Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

[1]  H. Ochman,et al.  The Evolution of Bacterial Genome Architecture , 2017, Front. Genet..

[2]  J. Gallie,et al.  Identification and Characterization of Domesticated Bacterial Transposases , 2017, bioRxiv.

[3]  M. Chandler,et al.  Single strand transposition at the host replication fork , 2016, Nucleic acids research.

[4]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[5]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[6]  K. Rudd,et al.  A role for REP sequences in regulating translation. , 2015, Molecular cell.

[7]  J. E. Peters,et al.  Vulnerabilities on the lagging-strand template: opportunities for mobile elements. , 2014, Annual review of genetics.

[8]  F. J. López de Saro,et al.  Chromosomal Replication Dynamics and Interaction with the β Sliding Clamp Determine Orientation of Bacterial Transposable Elements , 2014, Genome biology and evolution.

[9]  P. Siguier,et al.  Bacterial insertion sequences: their genomic impact and diversity , 2014, FEMS microbiology reviews.

[10]  E. De Gregorio,et al.  GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes , 2013, BMC Genomics.

[11]  F. Dyda,et al.  Breaking and joining single-stranded DNA: the HUH endonuclease superfamily , 2013, Nature Reviews Microbiology.

[12]  B. Schneider,et al.  Evolution of REP diversity: a comparative study , 2013, BMC Genomics.

[13]  P. Siguier,et al.  ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB , 2013, Molecular microbiology.

[14]  P. Siguier,et al.  IS200/IS605 family single-strand transposition: mechanism of IS608 strand transfer , 2013, Nucleic acids research.

[15]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[16]  R. Ghirlando,et al.  The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease , 2012, Nucleic acids research.

[17]  Young Cheol Kim,et al.  Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions , 2012, PLoS genetics.

[18]  O. Zhaxybayeva,et al.  Gene transfer agents: phage-like elements of genetic exchange , 2012, Nature Reviews Microbiology.

[19]  S. Sandler,et al.  Mu Insertions Are Repaired by the Double-Strand Break Repair Pathway of Escherichia coli , 2012, PLoS genetics.

[20]  G. Fichant,et al.  Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences† , 2011, Nucleic acids research.

[21]  P. Rainey,et al.  Curiosities of REPINs and RAYTs , 2011, Mobile genetic elements.

[22]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[23]  F. Dyda,et al.  Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing , 2011, Nucleic acids research.

[24]  P. Rainey,et al.  Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria , 2011, PLoS genetics.

[25]  Fred Dyda,et al.  DNA recognition and the precleavage state during single‐stranded DNA transposition in D. radiodurans , 2010, The EMBO journal.

[26]  P. Siguier,et al.  Single-Stranded DNA Transposition Is Coupled to Host Replication , 2010, Cell.

[27]  E. De Gregorio,et al.  A giant family of short palindromic sequences in Stenotrophomonas maltophilia. , 2010, FEMS microbiology letters.

[28]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[29]  J. Nunvář,et al.  Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes , 2010, BMC Genomics.

[30]  M. Chandler,et al.  Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence , 2010, PLoS genetics.

[31]  J. E. Peters,et al.  Transposition into Replicating DNA Occurs through Interaction with the Processivity Factor , 2009, Cell.

[32]  F. Dyda,et al.  Resetting the site: redirecting integration of an insertion sequence in a predictable way. , 2009, Molecular cell.

[33]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[34]  Torsten Schwede,et al.  Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective , 2009, Electrophoresis.

[35]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[36]  Georgios S. Vernikos,et al.  Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens , 2009, Genome Biology.

[37]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[38]  A. Danchin,et al.  Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths , 2009, PLoS genetics.

[39]  Sebastian Will,et al.  RNAalifold: improved consensus structure prediction for RNA alignments , 2008, BMC Bioinformatics.

[40]  F. Dyda,et al.  In vitro reconstitution of a single-stranded transposition mechanism of IS608. , 2008, Molecular cell.

[41]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[42]  F. Dyda,et al.  Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection , 2008, Cell.

[43]  Patricia Siguier,et al.  ISfinder: the reference centre for bacterial insertion sequences , 2005, Nucleic Acids Res..

[44]  R. Ghirlando,et al.  Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. , 2005, Molecular cell.

[45]  David Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[46]  E. Pareja,et al.  Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation. , 2005, Research in microbiology.

[47]  Matt Nolan,et al.  Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  C. Loot,et al.  IS911 partial transposition products and their processing by the Escherichia coli RecG helicase , 2004, Molecular microbiology.

[49]  C. von Eichel-Streiber,et al.  The IStron CdISt1 of Clostridium difficile: molecular symbiosis of a group I intron and an insertion element. , 2004, Anaerobe.

[50]  S. Bell Faculty Opinions recommendation of Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. , 2003 .

[51]  A. J. Carpousis,et al.  The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP‐stabilizers , 2003, Molecular microbiology.

[52]  M. O’Donnell,et al.  Competitive processivity‐clamp usage by DNA polymerases during DNA replication and repair , 2003, The EMBO journal.

[53]  Laurence H Pearl,et al.  Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the β‐clamp , 2003, The EMBO journal.

[54]  J. Lawrence,et al.  Lateral gene transfer: when will adolescence end? , 2003, Molecular microbiology.

[55]  Keith M. Derbyshire,et al.  The outs and ins of transposition: from Mu to Kangaroo , 2003, Nature Reviews Molecular Cell Biology.

[56]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[57]  R. Kotin,et al.  Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep. , 2002, Molecular cell.

[58]  J. Ramos,et al.  Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. , 2002, Nucleic acids research.

[59]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[60]  D. Ecker,et al.  RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.

[61]  B. Dalrymple,et al.  A universal protein–protein interaction motif in the eubacterial DNA replication and repair systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[62]  R. Page,et al.  Trees within trees: phylogeny and historical associations. , 1998, Trends in ecology & evolution.

[63]  Sean R. Eddy,et al.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .

[64]  O. Espéli,et al.  In vivo cleavage of Escherichia coli BIME‐2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site , 1997, Molecular microbiology.

[65]  R. Durbin,et al.  Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.

[66]  W. Messer,et al.  Interaction of the Initiator Protein DnaA of Escherichia coli with Its DNA Target (*) , 1995, The Journal of Biological Chemistry.

[67]  E. Gilson,et al.  Structural and functional diversity among bacterial interspersed mosaic elements (BIMEs) , 1994, Molecular microbiology.

[68]  F. Boccard,et al.  Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units. , 1993, The EMBO journal.

[69]  D. Haussler,et al.  Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.

[70]  Eugene V. Koonin,et al.  Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria , 1992, Nucleic Acids Res..

[71]  D. Lilley,et al.  DNA replication, 2nd edn , 1992 .

[72]  Eric Gilson,et al.  DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization , 1990, Nucleic Acids Res..

[73]  C. Higgins,et al.  Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review. , 1988, Gene.

[74]  E. Gilson,et al.  A subfamily of E. coli palindromic units implicated in transcription termination? , 1986, Annales de l'Institut Pasteur. Microbiology.

[75]  B. Marrs Genetic recombination in Rhodopseudomonas capsulata. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[76]  J. Lederberg,et al.  GENETIC EXCHANGE IN SALMONELLA , 1952, Journal of bacteriology.

[77]  G. Lumb,et al.  Hypoplasia of the exocrine tissue of the pancreas. , 1952, The Journal of pathology and bacteriology.

[78]  J. Lederberg,et al.  Gene Recombination in Escherichia Coli , 1946, Nature.

[79]  F. Griffith The Significance of Pneumococcal Types , 1928, Journal of Hygiene.

[80]  P. Siguier,et al.  The IS200/IS605 Family and “Peel and Paste” Single-strand Transposition Mechanism , 2015, Microbiology spectrum.

[81]  P. Siguier,et al.  Everyman's Guide to Bacterial Insertion Sequences , 2015, Microbiology spectrum.

[82]  Antoine M. van Oijen,et al.  Replication-fork dynamics. , 2014, Cold Spring Harbor perspectives in biology.

[83]  P. Siguier,et al.  Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments. , 2012, Methods in molecular biology.

[84]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[85]  F. Dyda,et al.  IS 1469 MDTNSLAHTK WNCKYHIVFA PKHRRKEIYG EKKQEISEIL RQLCELKGVR IVEAHACVDH IHMLVEIPPK IS 200 S MDTNSLAHTK WNCKYHIVFA PKHRRKEIYG EKKQEISEIL RQLCEWKGVR IVEAHACVDH IHMLVEIPPK IS 1004 GDYRSSSHVY WRCKYHIVWT PKFRFKILKG NVAKELNRSI YILCNMKDCE VLELNVQPDH VHLVAIIPPK IS 606 DDMRHGRHCV FLMHTHLVFV TKYRRKAFNK EVID , 2005 .

[86]  Jeremy Fairbank,et al.  Historical Perspective , 1987, Do We Really Understand Quantum Mechanics?.

[87]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[88]  M. Chandler,et al.  Insertion Sequences , 1998, Microbiology and Molecular Biology Reviews.

[89]  E. Koonin,et al.  Computer-assisted dissection of rolling circle DNA replication. , 1993, Bio Systems.

[90]  M. Gefter,et al.  DNA Replication , 2019, Advances in Experimental Medicine and Biology.