What tangled web: Barriers to rampant horizontal gene transfer

BioEssays

Volumn 27, Issue 7, 2005, Pages 741-747

  Kurland, Charles G ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

REPETITIVE DNA;

DNA SEQUENCE; ESCHERICHIA COLI; EUKARYOTIC CELL; GENE REPLICATION; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE REPEAT; PHYLOGENY; PROKARYOTIC CELL; REVIEW; TRANSPOSON; ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENOME; HUMAN; MOLECULAR EVOLUTION; MUTATION; THEORETICAL MODEL;

EUKARYOTA; VERTEBRATA;

ANIMALS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME; HUMANS; MODELS, GENETIC; MODELS, THEORETICAL; MUTATION; PHYLOGENY;

EID: 23044437168     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20258     Document Type: Review

References (48)

1. Dawkins R. 1976. The Selfish Gene. New York: Oxford University Press.
2. Doolittle WF, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
3. Orgel LE, Crick FHC. 1980. Selfish DNA: the ultimate parasite. Nature 284:604-607.
4. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
5. Snel B, Bork P, Huynen M. 1999. Genome phylogeny based on gene content. Nat Genet 21:108-110.
6. Snel B, Bork P, Huynen M. 2002. Genomes in flux: the evolution of Archaeal and Proteobacterial gene content. Genome Res. 12:17-25.
7. Fitz-Gibbon ST, House CH. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-4222.
8. Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole pProteome comparisons. Genome Res. 9:550-557.
9. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. 2001. Universal trees based on large combined protein sequence data sets. Nat Genet 28:281-285.
10. Korbel JO, Snel B, Huynen MA, Bork P. 2002. SHOT: A Web Server for the construction of genome phylogenies. Trends Genet. 18:158-162.
11. Gogarten JP, Doolittle WF, Lawrence JG. 2002. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226-2238.
12. Kurland CG, Canback B, Berg OG. 2003. Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 100:9658-9662.
13. Kurland CG. 2004. Paradigm Lost. In: Microbial Evolution: Concepts and Controversies, Ed. Jan Sapp. New York: Oxford University Press.
14. Kurland CG. 2000. Something for everyone. EMBO Reports 1:92-95.
15. Canback B, Andersson SGE, Kurland CG. 2002. The global phylogeny of glycolytic enzymes. Proc Natl Acad Sci USA 99:609-6102.
16. Berg O, Kurland CG. 2002. Evolution of microbial genomes: Sequence acquisition and loss. Mol Biol Evol 19:2265-2276.
17. Hamilton WD. 1964. The genetical evolution of social behavior, I. J Theoretical Biology 7:1-16.
18. Hamilton WD. 1964. The genetical evolution of social behavior, II. J Theoretical Biology 7:17-52.
19. Taddei F, Radman M, Maynard-Smith J, Touponce B, Gouyon PH, Godelle B. 1997. Role of mutator alleles in adaptive evolution. Nature (London) 387:700-702.
20. Ishikawa H. 2003. Insect Symbiosis: an Introduction. In: Boutzis K, Miller TA, editors. Insect Symbiosis. Boca Raton: CRC Press LLC. p 1-21.
21. Charlesworth BP, Sniegowski PD, Stephan W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215-220.
22. Charlesworth B, Langley CH. 1989. The population genetics of Drosophila transposable elements. Ann Rev Genet 23:251-287.
23. Green MM. 1980. Transposable elements in Drosophila and other insects. Ann Rev Genet 14:109-120.
24. Gregory TR. 2002. Genome size and developmental complexity. Genetica 115:131-146.
25. Brenner S, Elgar G, Sanford R, Macrae A, Venkatesh B, Aparacio S. 1993. Characterization of the pufferfish (Fugu) as a compact model vertebrate genome. Nature 366:265-268.
26. Neafsey DE, Palumbi SR. 2003. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetradontid puffer fish. Genome Research 13:821-830.
27. Andersson SGE, Kurland CG. 1998. Reductive evolution of resident genomes. Trends Microbiol 6:263-268.
28. Mira A, Ochman H, Moran NA. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet 17:589-596.
29. Petrov DA, Hartl DL. 1998. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species group. Mol Biol Evol 15:293-302.
30. Petrov DA, Sangster TA, Johnston JS, Hartl DL, Shaw KL. 2000. Evidence for DNA loss as a determinant of genome size. Science 287:1060-1062.
31. Gregory TR. 2004. Insertion deletion biases and the evolution of genome size. Gene 324:15-34.
32. Matzke MA, Mettte MF, Aufsatz W, Jakowitsch J, Matzke AJM. 1999. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica 107:271-287.
33. Hartl DL. 2000. Molecular melodies in high and low C. Nature Rev Genet 1:145-149.
34. Nuzhdin SV. 1999. Sure facts, speculations and open questions about the evolution of transposable copy number. Genetica 107:129-137.
35. Björkman J, Nagaev I, Berg OG, Hughes D, Andersson DI. 2000. Effects of environment on compensatory mutations to ameliorate the costs of antibiotic resistance. Science 287:1479-1482.
36. Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383-397.
37. Lawrence JG, Ochman H. 1998. Molecular archaeology of the Escherichia coli. Genome Proc Natl Acad Sci USA 95:9413-9417.
38. Hooper SD, Berg OG. 2002. Gene import or deletion-a study of the difference genes in Escherichia coll Strains K12 and 0157:H7. J Mol Evol 54:734-744.
39. Ochman H, Jones IB. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J 19:6637-6643.
40. Perna NT, Plunkett G, III, Burland V, et al. 2000. Genome sequence of enterohaemorrhagic Escherichia coli 0157:H7. Nature (London) 409:529-533.
41. Woese CR. 1998. The universal ancestor. Proc Natl Acad Sci USA 95:6854-6859.
42. Woese CR. 2000. Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392-8396.
43. Asai T, Zaporojets D, Squires C, Squires CL. 1999. An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci USA 96:1971-1976.
44. Rao AR, Varshney U. 2001. Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli. EMBO J 20:2977-2986.
45. Ohnishi M, Janosi L, Shuda M, Matsumoto H, Terawaki T, Kaji A. 1999. A. molecular cloning, sequencing, purification and characterization of Pseudomonas aeruginosa ribosome recycling factor. J Bacteriol 181:1281-1291.
46. Kurland CG. 1992. Translational accuracy and the fitness of bacteria. Annu Rev Genet 26:29-50.
47. Andersson DI, Levin BR. 1999. The biological cost of antibiotic resistance. Curr Op Microbiol 2:487-491.
48. Bergstrom CT, Lipsitch M, Levin BR. 2000. Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155:1505-1519.