Yeast genome evolution in the postgenome eraSeoighe and Wolfe 549 - PDF document

Yeast genome evolution in the post-genome eraSeoighe and Wolfe 549 [22]. The pattern of blocks was assessed to see whether theirarrangement in the ancestral genome prior to duplicationarrangement in the ancestral genome prior to duplicationequally parsimonious series of reciprocal translocations, sug-S.cerevisiaeup because they lack a sufficient number of genes that havemissing information means that the minimum number ofreciprocal translocation steps required to rearrange the cur-rent map of duplicated blocks into a symmetrical pattern (i.e.70–100 [23]). The problem of estimating the minimal num--•]. Although an interesting problem, it is,perhaps, biologically uninformative. By Southern hybridisation of probes to pulsed-field gels,Ryu Figure 1 Schematic representation of gene order(based on Keogh eogh )–represent genes, with different fonts used todistinguish between homologues. Forsimplicity, no interchromosomal translocationshave been shown. Species1 diverged fromspecies2 and 3 before genome duplicationoccurred. Species2 and 3 are descendedfrom the same genome duplication event, andspecies-specific losses. We hypothesise thatC.glabratathe same genome duplication event asS.cerevisiaeC.glabratachromosomes [47] and two rDNA arrays[48,49]; for two gene pairs in S.cerevisiaeDED1DBP1PDR15C.glabratacontains a sequence significantlypair than to the other, as expected ifspecies [49–53], but one example ofduplicated block has been identified(KHaynes, personal communicat

ion). ABCDEFGHIJ ABCDEFGHIJ ABCDEFGHIJ Species with duplicated genome(could be auto- or allo-polyploid)Differentialgene loss ACDFGHJ ABDEFIJ ACDFGHJ ABDEFIJ ABDEFIJ ACDFGHJ ACDFGHJ ABEFIJ ACFGHJ ABDEIJ ABCDEFGHIJ Genes A, D, F, J Further differential gene lossCurrent Opinion in Microbiology mc2514.qxd 11/09/1999 2:48 PM Page 549 that were previously classified as nonessential may in factmake a small contribution to evolutionary fitness. It isapparent from the functional classifications of duplicatedproteins and from the excess of duplicated genes classi-fied as nonessential (Table1) that genes that werefunctions. Of the 280 duplicated pairs for which the Yeasteastfor both proteins, the categories are different for only 26pairs and most of these differences do not appear signifi-cant when examined more closely. Taken together thesewere retained to improve the efficiency with which exist-S.cere-functional categories (Table1), indicating some non-ran-genes. Some functional categories are over-duplicated,cated [31] but do not form part of larger paired regions.Many of the over-duplicated functional categories(Table1) include very highly expressed genes, such as heat1) include very highly expressed genes, such as heat••]. The tendency to retain high-expression genes induplicate (or alternatively, the tendency for each copy of aper cell (Figure2). Thus it appears that increased geneand which were lost. It must, however, be noted from Fig-ure2 that a majority of duplicated gene

s have expressionC.glabrata(Figure1).pairs are missing the intron in one copy (Table2). By com-C.albicansS. cerevisiaeSEC14SEC14from YKL091Cand all the available orthologues of SEC14(K.lactis, C.glabrata, C.albicansalbicansthe hemiascomycete SEC14sequences cluster togetherwith YKL091Cas an outgroup. Nonetheless, the intron mustYeast genome evolution in the post-genome eraSeoighe and Wolfe 551 Over-representation of highly expressed genes among duplicates. Thehave been retained in duplicate after genome duplication (black line).Expression data is from Holstege a is from Holstege ••] and was grouped intobins of genes expressed at 0–4, 4–8, 8–12 (etc.) mRNA moleculesper cell. The large bin representing the lowest expression category(0–4 mRNA molecules per cell) is not shown and contained 87% of all genes and 76% of the duplicated genes. 01020304050607080 0.040.060.08 mRNA molecules per cell Table 2 Gene pairs differing by the existence of an intron. Gene containing intronGene lacking intronSNC1SNC2ECM33YDR055WYHR097CYDR348CMRK1MDS1RPL22AYFL034C-BCOX5BCOX5ARPL36AYPL249C-AYML056CYLR432WRPL21BRPL21AANC1 SAS5SEC14YKL091C An outgroup is not available for this pair. This pair is probably not a Yeast genome evolution in the post-genome eraSeoighe and Wolfe 553 12.Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS,complete protein sets of worm and yeastdivergence.Science1998, 13.Ohno S: Unwin; 1970.14.Lundin LG: Evolution of the vertebrate genome

as reflected inparalogous chromosomal regions in man and the house mouse.1993, 15.Ahn S, Tanksley SD: Comparative linkage maps of the rice andProc Natl Acad Sci1993, :7980-7984.16.Ryu SL, Murooka Y, Kaneko Y: Reciprocal translocation atduplicated RPL2loci might cause speciation of 1998,:345-351.17.Wolfe KH, Shields DC: duplication of the entire yeast genome.1997, 387:708-713.18.Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner A, Hani J,Heumann K, Kleine K, Maierl A, Oliver SG1997, 387 (suppl):7-65.19.Coissac E, Maillier E, Netter P: A comparative study of duplicationsin bacteria and eukaryotesthe importance of telomeres.1997, :1062-1074.20.Keogh RS, Seoighe C, Wolfe KH: Evolution of gene order andchromosome number in Kluyveromycesrelated fungi.Yeast1998, :443-457.21.Ozier-Kalogeropoulos O, Malpertuy A, Boyer J, Tekaia F, Dujon B:Kluyveromyces lactis Nucleic Acids1998, The K.lactisgenome was surveyed by random sequencing. The most informa-tive data came from sequencing both ends of plasmid clones with 2–3 kb inserts,22.Seoighe C, Wolfe KH: Updated map of duplicated regions in the1999, in press.23.Seoighe C, Wolfe KH: Extent of genomic rearrangement aftergenome duplication in yeast.Proc Natl Acad Sci USA1998,:4447-4452.24.El-Mabrouk N, Bryant D, Sankoff D: Reconstructing the preRECOMB ‘99: Proceedings of the ThirdInternational Conference on Computational Molecular Biology:1999,11–14 April: Lyon, France. Edited by Istrail S, Pevzner P, Waterman M.New York: ACMPress; 199

9:154-163.The authors, in a rigorous treatment of the problem of estimating the ‘pre-doubling’ organisation of the yeast genome, calculated that an absolute min-imum of 38 reciprocal translocations must have occurred to scamble geneorder after genome duplication. They also suggested an algorithm for con-structing the pre-doubling genome, and proposed one such ancestor. Alsoof interest here, however, would be a description of the class of equivalent25.Ryu SL, Murooka Y, Kaneko Y: Genomic reorganization betweenYeast1996, :757-764.26.Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS,complete protein sets of worm and yeastdivergence.Science1998, 27.Dujon B: The yeast genome projectTrends1996, :263-270.28.Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J:Preservation of duplicate genes by complementary degenerativemutations.1999, :1531-1545.29.Thatcher JW, Shaw JM, Dickinson WJ: Marginal fitnessProc Natl Acad Sci1998, :253-257.30.Hodges PE, McKee AH, Davis BP, Payne WE, Garrels JI: The YeastProteome Database (YPD)a model for the organization andpresentation of genome-wide functional data.Nucleic Acids Res1999, :69-73.31.Planta RJ, Mager WH: The list of cytoplasmic ribosomal proteinsYeast1998, :471-477.32.Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ,GreenMR, Golub TR, Lander ES, Young RA: regulatory circuitry of a eukaryotic genome.Cell1998,:717-728.Although it was not the primary aim of the study, this paper is one of the bestexamples so fa

r of the power of microarray technology to study gene expres-sion on a global scale. The authors estimated the number of mRNA mole-cules per cell, and mRNA half-life, for every gene in the S.cerevisiaegenome under conditions of growth to mid-log phase in YPD media, usingAffymetrix high-density oligonucleotide arrays. Included in the wealth of datasion levels of cytosolic and mitochondrial ribosomal proteins average 29 and1.4 mRNA molecules per cell, respectively.33.Bankaitis VA, Malehorn DE, Emr SD, Greene R: The cerevisiae SEC14 gene encodes a cytosolic factor that is requiredfor transport of secretory proteins from the yeast Golgi complex.Cell Biol1989, :1271-1281.34.Sharp PM, Lloyd AT: yeast chromosome IIIevolution of chromosome primarystructure.Nucleic Acids Res1993, :179-183.35.Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G,The mosaic genome of warm-bloodedScience1985, :953-958.36.Bradnam KR, Seoighe C, Sharp PM, Wolfe KH: chromosomes.1999, :666-675.37.Li W, Stolovitzky G, Bernaola-Galvan P, Oliver JL: heterogeneity within, and uniformity between, DNA sequences ofyeast chromosomes.1998, 38.Kielland-Brandt M, Nielsson-Tillgren T, Gjermansen C, Holmberg S,Pedersen MB: Genetics of Brewing Yeasts.The YeastsWheals AE, Rose AH, Harrison JS. London: Academic Press;1995:223-254. 39.Tamai Y, Momma T, Yoshimoto H, Kaneko Y: types of chromosome in the bottom fermenting yeastYeast1998, 40.Petersen RF, Marinoni G, Nielsen ML, Piskur J: approaches for analyzing diversity and phy

logeny among yeastYeasts. Edited by Ernst JF, Schmidt A. Basel: Karger; 1999.Viable hybrid yeast strains containing most chromosomes from both parentsviability is low. In hybridisation between species, the hybrids lose all or most of one set of parental chromosomesduring mitosis. Petersen suggest that some genes may be retained intwo copies either by limited aneuploidy or by integration into the chromo-41.Masneuf I, Hansen J, Groth C, Piskur J, Dubourdieu D: among wine and cider production strains.1998, :3887-3892.42.Groth C, Hansen J, Piskur J: A natural chimeric yeast containinggenetic material from three species.Int J Syst Bacteriol1999,inpress.Sequence analysis of a yeast isolated from cider (CID1) shows that its nucleargenome contains sequences derived from both S.cerevisiaeS.bayanusIts mitochondrial DNA is derived from a third species, Saccharomycessp. IFO1802. Exchange of genetic material between Saccharomyces43.Gilley J, Fried M: Extensive gene order differences within regionsimplications for chromosomal evolution and the cloning of1999, 44.Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK,Langeland J, Prince V, Wang YLZebrafish hox clusters andScience1998, :1711-1714.45.Kordis D, Gubensek F: Unusual horizontal transfer of a longinterspersed nuclear element between distant vertebrate classes.Proc Natl Acad Sci USA1998, :10704-10709.46.Lawn RM, Schwartz K, Patthy L: Convergent evolution ofapolipoprotein(a) in primates and hedgehog.Proc Natl Acad SciUSA1997, :11992-1199