Prokaryote Genome Fluidity: Toward a System Approach of the Mobilome (original) (raw)
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. (2005) The microbial pan-genome. Curr Opin Genet Dev, 15:589–594. ArticlePubMedCAS Google Scholar
Bapteste E, O’Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupre J, Dagan T, Boucher Y, Martin W. (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct, 4:34. ArticlePubMed Google Scholar
Baquero F. (2009) Environmental stress and evolvability in microbial systems. Clin Microbiol Infect, 15(Suppl. 1):5–10. ArticlePubMed Google Scholar
Nagata Y, Endo R, Ito M, Ohtsubo Y, Tsuda M. (2007) Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Appl Microbiol Biotechnol, 76:741–752. ArticlePubMedCAS Google Scholar
Wackett LP, Sadowsky MJ, Martinez B, Shapir N. (2002) Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Appl Microbiol Biotechnol, 58:39–45. ArticlePubMedCAS Google Scholar
Frost LS, Leplae R, Summers AO, Toussaint A. (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol, 3:722–732. ArticlePubMedCAS Google Scholar
Langille MG, Hsiao WW, Brinkman FS. (2008) Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics, 9:329. ArticlePubMed Google Scholar
Arvey AJ, Azad RK, Raval A, Lawrence JG. (2009) Detection of genomic islands via segmental genome heterogeneity. Nucleic Acids Res, 37:5255–5266. ArticlePubMedCAS Google Scholar
Matic I, Taddei F, Radman M. (1996) Genetic barriers among bacteria. Trends Microbiol, 4:69–72. ArticlePubMedCAS Google Scholar
Saavedra De Bast M, Mine N, Van Melderen L. (2008) Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J Bacteriol, 190:4603–4609. ArticlePubMed Google Scholar
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315:1709–1712. ArticlePubMedCAS Google Scholar
Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF. (2008) A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem, 283:20361–20371. ArticlePubMedCAS Google Scholar
Marraffini LA, Sontheimer EJ. (2010) Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature, 463:568–571. ArticlePubMedCAS Google Scholar
Nekrasov SV, Agafonova OV, Belogurova NG, Delver EP, Belogurov AA. (2007) Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system. J Mol Biol, 365:284–297. ArticlePubMedCAS Google Scholar
Toussaint A, Merlin C. (2002) Mobile elements as a combination of functional modules. Plasmid, 47:26–35. ArticlePubMedCAS Google Scholar
Thomas CM. (2000) The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread. Harwood Academic Publishers, Amsterdam. Book Google Scholar
Merlin C, Mahillon J, Nesvera J, Toussaint A. (2000) Gene Recruiters and Transporters: The Modular Structure of Bacterial Mobile Elements. In The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread. Edited by Thomas CM, Harwood Academic Publishers, Amsterdam, 363–409. Google Scholar
Avery OT, Macleod CM, McCarty M. (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type Iii. J Exp Med, 79:137–158. ArticlePubMedCAS Google Scholar
Kovacs AT, Smits WK, Mironczuk AM, Kuipers OP. (2009) Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Environ Microbiol, 11:1911–1922. ArticlePubMedCAS Google Scholar
Averhoff B. (2009) Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus. FEMS Microbiol Rev, 33:611–626. ArticlePubMedCAS Google Scholar
Claverys JP, Martin B, Polard P. (2009) The genetic transformation machinery: composition, localization, and mechanism. FEMS Microbiol Rev, 33:643–656. ArticlePubMedCAS Google Scholar
Alvarez-Martinez CE, Christie PJ. (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev, 73:775–808. ArticlePubMedCAS Google Scholar
Hamilton HL, Dillard JP. (2006) Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination. Mol Microbiol, 59:376–385. ArticlePubMedCAS Google Scholar
Rohwer F, Thurber RV. (2009) Viruses manipulate the marine environment. Nature, 459:207–212. ArticlePubMedCAS Google Scholar
de la Cruz F, Frost LS, Meyer RJ, Zechner EL. (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev, 34:18–40. ArticlePubMed Google Scholar
Abajy MY, Kopec J, Schiwon K, Burzynski M, Doring M, Bohn C, Grohmann E. (2007) A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in gram-positive bacteria. J Bacteriol, 189:2487–2496. ArticlePubMedCAS Google Scholar
Ong CL, Beatson SA, McEwan AG, Schembri MA. (2009) Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl Environ Microbiol, 75:6783–6791. ArticlePubMedCAS Google Scholar
Weinbauer MG, Rassoulzadegan F. (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol, 6:1–11. ArticlePubMed Google Scholar
Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasic L, Thingstad TF, Rohwer F, Mira A. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol, 7:828–836. ArticlePubMedCAS Google Scholar
Garcillan-Barcia MP, Francia MV, de la Cruz F. (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev, 33:657–687. ArticlePubMedCAS Google Scholar
Ravin NV. (2003) Mechanisms of replication and telomere resolution of the linear plasmid prophage N15. FEMS Microbiol Lett, 221:1–6. ArticlePubMedCAS Google Scholar
Baker S, Hardy J, Sanderson KE, Quail M, Goodhead I, Kingsley RA, Parkhill J, Stocker B, Dougan G. (2007) A novel linear plasmid mediates flagellar variation in Salmonella typhi. PLoS Pathog, 3:e59. Google Scholar
Bentley SD, Brown S, Murphy LD, Harris DE, Quail MA, Parkhill J, Barrell BG, McCormick JR, Santamaria RI, Losick R, Yamasaki M, Kinashi H, Chen CW, Chandra G, Jakimowicz D, Kieser HM, Kieser T, Chater KF. (2004) SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol Microbiol, 51:1615–1628. ArticlePubMedCAS Google Scholar
Huang CH, Chen CY, Tsai HH, Chen C, Lin YS, Chen CW. (2003) Linear plasmid SLP of Streptomyces lividans is a composite replicon. Mol Microbiol, 47:1563–1576. ArticlePubMedCAS Google Scholar
Craig NL, Craigie R, Gellert M, Lambowitz AM. (2003) Mobile DNA II. ASM Press, Washington, DC. Google Scholar
Martinsohn JT, Radman M, Petit MA. (2008) The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet, 4:e1000065. ArticlePubMed Google Scholar
Leplae R, Lima-Mendez G, Toussaint A. (2006) A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol Rev, 30:980–994. ArticlePubMedCAS Google Scholar
Austin S, Ziese M, Sternberg N. (1981) A novel role for site-specific recombination in maintenance of bacterial replicons. Cell, 25:729–736. ArticlePubMedCAS Google Scholar
Toro N, Jimenez-Zurdo JI, Garcia-Rodriguez FM. (2007) Bacterial group II introns: not just splicing. FEMS Microbiol Rev, 31:342–358. ArticlePubMedCAS Google Scholar
Shapiro JA. (1979) Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci U S A, 76:1933–1937. ArticlePubMedCAS Google Scholar
Symonds N, Toussaint A, van de Putte P, Howe MM. (1987) Phage Mu. Cold Spring Harbor Laboratory Press, New York. Google Scholar
Guynet C, Hickman AB, Barabas O, Dyda F, Chandler M, Ton-Hoang B. (2008) In vitro reconstitution of a single-stranded transposition mechanism of IS608. Mol Cell, 29:302–312. ArticlePubMedCAS Google Scholar
Ton-Hoang, B., Pasternak, C., Siguier, P., Guynet, C., Hickman, AB., Dyda, F., Sommer, S., and Chandler, M. (2010) Cell 142(3), 398–408. PMID 069190 Google Scholar
Ehrlich SD, Bierne H, d’Alencon E, Vilette D, Petranovic M, Noirot P, Michel B. (1993) Mechanisms of illegitimate recombination. Gene, 135:161–166. Google Scholar
Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M. (2006) Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol, 60:1136–1151. ArticlePubMedCAS Google Scholar
Koonin EV, Wolf YI. (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res, 36:6688–6719. ArticlePubMedCAS Google Scholar
Smith MC, Thorpe HM. (2002) Diversity in the serine recombinases. Mol Microbiol, 44:299–307. ArticlePubMedCAS Google Scholar
Hallet B, Sherratt DJ. (1997) Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol Rev, 21:157–178. ArticlePubMedCAS Google Scholar
Rice P, Craigie R, Davies DR. (1996) Retroviral integrases and their cousins. Curr Opin Struct Biol, 6:76–83. ArticlePubMedCAS Google Scholar
Rajeev L, Malanowska K, Gardner JF. (2009) Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbiol Mol Biol Rev, 73:300–309. ArticlePubMedCAS Google Scholar
Consortium GO. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res, 38:D331–D335. Article Google Scholar
Toussaint A, Lima-Mendez G, Leplae R. (2007) PhiGO, a phage ontology associated with the ACLAME database. Res Microbiol, 158(7):567–571. ArticlePubMedCAS Google Scholar
Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y. (2009) ACID: annotation of cassette and integron data. BMC Bioinformatics, 10:118. ArticlePubMed Google Scholar
Reiter WD, Palm P, Yeats S. (1989) Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res, 17:1907–1914. ArticlePubMedCAS Google Scholar
Mantri Y, Williams KP. (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res, 32(Database issue):D55–D58. Google Scholar
Langille MG, Brinkman FS. (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics, 25:664–665. ArticlePubMedCAS Google Scholar
Fouts DE. (2006) Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res, 34(20):5839–5851. ArticlePubMedCAS Google Scholar
Bose M, Barber RD. (2006) Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol, 6:0020. Google Scholar
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. (2008) Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics, 24:863–865. ArticlePubMedCAS Google Scholar
Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D. (2003) Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res, 13:428–442. ArticlePubMedCAS Google Scholar
Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, Rajakumar K. (2007) MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res, 35:W97–W104. ArticlePubMed Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res, 14:1394–1403. ArticlePubMedCAS Google Scholar
Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit MA, El Karoui M. (2005) Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics, 6:171. ArticlePubMedCAS Google Scholar
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res, 34:D32–D36. ArticlePubMedCAS Google Scholar
Kichenaradja P, Siguier P, Perochon J, Chandler M. (2010) ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res, 38:D62–D68. ArticlePubMedCAS Google Scholar
Cortez D, Forterre P, Gribaldo S. (2009) A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol, 10:R65. ArticlePubMed Google Scholar
Hacker J, Hochhut B, Middendorf B, Schneider G, Buchrieser C, Gottschalk G, Dobrindt U. (2004) Pathogenomics of mobile genetic elements of toxigenic bacteria. Int J Med Microbiol, 293:453–461. ArticlePubMedCAS Google Scholar
Ikeda H, Tomizawa J. (1968) Prophage P1, and extrachromosomal replication unit. Cold Spring Harb Symp Quant Biol, 33:791–798. PubMedCAS Google Scholar
Rybchin VN, Svarchevsky AN. (1999) The plasmid prophage N15: a linear DNA with covalently closed ends. Mol Microbiol, 33:895–903. ArticlePubMedCAS Google Scholar
Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D. (2003) The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol, 69:4837–4845. ArticlePubMedCAS Google Scholar
Brochet M, Da Cunha V, Couve E, Rusniok C, Trieu-Cuot P, Glaser P. (2009) Atypical association of DDE transposition with conjugation specifies a new family of mobile elements. Mol Microbiol, 71:948–959. ArticlePubMedCAS Google Scholar
Novick RP, Subedi A. (2007) The SaPIs: mobile pathogenicity islands of Staphylococcus. Chem Immunol Allergy, 93:42–57. ArticlePubMedCAS Google Scholar
Siguier P, Filee J, Chandler M. (2006) Insertion sequences in prokaryotic genomes. Curr Opin Microbiol, 9:526–531. ArticlePubMedCAS Google Scholar
Thieffry D, Thomas R. (1995) Dynamical behaviour of biological regulatory networks – II. Immunity control in bacteriophage lambda. Bull Math Biol, 57:277–297. CAS Google Scholar
Su S, Khan SR, Farrand SK. (2008) Induction and loss of Ti plasmid conjugative competence in response to the acyl-homoserine lactone quorum-sensing signal. J Bacteriol, 190:4398–4407. ArticlePubMedCAS Google Scholar
McLeod SM, Burrus V, Waldor MK. (2006) Requirement for Vibrio cholerae integration host factor in conjugative DNA transfer. J Bacteriol, 188:5704–5711. ArticlePubMedCAS Google Scholar
Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbe J, Ploy MC, Mazel D. (2009) The SOS response controls integron recombination. Science, 324:1034. ArticlePubMedCAS Google Scholar
Dorman CJ. (2009) Nucleoid-associated proteins and bacterial physiology. Adv Appl Microbiol, 67:47–64. ArticlePubMedCAS Google Scholar
Gamas P, Caro L, Galas D, Chandler M. (1987) Expression of F transfer functions depends on the Escherichia coli integration host factor. Mol Gen Genet, 207:302–305. ArticlePubMedCAS Google Scholar
Nagy Z, Chandler M. (2004) Regulation of transposition in bacteria. Res Microbiol, 155:387–398. ArticlePubMedCAS Google Scholar
Hendrix RW, Lawrence JG, Hatfull GF, Casjens S. (2000) The origins and ongoing evolution of viruses. Trends Microbiol, 8:504–508. ArticlePubMedCAS Google Scholar
Lawrence JG, Hatfull GF, Hendrix RW. (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol, 184:4891–4905. ArticlePubMedCAS Google Scholar
Doolittle WF. (1999) Phylogenetic classification and the universal tree. Science, 284:2124–2129. ArticlePubMedCAS Google Scholar
Gogarten JP, Doolittle WF, Lawrence JG. (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol, 19:2226–2238. ArticlePubMedCAS Google Scholar
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol, 25:762–777. ArticlePubMedCAS Google Scholar
Leplae R, Lima-Mendez G, Toussaint A. (2010) ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res, 38:D57–D61. ArticlePubMedCAS Google Scholar
Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E. (2010) Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A, 107:127–132. ArticlePubMedCAS Google Scholar
Kay E, Chabrillat G, Vogel TM, Simonet P. (2003) Intergeneric transfer of chromosomal and conjugative plasmid genes between Ralstonia solanacearum and Acinetobacter sp. BD413. Mol Plant Microbe Interact, 16:74–82. Google Scholar
Molin S, Tolker-Nielsen T. (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr Opin Biotechnol, 14:255–261. ArticlePubMedCAS Google Scholar
Curcio MJ, Derbyshire KM. (2003) The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol, 4:865–877. ArticlePubMedCAS Google Scholar
May EW, Craig NL. (1996) Switching from cut-and-paste to replicative Tn7 transposition. Science, 272:401–404. ArticlePubMedCAS Google Scholar
Juhas M, Power PM, Harding RM, Ferguson DJ, Dimopoulou ID, Elamin AR, Mohd-Zain Z, Hood DW, Adegbola R, Erwin A, Smith A, Munson RS, Harrison A, Mansfield L, Bentley S, Crook DW. (2007) Sequence and functional analyses of Haemophilus spp. genomic islands. Genome Biol, 8:R237. Google Scholar
Bouvier M, Demarre G, Mazel D. (2005) Integron cassette insertion: a recombination process involving a folded single strand substrate. EMBO J, 24:4356–4367. ArticlePubMedCAS Google Scholar
Lang AS, Beatty JT. (2007) Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol, 15:54–62. ArticlePubMedCAS Google Scholar
Polard P, Ton-Hoang B, Haren L, Betermier M, Walczak R, Chandler M. (1996) IS911-mediated transpositional recombination in vitro. J Mol Biol, 264:68–81. ArticlePubMedCAS Google Scholar
Duval-Valentin G, Marty-Cointin B, Chandler M. (2004) Requirement of IS911 replication before integration defines a new bacterial transposition pathway. EMBO J, 23:3897–3906. ArticlePubMedCAS Google Scholar