Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae

Eukaryotic Cell

Volumn 4, Issue 6, 2005, Pages 1102-1115

  Hall, Charles ^a   Brachat, Sophie ^b   Dietrich, Fred S ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYL SULFATASE; DIHYDROOROTATE DEHYDROGENASE; FUNGAL PROTEIN; OXIDOREDUCTASE; SULFATASE;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CHEMISTRY; CROSS BREEDING; DNA SEQUENCE; FUNGAL GENE; GENETIC COMPLEMENTATION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BAYES THEOREM; CROSSES, GENETIC; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE TRANSFER, HORIZONTAL; GENES, FUNGAL; GENETIC COMPLEMENTATION TEST; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SULFATASES;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CANDIDA ALBICANS; EREMOTHECIUM GOSSYPII; EUKARYOTA; LACTOBACILLALES; SACCHAROMYCES BAYANUS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETACEAE; SACCHAROMYCETES;

EID: 20444468864     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.4.6.1102-1115.2005     Document Type: Article

References (62)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329-3330.
3. Benson, D. A., M. S. Boguski, D. J. Lipman, and J. Ostell. 1997. GenBank. Nucleic Acids Res. 25:1-6.
4. Boer, V. M., J. H. de Winde, J. T. Pronk, and M. D. Piper. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278:3265-3274.
5. Bolotin, A., P. Wincker, S. Mauger, O. Jaillon, K. Malarme, J. Weissenbach, S. D. Ehrlich, and A. Sorokin. 2001. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11:731-753.
6. Boucher, Y., and W. F. Doolittle. 2000. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol Microbiol. 37:703-716.
7. Braun, E. L., A. L. Halpern, M. A. Nelson, and D. O. Natvig. 2000. Largescale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res. 10:416-430.
8. Burke, D. T., D. Dawson, and T. Stearns. 2000. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual. Cold Spring Laboratory Press, New York, N.Y.
9. Cherest, H., and Y. Surdin-Kerjan. 1992. Genetic analysis of a new mutation conferring cysteine auxotrophy in Saccharomyces cerevisiae: updating of the sulfur metabolism pathway. Genetics 130:51-58.
10. Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76.
11. Dietrich, F. S., S. Voegeli, S. Brachat, A. Lerch, K. Gates, S. Steiner, C. Mohr, R. Pohlmann, P. Luedi, S. Choi, R. A. Wing, A. Flavier, T. D. Gaffney, and P. Philippsen. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307.
12. Diezmann, S., C. J. Cox, G. Schonian, R. J. Vilgalys, and T. G. Mitchell. 2004. Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis. J. Clin. Microbiol. 42:5624-5635.
13. Dreiseikelmann, B. 1994. Translocation of DNA across bacterial membranes. Microbiol. Rev. 58:293-316.
14. Dujon, B., D. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. De Montigny, C. Marck, C. Neuveglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J. M. Beckerich, E. Beyne, C. Bleykasten, A. Boisrame, J. Boyer, L. Cattolico, F. Confanioleri, A. De Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J. M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G. F. Richard, M. L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wesolowski-Louvel, E. Westnof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker, and J. L. Souciet. 2004. Genome evolution in yeasts. Nature 430:35-44.
15. Fukami, K., and Y. Tateno. 1989. On the maximum likelihood method for estimating molecular trees: uniqueness of the likelihood point. J. Mol. Evol. 28:460-464.
16. Galagan, J. E., S. E. Calvo, K. A. Borkovich, E. U. Selker, N. D. Read, D. Jaffe, W. FitzHugh, L. J. Ma, S. Smirnov, S. Purcell, B. Rehman, T. Elkins, R. Engels, S. Wang, C. B. Nielsen, J. Butler, M. Endrizzi, D. Qui, P. Ianakiev, D. Bell-Pedersen, M. A. Nelson, M. Werner-Washburne, C. P. Selitrennikoff, J. A. Kinsey, E. L. Braun, A. Zelter, U. Schulte, G. O. Kothe, G. Jedd, W. Mewes, C. Staben, E. Marcotte, D. Greenberg, A. Roy, K. Foley, J. Naylor, N. Stange-Thomann, R. Barrett, S. Gnerre, M. Kamal, M. Kamvysselis, E. Mauceli, C. Bielke, S. Rudd, D. Frishman, S. Krystofova, C. Rasmussen, R. L. Metzenberg, D. D. Perkins, S. Kroken, C. Cogoni, G. Macino, D. Catcheside, W. Li, R. J. Pratt, S. A. Osmani, C. P. DeSouza, L. Glass, M. J. Orbach, J. A. Berglund, R. Voelker, O. Yarden, M. Plamann, S. Seiler, J. Dunlap, A. Radford, R. Aramayo, D. O. Natvig, L. A. Alex, G. Mannhaupt, D. J. Ebbole, M. Freitag, I. Paulsen, M. S. Sachs, E. S. Lander, C. Nusbaum, and B. Birren. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868.
17. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:563-567.
18. Gojkovic, Z., W. Knecht, E. Zameitat, J. Warneboldt, J. B. Coutelis, Y. Pynyaha, C. Neuveglise, K. Moller, M. Loffler, and J. Piskur. 2004. Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol. Genet. Genomics 271:387-393.
19. Gonnet, G. H., M. A. Cohen, and S. A. Benner. 1992. Exhaustive matching of the entire protein sequence database. Science 256:1443-1445.
20. Gray, M. W. 1993. Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3:884-890.
21. Heinemann, J. A., and G. F. Sprague, Jr. 1989. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340:205-209.
22. Horner, D. S., P. G. Foster, and T. M. Embley. 2000. Iron hydrogenases and the evolution of anaerobic eukaryotes. Mol. Biol. Evol. 17:1695-1709.
23. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
24. Jensen, K. F., and O. Bjornberg. 1998. Evolutionary and functional families of dihydroorotate dehydrogenase. Paths Pyrimidines 6:20-28.
25. Kahnert, A., and M. A. Kertesz. 2000. Characterization of a sulfur-regulated oxygenative alkylsulfatase from Pseudomonas putida S-313. J. Biol. Chem. 275:31661-31667.
26. Katz, L. A. 2002. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int. J. Syst. Evol. Microbiol. 52:1893-1900.
27. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
28. Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254.
29. Klotz, M. G., G. R. Klassen, and P. C. Loewen. 1997. Phylogenetic relationships among prokaryotic and eukaryotic catalases. Mol. Biol. Evol. 14:951-958.
30. Koonin, E. V., K. S. Makarova, and L. Aravind. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55:709-742.
31. Kurtzman, C. P., and C. J. Robnett. 2003. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analysis. FEMS Yeast Res. 3:417-432.
32. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50:479-496.
33. Moore, J. D., and S. A. Endow. 1996. Kinesin proteins: a phylum of motors for microtubule-based motility. Bioessays 18:207-219.
34. Morell, V. 1996. TreeBASE: the roots of phylogeny. Science 273:569.
35. Mower, J. P., S. Stefanovic, G. J. Young, and J. D. Palmer. 2004. Gene transfer form parasitic to host plants. Nature 432:165-166.
36. Mullis, K., F. Faloona, S. Scharf, R. Saiki, G. Horn, and H. Erlich. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp. Quant. Biol. 51(Part 1):263-273.
37. Nagy, M., F. Lacroute, and D. Thomas. 1992. Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts. Proc. Natl. Acad. Sci. USA 89:8966-8970.
38. Nara, T., T. Hshimoto, and T. Aoki. 2000. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257:209-222.
39. Nevoigt, E., A. Fassbender, and U. Stahl. 2000. Cells of the yeast Saccharomyces cerevisiae are transformable by DNA under non-artificial conditions. Yeast 16:1107-1110.
40. Ochman, H. 2001. Lateral and oblique gene transfer. Curr. Opin. Genet. Dev. 11:616-619.
41. Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
42. Paietta, J. V. 1989. Molecular cloning and regulatory analysis of the arylsulfatase structural gene of Neurospora crassa. Mol. Cell. Biol. 9:3630-3637.
43. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
44. Pogorevc, M., and K. Faber. 2003. Purification and characterization of an inverting stereo- and enantioselective sec-alkylsulfatase from the gram-positive bacterium Rhodococcus ruber DSM 44541. Appl. Environ. Microbiol. 69:2810-2815.
45. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
46. Reiss, J. 1974. Cytochemical detection of hydrolases in fungus cells. 3. Aryl sulfatase. J. Histochem. Cytochem. 22:183-188.
47. Rip, J. W., and B. A. Gordon. 1998. A simple spectrophotometric enzyme assay with absolute specificity for arylsulfatase A. Clin. Biochem. 31:29-31.
48. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
49. Roy, A. 1992. Nucleotide sequence of the URA1 gene of Saccharomyces cerevisiae. Gene 118:149-150.
50. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
51. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
52. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
53. Swofford, D. L. 1999. PAUP* Phylogenetics analysis using parsimony (*and other methods). Sinauer, Sunderland, MA.
54. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
55. Visser, W., W. A. Scheffers, W. H. Batenburg-van der Vegte, and J. P. van Dijken. 1990. Oxygen requirements of yeasts. Appl. Environ. Microbiol. 56:3785-3792.
56. Wach, A., A. Brachat, R. Pohlmann, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793-1808.
57. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:691-699.
58. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, R. W. Davis, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
59. Wood, V., K. M. Rutherford, A. Ivens, M. A. Ragjandream, and B. Barrell. 2001. A re-annotation of the Saccharomyces cerevisiae genome. Comp. Funct. Genomics 2:143-154.
60. Wuyts, J., Y. Van de Peer, T. Winkelmans, and R. De Wachter. 2002. The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30:183-185.
61. Zameitat, E., W. Knecht, J. Piskur, and M. Loffler. 2004. Two different dihydroorotate dehydrogenases from yeast Saccharomyces kluyveri. FEBS Lett. 568:129-134.
62. Zhu, J., P. M. Oger, B. Schrammeijer, P. J. Hooykaas, S. K. Farrand, and S. C. Winans. 2000. The bases of crown gall tumorigenesis. J. Bacteriol. 182:3885-3895.