On the need for widespread horizontal gene transfers under genome size constraint

Biology Direct

Volumn 4, Issue , 2009, Pages 28-

  Isambert, Hervé ^a   Stein, Richard R ^a  

^a INSTITUT CURIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PROKARYOTA;

ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; PHYSIOLOGY; PROKARYOTIC CELL;

GENE TRANSFER, HORIZONTAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; PROKARYOTIC CELLS;

EID: 70349581783     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-4-28     Document Type: Article

References (42)

1. Dagan T, Martin W. The tree of one percent. Genome Biol 2006, 7(10):118. 10.1186/gb-2006-7-10-118, 1794558, 17081279.
2. Glansdor3 N, Xu Y, Labedan B. The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 2008, 3:29. 10.1186/1745-6150-3-29, 2478661, 18613974.
3. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008, 36(21):6688-719. 10.1093/nar/gkn668, 2588523, 18948295.
4. Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 2008, 9(8):605-18. 10.1038/nrg2386, 18591983.
5. Salzberg SL, White O, Peterson J, Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss?. Science 2001, 292(5523):1903-6. 10.1126/science.1061036, 11358996.
6. Gladyshev EA, Meselson M, Arkhipova IR. Massive horizontal gene transfer in bdelloid rotifers. Science 2008, 320(5880):1210-3. 10.1126/science.1156407, 18511688.
7. Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T, Nagamine T, Nelson N, Newbold CJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 2006, 7:22. 10.1186/1471-2164-7-22, 1413528, 16472398.
8. Rivera MC, Lake JA. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 2004, 431(7005):152-5. 10.1038/nature02848, 15356622.
9. Gogarten JP, Doolittle WF, Lawrence JG. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002, 19(12):2226-38.
10. Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV. Evidence for massive gene exchange between archaeal and bacterial hyper-thermophiles. Trends Genet 1998, 14(11):442-4. 10.1016/S0168-9525(98)01553-4, 9825671.
11. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399(6734):323-9. 10.1038/20601, 10360571.
12. Nesbo CL, L'Haridon S, Stetter KO, Doolittle WF. Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol 2001, 18(3):362-75.
13. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311(5765):1283-7. 10.1126/science.1123061, 16513982.
14. Marri PR, Hao W, Golding GB. The role of laterally transferred genes in adaptive evolution. BMC Evol Biol 2007, 7(Suppl 1):S8. 10.1186/1471-2148-7-S1-S8, 1796617, 17288581.
15. Novozhilov AS, Karev GP, Koonin EV. Mathematical Modeling of Evolution of Horizontally Transferred Genes. Mol Biol Evol 2005, 22(8):1721-1732. 10.1093/molbev/msi167, 15901840.
16. Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 2005, 3(9):679-87. 10.1038/nrmicro1204, 16138096.
17. Hao W, Golding GB. The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res 2006, 16(5):636-43. 10.1101/gr.4746406, 1457040, 16651664.
18. Achaz G, Rocha EPC, Netter P, Coissac E. Origin and fate of repeats in bacteria. Nucleic Acids Res 2002, 30(13):2987-94. 10.1093/nar/gkf391, 117046, 12087185.
19. Gevers D, Vandepoele K, Simillon C, de Peer YV. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 2004, 12(4):148-54. 10.1016/j.tim.2004.02.007, 15116722.
20. Ochman H, Davalos LM. The nature and dynamics of bacterial genomes. Science 2006, 311(5768):1730-3. 10.1126/science.1119966, 16556833.
21. Touchon M, Rocha EPC. Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 2007, 24(4):969-81. 10.1093/molbev/msm014, 17251179.
22. Lynch M. Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol 2006, 60:327-49. 10.1146/annurev.micro.60.080805.142300, 16824010.
23. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappe MS, Short JM, Carrington JC, Mathur EJ. Genome streamlining in a cosmopolitan oceanic bacterium. Science 2005, 309(5738):1242-5. 10.1126/science.1114057, 16109880.
24. Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral JP, Bouget FY, Piganeau G, Baets BD, Picard A, Delseny M, Demaille J, de Peer YV, Moreau H. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci USA 2006, 103(31):11647-52. 10.1073/pnas.0604795103, 1544224, 16868079.
25. Vellai T, Vida G. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proc R Soc Lond B 1999, 266(1428):1571-7.
26. van Nimwegen E. Scaling laws in the functional content of genomes. Trends Genet 2003, 19(9):479-84. 10.1016/S0168-9525(03)00203-8, 12957540.
27. Ranea JAG, Grant A, Thornton JM, Orengo CA. Microeconomic principles explain an optimal genome size in bacteria. Trends Genet 2005, 21:21-5. 10.1016/j.tig.2004.11.014, 15680509.
28. Evlampiev K, Isambert H. Conservation and topology of protein interaction networks under duplication-divergence evolution. Proc Natl Acad Sci USA 2008, 105(29):9863-8. 10.1073/pnas.0804119105, 2481380, 18632555.
29. Evlampiev K, Isambert H. Modeling protein network evolution under genome duplication and domain shuffing. BMC Syst Biol 2007, 1:49. 10.1186/1752-0509-1-49, 2245809, 17999763.
30. Itaya M, Tsuge K, Koizumi M, Fujita K, Kagaku M. Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci USA 2005, 102:15971-15976. 10.1073/pnas.0503868102, 1276048, 16236728.
31. Hao W, Golding GB. Uncovering rate variation of lateral gene transfer during bacterial genome evolution. BMC Genomics 2008, 9(NIL):235. 10.1186/1471-2164-9-235, 2426709, 18492275.
32. Zhu X, Gerstein M, Snyder M. Getting connected: analysis and principles of biological networks. Genes Dev 2007, 21(9):1010-24. 10.1101/gad.1528707, 17473168.
33. Lagomarsino MC, Jona P, Bassetti B, Isambert H. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci USA 2007, 104(13):5516-20. 10.1073/pnas.0609023104, 1838485, 17372223.
34. Sellerio AL, Bassetti B, Isambert H, Lagomarsino MC. A comparative evolutionary study of transcription networks: The global role of feedback and hierachical structures. Mol BioSyst 2009, 5(2):170-179. 10.1039/b815339f, 19156263.
35. Maslov S, Krishna S, Pang TY, Sneppen K. Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci USA 2009, 106(24):9743-9748. 10.1073/pnas.0903206106, 19482938.
36. Lynch M. The evolution of genetic networks by non-adaptive processes. Nat Rev Genet 2007, 8(10):803-13. 10.1038/nrg2192, 17878896.
37. Uhen MD. Evolution of marine mammals: back to the sea after 300 million years. Anat Rec (Hoboken) 2007, 290(6):514-22.
38. Collin R, Miglietta MP. Reversing opinions on Dollo's Law. Trends in Ecology & Evolution 2008, 23(11):602-609.
39. Stern DL, Orgogozo V. The loci of evolution: How predictable is genetic evolution?. Evolution 2008, 62(9):2155-2177. 2613234, 18616572.
40. Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. Death and Resurrection of the Human IRGM Gene. PLoS Genet 2009, 5. 2644816, 19266026.
41. Pagel M. Limpets break Dollo's law. Trends in Ecology & Evolution 2004, 19(6):278-280.
42. Kohlsdorf T, Wagner G. Evidence for the reversibility of digit loss: a phylogenetic study of limb evolution in Bachia (Gymnophthalmidae: Squamata). Evolution 2006, 60(9):1896-1912.