Investigation: Rémi Denise ,
Writing -original draft: Rémi Denise ,
References 1. Gould SJ, Vrba ES. Exaptation-a Missing Term in the Science of Form, Paleobiology, vol.8, issue.1, pp.4-15, 1982. ,
An integrated view of protein evolution, Nat Rev Genet, vol.7, p.16619049, 2006. ,
Evolution and tinkering, Science, vol.196, issue.4295, p.860134, 1977. ,
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, issue.6784, p.10830951, 2000. ,
Horizontal gene transfer, genome innovation and evolution, Nat Rev Microbiol, vol.3, issue.9, p.16138096, 2005. ,
Horizontal gene transfer accelerates genome innovation and evolution, Mol Biol Evol, vol.20, issue.10, p.12777514, 2003. ,
Adaptive evolution of complex innovations through stepwise metabolic niche expansion, Nat Commun, vol.7, p.27197754, 2016. ,
The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems, PLoS Genet, vol.8, issue.9, p.23028376, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374947
Evolution of conjugation and type IV secretion systems, Mol Biol Evol, vol.30, issue.2, p.22977114, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374951
The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system, Proc Natl Acad Sci U S A, vol.106, issue.11, p.19251647, 2009. ,
Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin, Proc Natl Acad Sci U S A, vol.106, issue.11, p.19251641, 2009. ,
Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella, Microbiology, vol.149, p.14600218, 2003. ,
The archaellum: an old motility structure with a new name, Trends Microbiol, vol.20, issue.7, p.22613456, 2012. ,
Exceptionally widespread nanomachines composed of type IV pilins: the prokaryotic Swiss Army knives, FEMS Microbiol Rev, vol.39, issue.1, p.25793961, 2015. ,
Recent progress in structure and dynamics of dual-membrane-spanning bacterial nanomachines, Curr Opin Struct Biol, vol.39, p.26995496, 2016. ,
The type II secretion system: biogenesis, molecular architecture and mechanism, Nat Rev Microbiol, vol.10, issue.5, p.22466878, 2012. ,
Identification of protein secretion systems in bacterial genomes, Sci Rep, vol.6, p.26979785, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01677379
Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification, Proc Natl Acad Sci U S A, vol.98, issue.5, p.11226268, 2001. ,
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging, Nucleic Acids Res, vol.32, issue.17, p.15466593, 2004. ,
Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure, BMC Evol Biol, vol.7, p.17605801, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00698404
Obstruction of pilus retraction stimulates bacterial surface sensing, Science, vol.358, issue.6362, p.29074778, 2017. ,
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS ONE, vol.9, issue.10, p.25330359, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, Methods Mol Biol, vol.1615, p.28667599, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01677379
Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, p.15531603, 2005. ,
Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization, Mol Microbiol, vol.83, issue.4, p.22211578, 2012. ,
The product of tadZ, a new member of the parA/minD superfamily, Aggregatibacter actinomycetemcomitans ,
, Mol Microbiol, vol.83, issue.4, p.22239271, 2012.
Product of the Pseudomonas aeruginosa gene pilD is a prepilin leader peptidase, Proc Natl Acad Sci U S A, vol.88, issue.8, p.1901657, 1991. ,
Cloning of an Aeromonas hydrophila type IV pilus biogenesis gene cluster: complementation of pilus assembly functions and characterization of a type IV leader peptidase/N-methyltransferase required for extracellular protein secretion, Mol Microbiol, vol.19, issue.4, p.8820654, 1996. ,
Identification of the Vibrio cholerae type 4 prepilin peptidase required for cholera toxin secretion and pilus formation, Mol Microbiol, vol.29, issue.6, p.9781884, 1998. ,
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, issue.1, p.25371430, 2015. ,
The Escherichia coli DNA translocase FtsK, Biochem Soc Trans, vol.38, issue.2, p.20298190, 2010. ,
Co-evolution of segregation guide DNA motifs and the FtsK translocase in bacteria: identification of the atypical Lactococcus lactis KOPS motif, Nucleic Acids Res, vol.40, issue.12, p.22373923, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01003421
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes, Proc Natl Acad Sci U S A, vol.86, issue.23, p.2531898, 1989. ,
Evolution of the vacuolar H +-ATPase: implications for the origin of eukaryotes, Proc Natl Acad Sci U S A, vol.86, issue.17, p.2528146, 1989. ,
Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria, PLoS ONE, vol.6, issue.12, p.22216142, 2011. ,
A Putative Type II Secretion System Is Involved in Cellulose Utilization in Cytophaga hutchisonii, Front Microbiol, vol.8, p.28848505, 2017. ,
Extracellular proteome analysis of Leptospira interrogans serovar Lai, OMICS, vol.17, issue.10, p.23895271, 2013. ,
Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches, Proc Natl Acad Sci, vol.109, issue.4, p.22232666, 2012. ,
Origin and fate of repeats in bacteria, Nucleic Acids Res, vol.30, issue.13, p.12087185, 2002. ,
The Widespread Colonization Island of Actinobacillus actinomycetemcomitans, Nat Genet, vol.34, issue.2, p.12717435, 2003. ,
Selfish operons: horizontal transfer may drive the evolution of gene clusters, Genetics, vol.143, issue.4, 1996. ,
The Pfam protein families database in 2019, Nucleic Acids Res, vol.47, issue.D1, p.30357350, 2019. ,
Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase, Proc Natl Acad Sci U S A, vol.101, issue.1, p.14684831, 2004. ,
Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli, Mol Microbiol, vol.111, issue.3, p.30561149, 2019. ,
Pseudopilin residue E5 is essential for recruitment by the type 2 secretion system assembly platform, Mol Microbiol, vol.101, issue.6, p.27260845, 2016. ,
Reconstitution of a minimal machinery capable of assembling periplasmic type IV pili, Proc Natl Acad Sci, vol.114, issue.25, p.28588140, 2017. ,
The two-domain tree of life is linked to a new root for the Archaea, Proc Natl Acad Sci, vol.112, issue.21, p.25964353, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02018983
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor, Proc Natl Acad Sci U S A, vol.108, issue.27, p.21690406, 2011. ,
Genetic analysis of a type IV pili-like locus in the archaeon Methanococcus maripaludis, Arch Microbiol, vol.196, issue.3, p.24493292, 2014. ,
Outer membrane components of the Tad (tight adherence) secreton of Aggregatibacter actinomycetemcomitans, J Bacteriol, vol.190, issue.3, p.18055598, 2008. ,
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes, Elife, vol.5, p.27580370, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01362343
A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, J Bacteriol, vol.194, issue.18, p.22773793, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374952
A bifunctional ATPase drives tad pilus extension and retraction ,
Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae, Nat Microbiol, vol.3, issue.7, p.29891864, 2018. ,
DNA-uptake machinery of naturally competent Vibrio cholerae, Proc Natl Acad Sci U S A, vol.110, issue.44, p.24127573, 2013. ,
A type IV pilus mediates DNA binding during natural transformation in Streptococcus pneumoniae, PLoS Pathog, vol.9, issue.6, p.23825953, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00947054
Biological roles of nontypeable Haemophilus influenzae type IV pilus proteins encoded by the pil and com operons, J Bacteriol, vol.194, issue.8, p.22328674, 2012. ,
Archaeal type IV pili and their involvement in biofilm formation, Front Microbiol, vol.6, p.25852657, 2015. ,
Pseudomonas aeruginosa orchestrates twitching motility by sequential control of type IV pili movements, Nat Microbiol, vol.4, issue.5, p.30804544, 2019. ,
The archaeal Ced system imports DNA, Proc Natl Acad Sci, vol.113, issue.9, p.26884154, 2016. ,
UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation, Mol Microbiol, vol.70, issue.4, p.18990182, 2008. ,
Novel Flp pilus biogenesisdependent natural transformation, Front Microbiol, vol.6, p.25713572, 2015. ,
Evolution of the Natural Transformation Protein, ComEC, in Bacteria. Front Microbiol, vol.9, p.30627116, 2018. ,
Bacterial "competence" genes: signatures of active transformation, or only remnants?, Trends in Microbiology, vol.11, issue.4, p.12706993, 2003. ,
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res, vol.42, issue.16, p.25120263, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374960
Sxy induces a CRP-S regulon in Escherichia coli, J Bacteriol, vol.191, issue.16, p.19502395, 2009. ,
Natural DNA uptake by Escherichia coli, PLoS ONE, vol.7, issue.4, p.22532864, 2012. ,
The structure of PilA from Acinetobacter baumannii AB5075 suggests a mechanism for functional specialization in Acinetobacter type IV pili, J Biol Chem, vol.294, issue.1, p.30413536, 2019. ,
Specific DNA recognition mediated by a type IV pilin, Proc Natl Acad Sci U S A, vol.110, issue.8, p.23386723, 2013. ,
Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli, PLoS Biol, vol.5, issue.9, p.17713986, 2007. ,
The evolution of gene clusters and genetic circularity in microorganisms, Genetics, vol.53, issue.3, p.5331527, 1966. ,
ComEA is a DNA receptor for transformation of competent Bacillus subtilis, Mol Microbiol, vol.31, issue.1, p.9987128, 1999. ,
Pseudomonas aeruginosa twitching motility: type IV pili in action, Annu Rev Microbiol, vol.66, p.22746331, 2012. ,
Type IV pili: paradoxes in form and function, Curr Opin Struct Biol, vol.18, issue.2, p.18249533, 2008. ,
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles, vol.18, p.25113822, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01977394
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, issue.4, p.23329690, 2013. ,
Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol Biol, vol.10, p.20626897, 2010. ,
HMMER web server: interactive sequence similarity searching, Nucleic Acids Res, vol.39, p.21593126, 2011. ,
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, p.421, 2009. ,
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, p.21513511, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00698365
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol Biol Evol, vol.27, issue.2, pp.221-225, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511794
Accelerated Profile HMM Searches, PLoS Comput Biol, vol.7, issue.10, p.22039361, 2011. ,
Noisy: identification of problematic columns in multiple sequence alignments, Algorithms Mol Biol, vol.3, p.18577231, 2008. ,
UFBoot2: Improving the Ultrafast Bootstrap Approximation, Mol Biol Evol, vol.35, issue.2, p.29077904, 2018. ,
ModelFinder: fast model selection for accurate phylogenetic estimates, Nat Methods, vol.14, issue.6, p.28481363, 2017. ,
RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res, vol.35, issue.9, p.17452365, 2007. ,
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, p.19505945, 2009. ,
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol Biol Evol, vol.14, issue.7, p.9254330, 1997. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00730410
An approximately unbiased test of phylogenetic tree selection, Syst Biol, vol.51, issue.3, p.12079646, 2002. ,
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philos Trans R Soc Lond B Biol Sci, vol.370, p.26323765, 1678. ,
URL : https://hal.archives-ouvertes.fr/hal-01218565