How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions - Extremophiles
- ️Albers, Sonja-Verena
- ️Tue May 28 2013
Aagaard C, Dalgaard JZ, Garrett RA (1995) Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius. Proc Natl Acad Sci USA 92:12285–12289
Ackermann HW (1996) Frequency of morphological phage descriptions in 1995. Arch Virol 141:209–218
Ackermann HW (2001) Frequency of morphological phage descriptions in the year 2000. Brief review. Arch Virol 146:843–857
Ackermann HW (2007) 5500 Phages examined in the electron microscope. Arch Virol 152:227–243
Ackermann HW, Prangishvili D (2012) Prokaryote viruses studied by electron microscopy. Arch Virol 157:1843–1849
Ajon M, Fröls S, van Wolferen M et al (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol 82:807–817
Alvarez L, Bricio C, Gómez MJ, Berenguer J (2011) Lateral transfer of the denitrification pathway genes among Thermus thermophilus strains. Appl Environ Microbiol 77:1352–1358
Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808
Anderson AW, Nordon HC, Cain RF et al (1956) Studies on a radio-resistant micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation. Food Technol 10:575–578
Aravind L, Tatusov RL, Wolf YI et al (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet 14:442–444
Arnold HP, She Q, Phan H et al (1999) The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol Microbiol 34:217–226
Assalkhou R, Balasingham S, Collins RF et al (2007) The outer membrane secretin PilQ from Neisseria meningitidis binds DNA. Microbiology 153:1593–1603
Atomi H, Matsumi R, Imanaka T (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol 186:4829–4833
Averhoff B (2009) Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilus. FEMS Microbiol Rev 33:611–626
Averhoff B, Friedrich A (2003) Type IV pili-related natural transformation systems: DNA transport in mesophilic and thermophilic bacteria. Arch Microbiol 180:385–393
Averhoff B, Müller V (2010) Exploring research frontiers in microbiology: recent advances in halophilic and thermophilic extremophiles. Res Microbiol 161:506–514
Ayora S, Carrasco B, Cárdenas PP et al (2011) Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev 35:1055–1081
Basen M, Sun J, Adams MWW (2012) Engineering a hyperthermophilic archaeon for temperature-dependent product formation. mBio 3:e00053–12
Basta T, Smyth J, Forterre P et al (2009) Novel archaeal plasmid pAH1 and its interactions with the lipothrixvirus AFV1. Mol Microbiol 71:23–34
Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332–14337
Bernstein H, Byers G, Michod R (1981) Evolution of sexual reproduction: importance of DNA repair, complementation, and variation. Am Nat 117:537–549
Bernstein H, Bernstein C, Michod RE (2012) DNA repair as the primary adaptive function of sex in bacteria and eukaryotes. In: Kimura S et al (eds) DNA repair: new research, Nova Science Publishers Inc, pp 1–49. ISBN: 978-1-62100-756-2
Bertani G, Baresi L (1987) Genetic transformation in the methanogen Methanococcus voltae PS. J Bacteriol 169:2730–2738
Bolduc B, Shaughnessy DP, Wolf YI et al (2012) Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 86:5562–5573
Bordenstein SR, Reznikoff WS (2005) Mobile DNA in obligate intracellular bacteria. Nat Rev Microbiol 3:688–699
Bricio C, Alvarez L, Gómez MJ, Berenguer J (2011) Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts. Biochem Soc Trans 39:249–253
Brochier-Armanet C, Forterre P (2007) Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2:83–93
Brock TD, Brock KM, Belly RT, Weiss RL (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84:54–68
Brüggemann H, Chen C (2006) Comparative genomics of Thermus thermophilus: plasticity of the megaplasmid and its contribution to a thermophilic lifestyle. J Bacteriol 124:654–661. doi:10.1016/j.jbiotec.2006.03.043
Brüssow H, Canchaya C, Hardt W-D (2004) Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68:560–602
Burkhardt J, Vonck J, Averhoff B (2011) Structure and function of PilQ, a secretin of the DNA transporter from the thermophilic bacterium Thermus thermophilus HB27. J Biol Chem 286:9977–9984
Burkhardt J, Vonck J, Langer JD et al (2012) Unusual N-terminal ααβαββα fold of PilQ from Thermus thermophilus mediates ring formation and is essential for piliation. J Biol Chem 287:8484–8494
Cadillo-Quiroz H, Didelot X, Held NL et al (2012) Patterns of gene flow define species of thermophilic Archaea. PLoS Biol 10:e1001265
Campbell BJ, Smith JL, Hanson TE et al (2009) Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 5:e1000362
Canchaya C, Fournous G, Chibani-Chennoufi S et al (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6:417–424
Capasso G, Favara R, Francofonte S, Inguaggiato S (1999) Chemical and isotopic variations in fumarolic discharge and thermal waters at Vulcano Island (Aeolian Islands, Italy) during 1996: evidence of resumed volcanic activity. J Volcanol Geoth Res 88:167–175
Ceballos RM, Marceau CD, Marceau JO et al (2012) Differential virus host-ranges of the Fuselloviridae of hyperthermophilic Archaea: implications for evolution in extreme environments. Front Microbiol 3:295
Cehovin A, Simpson PJ, McDowell MA et al (2013) Specific DNA recognition mediated by a type IV pilin. Proc Natl Acad Sci USA 110:3065–3070
César CE, Álvarez L, Bricio C et al (2011) Unconventional lateral gene transfer in extreme thermophilic bacteria. Int Microbiol 14:187–199
Charpentier X, Kay E, Schneider D, Shuman HA (2011) Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila. J Bacteriol 193:1114–1121
Chen I, Dubnau D (2004) DNA uptake during bacterial transformation. Nat Rev Microbiol 2:241–249
Chen L, Brugger K, Skovgaard M et al (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 187:4992–4999
Claverys J-P, Prudhomme M, Martin B (2006) Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol 60:451–475
Claverys J-P, Martin B, Polard P (2009) The genetic transformation machinery: composition, localization, and mechanism. FEMS Microbiol Rev 33:643–656
Cohan FM (1994a) Genetic exchange and evolutionary divergence in prokaryotes. Trends Ecol Evol 9:175–180
Cohan FM (1994b) The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am Nat 143:965–986
Danner DB, Deich RA, Sisco KL, Smith HO (1980) An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation. Gene 11:311–318
Datta N, Kontomichalou P (1965) Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae. Nature 208:239–241
de la Cruz F, Frost LS, Meyer RJ, Zechner EL (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34:18–40
Deatherage BL, Cookson BT (2012) Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life. Infect Immun 80:1948–1957
Déclais AC, Marsault J, Confalonieri F et al (2000) Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling. J Biol Chem 275:19498–19504
Deich RA, Smith HO (1980) Mechanism of homospecific DNA uptake in Haemophilus influenzae transformation. Mol Gen Genet 177:369–374
Dickerson RE (1980) Evolution and gene transfer in purple photosynthetic bacteria. Nature 283:210–212
Diruggiero J, Dunn D, Maeder DL et al (2000) Evidence of recent lateral gene transfer among hyperthermophilic archaea. Mol Microbiol 38:684–693
Dorer MS, Fero J, Salama NR (2010) DNA damage triggers genetic exchange in Helicobacter pylori. PLoS Pathog 6:e1001026
Dorward DW, Garon CF, Judd RC (1989) Export and intercellular transfer of DNA via membrane blebs of Neisseria gonorrhoeae. J Bacteriol 171:2499–2505
Drake JW (2009) Avoiding dangerous missense: thermophiles display especially low mutation rates. PLoS Genet 5:e1000520
Dubey GP, Ben-Yehuda S (2011) Intercellular nanotubes mediate bacterial communication. Cell 144:590–600
Dubnau D (1991) Genetic competence in Bacillus subtilis. Microbiol Rev 55:395–424
Dubnau D (1999) DNA uptake in bacteria. Annu Rev Microbiol 53:217–244
Dykhuizen DE, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173:7257–7268
Eisenstark A (1967) Bacteriophage techniques. In: Maramorosch K, Koprowski H (eds) Methods in virology, vol 1. Academic Press, NY, pp 449–525
Elkins C, Thomas CE, Seifert HS, Sparling PF (1991) Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence. J Bacteriol 173:3911–3913
Ellen AF, Albers S-V, Huibers W et al (2009) Proteomic analysis of secreted membrane vesicles of archaeal Sulfolobus species reveals the presence of endosome sorting complex components. Extremophiles 13:67–79
Finkel SE, Kolter R (2001) DNA as a nutrient: novel role for bacterial competence gene homologs. J Bacteriol 183:6288–6293
Fitzmaurice WP, Benjamin RC, Huang PC, Scocca JJ (1984) Characterization of recognition sites on bacteriophage HP1c1 DNA which interact with the DNA uptake system of Haemophilus influenzae Rd. Gene 31:187–196
Forterre P (2002) A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 18:236–723
Friedrich A, Hartsch T, Averhoff B (2001) Natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in Acinetobacter sp. strain BD413 and Thermus thermophilus HB27. Appl Environ Microbiol 67:3140–3148
Friedrich A, Prust C, Hartsch T et al (2002) Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Appl Environ Microbiol 68:745–755
Friedrich A, Rumszauer J, Henne A, Averhoff B (2003) Pilin-like proteins in the extremely thermophilic bacterium Thermus thermophilus HB27: implication in competence for natural transformation and links to type IV pilus biogenesis. Appl Environ Microbiol 69:3695–3700
Fröls S, Ajon M, Wagner M et al (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol 70:938–952
Fröls S, White MF, Schleper C (2009) Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochem Soc Trans 37:36–41
Garcia-Vallvé S, Romeu A, Palau J (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10:1719–1725
Gaudin M, Gauliard E, Schouten S et al (2012) Hyperthermophilic archaea produce membrane vesicles that can transfer DNA. Environ Microbiol Rep 5:109–116
Geslin C, Le Romancer M, Erauso G et al (2003) PAV1, the first virus-like particle isolated from a hyperthermophilic Euryarchaeote, “Pyrococcus abyssi”. J Bacteriol 185:3888–3894
Geslin C, Gaillard M, Flament D et al (2007) Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi. J Bacteriol 189:4510–4519
Ghane F, Grogan DW (1998) Chromosomal marker exchange in the thermophilic archaeon Sulfolobus acidocaldarius: physiological and cellular aspects. Microbiology 144:1649–1657
Gomis-Rüth FX, Coll M (2006) Cut and move: protein machinery for DNA processing in bacterial conjugation. Curr Opin Struct Biol 16:744–772
Gorlas A, Koonin EV, Bienvenu N et al (2012) TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ Microbiol 14:503–516
Gounder K, Brzuszkiewicz E, Liesegang H et al (2011) Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics 12:577
Greve B, Jensen S, Brügger K et al (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1:231–239
Gribaldo S, Brochier-Armanet C (2006) The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci 361:1007–1022
Grogan DW (1996) Exchange of genetic markers at extremely high temperatures in the archaeon Sulfolobus acidocaldarius. J Bacteriol 178:3207–3211
Grogan DW, Stengel KR (2008) Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/lambdaRed and Sulfolobus acidocaldarius recombination systems. Mol Microbiol 69:1255–1265
Grogan DW, Carver GT, Drake JW (2001) Genetic fidelity under harsh conditions: analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc Natl Acad Sci USA 98:7928–7933
Guglielmini J, Quintais L, Garcillán-Barcia MP et al (2011) The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7:e1002222
Guglielmini J, de la Cruz F, Rocha EPC (2013) Evolution of conjugation and Type IV secretion systems. Mol Biol Evol 30:315–331
Guiral S, Mitchell TJ, Martin B, Claverys J-P (2005) Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. Proc Natl Acad Sci USA 102:8710–8715
Halary S, Leigh JW, Cheaib B et al (2010) Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci USA 107:127–132
Happonen LJ, Redder P, Peng X et al (2010) Familial relationships in hyperthermo- and acidophilic archaeal viruses. J Virol 84:4747–4754
Håvarstein LS, Martin B, Johnsborg O et al (2006) New insights into the pneumococcal fratricide: relationship to clumping and identification of a novel immunity factor. Mol Microbiol 59:1297–1307
Heine M, Chandra SBC (2009) The linkage between reverse gyrase and hyperthermophiles: a review of their invariable association. J Microbiol 47:229–234
Held NL, Whitaker RJ (2009) Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol 11:457–466
Herriott RM, Meyer EM, Vogt M (1970) Defined nongrowth media for stage II development of competence in Haemophilus influenzae. J Bacteriol 101:517–524
Hidaka Y, Hasegawa M, Nakahara T, Hoshino T (1994) The entire population of Thermus thermophilus cells is always competent at any growth phase. Biosci Biotechnol Biochem 58:1338–1339
Hofreuter D, Odenbreit S, Püls J et al (2000) Genetic competence in Helicobacter pylori: mechanisms and biological implications. Res Microbiol 151:487–491
Jaatinen ST, Happonen LJ, Laurinmäki P et al (2008) Biochemical and structural characterisation of membrane-containing icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus. Virology 379:10–19
Jain R, Rivera MC, Moore JE, Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20:1598–1602
Jalasvuori M, Jaatinen ST, Laurinavicius S et al (2009) The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J Virol 83:9388–9397
Johnsborg O, Eldholm V, Håvarstein LS (2007) Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 158:767–778
Jonuscheit M, Martusewitsch E, Stedman KM, Schleper C (2003) A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol Microbiol 48:1241–1252
Jorth P, Whiteley M (2012) An evolutionary link between natural transformation and CRISPR adaptive immunity. mBio 3:
Kahn ME, Maul G, Goodgal SH (1982) Possible mechanism for donor DNA binding and transport in Haemophilus. Proc Natl Acad Sci USA 79:6370–6374
Kampmann M, Stock D (2004) Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res 32:3537–3545
Kikuchi A, Asai K (1984) Reverse gyrase—a topoisomerase which introduces positive superhelical turns into DNA. Nature 309:677–681
Koerdt A, Gödeke J, Berger J et al (2010) Crenarchaeal biofilm formation under extreme conditions. PLoS ONE 5:e14104
Kolling GL, Matthews KR (1999) Export of virulence genes and shiga toxin by membrane vesicles of Escherichia coli O157:H7. Appl Environ Microbiol 65:1843–1848
König H, Messner P, Stetter KO (1988) The fine structure of the fibers of Pyrodictium occultum. FEMS Microbiol Lett 49:207–212
Koonin EV (2009) On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci 1178:47–64
Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688–6719
Koyama Y, Hoshino T, Tomizuka N, Furukawa K (1986) Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166:338–340
Krüger N-J, Stingl K (2011) Two steps away from novelty—principles of bacterial DNA uptake. Mol Microbiol 80:860–867
Krupovic M, Bamford DH (2008) Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota. Virology 375:292–300
Krupovic M, Forterre P, Bamford DH (2010) 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 397:144–160
Krupovic M, Prangishvili D, Hendrix RW, Bamford DH (2011) Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 75:610–635
Krupovic M, Gonnet M, Hania WB et al (2013) Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS ONE 8:e49044
Kulp A, Kuehn MJ (2010) Biological functions and biogenesis of secreted bacterial outer membrane vesicles. Annu Rev Microbiol 64:163–184
Lang AS, Zhaxybayeva O, Beatty JT (2012) Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 10:472–482
Lawley T, Klimke W, Gubbins M, Frost L (2003) F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett 224:1–15
Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413–9417
Levin BR (1981) Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99:1–23
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715
Lipps G (2006) Plasmids and viruses of the thermoacidophilic crenarchaeote Sulfolobus. Extremophiles 10:17–28
Lipscomb GL, Stirrett K, Schut GJ et al (2011) Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl Environ Microbiol 77:2232–2238
Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58:563–602
MacFadyen LP, Chen D, Vo HC et al (2001) Competence development by Haemophilus influenzae is regulated by the availability of nucleic acid precursors. Mol Microbiol 40:700–707
Maier B, Potter L, So M et al (2002) Single pilus motor forces exceed 100 pN. Proc Natl Acad Sci USA 99:16012–16017
Majewski J, Cohan FM (1998) The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148:13–18
Majewski J, Cohan FM (1999) Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152:1459–1474
Marguet E, Gaudin M, Gauliard E et al (2013) Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus. Biochem Soc Trans 41:436–442
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–1845
Martin B, García P, Castanié MP, Claverys JP (1995) The recA gene of Streptococcus pneumoniae is part of a competence-induced operon and controls lysogenic induction. Mol Microbiol 15:367–379
Mashburn-Warren LM, Whiteley M (2006) Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 61:839–846
Matsushita I, Yanase H (2009) A novel insertion sequence transposed to thermophilic bacteriophage {phi}IN93. J Biochem 146:797–803
McDaniel LD, Young E, Delaney J et al (2010) High frequency of horizontal gene transfer in the oceans. Science 330:50
Meibom KL, Blokesch M, Dolganov NA et al (2005) Chitin induces natural competence in Vibrio cholerae. Science 310:1824–1827
Mell JC, Hall IM, Redfield RJ (2012) Defining the DNA uptake specificity of naturally competent Haemophilus influenzae. Nucleic Acids Res 40:8536–8549
Michod RE, Wojciechowski MF, Hoelzer MA (1988) DNA repair and the evolution of transformation in the bacterium Bacillus subtilis. Genetics 118:31–39
Minakhin L, Goel M, Berdygulova Z et al (2008) Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol 378:468–480
Mortier-Barrière I, Velten M, Dupaigne P et al (2007) A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell 130:824–836
Murray NE (2002) Immigration control of DNA in bacteria: self versus non-self. Microbiology 148:3–20
Muskhelishvili G, Palm P, Zillig W (1993) SSV1-encoded site-specific recombination system in Sulfolobus shibatae. Mol Gen Genet 237:334–342
Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760–766
Napoli A, Valenti A, Salerno V et al (2004) Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus solfataricus. J Biol Chem 279:33192–33198
Naryshkina T, Liu J, Florens L et al (2006) Thermus thermophilus bacteriophage phiYS40 genome and proteomic characterization of virions. J Mol Biol 364:667–677
Nesbø CL, L’Haridon S, Stetter KO, Doolittle WF (2001) Phylogenetic analyses of two “Archaeal” genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol 18:362–375
Nickell S, Hegerl R, Baumeister W, Rachel R (2003) Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J Struct Biol 141:34–42
Norman A, Hansen LH, Sørensen SJ (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci 364:2275–2289
Nunn DN, Lory S (1991) Product of the Pseudomonas aeruginosa gene pilD is a prepilin leader peptidase. Proc Natl Acad Sci USA 88:3281–3285
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304
Omelchenko MV, Wolf YI, Gaidamakova EK et al (2005) Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol 5:57
Onai K, Morishita M, Kaneko T et al (2004) Natural transformation of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1: a simple and efficient method for gene transfer. Mol Gen Genet 271:50–59
Oshima T, Imahori K (1974) Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24:102–112
Palchevskiy V, Finkel SE (2006) Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient. J Bacteriol 188:3902–3910
Palchevskiy V, Finkel SE (2009) A role for single-stranded exonucleases in the use of DNA as a nutrient. J Bacteriol 191:3712–3716
Pallen MJ, Wren BW (2007) Bacterial pathogenomics. Nature 449:835–842
Palm P, Schleper C, Grampp B et al (1991) Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185:242–250
Peng X, Blum H, She Q et al (2001) Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291:226–234
Pérez-Cruz C, Carrión O, Delgado L et al (2013) A new type of outer membrane vesicles produced by the Gram-negative bacterium Shewanella vesiculosa M7T: implications for DNA content. Appl Environ Microbiol AEM. doi: 10.1128/AEM.03657-12
Pérez-Mendoza D, de la Cruz F (2009) Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any? BMC Genomics 10:71
Popa O, Dagan T (2011) Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol 14:615–623
Prangishvili D, Albers SV, Holz I et al (1998) Conjugation in archaea: frequent occurrence of conjugative plasmids in Sulfolobus. Plasmid 40:190–202
Prangishvili D, Holz I, Stieger E et al (2000) Sulfolobicins, specific proteinaceous toxins produced by strains of the extremely thermophilic archaeal genus Sulfolobus. J Bacteriol 182:2985–2988
Prangishvili D, Forterre P, Garrett RA (2006a) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4:837–848
Prangishvili D, Garrett RA, Koonin EV (2006b) Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117:52–67
Provvedi R, Dubnau D (1999) ComEA is a DNA receptor for transformation of competent Bacillus subtilis. Mol Microbiol 31:271–280
Puigbò P, Wolf YI, Koonin EV (2010) The tree and net components of prokaryote evolution. Genome Biol Evol 2:745–756
Rachel R, Wyschkony I, Riehl S, Huber H (2002) The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. Archaea 1:9–18
Ramírez-Arcos S, Fernández-Herrero LA, Marín I, Berenguer J (1998) Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180:3137–3143
Redder P, Peng X, Brügger K et al (2009) Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environ Microbiol 11:2849–2862
Redfield RJ (1988) Evolution of bacterial transformation: is sex with dead cells ever better than no sex at all? Genetics 119:213–221
Redfield RJ (1993a) Genes for breakfast: the have-your-cake-and-eat-it-too of bacterial transformation. J Hered 84:400–404
Redfield RJ (1993b) Evolution of natural transformation: testing the DNA repair hypothesis in Bacillus subtilis and Haemophilus influenzae. Genetics 133:755–761
Redfield RJ, Schrag MR, Dean AM (1997) The evolution of bacterial transformation: sex with poor relations. Genetics 146:27–38
Renelli M, Matias V, Lo RY, Beveridge TJ (2004) DNA-containing membrane vesicles of Pseudomonas aeruginosa PAO1 and their genetic transformation potential. Microbiology 150:2161–2169
Rosenshine I, Tchelet R, Mevarech M (1989) The mechanism of DNA transfer in the mating system of an archaebacterium. Science 245:1387–1389
Rumbo C, Fernández-Moreira E, Merino M et al (2011) Horizontal transfer of the OXA-24 carbapenemase gene via outer membrane vesicles: a new mechanism of dissemination of carbapenem resistance genes in Acinetobacter baumannii. Antimicrob Ag Chemother 55:3084–3090
Rumszauer J, Schwarzenlander C, Averhoff B (2006) Identification, subcellular localization and functional interactions of PilMNOWQ and PilA4 involved in transformation competency and pilus biogenesis in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273:3261–3272
Sakaki Y, Oshima T (1975) Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8. J Virol 15:1449–1453
Santangelo TJ, Cubonová L, Reeve JN (2008) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microbiol 74:3099–3104
Santangelo TJ, Cubonová L, Reeve JN (2010) Thermococcus kodakarensis genetics: TK1827-encoded beta-glycosidase, new positive-selection protocol, and targeted and repetitive deletion technology. Appl Environ Microbiol 76:1044–1052
Sato T, Fukui T, Atomi H, Imanaka T (2003) Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 185:210–220
Sato T, Fukui T, Atomi H, Imanaka T (2005) Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl Environ Microbiol 71:3889–3899
Schleper C, Holz I, Janekovic D et al (1995) A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J Bacteriol 177:4417–4426
Schmidt KJ, Beck KE, Grogan DW (1999) UV stimulation of chromosomal marker exchange in Sulfolobus acidocaldarius: implications for DNA repair, conjugation and homologous recombination at extremely high temperatures. Genetics 152:1407–1415
Schröder G, Lanka E (2005) The mating pair formation system of conjugative plasmids-A versatile secretion machinery for transfer of proteins and DNA. Plasmid 54:1–25
Schwarzenlander C, Averhoff B (2006) Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273:4210–4218
Schwarzenlander C, Haase W, Averhoff B (2009) The role of single subunits of the DNA transport machinery of Thermus thermophilus HB27 in DNA binding and transport. Environ Microbiol 11:801–808
Sedwick P, Stuben D (1996) Chemistry of shallow submarine warm springs in an arc-volcanic setting: Volcano Island, Aeolian Archipelago, Italy. Mar Chem 53:15
Seitz P, Blokesch M (2012) Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol Rev 37:336–363
She Q, Phan H, Garrett RA et al (1998) Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles 2:417–425
She Q, Shen B, Chen L (2004) Archaeal integrases and mechanisms of gene capture. Biochem Soc Trans 32:222–226
She Q, Zhu H, Xiang X (2006) Integration mechanisms: possible role in genome evolution. In: Garrett RA, Klenk H-P (eds) Archaea. Blackwell Publishing Ltd, Malden, pp 113–124
Shetty A, Chen S, Tocheva EI et al (2011) Nanopods: a new bacterial structure and mechanism for deployment of outer membrane vesicles. PLoS ONE 6:e20725
Siebers B, Zaparty M, Raddatz G et al (2011) The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PLoS ONE 6:e24222
Silverman PM (1997) Towards a structural biology of bacterial conjugation. Mol Microbiol 23:423–429
Soler N, Marguet E, Verbavatz J-M, Forterre P (2008) Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales. Res Microbiol 159:390–399
Soler N, Gaudin M, Marguet E, Forterre P (2011) Plasmids, viruses and virus-like membrane vesicles from Thermococcales. Biochem Soc Trans 39:36–44
Stedman KM, She Q, Phan H et al (2000) pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota. J Bacteriol 182:7014–7020
Stetter KO (2006a) Hyperthermophiles in the history of life. Philos Trans R Soc Lond B Biol Sci 361:1837–1843
Stetter KO (2006b) History of discovery of the first hyperthermophiles. Extremophiles 10:357–362
Stetter KO (2013) A brief history of the discovery of hyperthermophilic life. Biochem Soc Trans 41:416–420
Stingl K, Muller S, Scheidgen-Kleyboldt G et al (2009) Composite system mediates two-step DNA uptake into Helicobacter pylori. Proc Natl Acad Sci USA 107:1184–1189
Suckow G, Seitz P, Blokesch M (2011) Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner. J Bacteriol 193:4914–4924
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3:711–721
Valenti A, De Felice M, Perugino G et al (2012) Synergic and opposing activities of thermophilic RecQ-like helicase and topoisomerase 3 proteins in Holliday junction processing and replication fork stabilization. J Biol Chem 287:30282–30295
van Passel MWJ (2008) An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae. Biol Direct 3:12
Vogelmann J, Ammelburg M, Finger C et al (2011) Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE. EMBO J 30:2246–2254
Waege I, Schmid G, Thumann S et al (2010) Shuttle vector-based transformation system for Pyrococcus furiosus. Appl Environ Microbiol 76:3308–3313
Wang Y, Duan Z, Zhu H et al (2007) A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 363:124–133
Weisburg WG, Giovannoni SJ, Woese CR (1989) The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 11:128–134
White MF (2011) Homologous recombination in the archaea: the means justify the ends. Biochem Soc Trans 39:15–19
White JR, Escobar-Paramo P, Mongodin EF et al (2008) Extensive genome rearrangements and multiple horizontal gene transfers in a population of Pyrococcus isolates from Vulcano Island, Italy. Appl Environ Microbiol 74:6447–6451
Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11:356–372
Wolfgang M, Lauer P, Park HS et al (1998) PilT mutations lead to simultaneous defects in competence for natural transformation and twitching motility in piliated Neisseria gonorrhoeae. Mol Microbiol 29:321–330
Worrell VE, Nagle DP, McCarthy D, Eisenbraun A (1988) Genetic transformation system in the archaebacterium Methanobacterium thermoautotrophicum Marburg. J Bacteriol 170:653–656
Wozniak RAF, Waldor MK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8:552–563
Yaron S, Kolling GL, Simon L, Matthews KR (2000) Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl Environ Microbiol 66:4414–4420
Yu MX, Slater MR, Ackermann H-W (2006) Isolation and characterization of Thermus bacteriophages. Arch Virol 151:663–679
Zaneveld JR, Nemergut DR, Knight R (2008) Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology 154:1–15
Zawadzki P, Roberts MS, Cohan FM (1995) The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140:917–932
Zhang C, Krause DJ, Whitaker RJ (2013) Sulfolobus islandicus: a model system for evolutionary genomics. Biochem Soc Trans 41:458–462
Zinder ND, Lederberg J (1952) Genetic exchange in Salmonella. J Bacteriol 64:679–699