Yeast genome evolution in the post-genome era

Current Opinion in Microbiology

Volumn 2, Issue 5, 1999, Pages 548-554

  Seoighe, Cathal ^a   Wolfe, Kenneth H ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA HYBRIDIZATION; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENE LOSS; GENE SEQUENCE; MICROBIAL GENETICS; NONHUMAN; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 0032879798     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(99)00015-6     Document Type: Review

References (53)

1. Goffeau A, Aert R, Agostini-Carbone ML, Ahmed A, Aigle M, Alberghina L, Allen E, Alt-Mörbe J, André B, Andrews Set al. The Yeast Genome Directory. Nature. 387(suppl):1997;5-105.
2. Kurtzman CP, Fell JW The Yeasts, a Taxonomic Study, edn 4. 1998;Elsevier, Amsterdam.
3. Kurtzman CP, Robnett CJ Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek. 73:1998;331-371. In a tour de force of systematics, Kurtzman and Robnett sequenced the variable D1/D2 domain of 26S ribosomal RNA from the type strains of virtually every ascomycete yeast species (about 500 species). Although the sequenced region is rather short (600 nucleotides) and the phylogenetic trees often have poor resolution on key branches, this work will provide a firm molecular footing for the future taxonomy of ascomycetes.
4. Cai J, Roberts IN, Collins MD Phylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences. Int J Syst Bacteriol. 46:1996;542-549.
5. James SA, Cai J, Roberts IN, Collins MD A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov. Int J Syst Bacteriol. 47:1997;453-460.
6. Sequencing of Candida albicans at Stanford's DNA Sequencing and Technology Center on World Wide Web URL: http://www-sequence.stanford.edu/group/candida/.
7. Sanger Centre Candida albicans Pilot Sequencing Project on World Wide Web URL: http://www.sanger.ac.uk/Projects/C_albicans/.
8. Tait E, Simon MC, King S, Brown AJ, Gow NA, Shaw DJ A Candida albicans genome project: cosmid contigs, physical mapping, and gene isolation. Fungal Genet Biol. 21:1997;308-314.
9. Dietrich FS, Voegeli S, Gaffney T, Mohr C, Rebischung C, Wing R, Choi S, Goff S, Philippsen P Gene map of chromosome I of Ashbya gossypii. Curr Genet. 35:1999;233.
10. Genoscope STS Sequencing from 13 Hemiascomycete Yeasts on World Wide Web URL: http://www.genoscope.cns.fr/externe/English/Projets/Projet_AR/AR. html.
11. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282:1998;2012-2018.
12. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith Tet al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028.
13. Ohno S Evolution by Gene Duplication. 1970;George Allen and Unwin, London.
14. Lundin LG Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics. 16:1993;1-19.
15. Ahn S, Tanksley SD Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci. 90:1993;7980-7984.
16. Ryu SL, Murooka Y, Kaneko Y Reciprocal translocation at duplicated RPL2 loci might cause speciation of Saccharomyces bayanus and Saccharomyces cerevisiae. Curr Genet. 33:1998;345-351.
17. Wolfe KH, Shields DC Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387:1997;708-713.
18. Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SGet al. Overview of the yeast genome. Nature. 387(suppl):1997;7-65.
19. Coissac E, Maillier E, Netter P A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres. Mol Biol Evol. 14:1997;1062-1074.
20. Keogh RS, Seoighe C, Wolfe KH Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast. 14:1998;443-457.
21. Ozier-Kalogeropoulos O, Malpertuy A, Boyer J, Tekaia F, Dujon B Random exploration of the Kluyveromyces lactis genome and comparison with that of Saccharomyces cerevisiae. Nucleic Acids Res. 26:1998;5511-5524. The K. lactis genome was surveyed by random sequencing. The most informative data came from sequencing both ends of plasmid clones with 2-3 kb inserts, because this provided information about gene order as well as gene content.
22. Seoighe C, Wolfe KH Updated map of duplicated regions in the yeast genome. Gene. 1999;. in press.
23. Seoighe C, Wolfe KH Extent of genomic rearrangement after genome duplication in yeast. Proc Natl Acad Sci USA. 95:1998;4447-4452.
24. El-Mabrouk N, Bryant D, Sankoff D Reconstructing the pre doubling genome. Istrail S, Pevzner P, Waterman M RECOMB '99: Proceedings of the Third International Conference on Computational Molecular Biology: 1999, 11-14 April: Lyon, France. 1999;154-163 ACM Press, New York. The authors, in a rigorous treatment of the problem of estimating the 'pre-doubling' organisation of the yeast genome, calculated that an absolute minimum of 38 reciprocal translocations must have occurred to scamble gene order after genome duplication. They also suggested an algorithm for constructing the pre-doubling genome, and proposed one such ancestor. Also of interest here, however, would be a description of the class of equivalent solutions for the pre-doubling genome. Common features of the class of most parsimonious solutions, if they exist, could suggest something about the real pre-doubling genome.
25. Ryu SL, Murooka Y, Kaneko Y Genomic reorganization between two sibling yeast species, Saccharomyces bayanus and Saccharomyces cerevisiae. Yeast. 12:1996;757-764.
26. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028.
27. Dujon B The yeast genome project: what did we learn? Trends Genet. 12:1996;263-270.
28. Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J Preservation of duplicate genes by complementary degenerative mutations. Genetics. 151:1999;1531-1545.
29. Thatcher JW, Shaw JM, Dickinson WJ Marginal fitness contributions of nonessential genes in yeast. Proc Natl Acad Sci. 95:1998;253-257.
30. Hodges PE, McKee AH, Davis BP, Payne WE, Garrels JI The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res. 27:1999;69-73.
31. Planta RJ, Mager WH The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast. 14:1998;471-477.
32. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95:1998;717-728. Although it was not the primary aim of the study, this paper is one of the best examples so far of the power of microarray technology to study gene expression on a global scale. The authors estimated the number of mRNA molecules per cell, and mRNA half-life, for every gene in the S. cerevisiae genome under conditions of growth to mid-log phase in YPD media, using Affymetrix high-density oligonucleotide arrays. Included in the wealth of data from this experiment is the finding that under these conditions, the expression levels of cytosolic and mitochondrial ribosomal proteins average 29 and 1.4 mRNA molecules per cell, respectively.
33. Bankaitis VA, Malehorn DE, Emr SD, Greene R The Saccharomyces cerevisiae SEC14 gene encodes a cytosolic factor that is required for transport of secretory proteins from the yeast Golgi complex. J Cell Biol. 108:1989;1271-1281.
34. Sharp PM, Lloyd AT Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. Nucleic Acids Res. 21:1993;179-183.
35. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F The mosaic genome of warm-blooded vertebrates. Science. 228:1985;953-958.
36. Bradnam KR, Seoighe C, Sharp PM, Wolfe KH G+C content variation along and among Saccharomyces cerevisiae chromosomes. Mol Biol Evol. 16:1999;666-675.
37. Li W, Stolovitzky G, Bernaola-Galvan P, Oliver JL Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes. Genome Res. 8:1998;916-928.
38. Kielland-Brandt M, Nielsson-Tillgren T, Gjermansen C, Holmberg S, Pedersen MB Genetics of Brewing Yeasts. Wheals AE, Rose AH, Harrison JS The Yeasts. 1995;223-254 Academic Press, London.
39. Tamai Y, Momma T, Yoshimoto H, Kaneko Y Co-existence of two types of chromosome in the bottom fermenting yeast Saccharomyces pastorianus. Yeast. 14:1998;923-933.
40. Petersen RF, Marinoni G, Nielsen ML, Piskur J Molecular approaches for analyzing diversity and phylogeny among yeast species. Erbst JF, Schmidt A Dimorphism in Human Pathogenic and Apathogenic Yeasts. 1999;Karger, Basel. Viable hybrid yeast strains containing most chromosomes from both parents were constructed between pairs of sensu stricto species, although spore viability is low. In hybridisation between sensu stricto and sensu lato species, the hybrids lose all or most of one set of parental chromosomes during mitosis. Petersen et al. suggest that some genes may be retained in two copies either by limited aneuploidy or by integration into the chromosomes of the other parent.
41. Masneuf I, Hansen J, Groth C, Piskur J, Dubourdieu D New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol. 64:1998;3887-3892.
42. Groth C, Hansen J, Piskur J A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol. 1999;. in press. Sequence analysis of a yeast isolated from cider (CID1) shows that its nuclear genome contains sequences derived from both S. cerevisiae and S. bayanus. Its mitochondrial DNA is derived from a third species, Saccharomyces sp. IFO 1802. Exchange of genetic material between Saccharomyces species may be more frequent than previously supposed.
43. Gilley J, Fried M Extensive gene order differences within regions of conserved synteny between the Fugu and human genomes: implications for chromosomal evolution and the cloning of disease genes. Hum Mol Genet. 8:1999;1313-1320.
44. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL Zebrafish hox clusters and vertebrate genome evolution. Science. 282:1998;1711-1714.
45. Kordis D, Gubensek F Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc Natl Acad Sci USA. 95:1998;10704-10709.
46. Lawn RM, Schwartz K, Patthy L Convergent evolution of apolipoprotein(a) in primates and hedgehog. Proc Natl Acad Sci USA. 94:1997;11992-11997.
47. Doi M, Homma M, Chindamporn A, Tanaka K Estimation of chromosome number and size by pulsed-field gel electrophoresis (PFGE) in medically important Candida species. J Gen Microbiol. 138:1992;2243-2251.
48. Maleszka R, Clark-Walker GD Yeasts have a four-fold variation in ribosomal DNA copy number. Yeast. 9:1993;53-58.
49. Miyazaki H, Miyazaki Y, Geber A, Parkinson T, Hitchcock C, Falconer DJ, Ward DJ, Marsden K, Bennett JE Fluconazole resistance associated with drug efflux and increased transcription of a drug transporter gene, PDH1, in Candida glabrata. Antimicrob Agents Chemother. 42:1998;1695-1701.
50. Zhou PB, Thiele DJ Isolation of a metal-activated transcription factor gene from Candida glabrata by complementation in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 88:1991;6112-6116.
51. Dundon W, Islam K Nucleotide sequence of the gene coding for SEC14p in Candida (Torulopsis) glabrata. Gene. 193:1997;115-118.
52. Nagahashi S, Lussier M, Bussey H Isolation of Candida glabrata homologs of the Saccharomyces cerevisiae KRE9 and KNH1 genes and their involvement in cell wall beta-1,6-glucan synthesis. J Bacteriol. 180:1998;5020-5029.
53. Cormack BP, Falkow S Efficient homologous and illegitimate recombination in the opportunistic yeast pathogen Candida glabrata. Genetics. 151:1999;979-987.