Chapter 19 : Genome-Wide Strategies for Studying Gene Function by Using Model Systems

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Genome-Wide Strategies for Studying Gene Function by Using Model Systems, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap19-1.gif /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap19-2.gif


This chapter outlines how complete genome sequences promote the development of broad genome-wide or functional-genomics approaches for investigating individual genes to entire gene sets. Classical approaches had focused on a small portion of the , , and genes. The power of genetically tractable model systems is that they facilitate the analysis of gene function at the level of the intact organism. In various adaptations of this method, PCR-generated replacement DNAs are used for constructing strains harboring simple point mutations or large deletions, making reporter gene constructs for any gene, inserting epitope or fluorescent tags in any protein, and studying the regulatory information controlling gene expression. Regulatable promoter replacement cassettes in combination with the availability of complete genome sequences will be important resources for studying gene function in yeasts and other eukaryotic systems. New methods for assessing gene expression, protein-protein interactions, and protein-nucleic acid interactions mean that it is now possible to use genome-wide approaches to study gene function. These global approaches should significantly accelerate progress toward a detailed understanding of the model organisms , , and . Genome-wide methods will generate exponentially increasing amounts of biological data. Effective systems of data storage, management, and analysis must keep pace with data generation so that the data and the tools necessary to apply these resources to individual research programs are accessible to all researchers.

Citation: Storms R. 1999. Genome-Wide Strategies for Studying Gene Function by Using Model Systems, p 347-365. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch19
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Aim, R. A.,, L.-S. L. Ling,, D. T. Moir,, B. L. King,, E. D. Brown,, P. C. Doig,, D. R. Smith,, B. Noonan,, B. C. Guild,, B. L. de-Jonge,, G. Carmel,, P. J. Tummino,, A. Caruso,, M. Uria-Nickelsen,, D. M. Mills,, C. Ives,, R. Gibson,, D. Merberg,, S. D. Mills,, O. Jiang,, D. E. Taylor,, G. F. Vovis,, and T. J. Trust. 1999. Genomic sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176180.
2. Altschul, S. F.,, T. L. Madden,, A. A. Schäffer,, 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. 25:33893402.
3. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Ponten,, U. C. Alsmark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson,, H. H. Winkler,, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.
4. 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. 21:33293330.
5. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
6. Bult, C. J.,, O. White,, G. J. Olsen,, L. Zhou,, R. D. Fleischmann,, G. G. Sutton,, J. A. Blake,, L. M. FitzGerald,, R. A. Clayton,, J. D. Gocayne,, A. R. Kerlavage,, B. A. Dougherty,, J. F. Tomb,, M. D. Adams,, C. I. Reich,, R. Overbeek,, E. F. Kirkness,, K. G. Weinstock,, J. M. Merrick,, A. Glodek,, J. L. Scott,, N. S. M. Geoghagen,, J. F. Weidman,, J. L. Fuhrmann,, D. Nguyen,, T. R. Utterback,, J. M. Kelly,, J. D. Peterson,, P. W. Peterson,, M. C. Hanna,, M. D. Cotton,, K. M. Roberts,, M. A. Hurst,, B. P. Kaine,, M. Borodovsky,, H.-P. Klenk,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 10581073.
7. Burns, N.,, B. Grimwade,, P. B. Ross-Macdonald,, E. Y. Choi,, K. Finberg,, G. S. Roeder,, and M. Snyder. 1994. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8:10871105.
8. Bussey, H.,, D. B. Kaback,, W. Zhong,, D. T. Vo,, M. W. Clark,, N. Fortin,, J. Hall,, B. F. Ouellette,, T. Keng,, A. B. Barton,, Y. Su,, C. J. Davies,, and R. K. Storms. 1995. The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92:38093813.
9. Chee, M.,, R. Yang,, E. Hubbell,, A. Berno,, X. C. Huang,, D. Stern,, J. Winkler,, D. J. Lockhart,, M. S. Morris,, and S. P. Fodor. 1996. Accessing genetic information with high-density DNA arrays. Science 274:610614.
10. Cole, S. T.,, R. Brosch,, J. Parkhill,, T. Garnier,, C. Churcher,, D. Harris,, S. V. Gordon,, K. Eiglmeier,, S. Gas,, C. E. Barry III,, F. Tekaia,, K. Badcock,, D. Basham,, D. Brown,, T. Chillingworth,, R. Connor,, R. Davies,, K. Devlin,, T. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, A. Krogh,, J. McLean,, S. Moule,, L. Murphy,, S. Oliver,, J. Osborne,, M. A. Quail,, M. A. Rajandream,, J. Rogers,, S. Rutter,, K. Seeger,, S. Skelton,, S. Squares,, R. Squares,, J. E. Sulston,, K. Taylor,, S. Whitehead,, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537544.
11. Deckert, G.,, P. V. Warren,, T. Gaasterland,, W. G. Young,, A. L. Lenox,, D. E. Graham,, R. Overbeek,, M. A. Snead,, M. Keller,, M. Aujay,, R. Huber,, R. A. Feldman,, J. M. Short,, G. J. Olson,, and R. V. Swanson. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353358.
12. DeRisi, J. L.,, V. R. Iyer,, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680686.
13. Fields, S.,, and O. Song. 1989. A novel genetic system to detect protein-protein interactions. Nature 340:245246.
14. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J.-F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenney,, G. Sutton,, W. FitzHugh,, C. A. Fields,, J. D. Gocayne,, J. D. Scott,, R. Shirley,, L.-I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Weidman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. R. Utterback,, M. C. Hanna,, D. T. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrmann,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith,, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
15. Fodor, S. P.,, R. P. Rava,, X. C. Huang,, A. C. Pease,, C. P. Holmes,, and C. L. Adams. 1993. Multiplexed biochemical assays with biological chips. Nature 364:555556.
16. Fodor, S. P. A.,, J. L. Read,, M. C. Pirrung,, L. Stryer,, A. T. Lu,, and D. Solas. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251:767773.
17. Fraser, C. M.,, S. Casjens,, W. M. Huang,, G. G. Sutton,, R. A. Clayton,, R. Lathigra,, O. White,, K. A. Ketchum,, R. Dodson,, E. K. Hickey,, M. Gwinn,, B. Dougherty,, J.-F. Tomb,, R. D. Fleischmann,, D. Richardson,, J. Peterson,, A. R. Kerlavage,, J. Quackenbush,, S. Salzberg,, M. Hanson,, R. van Vugt,, N. Palmer,, M. D. Adams,, J. D. Gocayne,, J. Weidman,, T. Utterback,, L. Watthey,, L. McDonald,, P. Artiach,, C. Bowman,, S. Garland,, C. Fujii,, M. D. Cotton,, K. K. Horst,, K. Roberts,, B. Hatch, H. O. Smith,, and J. C. Venter. 1997. Genomic sequence of a Lyme disease spirochete, Borrelia burgdorferi. Nature 390:580586.
18. Fraser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, J. L. Fritchman,, J. F. Weidman,, K. V. Small,, M. Sandusky,, J. L. Fuhrmann,, D. T. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J.-F. Tomb,, B. A. Dougherty,, K. F. Bott,, P.-C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. Hutchison III,, and J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397403.
19. Fraser, C. M.,, S. J. Norris,, G. M. Weinstock,, O. White,, G. G. Sutton,, R. Dodson,, M. Gwinn,, E. K. Hickey,, R. Clayton,, K. A. Ketchum,, E. Sodergren,, J. M. Hardham,, M. P. McLeod,, S. Salzberg,, J. Peterson,, H. Khalak,, D. Richardson,, J. K. Howell,, M. Chidambaram,, T. Utterback,, L. McDonald,, P. Artiach,, C. Bowman,, M. D. Cotton,, C. Fujii,, S. Garland,, B. Hatch,, K. Horst, K. Roberts,, L. Watthey,, J. Weidman,, H. O. Smith,, and J. C. Venter. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375388.
20. Fromont-Racine, M.,, J.-C. Rain,, and P. Legrain. 1997. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16:277282.
21. Gari, E.,, L. Piedrafita,, M. Aldea,, and E. Herrero. 1997. A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast 13:837848.
22. Gietz, D.,, A. St. Jean,, R. A. Woods,, and R. H. Schiestl. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20:1425.
23. Gietz, R. D.,, and R. A. Woods,. 1994. High efficiency transformation in yeast, p. 121134. In J. A. Johnston (ed.), Molecular Genetics of Yeast: Practical Approaches. Oxford University Press, Oxford, United Kingdom.
24. Goebl, M. G.,, and T. D. Petes. 1986. Most of the yeast genomic sequences are not essential for cell growth and division. Cell 46:983992.
25. GofFeau, A.,, R. Aert,, M. L. Agostini-Carbone,, A. Ahmed,, M. Aigle,, L. Alberghina,, K. Albermann,, M. Albers,, M. Aldea,, D. Alexandraki,, G. Aljinovic,, E. Allen,, R. Altmann,, J. Alt-Mörbe,, B. André,, S. Andrews,, W. Ansorge,, G. Antoine,, R. Anwar,, A. Aparicio,, R. Araujo,, J. Arino,, W. Arnold,, J. Arroyo,, E. Aviles,, U. Backes,, M. C. Baclet,, K. Badcock,, A. Bahr,, V. Baladron,, J. P. G. Ballesta,, A. T. Bankier,, A. Banrevi,, M. Bargués,, L. Baron,, T. Barreiros,, B. G. Barrell,, C. Barthe,, A. B. Barton,, A. Baur,, A.-M. Bécam,, A. Becker,, I. Becker,, J. Beinhauer,, V. Benes,, P. Bénit,, G. Berben,, E. Bergantino,, P. Bergez,, A. Berno,, I. Bertani,, N. Biteau,, A. J. Bjourson,, H. Blöcker,, C. Blugeon,, C. Bonn,, E. Boles,, P. A. Bolle,, M. Bolotin-Fukuhara,, R. Bordonné,, J. Boskovie,, P. Bossier,, D. Botstein,, G. Bou,, S. Bowman,, J. Boyer,, P. Brandt,, T. Brandt,, M. Brendel,, T. Brennan,, R. Brinkman,, A. Brown,, A. J. P. Brown,, D. Brown,, M. Brückner,, C. V. Bruschi,, J. M. Buhler,, M. J. Buitrago,, F. Bussereau,, H. Bussey,, A. Camasses,, C. Carcano,, G. Carignani,, J. Carpenter,, A. Casamayor,, C. Casas,, L. Castagnoli,, H. Cederberg,, E. Cerdan,, N. Chalwatzis,, R. Chanet,, E. Chen,, G. Chéret,, J. M. Cherry,, T. Chillingworth,, C. Christiansen,, J.-C. Chuat,, E. Chung,, C. Churcher,, C. M. Churcher,, M. W. Clark,, M. L. Clemente,, A. Coblenz,, M. Coglievina,, E. Coissac,, L. Colleaux,, R. Connor,, R. Contreras,, J. Cooper,, T. Copsey,, F. Coster,, R. Coster,, J. Couch,, M. Crouzet,, C. Cziepluch,, B. Daignan-Fornier,, F. Dal Paro,, D. V. Dang,, M. D'Angelo,, C. J. Davies,, K. Davis,, R. W. Davis,, A. De Antoni,, S. Dear,, K. Dedman,, E. Defoor,, M. de Haan,, T. Delàveau,, S. Del Bino,, M. Delgado,, H. Delius,, D. Delneri,, F. Del Rey,, J. Demolder,, N. Démolis,, K. Devlin,, P. de Wergifosse,, F. S. Dietrich,, H. Ding,, C. Dion,, T. Dipaolo,, F. Doignon,, C. Doira,, H. Domdey,, J. Dover,, Z. Du,, E. Dubois,, B. Dujon,, M. Duncan,, P. Durand,, A. Düsterhöft,, S. Düsterhus,, T. Eki,, M. El Bakkoury,, L. G. Eide,, K.-D. Entian,, P. Eraso,, D. Erdmann,, H. Erfle,, V. Escribano,, M. Esteban,, L. Fabiani,, F. Fabre,, C. Fairhead,, B. Fartmann,, A. Favello,, G. Faye,, H. Feldmann,, L. Fernandes,, F. Feroli,, M. Feuermann,, T. Fiedler,, W. Fiers,, U. N. Fleig,, M. Flöth,, G. M. Fobo,, N. Fortin,, F. Foury,, M. C. Francingues-Gaillard,, L. Franco,, A. Fraser,, J. D. Friesen,, C. Fritz,, L. Frontali,, H. Fukuhara,, L. Fulton,, L. J. Fuller,, C. Gabel,, C. Gaillardin,, L. Gaillon,, F. Galibert,, F. Galisson,, P. Galland,, F.-J. Gamo,, C. Gancedo,, J. M. Garcia-Cantalejo,, M. I. Garcia-Gonzalez,, J. J. Garcia-Ramirez,, M. Garcia-Saéz,, H. Gassenhuber,, M. Gatius,, S. Gattung,, C. Geisel,, M. E. Gent,, S. Gentles,, M. Ghazvini,, D. Gigot,, V. Gilliquet,, N. Glansdorff,, A. Gómez-Peris,, A. Gonzalez,, S. E. Goulding,, C. Granotier,, T. Greco,, M. Grenson,, P. Grisanti,, L. A. Grivell,, D. Grothues,, U. Gueldener,, P. Guerreiro,, E. Guzman,, M. Haasemann,, B. Habbig,, H. Hagiwara,, J. Hall,, K. Halls-worth,, K. Hamberg,, N. Hamlin,, N. J. Hand,, V. Hanemann,, J. Hani,, T. Hankeln,, M. Hansen,, D. Harris,, D. E. Harris,, G. Hartzell,, D. Hatat,, U. Hattenhorst,, J. Hawkins,, U. Hebling,, J. Hegemann,, C. Hein,, A. Hennemann,, K. Hennessy,, C. J. Herbert,, K. Hernandez,, Y. Hernando,, e. Herrero,, K. Heumann,, D. Heuss-Neitzel,, N. Hewitt,, R. Hiesel,, H. Hilbert,, F. Hilger,, F. Hillier,, K. Hinni,, C. Ho,, J. Hoenicka,, B. Hofmann,, J. Hoheisel,, S. Hohmann,, C. P. Hollenberg,, K. Holmstrom,, O. Horaitis,, T. S. Horsnell,, M.-E. Huang,, B. Hughes,, S. Hunicke-Smith,, S. Hunt,, S. E. Hunt,, K. Huse,, R. W. Hyman,, F. Iborra,, K. J. Indge,, I. Iraqui Houssaini,, K. Isono,, C. Jacq,, M. Jacquet,, A. Jacquier,, K. Jagels,, W. Jàger,, C. M. James,, J. C. Jauniaux,, Y. Jia,, M. Jier,, A. Jimenez,, A. Johnson,, L. Johnson,, M. Johnson,, L. Jones,, F. Jones,, J.-L. Jonniaux,, D. B. Kaback,, T. Kallesoe,, S. Kalman,, A. Kalogeropoulos,, L. Karpfinger-Hartl,, D. Kashkari,, C. Katsoulou,, A. Kayser,, A. Kelly,, T. Keng,, H. KeucheL,, P. Kiesau,, L. Kirchrath,, J. Kirsten,, K. Kleine,, U. Kleinhans,, R. Klima,, C. Komp,, E. Kordes,, S. Korol,, P. Kotter,, C. Kramer,, B. Kramer,, W. Kramer,, P. Kreisl,, T. Kucaba,, H. Kuester,, O. Kurdi,, P. Laamanen,, M. J. Lafuente,, O. Landt,, G. Lanfranchi,, Y. Langston,, D. Lashkari,, P. Latreille,, G. Lauquin,, T. Le,, P. Legrain,, Y. Legros,, A. Lepingle,, H. Lesveque,, H. Leuther,, H. Lew,, C. Lewis,, Z. Y. Li,, S. Liebl,, A. Lin,, D. Lin,, M. Logghe,, A. J. E. Lohan,, J. E. Louis,, G. Lucchini,, K. Lutzenkirchen,, R. Lyck,, G. Lye,, A. C. Maarse,, M. J. Maat,, C. Macri,, A. Madania,, M. Maftahi,, A. Maia e Silva,, E. Maillier,, L. Mallet,, G. Mannhaupt,, V. Manus,, R. Marathe,, C. Marck,, A. Marconi,, E. Mardis,, E. Martegani,, R. Martin,, A. Mathieu,, K. T. C. Maurer,, M. J. Mazón,, C. Mazzoni,, D. McConnell,, S. McDonald,, R. A. McKee,, A. D. K. McReynolds,, P. Melchioretto,, S. Menezes,, F. Messenguy,, H. W. Mewes,, G. Michaux,, N. Miller,, O. Minenkova,, T. Miosga,, S. Mirtipati,, S. Möller-Rieker,, S. Möstl,, F. Molemans,, A. Monnet,, A.-L. Monnier,, M. A. Montague,, M. Moro,, D. Mosedale,, D. Möstl,, S. Moule,, L. Mouser,, Y. Murakami,, S. Muller-Auer,, J. Mulligan,, L. Murphy,, M. Muzi Falconi,, M. Naitou,, K. Nakahara,, A. Namath,, F. Nasr,, L. Navas,, A. Nawrocki,, J. Nelson,, U. Nentwich,, P. Netter,, R. Neu,, C. S. Newlon,, M. Nhan,, D. Niblett,, J.-M. Nicaud,, R. K. Niedenthal,, C. Nombela,, D. Noone,, R. Norgren,, B. NuBbaumer,, B. Obermaier,, C. Odell,, P. Ömer,, C. Oh,, K. Oliver,, S. G. Oliver,, B. F. Ouellette,, M. Ozawa,, V. Paces,, C. Pallier,, D. Pandolfo,, L. Panzeri,, S. Paoluzi,, A. G. Parle-McDermott,, S. Pascolo,, N. Paricio,, A. Pauley,, L. Paulin,, B. M. Pearson,, D. Pearson,, D. Peluso,, J. Perea,, M. Pérez-Alonso,, J. E. Pérez-Ortin,, A. Perrin,, F. X. Petel,, B. Pettersson,, F. Pfeiffer,, P. Philippsen,, A. Piérard,, E. Piravandi,, R. J. Planta,, P. Plevani,, O. Poch,, B. Poetsch,, F. M. Pohl,, T. M. Pohl,, R. Pöhlmann,, R. Poirey,, D. Portetelle,, F. Portillo,, S. Potier,, M. Proft,, H. Prydz,, A. Pujol,, B. Purnelle,, V. Puzos,, M. A. Rajandream,, M. Ramezani Rad,, S. W. Rasmussen,, A. Raynal,, C. Rebischung,, S. Rechmann,, M. Remacha,, J. L. Revuelta,, P. Rice,, G.-F. Richard,, C. Richards,, P. Richterich,, M. Rieger,, L. Rifkin,, l. Riles,, T. Rinaldi,, M. Rinke,, J. Robben,, A. B. Roberts,, D. Roberts,, F. Rodriguez,, E. Rodriguez-Belmonte,, C. Rodrigues-Pousada,, A. M. Rodriguez-Torres,, M. Rose,, R. Rossau,, N. Rowley,, T. Rupp,, M. Ruzzi,, W. Saeger,, J. E. Saiz,, M. Saliola,, D. Salom,, H. P. Saluz,, M. Sânchez-Perez,, M. A. Santos,, E. Sanz,, J. E. Sanz,, A.-M. Saren,, F. Sartorello,, M. Sasanuma,, S.-I. Sasanuma,, T. Scarcez,, I. Schaaf-Gerstenschlàger,, B. Schâfer,, M. Schâfer,, M. Scharfe,, B. Scherens,, N. Schroff,, M. Sen-Gupta,, T. Shibata,, T. Schmidheini,, E. R. Schmidt,, C. Schneider,, P. Scholier,, S. Schramm,, A. Schreer,, M. Schroder,, C. Schwager,, S. Schwarz,, C. Schwarzlose,, B. Schweitzer,, M. Schweizer,, A.-M. Sdicu,, P. Sehl,, C. Sensen,, J. G. Sgouros,, T. Shogren,, L. Shore,, Y. Su,, J. Skala,, J. Skelton,, P. P. Slonimski,, P. H. M. Smits,, V. Smith,, H. Soares,, E. Soeda,, A. Soler-Mira,, F. Sor,, N. Soriano,, J. L. Souciet,, C. Soustelle,, R. Spiegelberg,, L. I. Stateva,, H. Y. Steensma,, J. Stegemann,, S. Steiner,, L. Stellyes,, F. Sterky,, R. K. Storms,, H. St. Peter,, R. Stucka,, A. Taich,, E. Talla,, I. Tarassov,, H. Tashiro,, P. Taylor,, C. Teodoru,, H. Tettelin,, A. Thierry,, G. Thireos,, E. Tobiasch,, D. Tovan,, E. Trevaskis,, Y. Tsuchiya,, M. Tzermia,, M. Uhlen,, A. Underwood,, M. Unseld,, J. H. M. Urbanus,, A. Urrestarazu,, S. Ushinsky,, M. Valens,, G. Valle,, A. Van Broekhoven,, M. Vandenbol,, Q. J. M. Van der Aart,, C. G. Van Der Linden,, L. Van Dyck,, M. Vanoni,, J. C. van Vliet-Reedijk,, A. Vassarotti,, M. Vaudin,, K. Vaughan,, P. Verhasselt,, I. Vetter,, F. Vierendeels,, D. Vignati,, C. Vilela,, S. Vissers,, C. Vleck,, D. T. Vo,, D. H. Vo,, M. Voet,, G. Volckaert,, D. Von Wettstein,, H. Voss,, P. Vreken,, A. Wach,, G. Wagner,, S. V. Walsh,, R. Wambutt,, H. Wang,, Y. Wang,, J. R. Warmington,, R. Waterston,, M. D. Watson,, N. Weber,, E. Wedier,, H. Wedier,, Y. Wei,, S. Whitehead,, B. L. Wicksteed,, S. Wiemann,, L. Wilcox,, C. Wilson,, R. Wilson,, A. Winant,, E. Winnett,, B. Winsor,, P. Wipfli,, S. Wölff,, P. Wohldman,, K. Wolf,, K. H. Wolfe,, L. F. Wright,, H. Wurst,, G. Xu,, M. Yamazaki,, M. A. Yelton,, K. Yokohama,, A. Yoshikawa,, S. Yuping,, P. Zaccaria,, M. Zagulski,, F. K. Zimmermann,, J. Zimmermann,, M. Zimmermann,, W.-W. Zhong,, A. Zollner,, and E. Zumstein. 1997. The Yeast Genome Directory. Nature 387(Suppl.): 1105.
26.Gofîeau, A., B. G. Barrell,, H. Bussey,, R. W. Davis,, B. Dujon,, H. Feldmann,, F. Galibert,, J. D. Hoheisel,, C. Jacq,, M. L. Johnston,, J. E. Louis,, H. W. Mewes,, Y. Murakami,, P. Philippsen,, H. Tettelin,, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546550.
27. Gold, L.,, D. Brown,, Y.-Y. He,, T. Shtatland,, B. S. Singer,, and Y. Wu. 1997. From oligonucleotide shapes to genomic SELEX: Novel biological regulatory loops. Proc. Natl. Acad. Sci. USA 94:5964.
28. Guarente, L. 1983. Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 101:181191.
29. Guarente, L.,, R. R. Yocum,, and P. Gifford. 1982. A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. Proc. Natl. Acad. Sci. USA 79:74107414.
30. Güldener, U.,, S. Heck,, T. Fiedler,, J. Beinhauer,, and J. H. Hegemann. 1996. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24:25192524.
31. Heiter, P.,, and M. Boguski. 1997. Functional genomics: it's all how you read it. Science 278: 601602.
32. Heumann, K.,, C. Harris,, and H. W. Mewes. 1996. A top-down approach to whole genome visualization. Ismb. 4:98108.
33. Hillenkamp, F.,, and M. Karas. 1990. Mass spectrometry of peptides and proteins by matrix-assisted ultraviolet laser desorption/ionization. Methods Enzymol. 193:280295.
34. Himmelreich, R.,, H. Hubert,, H. Plagens,, E. Pirkl,, B. C. Li,, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:44204449.
35. Itaya, M. 1995. An estimation of minimal genome size required for life. FEBS Lett. 362: 257260.
36. Itaya, M.,, and T. Tanaka. 1990. Gene-directed mutagenesis on the chromosome of Bacillus subtilis 168. Mol. Gen. Genet. 223:268272.
37. Johnston, M. 1996. Towards a complete understanding of how a simple eukaryotic cell works. Trends Genet. 12:242243.
38. Kaback, D. B.,, P. W. Oeller,, H. Yde Steensma,, J. Hirschman,, D. Ruezinsky,, K. G. Coleman,, and J. R. Pringle. 1984. Temperature-sensitive lethal mutations on yeast chromosome I appear to define only a small number of genes. Genetics 108:6790.
39. Kaneko, T.,, S. Sato,, H. Kotani,, A. Tanaka,, E. Asamizu,, Y. Nakamura,, N. Miyajima,, M. Hirosawa,, M. Sugiura,, S. Sasamoto,, T. Kimura,, T. Hosouchi,, A. Matsuno,, A. Muraki,, N. Nakazaki,, K. Naruo,, S. Okumura,, S. Shimpo,, C. Takeuchi,, T. Wada,, A. Watanabe,, M. Yamada,, M. Yasuda,, and S. Tabata. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109136.
40. Karas, M.,, and F. Hillenkamp. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60:22992301.
41. Kawarabayasi, Y.,, M. Sawada,, H. Horikawa,, Y. Haikawa,, Y. Hino,, S. Yamamoto,, M. Sekine,, S. Baba,, H. Kosugi,, A. Hosoyama,, Y. Nagai,, M. Sakai,, K. Ogura,, R. Otsuka,, H. Nakazawa,, M. Takamiya,, Y. Ohfuku,, T. Funahashi,, T. Tanaka,, Y. Kudoh,, J. Yamazaki,, N. Kushida,, A. Oguchi,, K. Aoki,, T. Yoshizawa,, Y. Nakamura,, F. T. Robb,, K. Horikoshi,, Y. Masuchi,, H. Shizuya,, and H. Kikuchi. 1998. Complete sequence and gene organization of the genome of a hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3 (supplement). DNA Res. 5:147155.
42. Klenk, H. P.,, R. A. Clayton,, J. Tomb,, O. White,, K. E. Nelson,, K. A. Ketchum,, R. J. Dodson,, M. Gwinn,, E. K. Hickey,, J. D. Peterson,, D. L. Richardson,, A. R. Kerlavage,, D. E. Graham,, N. C. Kyrpides,, R. D. Fleischmann,, J. Quackenbush,, N. H. Lee,, G. G. Sutton,, S. Gill,, E. F. Kirkness,, B. A. Dougherty,, K. McKenney,, M. D. Adams,, B. Loftus,, S. Peterson,, C. I. Reich,, L. K. McNeil, J. H. Badger, A. Glodek,, L. Zhou,, R. Overbeek,, J. D. Gocayne,, J. F. Weidman,, L. McDonald,, T. Utterback,, M. D. Cotton,, T. Spriggs,, P. Artiach,, B. P. Kaine,, S. M. Sykes,, P. W. Peterson,, K. P. D'Andrea,, C. Bowman,, C. Fujii,, S. A. Garland, T. M. Mason, G. J. Olsen,, C. M. Fraser,, H. O. Smith,, C. R. Woese,, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364370.
43. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessieres,, A. Bolotin,, S. Borchert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Broufflet,, C. V. Bruschi,, B. Caldwell,, V. Capuano,, N. M. Carter,, S. K. Choi,, J. J. Codani,, I. F. Connexion,, N. J. Cummings,, R. A. Daniel,, F. Denizot,, F. M. Devine,, A. Dusterhoft,, S. D. Ehrlich,, P. T. Emmerson,, K. D. Entian,, J. Errington,, C. Fabret,, E. Ferrari,, D. Foulger,, C. Fritz,, M. Fujita,, Y. Fujita,, S. Fuma,, A. Galizzi,, N. Galleron,, N. Ghim,, P. Glaser,, A. Goffeau,, E. J. Golightly,, G. Grandi,, G. Guiseppi,, B. J. Guy,, K. Haga,, J. Haiech,, C. R. Harwood,, A. Henaut,, H. Hilbert,, S. Holsappel,, S. Hosono,, M. F. Hullo,, M. Itaya,, L. Jones,, B. Joris,, D. Karamata,, Y. Kasahara,, M. Klaerr-Blanchard,, C. Klein,, Y. Kobayashi,, P. Koetter,, G. Koningstein,, S. Krogh,, M. Kumano,, K. Kurita,, A. Lapidus,, S. Lardinois,, J. Lauber,, V. Lazarevic,, S. M. Lee,, A. Levine,, H. Liu,, S. Masuda,, C. Mauel,, C. Me digue,, N. Medina,, R. P. Mellado,, M. Mizuno,, D. Moestl,, S. Nakai,, M. Noback,, D. Noone,, M. O'Reilly,, K. Ogawa,, A. Ogiwara,, B. Oudega,, S. H. Park,, V. Parro,, T. Pohl,, D. Portetelle,, S. Porwollik,, A. M. Prescott,, E. Presecan,, P. Pujic,, B. Purnelle,, G. Rapoport,, M. Rey,, S. Reynolds,, M. Rieger,, C. Rivolta,, E. Rocha,, B. Roche,, M. Rose,, Y. Sadaie,, T. Sato,, E. Scanlan,, S. Schleich,, R. Schroeter,, F. Scoffone,, J. Sekiguchi,, A. Sekowska,, S. J. Seror,, P. Serror,, B. S. Shin,, B. Soldo,, A. Sorokin,, E. Tacconi,, T. Takagi,, H. Takahashi,, K. Takemaru,, M. Takeuchi,, A. Tamakoshi,, T. Tanaka,, P. Terpstra,, A. Tognoni,, V. Tosato,, S. Uchiyama,, M. Vandenbol,, F. Vannier,, A. Vassarotti,, A. Viari,, R. Wambutt,, E. Wedler,, H. Wedler,, T. Weitzenegger,, P. Winters,, A. Wipat,, H. Yamamoto,, K. Yamane,, K. Yasumoto,, K. Yata,, K. Yoshida,, H. F. Yoshikawa,, E. Zumstein,, H. Yoshikawa,, and A. Danchin. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:364370.
44. Lafontaine, D.,, and D. Tollervey. 1996. One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins. Nucleic Acids Res. 24: 34693471.
45. Link, A. J.,, D. Phillips,, and G. M. Church. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J. Bacteriol. 179:62286237.
46. Lipshutz, R. J.,, D. Morris,, M. Chee,, E. Hubbell,, M. J. Kozal,, N. Shah,, N. Shen,, R. Yang,, and S. P. Fodor. 1995. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19:442447.
47. Lussier, M.,, A. M. White,, J. Sheraton,, I. di Paolo,, J. Treadwell,, S. B. Southard,, C. I. Horenstein,, J. Chen-Weiner,, A. F. Ram,, J. C. Kapteyn,, T. W. Roemer,, D. H. Vo,, D. C. Bondoc,, J. Hall,, W. W. Zhong,, A. M. Sdicu,, J. Davies,, F. M. Klis,, P. W. Robbins,, and H. Bussey. 1997. Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae Genetics 147:435450.
48. Marshall, A.,, and J. Hodgson. 1998. DNA chips: an array of possibilities. Nat. Biotechnol. 16: 2731.
49. Miller, J. H. 1992. A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
50. 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. Part 1. Cold Spring Harbor Symp. Quant. Biol. 51:263273.
51. Nagahashi, S.,, H. Nakayama,, K. Hamada,, H. Yang,, M. Arisawa,, and K. Kitada. 1997. Regulation by tetracycline of gene expression in Saccharomyces cerevisiae. Mol. Gen. Genet. 255: 372375.
52. Naitou, M.,, H. Hagiwara,, F. Hanaoka,, T. Eki,, and Y. Murakami. 1997. Expression profiles of transcripts from 126 open reading frames in the entire chromosome VI of Saccharomyces cerevisiae by systematic northern analyses. Yeast 13: 12751290.
53. Niedenthal, R. K.,, l. Riles,, M. Johnson,, and J. H. Hegemarm. 1996. Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast. Yeast 1996. 12:773786.
54. Oliver, S. 1996. A network approach to the systematic analysis of yeast gene function. Trends Genet. 12:241242.
55. Oliver, S.G. 1996. From DNA sequence to biological function. Nature 379:597600.
56. Pearson, W. R. 1998. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276:7184.
57. Pearson, W. R.,, and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:24442448.
58. Rieger, K. J.,, A. Kaniak,, J. Y. Coppee,, G. Aljinovic,, A. Baudin-Baillieu,, G. Orlowska,, R. Gromadka,, O. Groudinsky,, J. P. Rago,, and P. P. Slonimski. 1997. Large-scale phenotypic analysis—the pilot project on yeast chromosome. III. Yeast 13:15471562.
59.Riley, M., and B. Lab e dan. 1996. Escherichia coli gene products: physiological functions and common ancestries, p. 21182202. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham III,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, D.C.
60. Rine, J. 1991. Gene overexpression in studies of Saccharomyces cerevisiae. Methods Enzymol. 194:239251.
61. Romanos, M. A.,, C. A. Scorer,, and J. J. Clare. 1992. Foreign gene expression in yeast: a review. Yeast 8:423488.
62. Ronne, H. 1995. Glucose repression in fungi. Trends Genet. 1995. 11:1217.
63. Rothstein, R. J. 1983. One-step gene disruption in yeast. Methods Enzymol. 101:202211.
64. Schneider, J. C.,, and L. Guarente. 1991. Vectors for expression of cloned genes in yeast: regulation, overproduction, and underproduction. Methods Enzymol. 194:373388.
65. Seifert, H. S.,, E. Y. Chen,, M. So,, and F. Hefiron. 1986. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 83:735739.
66. Shalon, D.,, S. J. Smith,, and P. O. Brown. 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:639645.
67. Sherman, F. 1991. Getting started with yeast. Methods Enzymol. 194:321.
68. Sherman, F.,, and J. Hicks. 1991. Micromanipulation and dissection of asci. Methods Enzymol. 194:2137.
69. Sherman, F.,, and P. Wakem. 1991. Mapping yeast genes. Methods Enzymol. 194:3857.
70. Shoemaker, D. D.,, D. A. Lashkari,, D. Morris,, M. Mittmann,, and R. W. Davis. 1996. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14:450456.
71. Smith, D. R.,, L. A. Doucette-Stamm,, C. Deloughery,, H.-M. Lee,, J. Dubois,, T. Aldredge,, R. Bashirzadeh,, D. Blakely,, R. Cook,, K. Gilbert,, D. Harrison,, L. Hoang,, P. Keagle,, W. Lumm,, B. Pothier,, D. Qiu,, R. Spadafora,, R. Vicare,, Y. Wang,, J. Wierzbowski,, R. Gibson,, N. Jiwani,, A. Caruso,, D. Bush,, H. Safer,, D. Patwell,, S. Prabhakar,, S. McDougall,, G. Shimer,, A. Goyal,, A. Pietrovski,, G. M. Church,, C. J. Daniels,, J.-I. Mao,, P. Rice,, J. Nolling,, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum δ H: functional analysis and comparative genomics. J. Bacteriol. 179:71357155.
72. Smith, V.,, D. Botstein,, and P. O. Brown. 1995. Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc. Natl. Acad. Sci. USA 92:64796483.
73. Smith, V.,, K. N. Chou,, D. Lashkari,, D. Botstein,, and P. O. Brown. 1996. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274:20692074.
74. Stephens, R. S.,, S. Kalman,, C. J. Lammel,, J. Fan,, R. Marathe,, L. Aravind,, W. P. Mitchell,, L. Olinger,, R. L. Tatusov,, Q. Zhao,, E. V. Koonin,, and R. W. Davis. 1998. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282:754759.
75. Tomb, J. F.,, O. White,, A. R. Kerlavage,, R. A. Clayton,, G. G. Sutton,, R. D. Fleischmann,, K. A. Ketchum,, H. P. Klenk,, S. Gill,, B. A. Dougherty,, K. Nelson,, J. Quackenbush,, L. Zhou,, E. F. Kirkness,, S. Peterson,, B. Loftus,, D. Richardson,, R. Dodson,, H. G. Khalak,, A. Glodek,, K. McKenney,, L. M. Fitzegerald,, N. Lee,, M. D. Adams,, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539547.
76. Tanaka, S.,, and K. Isono. 1993. Correlation between observed transcripts and sequenced ORFs of chromosome III of Saccharomyces cerevisiae. Nucleic Acids Res. 21:11491153.
77. Tuerk, C.1997. Using the SELEX combinatorial chemistry process to find high affinity nucleic acid ligands to target molecules. Methods Mol. Biol. 67:219230.
78. Tuerk, C.,, and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505510.
79. Ushinsky, S., C., H. Bussey,, A. A. Ahmed,, Y. Wang,, J. Friesen,, and R. K. Storms. 1977. Functional analysis of a 38 kilobase region on chromosome XVI in Saccharomyces cerevisiae. Genes Fund. 4: 273284.
80. Velculescu, V. E.,, L. Zhang,, B. Vogelstein,, and K. W. Kinzler. 1995. Serial analysis of gene expression. Science 270:484487.
81. Velculescu, V.E.,, L. Zhang,, W. Zhou,, J. Vogelstein,, M.A. Basrai,, D. E. Bassett, Jr.,, P. Hieter,, B. Vogelstein,, and K. W. Kinzler. 1997. Characterization of the yeast transcriptome. Cell 88:243251.
82. Wach, A.,, A. Brachat,, R. Pohlmann,, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae . Yeast 10:17931808.
83. Witke, W.,, A. V. Podtelejnikov,, A. Di Nardo,, J. D. Sutherland,, C. B. Gurniak,, C. Dotti,, and M. Mann. 1998. In mouse brain profilin I and profilin II associate with regulators of the endocytic pathway and actin assembly. EMBO J. 17:967976.
84. Wodicka, L.,, H. Dong,, M. Mittmann,, M. H. Ho,, and D. J. Lockhart. 1997. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15:13591367.
85. Wolfe, K. H.,, and D. C. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708713.
86. Yoshikawa, A.,, and K. Isono. 1990. Chromosome III of Saccharomyces cerevisiae: an ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes. Yeast 6:383401.
87. Zachariae, W.,, A. Shevchenko,, P. D. Andrews,, R. Ciosk,, M. Galova,, M. J. Stark,, M. Mann,, and K. Nasmyth. 1998. Mass spectrometric analysis of the anaphase-promoting complex from yeast: identification of a subunit related to cullins. Science 279:12161219.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error