Lateral gene transfers and the evolution of eukaryotes: Theories and data

International Journal of Systematic and Evolutionary Microbiology

Volumn 52, Issue 5, 2002, Pages 1893-1900

  Katz, Laura A ^a  

^a SMITH COLLEGE   (United States)

Author keywords

Chimerism; Gene genealogies; Horizontal gene transfer; Origin of eukaryotes

Indexed keywords

ARTICLE; CELL NUCLEUS; CELL ORGANELLE; CHIMERA; CONTROLLED STUDY; DONOR; EUKARYOTE; EUKARYOTIC CELL; GENE SEQUENCE; GENE TRANSFER; GENETIC VARIABILITY; HYPOTHESIS; MICROBIAL GENETICS; MICROFLORA; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; RECIPIENT; THEORY; VERTICAL TRANSMISSION;

ANIMALS; ECOSYSTEM; EUKARYOTIC CELLS; EVOLUTION; GENE TRANSFER, HORIZONTAL; GENETICS, MICROBIAL; GENOME, HUMAN; HUMANS; METABOLISM; MODELS, GENETIC; ORGANELLES;

DARWINIA; EUKARYOTA; PROKARYOTA;

EID: 0036739501     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.02113-0     Document Type: Article

References (76)

1. Adams, K. L., Song, K., Roessler, P. G., Nugent, J. M., Doyle, J. L., Doyle, J. J. & Palmer, J. D. (1999). Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc Natl Acad Sci U S A 96, 13863-13868.
2. Andersson, J. O., Doolittle, W. F. & Nesbo, C. L. (2001). Genomics - Are there bugs in our genome? Science 292, 1848-1850.
3. Bertolla, F. & Simonet, P. (1999). Horizontal gene transfers in the environment: natural transformation as a putative process for gene transfers between transgenic plants and microorganisms. Res Microbiol 150, 375-384.
4. Best, A. A. & Olsen, G. J. (2001). Similar subunit architecture of archaeal and eukaryal RNA polymerases. FEMS Microbiol Lett 195, 85-90.
5. Boucher, Y. & Doolittle, W. F. (2000). The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol Microbiol 37, 703-716.
6. Brown, J. R. & Doolittle, W. F. (1997). Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev 61, 456-502.
7. Brown, J. R., Masuchi, Y., Robb, F. T. & Doolittle, W. F. (1994). Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J Mol Evol 38, 566-576.
8. Bui, E. T., Bradley, P. J. & Johnson, P. J. (1996). A common evolutionary origin for mitochondria and hydrogenosomes. Proc Natl Acad Sci U S A 93, 9651-9656.
9. Cavalier-Smith, T. (1983). A 6-kingdom classification and a unified phylogeny. In Endocytobiology II: Intracellular Space as Oligogenetic Ecosystem, pp. 1027-1034. Edited by H. E. A. Schenk & W. Schwemmler. Berlin: Walter de Gruyter Press.
10. Chateau, S., Sangwan, R. S. & Sangwan-Norreel, B. S. (2000). Competence of Arabidopsis thaliana genotypes and mutants from Agrobacterium tumefaciens-mediated gene transfer: role of phytohormones. J Exp Bot 51, 1961-1968.
11. Clark, C. G. & Roger, A. J. (1995). Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc Natl Acad Sci U S A 92, 6518-6521.
12. De Block, M. (1994). The cell biology of plant transformation: current state, problems, prospects and the implications for plant breeding. Euphytica 71, 1-14.
13. de Koning, A. P., Brinkman, F. S. L., Jones, S. J. M. & Keeling, P. J. (2000). Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol Biol Evol 17, 1769-1773.
14. DiRuggiero, J., Brown, J. R., Bogert, A. P. & Robb, F. T. (1999). DNA repair systems in archaea: mementos from the last universal common ancestor? J Mol Evol 49, 474-84.
15. Doolittle, W. F. (1998). You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14, 307-311.
16. Doolittle, W. F. (1999). Lateral genomics. Trends Biochem Sci 24, M5-M8.
17. Eisen, J. A. (2000). Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Microbiol 10, 606-611.
18. Garcia-Vallvé, S., Romeu, A. & Palau, J. (2000a). Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10, 1719-1725.
19. Garcia-Vallvé, S., Romeu, A. & Palau, J. (2000b). Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17, 352-361.
20. Gerbod, D., Edgcomb, V. P., Noel, C., Vanacova, S., Wintjens, R., Tachezy, J., Sogin, M. L. & Viscogliosi, E. (2001). Phylogenetic relationships of class II fumarase genes from trichomonad species. Mol Biol Evol 18, 1574-1584.
21. Germot, A., Philippe, H. & Le Guyader, H. (1996). Presence of a mitochondrial -type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes. Proc Natl Acad Sci U S A 93, 14614-14617.
22. Germot, A., Philippe, H. & Le Guyader, H. (1997). Evidence for loss of mitochondria in microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol 87, 159-168.
23. Golding, G. B. & Gupta, R. S. (1995). Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol Biol Evol 12, 1-6.
24. Gray, M. W. (1999). Evolution of organellar genomes. Curr Opin Genet Dev 9, 678-87.
25. Graybeal, A. (1998). Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47, 9-17.
26. Gupta, R. S. & Golding, G. B. (1996). The origin of the eukaryotic cell. Trends Biochem Sci 21, 166-171.
27. Hashimoto, T., Sänchez, L. B., Shirakura, T., Müller, M. & Hasegawa, M. (1998). Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc Natl Acad Sci U S A 95, 6860-6865.
28. Henze, K. & Martin, W. (2001). How do mitochondrial genes get into the nucleus? Trends Genet 17, 383-387.
29. Hilario, E. & Gogarten, J. P. (1993). Horizontal transfer of ATPase genes - the tree of life becomes a net of life. Biosystems 31, 111-119.
30. Hirt, R. P., Healy, B., Vossbrinck, C. R., Canning, E. U. & Embley, T. M. (1997). A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria. Curr Biol 7, 995-998.
31. Hirt, R. P., Logsdon, J. M., Healy, B., Dorey, M. W., Doolittle, W. F. & Embley, T. M. (1999). Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A 96, 580-585.
32. Hoffmann, T., Golz, C. & Schieder, O. (1994). Foreign DNA-sequences are received by a wild-type strain of Aspergillus niger after coculture with transgenic higher-plants. Current Genetics 27, 70-76.
33. Horner, D. S. & Embley, T. M. (2001). Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol Biol Evol 18, 1970-1975.
34. Horner, D. S., Hirt, R. P., Kilvington, S., Lloyd, D. & Embley, T. M. (1996). Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proc R Soc Lond B 263, 1053-1059.
35. Horner, D. S., Hirt, R. P. & Embley, T. M. (1999). A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Mol Biol Evol 16, 1280-1291.
36. Horner, D. S., Foster, P. G. & Embley, T. M. (2000). Iron hydrogenases and the evolution of anaerobic eukaryotes. Mol Biol Evol 17, 1695-1709.
37. Katz, L. A. (1998). Changing perspectives on the origin of eukaryotes. Trends Ecol Evol 13, 493-497.
38. Katz, L. A. (1999). The tangled web: gene genealogies and the origin of eukaryotes. Am Nat 154, S137-SI45.
39. Keeling, P. J. (1998). A kingdom's progress: Archezoa and the origin of eukaryotes. BioEssays 20, 87-95.
40. Keeling, P. J. & Doolittle, W. F. (1997). Evidence that eukaryotic triosephosophate isomerase is of alpha-proteobacterial origin. Proc Natl Acad Sci U S A 94, 1270-1275.
41. Klotz, M. G., Klassen, G. R. & Loewen, P. C. (1997). Phylogenetic relationships among prokaryotic and eukaryotic catalases. Mol Biol Evol 14, 951-958.
42. Kurland, C. G. & Andersson, S. G. E. (2000). Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64, 786-820.
43. Lander, E. S., Linton, L. M., Birren, B. & 239 other authors (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
44. Lang, B. F., Gray, M. W. & Burger, G. (1999). Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33, 351-397.
45. Lange, B. M., Rujan, T., Martin, W. & Croteau, R. (2000). Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc Natl Acad Sci U S A 97, 13172-13177.
46. Lawrence, J. G. (1999). Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 2, 519-523.
47. Lawrence, J. G. & Ochman, H. (1998). Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95, 9413-9417.
48. Margulis, L. (1996). Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc Natl Acad Sci U S A 97, 1071-1076.
49. Margulis, L., Dolan, M. F. & Guerrero, R. (2000). The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitocbondriate protists. Proc Natl Acad Sci U S A 97, 6954-6959.
50. Martin, W. (1999). Mosaic bacterial chromosomes: a challenge on route to a tree of genomes. Bioessays 21, 99-104.
51. Martin, W. & Müller, M. (1998). The hydrogen hypothesis for the first eukaryote. Nature 392, 37-41.
52. Martin, W. & Herrmann, R. G. (1989). Gene transfer from organelles to the nucleus: how much, what happens and why? Plant Physiol 118, 9-17.
53. Moreira, D. & Lopez-Garcia, P. (1998). Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J Mol Evol 47, 517-530.
54. Morrison, H. G., Roger, A. J., Nystul, T. G., Gillin, F. D. & Sogin, M. L. (2001). Giardia lamblia expresses a proteobacterial-like DnaK homolog. Mol Biol Evol 18, 530-541.
55. Nevoigt, E., Fassbender, A. & Stahl, U. (2000). Cells of the yeast Saccharomyces cerevisiae are transformable by DNA under non-artificial conditions. Yeast 16, 1107-1110.
56. Paget, E., Lebrun, M., Freyssinet, G. & Simonet, P. (1998). The fate of recombinant plant DNA in soil. Eur J Soil Biol 34, 81-88.
57. Patterson, D. J. (1999). The diversity of eukaryotes. Am Nat 154, S96-S124.
58. Poe, S. (1998a). The effect of taxonomic sampling on accuracy of phylogeny estimation: test case of a known phylogeny. Mol Biol Evol 15, 1086-1090.
59. Poe, S. (1998b). Sensitivity of phylogeny estimation to taxonomic sampling. Syst Biol 47, 18-31.
60. Ribeiro, S. & Golding, G. B. (1998). The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 15, 779-788.
61. Roger, A. J. (1999). Reconstructing early events in eukaryotic evolution. Am Nat 154, S146-S163.
62. Roger, A. J. & Brown, J. R. (1996). A chimeric origin for eukaryotes re-examined. Trends Biochem Sci 21, 370-371.
63. Roger, A. J., Svard, S. G., Tovar, J., Clark, C. G., Smith, M. W., Gillin, F. D. & Sogin, M. L. (1998). A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc Natl Acad Sci U S A 95, 229-234.
64. Roger, A., Morrison, H. G. & Sogin, M. L. (1999). Primary structure and phylogenetic relationships or a malate dehydrogenase gene from Giardia lamblia. J Mol Evol 48, 750-755.
65. Rosewich, U. L. & Kistler, H. C. (2000). Role of horizontal gene transfer in the evolution of fungi. Anna Rev Phytopathol 38, 325-363.
66. Rujan, T. & Martin, W. (2001). How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet 17, 113-120.
67. Salzberg, S. L., White, O., Peterson, J. & Eisen, J. A. (2001). Microbial genes in the human genome: lateral transfer or gene loss? Science 292, 1903-1906.
68. Stanhope, M. J., Lupas, A., Italia, M. J., Koretke, K. K., Volker, C. & Brown, J. R. (2001). Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411, 940-944.
69. Stibitz, T. B., Keeling, P. J. & Bhattacharya, D. (2000). Symbiotic origin of a novel actin gene in the cryptophyte Pyrenomonas helgolandii. Mol Biol Evol 17, 1731-1738.
70. Swofford, D. L., Olsen, G. J., Waddell, P. J. & Hillis, D. M. (1996). Phylogenetic inference. In Molecular Systematics, pp. 407-514. Edited by D. M. Hillis, C. Moritz & B. K. Mable. Sunderland, MA: Sinauer Associates.
71. Thorsness, P. E. & Fox, T. D. (1990). Escape of DNA from mitochondria to the nucleus in Saccharomyees cerevisiae. Nature 346, 376-379.
72. Woese, C. R. (1998). The universal ancestor. Proc Natl Acad Sci USA 95, 6854-6859.
73. Wolf, Y. I. & Koonin, E. V. (2001). Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group. Trends Genet 17, 431-433.
74. Yoder, A. D. & Irwin, J. A (1999). Phylogeny of the Lemuridae: effects of character and taxon sampling on resolution of species relationships within Eulemur. Cladistics 15, 351-361.
75. Zillig, W. (1991). Comparative biochemistry of Archaea and Bacteria. Curr Opin Genet Dev 1, 544-551.
76. Zillig, W., Klenk, H. P., Palm, P., Leffers, H., Puhler, G., Gropp, F. & Garrett, R. A. (1989). Did eukaryotes originate by a fusion event. Endocytobiosis Cell Res 6, 1-25.