Gene gain and loss events in Rickettsia and Orientia species

Biology Direct

Volumn 6, Issue , 2011, Pages

  Georgiades, Kalliopi ^a,b   Merhej, Vicky ^a   El Karkouri, Khalid ^a   Raoult, Didier ^a   Pontarotti, Pierre ^b  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA; ORIENTIA; PROKARYOTA; RICKETTSIA; RICKETTSIACEAE; RICKETTSIALES;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; ORIENTIA TSUTSUGAMUSHI; PHYLOGENY; RICKETTSIA; SPECIES DIFFERENCE;

EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; ORIENTIA TSUTSUGAMUSHI; PHYLOGENY; RICKETTSIA; SPECIES SPECIFICITY;

EID: 79551682170     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-6     Document Type: Article

References (51)

1. Raoult D, Ndihokubwayo JB, Tissot-Dupont H, Roux V, Faugere B, Abegbinni R, Birtles RJ. Outbreak of epidemic typhus associated with trench fever in Burundi. Lancet 1998, 352:353-358. 10.1016/S0140-6736(97)12433-3, 9717922.
2. Merhej V, Raoult D. Rickettsial evolution in the light of comparative genomics. Biol Rev 2010,
3. Kikuchi Y, Sameshima S, Kitade O, Kojima J, Fukatsu T. Novel clade of Rickettsia spp. from leeches. Appli Environ Microbiol 2002, 68:999-1004.
4. Kuchler SM, Kehl S, Dettner K. Characterization and localization of Rickettsia sp. In water beetles of genus Deronectes (Coleoptera: Dytiscidae). Fems Microbiol Ecol 2009, 68:201-211. 10.1111/j.1574-6941.2009.00665.x, 19573201.
5. Fournier PE, Raoult D. Current Knowledge on Phylogeny and Taxonomy of Rickettsia spp. Ann N Y Acad Sci 2009, 1166:1-11. 10.1111/j.1749-6632.2009.04528.x, 19538259.
6. Moran NA. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA 1996, 93:2873-2878. 10.1073/pnas.93.7.2873, 39726, 8610134.
7. Andersson SG, Kurland CG. Reductive evolution of resident genomes. Trends Microbiol 1998, 6:263-268. 10.1016/S0966-842X(98)01312-2, 9717214.
8. Andersson JO, Anersson SG. Genome degradation is an ongoing process in Rickettsia. Mol Biol Evol 1999, 16(9):1178-1191.
9. Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D. Reductive genome evolution from the mother of Rickettsia. Plos Genetics 2007, 3. 10.1371/journal.pgen.0030014, 1779305, 17238289.
10. Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SG. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet 2007, 23:511-520. 10.1016/j.tig.2007.08.002, 17822801.
11. Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct 2009, 4:13. 10.1186/1745-6150-4-13, 2688493, 19361336.
12. Ogata H, Audic S, Renesto-Audiffren P, Fournier PE, Barbe V, Samson D, Roux V, Cossart P, Weissenbach J, Claverie JM, Raoult D. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 2001, 293:2093-2098. 10.1126/science.1061471, 11557893.
13. Bechah Y, Karkouri EK, Mediannikov O, Quentin L, Pelletier N, Robert C, Médigue C, Mege JL, Raoult D. Genomic, proteomic and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities. Genome Res 2010, 20:655-663. 10.1101/gr.103564.109, 2860167, 20368341.
14. Fournier PE, Raoult D. Identification of rickettsial isolates at the species level using multi-spacer typing. BMC Microbiology 2007, 7:72. 10.1186/1471-2180-7-72, 1950309, 17662158.
15. Boussau B, Karlberg OE, Frank CA, Legault BA, Andersson SGE. Computational inference of scenarios for α-proteobacterial genome evolution. Proc Natl Acad Sci USA 2004, 101:9722-9727. 10.1073/pnas.0400975101, 470742, 15210995.
16. Ogata H, Renesto P, Audic S, Robert C, Blanc G, Fournier PE, Parinello H, Claverie JM, Raoult D. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. Plos Biol 2005, 3:e218. 10.1371/journal.pbio.0030248, 1174820, 16000017.
17. Ogata H, La SB, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. Plos Genet 2006, 2:e76. 10.1371/journal.pgen.0020076, 1458961, 16703114.
18. Blanc G, Ogata H, Robert C, Audic S, Claverie JM, Raoult D. Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res 2007, 17:1657-1664. 10.1101/gr.6742107, 2045148, 17916642.
19. Wolf YI, Aravind L, Koonin EV. Rickettsiae and Chlamydiae - evidence of horizontal gene transfer and gene exchange. Trends Genet 1999, 15:173-175. 10.1016/S0168-9525(99)01704-7, 10322483.
20. Cho NH, Kim HR, Lee JH, Kim SY, Kim J, Cha S, Kim SY, Darby AV, Fuxelius HH, Yin J, Kim JH, Kim J, Lee SJ, Koh YS, Jang WJ, Park KH, Andersson SG, Choi MS, Kim IS. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci USA 2007, 104:7981-7986. 10.1073/pnas.0611553104, 1876558, 17483455.
21. Kuo CH, Ochman H. The fate of new bacterial genes. FEMS Microbiol Rev 2009, 33:38-43. 10.1111/j.1574-6976.2008.00140.x, 19054121.
22. Seong SY, Choi MS, Kim IS. Orientia tsutsugamushi infection: overview and immune responses. Microbes Infect 2001, 3:11-21. 10.1016/S1286-4579(00)01352-6, 11226850.
23. Damler J, Barbet A, Bekker C, Dasch G, Palmer G, Ray S, Rikihisa Y, Runargirwa F. Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, description of 6 new species combination and designation of Ehrlichia equi and HGE agent as subjective synonyms of H. phagocytophila. Int J Syst Evol Microbiol 2001, 51:2145-2165.
24. Merhej V, Khalid EK, Raoult D. Whole genome-based phylogenetic analysis of Rickettsiae. Clin Microbiol Infect 2009, 15:336-337. 10.1111/j.1469-0691.2008.02265.x, 19456801.
25. Ochman H, Lerat E, Daubin V. Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci USA 2005, 102:6595-6599. 10.1073/pnas.0502035102, 1131874, 15851673.
26. Knowles DG, McLysaght A. Recent de novo origin of human protein-coding genes. Genome Res 2009, 19:1752-1759. 10.1101/gr.095026.109, 2765279, 19726446.
27. Mirkin BG, Fenner TI, Galperin MY, Koonin EV. 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. 10.1186/1471-2148-3-2, 149225, 12515582.
28. Pal C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 2005, 37:1372-1375. 10.1038/ng1686, 16311593.
29. Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res 2006, 16:1099-1108. 10.1101/gr.5322306, 1557764, 16899658.
30. Whitaker JW, McConkey GA, Westhead DR. The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biol 2009, 10:R36. 10.1186/gb-2009-10-4-r36, 2688927, 19368726.
31. Iwasaki W, Takagi T. Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages. Plos Genet 2009, 5(Suppl 3):e1000402. 10.1371/journal.pgen.1000402, 2644373, 19266023.
32. Snel B, Bork P, Huynen MA. Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res 2002, 12:17-25. 10.1101/gr.176501, 11779827.
33. Marri RP, Hao W, Golding GB. Gene gain and gene loss in Streptococcus: Is it driven by habitat?. Mol Biol Evol 2006, 23(12):2379-2391. 10.1093/molbev/msl115, 16966682.
34. Kettler GC, Martny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglish C, Church GM, Richardson P, Chisholm SW. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. Plos Genet 2007, 3(12):2515-2517.
35. Cordero OX, Hogeweg P. The impact of long-distance horizontal gene transfer on prokaryotic genome size. Proc Natl Acad Sci USA 2009, 106:21748-21753. 10.1073/pnas.0907584106, 2799812, 20007373.
36. Fuxelius HH, Alistair CD, Cho NH, Andersson SGE. Visualisation of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol 2008, 9:R42. 10.1186/gb-2008-9-2-r42, 2374718, 18302730.
37. Medici D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 2005, 15:589-594. 10.1016/j.gde.2005.09.006, 16185861.
38. Thomas V, Greub G. Amoebae/amoebal symbionts genetic transfers: lessons from giant viruses neighbors. Intervirology 2010, 53:254-267. 10.1159/000312910, 20551677.
39. Moliner C, Fournier PE, Raoult D. Genome analysis of microorganisms living in Amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 2010, 34:281-294.
40. Merkeev IV, Mironov AA. Orphan genes: Function, evolution, and composition. Mol Biol 2008, 42:127-132.
41. Rocha MTG, Cooper JE, Smith NH, Feil EJ. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol 2006, 239:226-235. 10.1016/j.jtbi.2005.08.037, 16239014.
42. Boyer M, Gimenez G, Suzan-Monti M, Raoult D. Classification and determination of possible origins of ORFans through analysis of nucleocytoplasmic large DNA viruses. Intervirology 2010, 53:310-320. 10.1159/000312916, 20551683.
43. Cortez D, Forterre P, Gribaldo S. A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in the Archaeal and bacterial genomes. Genome Biol 2009, 10:R65. 10.1186/gb-2009-10-6-r65, 2718499, 19531232.
44. Moran NA, Wernegreen JJ. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol 2000, 15:321-326. 10.1016/S0169-5347(00)01902-9, 10884696.
45. Moran NA, Mira A. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol 2001, 2(12):research0054.1-0054.12.
46. The NCBI site. , ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
47. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
48. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author 1993, Department of Genetics. University of Washington, Seattle.
49. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet 1999, 21:108-110. 10.1038/5052, 9916801.
50. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
51. Goldman N, Yang ZH. Codon-Based Model of Nucleotide Substitution for Protein-Coding Dna-Sequences. Mol Biol Evol 1994, 11:725-736.