Biased gene transfer in microbial evolution

Nature Reviews Microbiology

Volumn 9, Issue 7, 2011, Pages 543-555

  Andam, Cheryl P ^a   Gogarten, J Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MINICHROMOSOME MAINTENANCE PROTEIN;

ALLELE; ARCHAEBACTERIUM; ARTICLE; HORIZONTAL GENE TRANSFER; LAST COMMON ANCESTOR; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROKARYOTE; RNA GENE; TAXONOMIC IDENTIFICATION; THERMOPHILIC BACTERIUM;

AMINO ACYL-TRNA SYNTHETASES; ARCHAEA; BACTERIA; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; PHYLOGENY;

PROKARYOTA;

EID: 79959256644     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro2593     Document Type: Article

References (108)

1. Jain, R., Rivera, M. C., Moore, J. E. & Lake, J. A. Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20, 1598-1602 (2003). (Pubitemid 41070820)
2. Yap, W. H., Zhang, Z. & Wang, Y. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181, 5201-5209 (1999). (Pubitemid 29416337)
3. Chan, C X., Darling, A. E., Beiko, R. G. & Ragan, M. A. Are protein domains modules of lateral genetic transfer? PLoS ONE 4, e4524 (2009).
4. Wang, Y. & Zhang, Z. Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology 146, 2845-2854 (2000).
5. Olendzenski, L. et al. Horizontal transfer of archaeal genes into the Deinococcaceae: detection by molecular and computer-based approaches. J. Mol. Evol. 51, 587-599 (2000). (Pubitemid 32001977)
6. Castillo-Ramirez, S., Vazquez-Castellanos, J. F., Gonzalez, V. & Cevallos, M. A. Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon. BMC Genomics 10, 536 (2009).
7. Omelchenko, M., Makarova, K., Wolf, Y., Rogozin, I. & Koonin, E. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 4, R55 (2003).
8. Igarashi, N. et al. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J. Mol. Evol. 52, 333-341 (2001). (Pubitemid 32368243)
9. Akagi, Y., Akamatsu, H., Otani, H. & Kodama, M. Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryot. Cell 8, 1732-1738 (2009).
10. Kaneko, S. & Itaya, M. Designed horizontal transfer of stable giant DNA released from Escherichia coli. J. Biochem. 147, 819-822 (2010).
11. Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R. & Koonin, E. V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442-444 (1998). (Pubitemid 28508919)
12. Nelson, K. E. et al. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329 (1999). (Pubitemid 29318123)
13. Beiko, R. G., Harlow, T. J. & Ragan, M. A. Highways of gene sharing in prokaryotes. Proc. Natl Acad. Sci. USA 102, 14332-14337 (2005). (Pubitemid 41429698)
14. Nesbo, C. L. et al. The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J. Bacteriol. 191, 1974-1978 (2009).
15. Boussau, B., Gueguen, L. & Gouy, M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol. Biol. 8, 272 (2008).
16. Zhaxybayeva, O. et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc. Natl Acad. Sci. USA 106, 5865-5870 (2009).
17. Nguyen, K. T., Piastro, K., Gray, T. A. & Derbyshire, K. M. Mycobacterial biofilms facilitate horizontal DNA transfer between strains of Mycobacterium smegmatis. J. Bacteriol. 192, 5134-5142 (2010).
18. Chafee, M. E., Funk, D. J., Harrison, R. G. & Bordenstein, S. R. Lateral phage transfer in obligate intracellular bacteria (Wolbachia): verification from natural populations. Mol. Biol. Evol. 27, 501-505 (2010).
19. Saisongkorh, W., Robert, C., La Scola, B., Raoult, D. & Rolain, J. M. Evidence of transfer by conjugation of Type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS ONE 5, e12666 (2010).
20. Brochier, C., Philippe, H. & Moreira, D. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16, 529-533 (2000).
21. Schouls, L. M., Schot, C. S. & Jacobs, J. A. Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J. Bacteriol. 185, 7241-7246 (2003). (Pubitemid 37509841)
22. Iyer, L. M., Koonin, E. V. & Aravind, L. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335, 73-88 (2004). (Pubitemid 38759754)
23. Makarova, K. S., Ponomarev, V. A. & Koonin, E. V. Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol. 2, RESEARCH 0033 (2001).
24. Boucher, Y., Douady, C. J., Sharma, A. K., Kamekura, M. & Doolittle, W. F. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J. Bacteriol. 186, 3980-3990 (2004). (Pubitemid 38746074)
25. Kanhere, A. & Vingron, M. Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol. Biol. 9, 9 (2009).
26. Danchin, E. G. et al. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc. Natl Acad. Sci. USA 107, 17651-17656 (2010).
27. Khomyakova, M., Bukmez, O., Thomas, L. K., Erb, T. J. & Berg, I. A. A methylaspartate cycle in haloarchaea. Science 331, 334-337 (2011).
28. Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226-2238 (2002). (Pubitemid 35440456)
29. Woese, C. R., Olsen, G. J., Ibba, M. & Soll, D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202-236 (2000). (Pubitemid 30143846)
30. O'Donoghue, P. & Luthey-Schulten, Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev. 67, 550-573 (2003).
31. Coscolla, M., Comas, I. & Gonzalez-Candelas, F. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Mol. Biol. Evol. 28, 985-1001 (2010).
32. Hendrickson, H. & Lawrence, J. G. Selection for chromosome architecture in bacteria. J. Mol. Evol. 62, 615-629 (2006). (Pubitemid 43965548)
33. Olendzenski, L., Zhaxybayeva, O. & Gogarten, J. P. in Horizontal Gene Transfer (eds Syvanen, M. & Kado, C. I.) 427-435 (Academic, New York, 2002).
34. Krupovic, M., Gribaldo, S., Bamford, D. H. & Forterre, P. The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements. Mol. Biol. Evol. 27, 2716-2732 (2010).
35. Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Rev. Microbiol. 3, 711-721 (2005). (Pubitemid 41195087)
36. McDaniel, L. D. et al. High frequency of horizontal gene transfer in the oceans. Science 330, 50 (2010).
37. Popa, O., Hazkani-Covo, E., Landan, G., Martin, W. & Dagan, T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21, 599-609 (2011).
38. Hooper, S., Mavromatis, K. & Kyrpides, N. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol. 10, R45 (2009).
39. Frost, L. S., Leplae, R., Summers, A. O. & Toussaint, A. Mobile genetic elements: the agents of open source evolution. Nature Rev. Microbiol. 3, 722-732 (2005). (Pubitemid 41195088)
40. Sobecky, P. A. & Hazen, T. H. Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol. Biol. 532, 435-453 (2009).
41. Malachowa, N. & DeLeo, F. R. Mobile genetic elements of Staphylococcus aureus. Cell. Mol. Life Sci. 67, 3057-3071 (2010).
42. Siefert, J. L. Defining the mobilome. Methods Mol. Biol. 532, 13-27 (2009).
43. Wozniak, R. A. & Waldor, M. K. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nature Rev. Microbiol. 8, 552-563 (2010).
44. Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl Acad. Sci. USA 102, 13950-13955 (2005). (Pubitemid 41377684)
45. Lapierre, P. & Gogarten, J. P. Estimating the size of the bacterial pan-genome. Trends Genet. 25, 107-110 (2009).
46. Puigbo, P., Wolf, Y. I. & Koonin, E. V. The tree and net components of prokaryote evolution. Genome Biol. Evol. 2, 745-756 (2010).
47. Lawrence, J. G. & Retchless, A. C. The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol. Biol. 532, 29-53 (2009).
48. Andam, C. P., Williams, D. & Gogarten, J. P. Biased gene transfer mimics patterns created through shared ancestry. Proc. Natl Acad. Sci. USA 107, 10679-10684 (2010).
49. Thomas, V. & Greub, G. Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours. Intervirology 53, 254-267 (2010).
50. Huang, J. & Gogarten, J. P. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol. 8, R99 (2007).
51. Martin, W., Brinkmann, H., Savonna, C. & Cerff, R. Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc. Natl Acad. Sci. USA 90, 8692-8696 (1993). (Pubitemid 23277736)
52. Fournier, G. P. & Gogarten, J. P. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J. Bacteriol. 190, 1124-1127 (2008). (Pubitemid 351170956)
53. Andam, C. P., Williams, D. & Gogarten, J. P. Natural taxonomy in light of horizontal gene transfer. Biol. Philos. 25, 589-602 (2010).
54. Omelchenko, M. V., Galperin, M. Y., Wolf, Y. I. & Koonin, E. V. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol. Direct 5, 31 (2010).
55. Farahi, K., Pusch, G. D., Overbeek, R. & Whitman, W. B. Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J. Mol. Evol. 58, 615-631 (2004). (Pubitemid 38609896)
56. Stern, A. et al. An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst. Biol. 59, 212-225 (2010).
57. Zhaxybayeva, O. Detection and quantitative assessment of horizontal gene transfer. Methods Mol. Biol. 532, 195-213 (2009).
58. Clark, R. & Neidthardt, F. Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior. J. Bacteriol. 172, 3237-3243 (1990). (Pubitemid 20179778)
59. Putzer, H., Brakhage, A. A. & Grunberg-Manago, M. Independent genes for two threonyl-tRNA synthetases in Bacillus subtilis. J. Bacteriol. 172, 4593-4602 (1990). (Pubitemid 20236757)
60. Yanagisawa, T. & Kawakami, M. How does Pseudomonas fluorescens avoid suicide from its antibiotic pseudomonic acid? Evidence for two evolutionarily distinct isoleucyl-tRNA synthetases conferring self-defense. J. Biol. Chem. 278, 25887-25894 (2003). (Pubitemid 36835350)
61. Thomas, C. M., Hothersall, J., Willis, C. L. & Simpson, T. J. Resistance to and synthesis of the antibiotic mupirocin. Nature Rev. Microbiol. 8, 281-289 (2010).
62. Gentry, D. R. et al. Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals subpopulations of Streptococcus pneumoniae with two distinct methionyl-tRNA synthetase genes. Antimicrob. Agents Chemother. 47, 1784-1789 (2003). (Pubitemid 36637796)
63. Brown, J. R. et al. Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens. EMBO Rep. 4, 692-698 (2003). (Pubitemid 36974754)
64. Vecchione, J. J. & Sello, J. K. A novel tryptophanyl-tRNA synthetase gene confers high-level resistance to indolmycin. Antimicrob. Agents Chemother. 53, 3972-3980 (2009).
65. Vecchione, J. J. & Sello, J. K. Regulation of an auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene via ribosome-mediated transcriptional attenuation. J. Bacteriol. 192, 3565-3573 (2010).
66. Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Selection in the evolution of gene duplications. Genome Biol. 3, RESEARCH0008 (2002).
67. Couturier, E. & Rocha, E. P. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol. Microbiol. 59, 1506-1518 (2006).
68. Zeng, Y., Roy, H., Patil, P. B., Ibba, M. & Chen, S. Characterization of two seryl-tRNA synthetases in albomycin-producing Streptomyces sp. strain ATCC 700974. Antimicrob. Agents Chemother. 53, 4619-4627 (2009).
69. Doolittle, W. F. et al. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Phil. Trans. R. Soc. B 358, 39-58 (2003). (Pubitemid 36178218)
70. Gogarten, J. P. & Townsend, J. P. Horizontal gene transfer, genome innovation and evolution. Nature Rev. Microbiol. 3, 679-687 (2005). (Pubitemid 41195085)
71. Fitch, W. M. & Upper, K. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harb. Symp. Quant. Biol. 52, 759-767 (1987). (Pubitemid 18262388)
72. Kandler, O. in Early Life on Earth, Nobel Symposium 84 (ed. Bengston, S.) 152-160 (Columbia Univ. Press, New York,1994).
73. Woese, C. The universal ancestor. Proc. Natl Acad. Sci. USA 95, 6854-6859 (1998). (Pubitemid 28278070)
74. Zhaxybayeva, O. & Gogarten, J. P. Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet. 20, 182-187 (2004). (Pubitemid 38369189)
75. Eriani, G., Delarue, M., Poch, O., Gangloff, J. & Moras, D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347, 203-206 (1990).
76. Fournier, G. P., Huang, J. & Gogarten, J. P. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Phil. Trans. R. Soc. B 364, 2229-2239 (2009).
77. Kim, H. S., Vothknecht, U. C., Hedderich, R., Celic, I. & Soll, D. Sequence divergence of seryl-tRNA synthetases in archaea. J. Bacteriol. 180, 6446-6449 (1998). (Pubitemid 29006055)
78. Korencic, D., Polycarpo, C., Weygand-Durasevic, I. & Soll, D. Differential modes of transfer RNASer recognition in Methanosarcina barkeri. J. Biol. Chem. 279, 48780-48786 (2004). (Pubitemid 39625756)
79. Bilokapic, S., Korencic, D., Soll, D. & Weygand- Durasevic, I. The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species from all three kingdoms of life. Eur. J. Biochem. 271, 694-702 (2004). (Pubitemid 38250912)
80. Jaric, J. et al. Identification of amino acids in the N-terminal domain of atypical methanogenic-type seryl-tRNA synthetase critical for tRNA recognition. J. Biol. Chem. 284, 30643-30651 (2009).
81. Ibba, M., Curnow, A. W. & Soll, D. Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem. Sci. 22, 39-42 (1997). (Pubitemid 27076803)
82. Gogarten, J., Fournier, G. & Zhaxybayeva, O. Gene transfer and the reconstruction of life's early history from genomic data. Space Sci. Rev. 135, 115-131 (2008).
83. Gevers, D. et al. Stepping stones towards a new prokaryotic taxonomy. Phil. Trans. R. Soc. B 361, 1911-1916 (2006). (Pubitemid 44787026)
84. Bapteste, E. et al. Prokaryotic evolution and the tree of life are two different things. Biol. Direct 4, 34 (2009).
85. Huang, J. & Gogarten, J. P. Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet. 22, 361-366 (2006). (Pubitemid 44015971)
86. Huang, J., Xu, Y. & Gogarten, J. P. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol. 22, 2142-2146 (2005). (Pubitemid 41437795)
87. Wolf, Y. I., Rogozin, I. B., Grishin, N. V. & Koonin, E. V. Genome trees and the tree of life. Trends Genet. 18, 472-479 (2002).
88. Korbel, J. O., Snel, B., Huynen, M. A. & Bork, P. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18, 158-162 (2002). (Pubitemid 34164642)
89. Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987). (Pubitemid 17082512)
90. Brochier, C., Forterre, P. & Gribaldo, S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5, R17 (2004).
91. Mongodin, E. F. et al. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl Acad. Sci. USA 102, 18147-18152 (2005). (Pubitemid 41798516)
92. Degnan, J. H. & Rosenberg, N. A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2, e68 (2006).
93. Herbeck, J. T., Degnan, P. H. & Wernegreen, J. J. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (γ-Proteobacteria). Mol. Biol. Evol. 22, 520-532 (2005). (Pubitemid 40299501)
94. Zhaxybayeva, O., Lapierre, P. & Gogarten, J. P. Genome mosaicism and organismal lineages. Trends Genet. 20, 254-260 (2004). (Pubitemid 38510439)
95. Zhaxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F. & Papke, R. T. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16, 1099-1108 (2006). (Pubitemid 44320397)
96. Hilario, E. & Gogarten, J. P. Horizontal transfer of ATPase genes - the tree of life becomes a net of life. Biosystems 31, 111-119 (1993). (Pubitemid 24045859)
97. Horn, M. et al. Illuminating the evolutionary history of chlamydiae. Science 304, 728-730 (2004). (Pubitemid 38560877)
98. Becker, B., Hoef-Emden, K. & Melkonian, M. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol. Biol. 8, 203 (2008).
99. Moustafa, A., Reyes-Prieto, A. & Bhattacharya, D. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS ONE 3, e2205 (2008).
100. de Koning, A. P., Brinkman, F. S., Jones, S. J. & Keeling, P. J. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol. Biol. Evol. 17, 1769-1773 (2000).
101. Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704 (2003). (Pubitemid 37365050)
102. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307-1320 (2008). (Pubitemid 351882003)
103. Lanave, C., Preparata, G., Saccone, C. & Serio, G. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20, 86-93 (1984). (Pubitemid 14116237)
104. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003). (Pubitemid 37038874)
105. Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105 (2005). (Pubitemid 40668057)
106. Posada, D. & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998). (Pubitemid 28552116)
107. Corvaglia, A. R. et al. A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains. Proc Natl Acad. Sci. USA 107, 11954-11958 (2010).
108. Pearson, T. et al. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol. 7, 78 (2009).