011. ,
Staphylococcal plasmids and their replication, Annu. Rev. Microbiol, vol.43, pp.537-565, 1989. ,
Pattern recognition receptors and control of adaptive immunity, Immunol. Rev, vol.227, pp.221-233, 2009. ,
Eukaryote-like serine/ threonine kinases and phosphatases in bacteria. Microbiol, Mol. Biol. Rev, vol.75, pp.192-212, 2011. ,
RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence, Nat. Rev. Microbiol, vol.11, pp.745-760, 2013. ,
Phosphorylation of Escherichia coli translation initiation factors by the bacteriophage T7 protein kinase, Biochemistry, vol.31, pp.4822-4827, 1992. ,
Interferon-inducible antiviral effectors, Nat. Rev. Immunol, vol.8, pp.559-568, 2008. ,
How cells respond to interferons, Annu. Rev. Biochem, vol.67, pp.227-264, 1998. ,
Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2), Mol. Microbiol, vol.44, pp.489-500, 2002. ,
In vitro phosphorylation of initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus horikoshii OT3, J. Biochem, vol.135, pp.479-485, 2004. ,
Posttranslational modification influences the effects of MgrA on norA expression in Staphylococcus aureus, J. Bacteriol, vol.190, pp.7375-7381, 2008. ,
Intrinsic antiviral immunity, Nat. Immunol, vol.13, pp.214-222, 2012. ,
Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases, Nat. Struct. Biol, vol.10, pp.168-174, 2003. ,
NIK1-mediated translation suppression functions as a plant antiviral immunity mechanism, Nature, vol.520, pp.679-682, 2015. ,
, Cell Host & Microbe, vol.20, p.481, 2016.