Alphaproteobacteria species as a source and target of lateral sequence transfers

Trends in Microbiology

Volumn 22, Issue 3, 2014, Pages 147-156

  Le, Phuong Thi ^a   Pontarotti, Pierre ^a   Raoult, Didier ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Alphaproteobacteria; Lateral gene transfer; Lateral sequence transfer; Sympatry; T4SS paradigm

Indexed keywords

ALPHAPROTEOBACTERIA; ARCHAEON; BACTERIAL GENOME; BACTERIAL SURVIVAL; CELL TRANSFER; CHIMERA; DNA SEQUENCE; DNA TRANSFER; ENDOSYMBIOSIS; GENE INTERACTION; GENETIC VARIABILITY; HUMAN; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; TYPE IV SECRETION SYSTEM; WOLBACHIA; ARTHROPOD; BACTERIAL GENE; BACTERIAL STRAIN; GENE TRANSFER; LIFESTYLE; MITOCHONDRIAL GENOME; MOSAICISM; NEMATODE; ORGANISMAL INTERACTION; PROTIST; SYMPATRY;

ALPHAPROTEOBACTERIA; LATERAL GENE TRANSFER; LATERAL SEQUENCE TRANSFER; SYMPATRY; T4SS PARADIGM;

ALPHAPROTEOBACTERIA; BACTERIAL SECRETION SYSTEMS; BIOLOGICAL EVOLUTION; GENE TRANSFER, HORIZONTAL;

BACTERIAL DNA;

EID: 84896713998     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2013.12.006     Document Type: Review

References (91)

1. Boussau B., et al. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:9722-9727.
2. Tettelin H., et al. Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol. 2008, 11:472-477.
3. Dobrindt U., et al. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2004, 2:414-424.
4. Merhej V., et al. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol. Direct 2009, 4:13.
5. Georgiades K., et al. Gene gain and loss events in Rickettsia and Orientia species. Biol. Direct 2011, 6:6.
6. Thomas C.M., Nielsen K.M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 2005, 3:711-721.
7. Chan C.X., et al. Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol. Evol. 2009, 1:429-438.
8. Merhej V., et al. The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences. Mol. Biol. Evol. 2011, 28:3213-3223.
9. Kondo N., et al. Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:14280-14285.
10. Fenn K., et al. Phylogenetic relationships of the Wolbachia of nematodes and arthropods. PLoS Pathog. 2006, 2:e94.
11. Dunning Hotopp J.C., et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 2007, 317:1753-1756.
12. Ogata H., et al. Selfish DNA in protein-coding genes of Rickettsia. Science 2000, 290:347-350.
13. Claverie J-M., Ogata H. The insertion of palindromic repeats in the evolution of proteins. Trends Biochem. Sci. 2003, 28:75-80.
14. Williams K.P., et al. A robust species tree for the alphaproteobacteria. J. Bacteriol. 2007, 189:4578-4586.
15. Merhej V., Raoult D. Rickettsial evolution in the light of comparative genomics. Biol. Rev. Camb. Philos. Soc. 2011, 86:379-405.
16. Renvoisé A., et al. Intracellular Rickettsiales: insights into manipulators of eukaryotic cells. Trends Mol. Med. 2011, 17:573-583.
17. Sassera D., et al. Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor. Mol. Biol. Evol. 2011, 28:3285-3296.
18. Pappas G., et al. Brucellosis. N. Engl. J. Med. 2005, 352:2325-2336.
19. Schülein R., et al. Invasion and persistent intracellular colonization of erythrocytes. A unique parasitic strategy of the emerging pathogen Bartonella. J. Exp. Med. 2001, 193:1077-1086.
20. Georgiades K., et al. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS ONE 2011, 6:e24857.
21. Thrash J.C., et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci. Rep. 2011, 1:13.
22. Viklund J., et al. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 2011, 29:599-615.
23. Giovannoni S.J., et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 2005, 309:1242-1245.
24. Blanc G., et al. Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res. 2007, 17:1657-1664.
25. Ogata H., et al. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol. 2005, 3:e248.
26. McLeod M.P., et al. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J. Bacteriol. 2004, 186:5842-5855.
27. Ogata H., et al. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet. 2006, 2:e76.
28. Masui S., et al. Distribution and evolution of bacteriophage WO in Wolbachia, the endosymbiont causing sexual alterations in arthropods. J. Mol. Evol. 2000, 51:491-497.
29. Rikihisa Y. Anaplasma phagocytophilum and Ehrlichia chaffeensis: subversive manipulators of host cells. Nat. Rev. Microbiol. 2010, 8:328-339.
30. Cho N-H., et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:7981-7986.
31. Saenz H.L., et al. Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors. Nat. Genet. 2007, 39:1469-1476.
32. Saisongkorh W., et al. Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS ONE 2010, 5:e12666.
33. Lang A.S., Beatty J.T. Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol. 2007, 15:54-62.
34. Lang A.S., et al. Gene transfer agents: phage-like elements of genetic exchange. Nat. Rev. Microbiol. 2012, 10:472-482.
35. Gray M.W., et al. Mitochondrial evolution. Science 1999, 283:1476-1481.
36. Embley T.M., Martin W. Eukaryotic evolution, changes and challenges. Nature 2006, 440:623-630.
37. Georgiades K., Raoult D. The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria. Biol. Direct 2011, 6:55.
38. Abhishek A., et al. Bacterial genome chimaerism and the origin of mitochondria. Can. J. Microbiol. 2011, 57:49-61.
39. Brindefalk B., et al. A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS ONE 2011, 6:e24457.
40. Kloesges T., et al. Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol. Biol. Evol. 2011, 28:1057-1074.
41. Dagan T., et al. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:10039-10044.
42. Esser C., et al. The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol. Lett. 2007, 3:180-184.
43. Nester E.W. DNA and protein transfer from bacteria to eukaryotes - the agrobacterium story. Mol. Plant Pathol. 2000, 1:87-90.
44. Darby A.C., et al. Characteristics of the genome of Arsenophonus nasoniae, son-killer bacterium of the wasp Nasonia. Insect Mol. Biol. 2010, 19(Suppl. 1):75-89.
45. Greub G., Raoult D. History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago. Appl. Environ. Microbiol. 2003, 69:5530-5535.
46. Deppenmeier U., et al. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 2002, 4:453-461.
47. Le P.T., et al. An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales. BMC Evol. Biol. 2012, 12:243.
48. Wong K., Golding G.B. A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history. Can. J. Microbiol. 2003, 49:269-280.
49. Shaul S., et al. Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms. BMC Evol. Biol. 2006, 6:22.
50. Dziewit L., et al. Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686. FEMS Microbiol. Lett. 2011, 324:56-63.
51. Adams K.L., Palmer J.D. Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol. Phylogenet. Evol. 2003, 29:380-395.
52. Kurland C.G., Andersson S.G. Origin and evolution of the mitochondrial proteome. Microbiol. Mol. Biol. Rev. 2000, 64:786-820.
53. Gabaldón T., Huynen M.A. Reconstruction of the proto-mitochondrial metabolism. Science 2003, 301:609.
54. Atteia A., et al. A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor. Mol. Biol. Evol. 2009, 26:1533-1548.
55. Thiergart T., et al. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol. Evol. 2012, 4:466-485.
56. Hazkani-Covo E., et al. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 2010, 6:e1000834.
57. Kleine T., et al. DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu. Rev. Plant Biol. 2009, 60:115-138.
58. Werren J.H., et al. Wolbachia: master manipulators of invertebrate biology. Nat. Rev. Microbiol. 2008, 6:741-751.
59. Baldo L., et al. Insight into the routes of Wolbachia invasion: high levels of horizontal transfer in the spider genus Agelenopsis revealed by Wolbachia strain and mitochondrial DNA diversity. Mol. Ecol. 2008, 17:557-569.
60. Frost C.L., et al. Multiple gains and losses of Wolbachia symbionts across a tribe of fungus-growing ants. Mol. Ecol. 2010, 19:4077-4085.
61. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010, 8:e1000313. International Aphid Genomics Consortium.
62. Kent B.N., et al. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol. Evol. 2011, 3:209-218.
63. Chafee M.E., et al. Lateral phage transfer in obligate intracellular bacteria (Wolbachia): verification from natural populations. Mol. Biol. Evol. 2010, 27:501-505.
64. Nikoh N., et al. Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes. Genome Res. 2008, 18:272-280.
65. Thomas V., Greub G. Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours. Intervirology 2010, 53:254-267.
66. Robinson K.M., et al. A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. PLoS Genet. 2013, 9:e1003877.
67. Glöckner G., et al. Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands. Int. J. Med. Microbiol. 2008, 298:411-428.
68. Gillespie J.J., et al. Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect. Immun. 2010, 78:1809-1823.
69. Moliner C., et al. Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol. Rev. 2010, 34:281-294.
70. Martin W. Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:8612-8614.
71. Timmis J.N., et al. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 2004, 5:123-135.
72. Dubey G.P., Ben-Yehuda S. Intercellular nanotubes mediate bacterial communication. Cell 2011, 144:590-600.
73. Kuehn M.J., Kesty N.C. Bacterial outer membrane vesicles and the host-pathogen interaction. Genes Dev. 2005, 19:2645-2655.
74. Frost L.S., et al. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 2005, 3:722-732.
75. Raoult D. The post-Darwinist rhizome of life. Lancet 2010, 375:104-105.
76. Orgel L.E., Crick F.H. Selfish DNA: the ultimate parasite. Nature 1980, 284:604-607.
77. Kurland C.G., et al. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:9658-9662.
78. Lawrence J.G., Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 1997, 44:383-397.
79. Mirkin B.G., et al. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 2003, 3:2.
80. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
81. Zhaxybayeva O., Doolittle W.F. Lateral gene transfer. Curr. Biol. 2011, 21:R242-R246.
82. Hacker J., Kaper J.B. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 2000, 54:641-679.
83. Ochman H., et al. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
84. McDaniel L.D., et al. High frequency of horizontal gene transfer in the oceans. Science 2010, 330:50.
85. Popa O., Dagan T. Trends and barriers to lateral gene transfer in prokaryotes. Curr. Opin. Microbiol. 2011, 14:615-623.
86. Hooper S.D., et al. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol. 2009, 10:R45.
87. Lercher M.J., Pál C. Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol. Biol. Evol. 2008, 25:559-567.
88. Tuller T., et al. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res. 2011, 39:4743-4755.
89. Tuller T. Codon bias, tRNA pools and horizontal gene transfer. Mob. Genet. Elements 2011, 1:75-77.
90. Jain R., et al. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:3801-3806.
91. Fitzpatrick D.A., et al. Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol. Biol. 2008, 8:181.