1,646
Views
12
CrossRef citations to date
0
Altmetric
Commentary

The role of mobile genetic elements in evolutionary longevity of heritable endobacteria

&
Article: e1136375 | Received 17 Nov 2015, Accepted 18 Dec 2015, Published online: 29 Jan 2016

References

  • Bordenstein SR, Reznikoff WS. Mobile DNA in obligate intracellular bacteria. Nat Rev Microbiol 2005; 3:688-99; PMID:16138097; http://dx.doi.org/10.1038/nrmicro1233
  • Newton IL, Bordenstein SR. Correlations between bacterial ecology and mobile DNA. Curr Microbiol 2011; 62:198-208; PMID:20577742; http://dx.doi.org/10.1007/s00284-010-9693-3
  • Moran NA, McCutcheon JP, Nakabachi A. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 2008; 42:165-90; PMID:18983256; http://dx.doi.org/10.1146/annurev.genet.41.110306.130119
  • McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 2012; 10:13-26; PMID:22064560; http://dx.doi.org/10.1038/nrmicro2670
  • Moran NA, Bennett GM. The tiniest tiny genomes. Annu Rev Microbiol 2014; 68:195-215; PMID:24995872; http://dx.doi.org/10.1146/annurev-micro-091213-112901
  • Muller HJ. The relation of recombination to mutational advance. Mutat Res 1964; 1:2-9; http://dx.doi.org/10.1016/0027-5107(64)90047-8
  • Naito M, Morton JB, Pawlowska TE. Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota. P Natl Acad Sci USA 2015; 112:7791-6; http://dx.doi.org/10.1073/pnas.1501676112
  • Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, Sandstrom JP, Moran NA, Andersson SGE. 50 million years of genomic stasis in endosymbiotic bacteria. Science 2002; 296:2376-9; PMID:12089438; http://dx.doi.org/10.1126/science.1071278
  • Perez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A, Latorre A. A small microbial genome: The end of a long symbiotic relationship? Science 2006; 314:312-3; PMID:17038625; http://dx.doi.org/10.1126/science.1130441
  • Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 2000; 407:81-6; PMID:10993077; http://dx.doi.org/10.1038/35024074
  • Moran NA, Munson MA, Baumann P, Ishikawa H. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. P Roy Soc Lond B Bio 1993; 253:167-71; http://dx.doi.org/10.1098/rspb.1993.0098
  • Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 2002; 32:402-7; PMID:12219091; http://dx.doi.org/10.1038/ng986
  • Lefevre C, Charles H, Vallier A, Delobel B, Farrell B, Heddi A. Endosymbiont phylogenesis in the Dryophthoridae weevils: Evidence for bacterial replacement. Mol Biol Evol 2004; 21:965-73; PMID:14739242; http://dx.doi.org/10.1093/molbev/msh063
  • Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, et al. Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol 2014; 6:76-93; PMID:24407854; http://dx.doi.org/10.1093/gbe/evt210
  • Plague GR, Dunbar HE, Tran PL, Moran NA. Extensive proliferation of transposable elements in heritable bacterial symbionts. J Bacteriol 2008; 190:777-9; PMID:17981967; http://dx.doi.org/10.1128/JB.01082-07
  • Dougherty KM, Plague GR. Transposable element loads in a bacterial symbiont of weevils are extremely variable. Appl Environ Microbiol 2008; 74:7832-4; PMID:18952872; http://dx.doi.org/10.1128/AEM.01049-08
  • Gil R, Belda E, Gosalbes MJ, Delaye L, Vallier A, Vincent-Monegat C, Heddi A, Silva FJ, Moya A, Latorre A. Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae. Int Microbiol 2008; 11:41-8; PMID:18683631
  • Burke GR, Moran NA. Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol Evol 2011; 3:195-208; PMID:21266540; http://dx.doi.org/10.1093/gbe/evr002
  • Manzano-Marín A, Latorre A. Settling down: The genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life. Genome Biol Evol 2014; 6:1683-98; http://dx.doi.org/10.1093/gbe/evu133
  • Fenn K, Blaxter M. Are filarial nematode Wolbachia obligate mutualist symbionts? Trends Ecol Evol 2004; 19:163-6; PMID:16701248; http://dx.doi.org/10.1016/j.tree.2004.01.002
  • Werren JH, Baldo L, Clark ME. Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 2008; 6:741-51; PMID:18794912; http://dx.doi.org/10.1038/nrmicro1969
  • Zug R, Hammerstein P. Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Bio Rev 2015; 90:89-111; http://dx.doi.org/10.1111/brv.12098
  • Vavre F, Fleury F, Lepetit D, Fouillet P, Boulétreau M. Phylogenetic evidence for horizontal transmission of Wolbachia in host-parasitoid associations. Mol Biol Evol 1999; 16:1711-23; PMID:10605113; http://dx.doi.org/10.1093/oxfordjournals.molbev.a026084
  • Clark MA, Moran NA, Baumann P. Sequence evolution in bacterial endosymbionts having extreme base compositions. Mol Biol Evol 1999; 16:1586-98; PMID:10555290; http://dx.doi.org/10.1093/oxfordjournals.molbev.a026071
  • Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, et al. The Wolbachia genome of Brugia malayi: Endosymbiont evolution within a human pathogenic nematode. PLoS Biology 2005; 3:599-614; http://dx.doi.org/10.1371/journal.pbio.0030121
  • Cordaux R. Gene conversion maintains nonfunctional transposable elements in an obligate mutualistic endosymbiont. Mol Biol Evol 2009; 26:1679-82; PMID:19414524; http://dx.doi.org/10.1093/molbev/msp093
  • Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, et al. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements. PLoS Biology 2004; 2:327-41; http://dx.doi.org/10.1371/journal.pbio.0020327
  • Leclercq S, Giraud I, Cordaux R. Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts. Mol Biol Evol 2011; 28:685-97; PMID:20819906; http://dx.doi.org/10.1093/molbev/msq238
  • Klasson L, Walker T, Sebaihia M, Sanders MJ, Quail MA, Lord A, Sanders S, Earl J, O'Neill SL, Thomson N, et al. Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol Biol Evol 2008; 25:1877-87; PMID:18550617; http://dx.doi.org/10.1093/molbev/msn133
  • Cordaux R, Pichon S, Ling A, Perez P, Delaunay C, Vavre F, Bouchon D, Greve P. Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont. Mol Biol Evol 2008; 25:1889-96; PMID:18562339; http://dx.doi.org/10.1093/molbev/msn134
  • Duron O. Lateral transfers of insertion sequences between Wolbachia, Cardinium and Rickettsia bacterial endosymbionts. Heredity 2013; 111:330-7; PMID:23759724; http://dx.doi.org/10.1038/hdy.2013.56
  • Weinert LA, Werren JH, Aebi A, Stone GN, Jiggins FM. Evolution and diversity of Rickettsia bacteria. BMC Biol 2009; 7:6; PMID:19187530; http://dx.doi.org/10.1186/1741-7007-7-6
  • Merhej V, Raoult D. Rickettsial evolution in the light of comparative genomics. Biol Rev Camb Philos Soc 2011; 86:379-405; PMID:20716256; http://dx.doi.org/10.1111/j.1469-185X.2010.00151.x
  • Nakayama K, Yamashita A, Kurokawa K, Morimoto T, Ogawa M, Fukuhara M, Urakami H, Ohnishi M, Uchiyama I, Ogura Y, et al. The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res 2008; 15:185-99; PMID:18508905; http://dx.doi.org/10.1093/dnares/dsn011
  • Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA. Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. P Natl Acad Sci USA 2009; 106:9063-8; http://dx.doi.org/10.1073/pnas.0900194106
  • Degnan PH, Leonardo TE, Cass BN, Hurwitz B, Stern D, Gibbs RA, Richards S, Moran NA. Dynamics of genome evolution in facultative symbionts of aphids. Environ Microbiol 2010; 12:2060-9; PMID:21966902
  • Desir∫ A, Faccio A, Kaech A, Bidartondo MI, Bonfante P. Endogone, one of the oldest plant-associated fungi, host unique Mollicutes-related endobacteria. New Phytol 2014; 205:1464-72; http://dx.doi.org/10.1111/nph.13136
  • Naumann M, Schüßler A, Bonfante P. The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. ISME J 2010; 4:862-71; PMID:20237515; http://dx.doi.org/10.1038/ismej.2010.21
  • Toomer KH, Chen X, Naito M, Mondo SJ, den Bakker HC, VanKuren NW, Lekberg Y, Morton JB, Pawlowska TE. Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi. Mol Ecol 2015; 24:3485-500; PMID:26011293; http://dx.doi.org/10.1111/mec.13250
  • Torres-Cortés G, Ghignone S, Bonfante P, Schüßler A. Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association. P Natl Acad Sci USA 2015; 112:7785-90; http://dx.doi.org/10.1073/pnas.1501540112
  • Sirand-Pugnet P, Citti C, Barre A, Blanchard A. Evolution of mollicutes: down a bumpy road with twists and turns. Res Microbiol 2007; 158:754-66; PMID:18023150; http://dx.doi.org/10.1016/j.resmic.2007.09.007
  • Nouvel LX, Sirand-Pugnet P, Marenda MS, Sagne E, Barbe V, Mangenot S, Schenowitz C, Jacob D, Barre A, Claverol S, et al. Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. BMC Genomics 2010; 11:86; PMID:20122262; http://dx.doi.org/10.1186/1471-2164-11-86
  • Dordet-Frisoni E, Sagne E, Baranowski E, Breton M, Nouvel LX, Blanchard A, Marenda MS, Tardy F, Sirand-Pugnet P, Citti C. Chromosomal transfers in mycoplasmas: when minimal genomes go mobile. mBio 2014; 5:e01958; PMID:25425234; http://dx.doi.org/10.1128/mBio.01958-14
  • Thomas A, Linden A, Mainil J, Bischof DF, Frey J, Vilei EM. Mycoplasma bovis shares insertion sequences with Mycoplasma agalactiae and Mycoplasma mycoides subsp. mycoides SC: Evolutionary and developmental aspects. FEMS Microbiol Lett 2005; 245:249-55; PMID:15837379; http://dx.doi.org/10.1016/j.femsle.2005.03.013
  • Tardy F, Mick V, Dordet-Frisoni E, Marenda MS, Sirand-Pugnet P, Blanchard A, Citti C. Integrative conjugative elements are widespread in field isolates of Mycoplasma species pathogenic for ruminants. Appl Environ Microb 2015; 81:1634-43; http://dx.doi.org/10.1128/AEM.03723-14
  • Dordet Frisoni E, Marenda MS, Sagne E, Nouvel LX, Guerillot R, Glaser P, Blanchard A, Tardy F, Sirand-Pugnet P, Baranowski E, et al. ICEA of Mycoplasma agalactiae: a new family of self-transmissible integrative elements that confers conjugative properties to the recipient strain. Mol Microbiol 2013; 89:1226-39; PMID:23888872; http://dx.doi.org/10.1111/mmi.12341
  • Calcutt MJ, Lewis MS, Wise KS. Molecular genetic analysis of ICEF, an integrative conjugal element that is present as a repetitive sequence in the chromosome of Mycoplasma fermentans PG18. J Bacteriol 2002; 184:6929-41; PMID:12446643; http://dx.doi.org/10.1128/JB.184.24.6929-6941.2002
  • Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barre A, Barbe V, Schenowitz C, Mangenot S, Couloux A, Segurens B, et al. Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 2007; 3:744-58; http://dx.doi.org/10.1371/journal.pgen.0030075
  • Carle P, Saillard C, Carrere N, Carrere S, Duret S, Eveillard S, Gaurivaud P, Gourgues G, Gouzy J, Salar P, et al. Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay. Appl Environ Microbiol 2010; 76:3420-6; PMID:20363791; http://dx.doi.org/10.1128/AEM.02954-09
  • Wozniak RAF, Waldor MK. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010; 8:552-63; PMID:20601965; http://dx.doi.org/10.1038/nrmicro2382
  • Citti C, Nouvel LX, Baranowski E. Phase and antigenic variation in mycoplasmas. Future Microbiol 2010; 5:1073-85; PMID:20632806; http://dx.doi.org/10.2217/fmb.10.71
  • Desiró A, Salvioli A, Ngonkeu EL, Mondo SJ, Epis S, Faccio A, Kaech A, Pawlowska TE, Bonfante P. Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi. ISME J 2014; 8:257-70; http://dx.doi.org/10.1038/ismej.2013.151
  • Mondo SJ, Toomer KH, Morton JB, Lekberg Y, Pawlowska TE. Evolutionary stability in a 400-million-year-old heritable facultative mutualism. Evolution 2012; 66:2564-76; PMID:22834753; http://dx.doi.org/10.1111/j.1558-5646.2012.01611.x
  • Ghignone S, Salvioli A, Anca I, Lumini E, Ortu G, Petiti L, Cruveiller S, Bianciotto V, Piffanelli P, Lanfranco L, et al. The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. ISME J 2012; 6:136-45; PMID:21866182; http://dx.doi.org/10.1038/ismej.2011.110
  • Garriss G, Waldor MK, Burrus V. Mobile antibiotic resistance encoding elements promote their own diversity. PLoS Genet 2009; 5:e1000775; PMID:20019796; http://dx.doi.org/10.1371/journal.pgen.1000775
  • Marini E, Palmieri C, Magi G, Facinelli B. Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes. Veterinary microbiology 2015; 178:99-104; PMID:25935120; http://dx.doi.org/10.1016/j.vetmic.2015.04.013
  • Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 2005; 3:711-21; PMID:16138099; http://dx.doi.org/10.1038/nrmicro1234