Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ, Proc. Natl. Acad. Sci. USA, vol.106, pp.16203-16208, 2009. ,
In vivo conformation and replication intermediates of circular mitochondrial plasmids in Neurospora and Cryphonectria parasitica, Fungal Biol, vol.116, pp.919-931, 2012. ,
His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology, vol.350, pp.228-239, 2006. ,
The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis, Nucleic Acids Res, vol.38, pp.6707-6718, 2010. ,
Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic Acids Res, vol.44, pp.10367-10376, 2016. ,
DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity, Proc. Natl. Acad. Sci. USA, vol.112, pp.3476-3484, 2015. ,
Disclosing early steps of protein-primed genome replication of the Gram-positive tectivirus Bam35, Nucleic Acids Res, vol.44, pp.9733-9744, 2016. ,
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases, EMBO J, vol.26, pp.3494-3505, 2007. ,
The highly conserved amino acid sequence motif Tyr-Gly-Asp-Thr-Asp-Ser in alphalike DNA polymerases is required by phage phi 29 DNA polymerase for protein-primed initiation and polymerization, Proc. Natl. Acad. Sci. USA, vol.87, pp.4610-4614, 1990. ,
Primer terminus stabilization at the phi 29 DNA polymerase active site. Mutational analysis of conserved motif KXY, J. Biol. Chem, vol.270, pp.2735-2740, 1995. ,
A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase, J. Mol. Biol, vol.290, pp.241-251, 1999. ,
Compilation, alignment, and phylogenetic relationships of DNA polymerases, Nucleic Acids Res, vol.21, pp.787-802, 1993. ,
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes, Curr. Opin. Struct. Biol, vol.8, pp.54-63, 1998. ,
Unlocking the sugar ''steric gate'' of DNA polymerases, Biochemistry, vol.50, pp.1135-1142, 2011. ,
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases, Trends Biochem. Sci, vol.33, pp.209-219, 2008. ,
Sae2 promotes dsDNA endonuclease activity within Mre11-Rad50-Xrs2 to resect DNA breaks, Nature, vol.514, pp.122-125, 2014. ,
Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases a, d, h, i, k, and REV1, J. Mol. Biol, vol.404, pp.34-44, 2010. ,
Mutational analysis of the human DNA polymerase alpha. The most conserved region in alpha-like DNA polymerases is involved in metal-specific catalysis, J. Biol. Chem, vol.268, pp.11028-11040, 1993. ,
An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein, J. Mol. Biol, vol.304, pp.289-300, 2000. ,
Ancient invasions: from endosymbionts to organelles, Science, vol.304, pp.253-257, 2004. ,
, Cell Reports, vol.21, pp.1574-1587, 20171585-11-07.
Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins, J. Mol. Evol, vol.54, pp.763-773, 2002. ,
Darwin's goldmine is still open: variation and selection run the world, Front. Cell. Infect. Microbiol, vol.2, p.106, 2012. ,
DNA primases, Annu. Rev. Biochem, vol.70, pp.39-80, 2001. ,
, , 2013.
, Mol. Cell, vol.52, pp.541-553
A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2, Nucleic Acids Res, vol.42, pp.3707-3719, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01332620
The Cryphonectria parasitica plasmid pUG1 contains a large ORF with motifs characteristic of family B DNA polymerases, Nucleic Acids Res, vol.25, pp.3275-3280, 1997. ,
Mitochondrial evolution, Cold Spring Harb. Perspect. Biol, vol.4, p.11403, 2012. ,
PrimPol-Prime Time to Reprime, Genes, 2017. ,
Primasepolymerases are a functionally diverse superfamily of replication and repair enzymes, Nucleic Acids Res, vol.43, pp.6651-6664, 2015. ,
Replication fork reactivation downstream of a blocked nascent leading strand, Nature, vol.439, pp.557-562, 2006. ,
Adenovirus DNA replication, Cold Spring Harb. Perspect. Biol, vol.5, p.13003, 2013. ,
Cellfree cloning using phi29 DNA polymerase, Proc. Natl. Acad. Sci. USA, vol.102, pp.17332-17336, 2005. ,
Origin and evolution of the archaeo-eukaryotic primase superfamily and related palmdomain proteins: structural insights and new members, Nucleic Acids Res, vol.33, pp.3875-3896, 2005. ,
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition, EMBO J, vol.25, pp.1335-1343, 2006. ,
Self-synthesizing DNA transposons in eukaryotes, Proc. Natl. Acad. Sci. USA, vol.103, pp.4540-4545, 2006. ,
Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size, Nucleic Acids Res, vol.39, pp.8291-8305, 2011. ,
The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes, Nucleic Acids Res, vol.44, pp.4551-4564, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977379
Polymerase q is a robust terminal transferase that oscillates between three different mechanisms during end-joining, p.13740, 2016. ,
Linear protein-primed replicating plasmids in eukaryotic microbes, Microbial Linear Plasmids, pp.187-226, 2007. ,
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases, Biol. Direct, vol.1, p.39, 2006. ,
, , 1992.
Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat. Rev. Microbiol, vol.13, pp.105-115, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977391
Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Curr. Opin. Microbiol, vol.31, pp.25-33, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977380
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses, Biol. Direct, vol.9, p.6, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00994115
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol, vol.12, p.36, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01001796
Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery, Curr. Opin. Microbiol, vol.38, pp.36-43, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977358
Mechanism and evolution of DNA primases, Biochim. Biophys. Acta, vol.1804, pp.1180-1189, 2010. ,
The A-Rule and Deletion Formation During Abasic and Oxidized Abasic Site Bypass by DNA Polymerase q, ACS Chem. Biol, vol.12, pp.1584-1592, 2017. ,
Two Neurospora mitochondrial plasmids encode DNA polymerases containing motifs characteristic of family B DNA polymerases but lack the sequence Asp-Thr-Asp, Proc. Natl. Acad. Sci. USA, vol.90, pp.4299-4303, 1993. ,
A novel type of replicative enzyme harbouring ATPase, primase and DNA polymerase activity, EMBO J, vol.22, pp.2516-2525, 2003. ,
Open Questions on the Origin of Eukaryotes, Trends Ecol. Evol, vol.30, pp.697-708, 2015. ,
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
Alternative solutions and new scenarios for translesion DNA synthesis by human PrimPol, DNA Repair (Amst.), vol.29, pp.127-138, 2015. ,
Repriming of DNA synthesis at stalled replication forks by human PrimPol, Nat. Struct. Mol. Biol, vol.20, pp.1383-1389, 2013. ,
Replisome-mediated translesion synthesis by a cellular replicase, J. Biol. Chem, vol.292, pp.13833-13842, 2017. ,
, , 2007.
, Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms, Virology, vol.364, pp.237-243
TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol, Nat. Commun, vol.7, p.13296, 2016. ,
A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity, Proc. Natl. Acad. Sci. USA, vol.102, pp.6407-6412, 2005. ,
Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation, J. Mol. Biol, vol.31, pp.291-304, 1968. ,
Protein-priming of DNA replication, Annu. Rev. Biochem, vol.60, pp.39-71, 1991. ,
Protein-Primed Replication of Bacteriophage F29 DNA, pp.137-167, 2016. ,
DNAbinding proteins essential for protein-primed bacteriophage F29 DNA replication, Front. Mol. Biosci, vol.3, p.37, 2016. ,
Molecular cloning: a laboratory manual, 2001. ,
, Cell Reports, vol.21, pp.1574-1587, 2017.
The LaBelle mitochondrial plasmid of Neurospora intermedia encodes a novel DNA polymerase that may be derived from a reverse transcriptase, Mol. Cell. Biol, vol.11, pp.1696-1706, 1991. ,
Enhanced sequencing coverage with digital droplet multiple displacement amplification, Nucleic Acids Res, vol.44, p.66, 2016. ,
Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 3 0-5 0 exonuclease and strand-displacement activities, EMBO J, vol.11, pp.4227-4237, 1992. ,
The ''A'' rule revisited: polymerases as determinants of mutational specificity, DNA Repair (Amst.), vol.1, pp.125-135, 2002. ,
T7 replisome directly overcomes DNA damage, Nat. Commun, vol.6, p.10260, 2015. ,
Inactivation of the 3 0-5 0 exonuclease of the replicative T4 DNA polymerase allows translesion DNA synthesis at an abasic site, J. Mol. Biol, vol.336, pp.1023-1034, 2004. ,
Translesion DNA polymerases in eukaryotes: what makes them tick?, Crit. Rev. Biochem. Mol. Biol, vol.52, pp.274-303, 2017. ,
The dark side of dioxygen biochemistry, Curr. Opin. Chem. Biol, vol.2, pp.253-262, 1998. ,
Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase, Nucleic Acids Res, vol.30, pp.3323-3332, 2002. ,
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69, Cell, vol.89, pp.1087-1099, 1997. ,
An overview of Y-Family DNA polymerases and a case study of human DNA polymerase h, Biochemistry, vol.53, pp.2793-2803, 2014. ,
Mechanisms by which herpes simplex virus DNA polymerase limits translesion synthesis through abasic sites, DNA Repair (Amst.), vol.7, pp.95-107, 2008. ,
Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers, Proc. Natl. Acad. Sci. USA, vol.114, pp.2310-2318, 2017. ,
, Cell Reports, vol.21, pp.1574-1587, 20171587-11-07.
, Cell Reports, vol.21
,
, , 1997.
PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402 ,
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009. ,
PrimPol, an archaic primase/polymerase operating in human cells, Mol Cell, vol.52, pp.541-553, 2013. ,
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
Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat Rev Microbiol, vol.13, pp.105-115, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977391
Unipro UGENE: a unified bioinformatics toolkit, Bioinformatics, vol.28, pp.1166-1167, 2012. ,
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information, Methods Mol Biol, vol.1079, pp.263-271, 2014. ,
The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res, vol.33, pp.244-248, 2005. ,
Purification of HisTagged Proteins, Methods Enzymol, vol.559, pp.1-15, 2015. ,
Protein production by auto-induction in high density shaking cultures, Protein Expr Purif, vol.41, pp.207-234, 2005. ,
Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, pp.1009-1010, 2011. ,