Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes

Molecular Biology and Evolution

Volumn 24, Issue 2, 2007, Pages 449-456

  Khachane, Amit N ^a   Timmis, Kenneth N ^a   Martins Dos Santos, Vítor A P ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Exponential decay; GC content; Genome size; Mitochondria; Obligate intracellular microbes

Indexed keywords

ALPHAPROTEOBACTERIA; ARTICLE; BUCHNERA APHIDICOLA; ENDOSYMBIONT; EVOLUTION; FOSSIL; GENOME; MICROORGANISM; MITOCHONDRION; NONHUMAN; PROKARYOTE; RICKETTSIA; SYMBIOSIS; TSETSE FLY; WIGGLESWORTHIA GLOSSINIDIA;

BASE COMPOSITION; BUCHNERA; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; EVOLUTION; EVOLUTION, MOLECULAR; EXTRACHROMOSOMAL INHERITANCE; GENOME; GENOME, BACTERIAL; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 16S; SYMBIOSIS;

BUCHNERA APHIDICOLA; EUKARYOTA; GLOSSINA (GENUS); PROKARYOTA; RICKETTSIA; WIGGLESWORTHIA; WIGGLESWORTHIA GLOSSINIDIA ENDOSYMBIONT OF GLOSSINA BREVIPALPIS;

EID: 33846809192     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl174     Document Type: Article

References (43)

1. Andersson JO, Andersson SG. 1999a. Genome degradation is an ongoing process in Rickettsia. Mol Biol Evol. 16:1178-1191.
2. Andersson JO, Andersson SG. 1999b. Insights into the evolutionary process of genome degradation. Curr Opin Genet Dev. 9:664-671.
3. Andersson JO, Andersson SG. 2001. Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. Mol Biol Evol. 8:829-839.
4. Andersson SG, Kurland CG. 1998. Reductive evolution of resident genomes. Trends Microbiol. 6:263-268.
5. Andersson SG, Kurland CG. 1999. Origins of mitochondria and hydrogenosomes. Curr Opin Microbiol. 2:535-541.
6. Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 396:133-140.
7. Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG. 2004. Computational inference of scenarios for α-proteobacterial genome evolution. Proc Natl Acad Sci USA. 101:9722-9727.
8. Clark MA, Moran NA, Baumann P. 1999. Sequence evolution in bacterial endosymbionts having extreme base compositions. Mol Biol Evol. 16:1586-1598.
9. Dagan T, Blekhman R, Graur D. 2006. The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens. Mol Biol Evol. 23:310-316.
10. Delmotte F, Rispe C, Schaber J, Silva FJ, Moya A. 2006. Tempo and mode of early gene loss in endosymbiotic bacteria from insects. BMC Evol Biol. 6:56.
11. Douglas AE, Raven JA. 2003. Genomes at the interface between bacteria and organelles. Philos Trans R Soc Lond B Biol Sci. 358:5-17.
12. Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H. 2004. The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA. 101:15386-15391.
13. Dyall SD, Brown MT, Johnson PJ. 2004. Ancient invasions: from endosymbionts to organelles. Science. 304:253-257.
14. Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature. 440:623-630.
15. Gil R, Sabater-Munoz B, Latorre A, Silva FJ, Moya A. 2002. Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci USA. 99:4454-4458.
16. Gómez-Valero L, Latorre A, Silva FJ. 2004. The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol Biol Evol. 21:2172-2181.
17. Gray MW, Burger G, Lang BF. 2001. The origin and early evolution of mitochondria. Genome Biol. 2:reviews1018.1-reviews1018.5.
18. Herbeck JT, Degnan PH, Wernegreenn JJ. 2005. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). Mol Biol Evol. 22:520-532.
19. Javaux EJ, Knoll AH, Walter MR. 2001. Morphological and ecological complexity in early eukaryotic ecosystems. Nature. 41:66-69.
20. Khachane AN, Timmis KN, Martins dos Santos VA. 2005. Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures. Nucleic Acids Res. 33:4016-4022.
21. Knight J. 2004. Giardia: not so special, after all? Nature. 429:236-237.
22. Kondo N, Nikoh N, Ijichi N, Shimada M, Fukatsu T. 2002. Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci USA. 99:14280-14285.
23. Konstantinidis KT, Tiedje JM. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA. 101:3160-3165.
24. Latorre A, Gil R, Silva FJ, Moya A. 2005. Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola. Heredity. 95:339-347.
25. Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 44:383-397.
26. Margulis L, Bermudes D. 1985. Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis. 1:101-124.
27. Moran NA. 1996. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA. 93:2873-2878.
28. Moran NA. 2002. Microbial minimalism: genome reduction in bacterial pathogens. [Review]. Cell. 108:583-586.
29. Moran NA, Mira A. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2:research0054.1-research0054. 12.
30. Moran NA, Munson MA, Baumann P, Ishikawa H. 1993. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc Lond Ser B Biol Sci. 253:167-171.
31. Moran NA, Wernegreen JJ. 2000. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol. 15:321-326.
32. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science. 314:267.
33. Nilsson AI, Koskiniemi S, Eriksson S, Kugelberg E, Hinton JC, Andersson DI. 2005. Bacterial genome size reduction by experimental evolution. Proc Natl Acad Sci USA. 102:12112-12116.
34. Ochman H, Elwyn S, Moran NA. 1999. Calibrating bacterial evolution. Proc Natl Acad Sci USA. 96:12638-12643.
35. Ochman H, Moran NA. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. [Review]. Science. 292:1096-1099.
36. Palmer JD. 1997. Organelle genomes: going, going, gone! Science. [Review]. 275:790-791.
37. Pérez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A, Latorre A. 2006. A small microbial genome: the end of a long symbiotic relationship? Science. 314:312-313.
38. Philippe H, Adoutte A. 1998. The molecular phylogeny of Eukaryota: solid facts and uncertainties. In: Coombs GH, Vickerman K, Sleigh MA, Warren A, editors. Evolutionary relationships among protozoa. London: Chapman & Hall. p. 25-56.
39. Silva FJ, Latorre A, Moya A. 2001. Genome size reduction through multiple events of gene disintegration in Buchnera APS. Trends Genet. 17:615-618.
40. Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, Sandstrom JP, Moran NA, Andersson SG. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science. 296:2376-2379.
41. Toft C, Fares MA. 2006. GRAST: a new way of genome reduction analysis using comparative genomics. Bioinformatics. 22:1551-1561.
42. Wernegreen JJ. 2002. Genome evolution in bacterial endosymbionts of insects. [Review]. Nat Rev Genet. 3:850-861.
43. Wernegreen JJ, Ochman H, Jones IB, Moran NA. 2000. Decoupling of genome size and sequence divergence in a symbiotic bacterium. J Bacteriol. 182:3867-3869.