Making serine integrases work for us, Curr. Opin. Microbiol, vol.38, pp.130-136, 2017. ,
Site-specific recombinases as tools for heterologous gene integration, Appl. Microbiol. Biotechnol, vol.92, pp.227-239, 2011. ,
Characterization of the genes and attachment sites for site-specific integration of plasmid pSE101 in Saccharopolyspora erythraea and Streptomyces lividans, Mol. Gen. Genet, vol.242, pp.185-193, 1994. ,
Nucleotide sequence of the rci gene encoding shufflon-specific DNA recombinase in the IncI1 plasmid R64: homology to the site-specific recombinases of intergrase family, Mol. Genet. Genomics, vol.213, pp.30-35, 1988. ,
Site-specific integration of the phage phi CTX genome into the Pseudomonas aeruginosa chromosome: characterization of the functional integrase gene located close to and upstream of attP, Mol. Gen. Genet, vol.246, pp.72-79, 1995. ,
Excision of the high-pathogenicity island of Yersinia pseudotuberculosis requires the combined actions of its cognate integrase and Hef, a new recombination directionality factor, Mol. Microbiol, vol.52, pp.1337-1348, 2004. ,
A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene, Nucleic Acids Res, vol.43, pp.4547-4557, 2015. ,
Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination, Mol. Microbiol, vol.15, pp.593-600, 1995. ,
Integrative and conjugative elements (ICEs): what they do and how they work, Annu. Rev. Genet, vol.49, pp.577-601, 2015. ,
Dynamic, structural, and regulatory aspects of lambda site-specific recombination, Annu. Rev. Biochem, vol.58, pp.913-949, 1989. ,
Circles: the replication-recombination-chromosome segregation connection, Proc. Natl. Acad. Sci. U.S.A, vol.98, pp.8189-8195, 2001. ,
In vivo identification of intermediate stages of the DNA inversion reaction catalyzed by the Salmonella Hin recombinase, Genetics, vol.149, pp.1649-1663, 1998. ,
The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells, 2014. ,
, , vol.2
A novel role for site-specific recombination in maintenance of bacterial replicons, Cell, vol.25, pp.729-736, 1981. ,
Integrons: agents of bacterial evolution, Nat. Rev. Microbiol, vol.4, pp.608-620, 2006. ,
Phage Integrases: Biology and Applications, J. Mol. Biol, vol.335, pp.667-678, 2004. ,
New applications for phage integrases, J. Mol. Biol, vol.426, pp.2703-2716, 2014. ,
Control of directionality in integrase-mediated recombination: examination of recombination directionality factors (RDFs) including Xis and Cox proteins, Nucleic Acids Res, vol.29, pp.2205-2216, 2001. ,
The cox protein of bacteriophage P2 inhibits the formation of the repressor protein and autoregulates the early operon, EMBO J, vol.6, pp.3191-3199, 1987. ,
Cooperative interactions between bacteriophage P2 integrase and its accessory factors IHF and Cox, Virology, vol.332, pp.284-294, 2005. ,
Bacteriophage P4 Vis protein is needed for prophage excision, Virology, vol.322, pp.82-92, 2004. ,
, Nucleic Acids Research, vol.46, issue.5, p.2535, 2018.
Cre recombinase and other tyrosine recombinases, Chem. Rev, vol.116, pp.12785-12820, 2016. ,
Requirements for catalysis in the Cre recombinase active site, Nucleic Acids Res, vol.38, pp.5817-5832, 2010. ,
Catalytic mechanism of DNA topoisomerase IB, Mol. Cell, vol.5, pp.1035-1041, 2000. ,
Similarities and differences among 105 members of the Int family of site-specific recombinases, Nucleic Acids Res, vol.26, pp.391-406, 1998. ,
The SSV1 viral integrase is not essential, Virology, vol.361, pp.103-111, 2007. ,
Mutational analysis of the archaeal tyrosine recombinase SSV1 integrase suggests a mechanism of DNA cleavage in trans, J. Biol. Chem, vol.279, pp.28936-28944, 2004. ,
Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase, J. Biol. Chem, vol.277, pp.16758-16767, 2002. ,
Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase, Acta Crystallogr. D Biol. Crystallogr, vol.68, pp.659-670, 2012. ,
Site-specific recombination by SSV2 Integrase: substrate requirement and domain functions, J. Virol, vol.89, pp.10934-10944, 2015. ,
Archaeal integrases and mechanisms of gene capture, Biochem. Soc. Trans, vol.32, pp.222-226, 2004. ,
Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon, Extremophiles, vol.2, pp.417-425, 1998. ,
Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria, J. Mol. Biol, vol.397, pp.144-160, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00506375
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes, Extremophiles, vol.18, pp.877-893, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977394
Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes, Arch. Virol, vol.161, pp.249-256, 2016. ,
Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain, Mol. Microbiol, vol.98, pp.1002-1020, 2015. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, pp.4673-4680, 1994. ,
DOI : 10.1093/nar/22.22.4673
URL : https://academic.oup.com/nar/article-pdf/22/22/4673/7122285/22-22-4673.pdf
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017. ,
DOI : 10.1093/nar/gkw1129
URL : https://academic.oup.com/nar/article-pdf/45/D1/D200/8846941/gkw1129.pdf
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf
The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res, vol.33, pp.244-248, 2005. ,
DOI : 10.1093/nar/gki408
URL : https://academic.oup.com/nar/article-pdf/33/suppl_2/W244/7622924/gki408.pdf
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information, Methods Mol. Biol, vol.1079, pp.263-271, 2014. ,
DOI : 10.1007/978-1-62703-646-7_17
URL : http://europepmc.org/articles/pmc4506754?pdf=render
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009. ,
DOI : 10.1093/bioinformatics/btp348
URL : https://academic.oup.com/bioinformatics/article-pdf/25/15/1972/564069/btp348.pdf
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol, vol.33, pp.1870-1874, 2016. ,
Identification, characterization, and application of the replicon region of the halophilic temperate sphaerolipovirus SNJ1, J. Bacteriol, vol.198, pp.1952-1964, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977378
Optimization of routine transformation of Escherichia coli with plasmid DNA, Biotechniques, vol.9, pp.570-577, 1990. ,
Construction of expression shuttle vectors for the Haloarchaeon natrinema sp. J7 based on its chromosomal origins of replication, Archaea, p.4237079, 2017. ,
Site-directed mutagenesis by overlap extension using the polymerase chain reaction, Gene, vol.77, pp.51-59, 1989. ,
DOI : 10.1016/0378-1119(89)90358-2
Construction and properties of a family of pACYC184-derived cloning vectors compatible with pBR322 and its derivatives, Gene, vol.102, pp.75-78, 1991. ,
Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene, J. Bacteriol, vol.185, pp.772-778, 2003. ,
Experimental characterization of cis-acting elements important for translation and transcription in halophilic archaea, PLoS Genet, vol.3, p.229, 2007. ,
Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205, Virology, vol.434, pp.233-241, 2012. ,
DOI : 10.1016/j.virol.2012.05.036
URL : https://doi.org/10.1016/j.virol.2012.05.036
Xer site specific recombination: double and single recombinase systems, Front. Microbiol, vol.8, p.453, 2017. ,
DOI : 10.3389/fmicb.2017.00453
URL : https://www.frontiersin.org/articles/10.3389/fmicb.2017.00453/pdf
Evidence for a Xer/dif system for chromosome resolution in archaea, PLoS Genet, vol.6, p.1001166, 2010. ,
Sequenceanalysis of an Archaeal virus isolated from a hypersaline lake in InnerMongolia, China. BMC Genomics, vol.8, p.410, 2007. ,
,
Natrialbamagadii virus phiCh1: first complete nucleotide sequence and functionalorganization of a virus infecting a haloalkaliphilic archaeon, Mol. Microbiol, vol.45, pp.851-863, 2002. ,
Haloarchaeal myovirus phiCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities, Mol. Microbiol, vol.83, pp.137-150, 2012. ,
Flipping chromosomes in deep-sea archaea, PLoS Genet, vol.13, p.1006847, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02109460
Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker, Mol. Microbiol, vol.35, pp.667-676, 2000. ,
Normalized nucleotide frequencies allow the definition of archaeal promoter elements for different archaeal groups and reveal base-specific TFB contacts upstream of the TATA box, Mol. Microbiol, vol.31, pp.1589-1592, 1999. ,
Analysis of the transcriptional regulator GlpR, promoter elements, and posttranscriptional processing involved in fructose-induced activation of the phosphoenolpyruvate-dependent sugar phosphotransferase system in Haloferax mediterranei, Appl. Environ. Microbiol, vol.80, pp.1430-1440, 2014. ,
Identification and characterization of mycobacteriophage L5 excisionase, Mol. Microbiol, vol.35, pp.350-360, 2000. ,
Integration and excision of the Mycobacterium tuberculosis prophage-like element, phiRv1, Mol. Microbiol, vol.45, pp.1515-1526, 2002. ,
Genetic determinants of immunity and integration of temperate Myxococcus xanthus phage Mx8, J. Bacteriol, vol.180, pp.614-621, 1998. ,
Site-specific recombination Xis-independent excisive recombination of bacteriophage lambda, J. Mol. Biol, vol.153, pp.67-78, 1981. ,
A phage protein that binds phiC31 integrase to switch its directionality, Mol. Microbiol, vol.80, pp.1450-1463, 2011. ,
The mechanism of varphiC31 integrase directionality: experimental analysis and computational modelling, Nucleic Acids Res, vol.44, pp.7360-7372, 2016. ,
Related haloarchaeal pleomorphic viruses contain different genome types, Nucleic Acids Res, vol.40, pp.5523-5534, 2012. ,
Characterization of a novel CDC gene (ORC1) partly homologous to CDC6 of Saccharomyces cerevisiae, Mol. Biol. Cell, vol.7, pp.409-418, 1996. ,
Viral biogeography revealed by signatures in Sulfolobus islandicus genomes, Environ. Microbiol, vol.11, pp.457-466, 2009. ,
Serine integrase chimeras with activity in E. coli and HeLa cells, Biol. Open, vol.3, pp.895-903, 2014. ,
Breaking the code of DNA binding specificity of TAL-type III effectors, Science, vol.326, pp.1509-1512, 2009. ,
An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope, Mol. Microbiol, vol.72, pp.307-319, 2009. ,
Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea, J. Virol, vol.86, pp.5067-5079, 2012. ,
A strange family, or how a new pleolipovirus reveals its friends and relatives, Mol. Microbiol, vol.98, pp.995-997, 2015. ,
Copy number amplification of the 2 micron circle plasmid of Saccharomyces cerevisiae, J. Theor. Biol, vol.119, pp.197-204, 1986. ,
A novel structural form of the 2 micron plasmid of the yeast Saccharomyces cerevisiae, Yeast, vol.10, pp.1341-1345, 1994. ,
Purification of the bacteriophage lambda xis gene product required for lambda excisive recombination, J. Biol. Chem, vol.257, pp.9658-9662, 1982. ,
Mobile elements in archaeal genomes, FEMS Microbiol. Lett, vol.206, pp.131-141, 2002. ,
Mechanisms of gene flow in archaea, Nat. Rev. Microbiol, vol.15, pp.492-501, 2017. ,
Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements, J. Virol, vol.90, pp.11043-11055, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977374
High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.16939-16944, 2013. ,
Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids, PLoS One, vol.8, p.49044, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00748527
Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses, Bioessays, vol.34, pp.867-870, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977405
A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells, Nat. Microbiol, vol.2, pp.1446-1455, 2017. ,