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  • A. Gofieau Et Al - Life With 6000 Genes

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    A. Gofieau et al- Life with 6000 Genes

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    A. Gofieau Et Al - Life With 6000 Genes

    Enviado por

    Yopghm698

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    Life with 6000 Genes A, Gofieau; B. G, Barrell; H. Bussey; R. W. Davis J.D. Hoheisel; C. Jacq; M. Johnston; E. J. Louis; H. W. Mewes; Y. Murakami; P. Philippsen; H. Tettelin; S. G. Oliver Science, New Series, Vol. 274, No. 5287, Genome Issue (Oct. 25, 1996), 546+563-567. Stable URL hp: flinks,jstor-org/siisici=0036-8075% 2819961025%293%3A274%3A5287%3CS46%SALW6G%3 CO%3B: Science is currently published by American Association for the Advancement of Science. ‘Your use of the ISTOR archive indicates your acceptance of JSTOR’s Terms and Conditions of Use, available at hup:/www stor orglabout/terms.html. ISTOR’s Terms and Conditions of Use provides, in par, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www jstor.org/joumnals/aaas.himl. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the sercen or printed page of such transmission. STOR is an independent not-for-profit organization dedicated to creating and preserving a digital archive of scholarly journals. For more information regarding JSTOR, please contact support @ jstor.org, hupulwww jstor.org/ Wed Aug 17 18:32:45 2005 by Fi across ho whoa goremo. A subst othe ‘eu wore sotced wich threo Me ‘eno a the VAC hang boan cher, sna ho poston was resoked toa cyogenat rere fs pose to acon nih ooh) & Canon ‘ar wae von foreach of tae YA, whch “lowed tes postion In cantmorgira tobe etomined Bacau ths td comand es data {or hvomesomos 10,21, and 28, an atomatie ‘Seaton was vec Cones at ro norracomtinant ‘stretoct to Ganstnon meron tia MCD fr aly Aatre 380 (upc), (1990) and havo Siracun extoganot locates [Orine Nao. Wn Ienerarco in an {OM pene nezunmin gor wee teed oes hs 28, KLE Merton Proc Net Acad, So US.A 88,7474 (000. Dette netneion and examples or provid cn ten eto 90. GID Shuler, JA Epa H. Cra, J Kans, ters Enya 206, 4 (15) ‘1. Fe ado sso ded ambiguous resus Bresutetopresenas an eararng masse band poor epee, 2. Teco be thereoutf otra vil per tb Leing nor ora saqyoos cuserrg over wich twa separate genes wee orenety are 10 freee unsere ety Typing arora na tameviors marker woul alow a (eco EST to map wth sonar ld sores hoo fan of to os ro for nk} ea como ro. Irozema ean it nu Te to locale the Trang iar, ned torneo. brome camod by tw enero png tthe amon mare, 4M rag and WA, Bekmere, oases 16, S49 irons. 8, V, Romano eal, Cytaganet. Cat Gane. 48, 148, (hose 28, § Batra, M. esha, 9. Garaahy, TS, Pre: Nat Acad Sat USA 81,6259 0038). 8 7. G0, Blingohy ta, Ar. Har. Gane. 62,288 {ioasi-8'8 Schnee: Natt Acad Sa Usa ea, 3147 (098) 58. L Strengon of st, Muze 378,754 (19955 0. Loitanand Gren 977, 2 (1099, 8 Hane et ats Somce 271, 300 (1900, 99, 5 Tugndtic et at, Hum. Mal Gano. 8, 1500 (iodsy,0.€ Basso, MS Bogut, P Het, etre 379, 59 (1006; Phir, O Basco se ao, Are Gane 13, 253 (106) 40. Tho socing sees wer ain acid eubetuon ‘ratoes base on the Abarth {en modal of exlulonay dstanco, Pam mates ‘maybe generat fran rane t Pads oe {relation of sbsanedmitnionfequencos ft 0 Dayhctot l,m aioe of Porn Sequence and Shictre M0, Dayo Ea Naor Becca! soar Foundation, Washing, OC, 1979) 9 Sravpc 3.pp 386-352.6.F Absa MOL Eo! 36,390 1083, Pad mation we iors or Storng macs bacon Soquoncs cach oe 1S epae pete pool a emafing rcs (Otter organ in Tab he PARDO mate ‘naa wed bacauoeitha een soon abe good ot (rerapurpose saecting (SF asc, Mol Bor'219, S06 1001), The BLAST crear Gen and. J States, Nature Gene 3,268 (1935), taics a rocoto soqwonco aus (EST or goroh tale to as costa! OF, ad hon ‘Compare ese with pees saoe he da Sua, TELASTN perms 9 smi rcton bat Fe ‘Sous couchos a eran query semeece agarst ‘Stare Waneatens of ach ey ha nasuctoo ‘Stouron ctabce Senos wey postr wih ES tesserace™ tes astro rman aed secon ‘aryexpoctten paar 41, MA, Perea Vance Arm, Ham, Gane 4, oot W001; We. Sweater eta, Pec At esa, Sei USA 90,1077 (1095) Fil oa. {Cat78, 1027 (0u8) N.Papaccpouls ot at. Se! ‘on 69,1825 1004; Sharer al C78 335, Life with 6000 Genes A. Goffeau,” 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, S. G. Oliver ‘The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeasts 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage ofthe yeast genome project isto elucidate the biological functions of all of these genes. Tle genome of the yeast Saccharomyces cerevisiae has been completely sequenced through an intemational effore involving some 600 scientist in Europe, North Amer tea, and Japan. [tithe largest genome to be completely sequenced s0 for (a record that ‘we hope will soon be bettered) and is the ete genome sequence of a et karyote, A number of public data libraries compiling the mapping. information and 546 nucleotide and protein sequence data from teach of the 16 yeast chromosomes (1-16) have been established (Table 1). “The position of S. cereisiae as a model eukaryote owes much to its intrinsic advan- tages as an experimental system, [tis a unicellular organism that (unlike many ‘more complex eukaryotes) can be grown on defined media, which gives the experiment cer complete control aver its chemical and SCIENCE + VOL.274 + 25 OCTOBER 1996 95S Manet ate 85,4881 Py t ayt 967. 70 (1086) 42, Tepotowta let fa camprehenave ge ap it at sates by to fat tat 82% cf pos that Fave ‘been posiony coned. 10 ‘dat ae ‘opresoridby eno ormera ESTsin GenBank ith! Dura. nesimh govsBESTISCEST gros 49, KH Fama A, ui, OT Koga, A (Sa As ce 22 Ste (1958) {4M Bora fa, Ganone Fe 6,791 (1998. 45, Coreonsus eoguaneos fom at ae he oven fing ESTs wore gored ten 294 Union ca. toe oF ho 29975) eased er pars, 138 (52%) of tooo ytd axccost FOR asa 46, We terk M. . Aodereon A J. Cobre, DF Coury, Dono, D. ey, Tern J Keayourfan, Tan, W. Ye. ard |S. Zorstova trom the Wiha ratte fo tia ast. thom We tn. Mle, Eyes, Lan, fa A. Scharf eoaetalconrcuten foward tho development of UniGene. Supt by NH fnarce HOODOWD fo ESL. NOOO to RIMM Fes to INS anc HGDDTST to TG and by tho Wha for Soma sarch fed the Weleore Tt 34 sa report ota {initan Sort ord om to Made esearch Couret ef Coreda, GP Sanat estan. ter of the Howard Hughes Meal tte, The ‘Stefan Genre Cae aeths Vina Fretito-MIT Goreme Carr ar thanks fore ‘lporucioaldce muchas with rds donated by Sandor Pharmocoieat. Goran eapptedby tha Resconton encase corsineMyopatioe nd tre Growpanent Suces suf Goroma. The Sanger Cont, Ganehon and Ooo gratohd Terauppat tom te Ewopaan Union VRHEST Eo {farmer Human Genome Grganzaten andthe Wotcors Trust sporereda srs ofranings rom (tober 12040 November 095 tho yee ‘slabraton vous t hae boo poste physical environment. S. cerevisiae has. life ‘cycle that is ideally suited to classical ge netic analysis, and this has permitted con- struction of a detailed genetic map that dlefines the haploid set of 16 chromosomes. Moreover, very efficient techniques have been developed that permit any of the 6000 genes to be replaced with a mutane allele, or completely deleted from the genome, with absolute accuracy (17-19). The combina tion ofa large number of chromosomes and a small genome size meant that it was pos- sible to divide sequencing responsibilities ‘conveniently among the different interna tional groups involved in the project. Old Questions and New Answers The genome. At the heginning of the se- quencing project, perhaps 1000 genes en- coding either RNA or protein products had been defined by genetic analysis (20). The complete genome sequence defines some 5885 open reading frames (ORFs) that are likely to specify protein products in the yeast cell. This means that a protein-encod- Ing gene is found for every 2 kb of the yeast genome, with almost 70% of the total se- ‘quence consisting of ORFs (21). The yeast enome is much more compact than those ofits more complex relatives in the eukary= ‘tic world. By contrast, the genoine of the nematode worm contains a potential pro- tein-encosing gene every 6 kb (22), and in the human genome, some 30 kb or more of sequence must be ‘examined in order to uncover such a gene. Analysis of the yeast genome reveals the existence of 6275 ORFs that theoretically could encode proteins longer than 99 amino acids. However, 390 ORFs are unlikely to be translated into proteins. Thus, only 5885 protein-encoding. genes are believed to exist. In addition, the yeast genome contains some 140 ribosomal RNA genes in a large tandem array on chromosome XII and 40_genes encoding small nuclear RNAs (spRNAs) scattered throughout the 16 chromosomes; 275 trans- fer RNA (tRNA) genes (belonging to 43 families) are aso widely distributed. Table 2, which provides details ofthe distribution of genes and other sequence elements among yeast’s 16 chromosomes, shows that the genome has been completely se- ‘quenced, with the exception of a set of identical genes repeated in tandem. ‘The compact nature of the S. cerevisiae senome is remarkable even when compared with the genomes of other yeasts and fungi Current data from the systematic sequence analysis of the genome of the fision yeast K Gafay apa Tataln, Uaversis Cache do Ls “an, Unto do Bost Pryaelogauo, Pace rch a ‘a, 22D, 138 Laas Now, Balu Baral Songer Con, Hrscon a Hon Car trig COTO 188 UK tse, Omarion ology, McGlunsosy, 1205, Doctir Pena ver, Meet HT, Can, FLW. Dass Deport of Boch, Stanford Un ‘ery, Bockman Carr, Room BON Stato, CA ‘taps sa07, USA. Dun, Unt de Géngteue Makcuare des Lowes [URAT 42 CNRS UPra2? Urverate Pot Mate ‘nett actu, 28 Pus Dostour Fu, 70724 Pare Coaoe 16, France Feldman, Urtorett Minehen, nati i Pro ge ane, Sear 2 S08 Mae, F Galan, Lapoatore do Sccimie Molcouste, UPR ‘1i-Facunt a Midece, CNRS, 2 Arun du Boe fear Léen Borar, 22043 Rares Coden, rao. 4°. fcneea, Wieser Genet Genome Sra Dontachos Kebserecrangszonrun, in Neusrhoret Fel, £06, 99120 Nedaberg. Goan. Cdaeg, Gide Maceo, Ecole Normaio Sy tres CMS UPA, 46 Ps Ub 75200 Pars asx, Franco. 1 Jofesion, Deparment Goats, Box 252, West lon Uneraty Medal Stoo, se Sct Avera, St tue MO er 10, USA. ES Lu, Yost Gonsts, latte of Moco Mak re, Jn Roce Hospi, Oxford OX ODU, Uk HOW Mees, Mae Panett Soon Nari: Foxit or Proton Scorers MIPS, Am Kept 1 2189 Morro, Goma Huan Genome seach FEN, Kojo Tous Seenes Oy 3-1 05 era, Japan P.Priposn, het or Apple Merbiobgy, ies fat Saee ngobemerse 0 ale Boa, Sntzerana 5.6 Gh Deparmant of Bocsemsty an Aptos okeular Bioby, Unity of Manchest te o SScence art Technology (MIT), Pet Ofce Box 8, Machete 0 160.U “To wram areqpanderce spo be SaaS. Schizosaccharomyces pombe indicate that the density of protein-encoding genes is ap- proximately one per 23 kb (23). The dit ference between these two yeast genomes can be ascribed co the pauety of introns in S. cerevisiae. In the fission yeast, approxi- rately 40% of genes contain introns (21), whereas only 4% of protein-encoding genes in S. cerevisiae ae similarly interrupted (Ta. ble 2). The Saccharomyces genes that do contain introns [notably, those encoding ribosomal proteins (24)] usually have only fone small intron close to the start of the coding sequence (often interrupting the i tiator codon) (25). It has even been sug- gested (26) that many yeast genes represent DNA copies thae have been generated by the action of reverse transcripases specified by retrotransposons (Ty elements) The chromosomes. A complete genome sequence provides more information than the sum of all che genes (or ORFS) that it contains. In particular, it permits an is vestigation of the higher order onganiza- tion of the S. cerevisiae genome. An ex- ample is the longerange variation in base Composition. Many yeast chromosomes consist of altemating large domains of GCerich and GC-poor DNA (2!, 27), generally correlating with che variation in gene density along these chromosomes. the case of chromosome Ill, it has been demonstrated that the periowiciey in base ‘composition is paralleled by a variation in recombination frequeney along the eh mosome arms, with the GC-rich peaks coinciding with regions of high recom ration in the midklle of each arm of the chromosome and AT-rich troughs eoin- ciding with the recombination-poor cen- tromerie and telomeric sequences, Sim chen and co-workers (28) have demo strated that the relative incidence of dou i ble-srand breaks, which are tho initiate genetic recombination in yeast (29), coreelates directly with the GC-rich regions of this chromosome, ‘The four smallest chromosomes (I, Ill Vi, and IX) exhibit average recombination frequencies some 1.3 to L.8 times greater than the average for the genome asa whole Kahack (30) has suggested that high levels of recombination have been selected for on these very small chromosomes to ensure at least one erossover pet meiosis and so per mit them to segregate corectly. Its known that areicial chromosomes (or chromo- some fragments) of approximately 150 kb in size are mitotically unstable (31, 32), which raises the related questions of whether there {sa minimal size for yeast chromosomes and how the. smallest chromosomes have achieved their current sie (see Table 2), ‘The organisation of chromosome I is very uunusuak The 31 kb at each ofits ends are very gene-poor, and Bussey etal. (5) have suggested that these terminal domains may act as “fillers” to increase the size, and hhence the stability, of this smallest yeast chromosome ‘Genetic redundancy is the rule at the ends of yeast chromosomes, For instance, the two terminal domains of chromosome I show considerable nucleotide sequence homology both to one another and to the terminal domains of other chromosomes (V and XI), The right terminal region of ehro- smosome | is duplicated at the left end of chromosome | (5) and at the right end of chromosome VIII (3). The sugar fermenta- tion genes MAL, SUC, and MEL all have @ ruber of telomere-atsoeiated copies, not all of which are expressed (33-35). An nteresting feature ofthe distebution of the Table 4. Finding yeast genome formation on the Iniemet. A fuller descrpton of these and other resouress may be found in (35, Intemet acresees FFP ites for he complete S. cares gonome sequence {tpsmips.emtinst.org (cractoryyeast) ‘pb ac uk (drectory/pubidatzbases/yeast) genome. stanford eau (deecteryyeastgename-seq) ‘Other S.cereusine ta leas MIPS, Marnsied, Germany Iii /we mipsilocnem mo deyeast) ‘Sanger Center, Finxon, UK ftp wien sanger.ac ul/yeast ome im) ‘Saccharomyoes Genome Database (S60), Stanford Unversity, USA tpl/genome- "wht stanford 2au/Saccharomyees) ‘SWISS. PROT, Uniersty of Geneva, Switzeand (ht: expasy heuge chisprt/sp-doou hin) ‘Yaast Protsin Database (YPD}, Proteome ne, avery, MA, USA (htipw: proteome corYEDhome ht ‘Genedz, Europeen Molecular Biology Laboratory, Heidelberg, Germany {hip:/srawrembt-heidetberg.de/~genequ) IEF, National Cener for Bid.ogeal formation, Baltenore, MD, USA {tstpv/wavened im nin. govXREFA) {Edtor's note: For readers who would Ike a user-fendly uid to the yeast databases, please see the specal feature atthe Sciorea Web st tp iw sclencemag org/scencevfeature/data

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