Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Science 20 December 1996:
Vol. 274. no. 5295, pp. 2069 - 2074
DOI: 10.1126/science.274.5295.2069

Reports

Functional Analysis of the Genes of Yeast Chromosome V by Genetic Footprinting

Victoria Smith, Karen N. Chou, Deval Lashkari, David Botstein, Patrick O. Brown *

Genetic footprinting was used to assess the phenotypic effects of Ty1 transposon insertions in 268 predicted genes of chromosome V of Saccharomyces cerevisiae. When seven selection protocols were used, Ty1 insertions in more than half the genes tested (157 of 268) were found to result in a detectable reduction in fitness. Results could not be obtained for fewer than 3 percent of the genes tested (7 of 268). Previously known mutant phenotypes were confirmed, and, for about 30 percent of the genes, new mutant phenotypes were identified.

V. Smith and K. N. Chou, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
D. Lashkari and D. Botstein, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
P. O. Brown, Howard Hughes Medical Institute and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
*   To whom correspondence should be addressed. E-mail: pbrown{at}cmgm.stanford.edu



References

  • ABEIJON, C, GUANOSINE DIPHOSPHATASE IS REQUIRED FOR PROTEIN AND SPHINGOLIPID GLYCOSYLATION IN THE GOLGI LUMEN OF SACCHAROMYCES-CEREVISIAE, JOURNAL OF CELL BIOLOGY 122: 307 (1993).
  • ATKINSON, K.D., YEAST MUTANTS AUXOTROPHIC FOR CHOLINE OR ETHANOLAMINE, JOURNAL OF BACTERIOLOGY 141: 558 (1980).
  • BOEKE, J.D., TY ELEMENTS TRANSPOSE THROUGH AN RNA INTERMEDIATE, CELL 40: 491 (1985).
  • BONNEFOY, N, OXA1, A SACCHAROMYCES-CEREVISIAE NUCLEAR GENE WHOSE SEQUENCE IS CONSERVED FROM PROKARYOTES TO EUKARYOTES CONTROLS CYTOCHROME-OXIDASE BIOGENESIS, JOURNAL OF MOLECULAR BIOLOGY 239: 201 (1994).
  • BOONCHIRD, C, CHARACTERIZATION OF THE YEAST ARG5,6 GENE - DETERMINATION OF THE NUCLEOTIDE-SEQUENCE, ANALYSIS OF THE CONTROL REGION AND OF ARG5,6 TRANSCRIPT, MOLECULAR & GENERAL GENETICS 226: 154 (1991).
  • BRANDRISS, M.C., ISOLATION AND PRELIMINARY CHARACTERIZATION OF SACCHAROMYCES-CEREVISIAE PROLINE AUXOTROPHS, JOURNAL OF BACTERIOLOGY 138: 816 (1979).
  • CHAPMAN, R.E., THE FUNCTIONING OF THE YEAST GOLGI-APPARATUS REQUIRES AN ER PROTEIN ENCODED BY ANP1, A MEMBER OF A NEW FAMILY OF GENES AFFECTING THE SECRETORY PATHWAY, EMBO JOURNAL 13: 4896 (1994).
  • DIETRICH, F, IN PRESS NATURE.
  • ELLEDGE, J, GENE DEV 4: 4740 (1990).
  • GARRETT, M.D., GDI1 ENCODES A GDP DISSOCIATION INHIBITOR THAT PLAYS AN ESSENTIAL ROLE IN THE YEAST SECRETORY PATHWAY, EMBO JOURNAL 13: 1718 (1994).
  • GOEBL, M.G., MOST OF THE YEAST GENOMIC SEQUENCES ARE NOT ESSENTIAL FOR CELL-GROWTH AND DIVISION, CELL 46: 983 (1986).
  • GRAHAM, L.A., VMA8 ENCODES A 32-KDA V-1 SUBUNIT OF THE SACCHAROMYCES-CEREVISIAE VACUOLAR H+-ATPASE REQUIRED FOR FUNCTION AND ASSEMBLY OF THE ENZYME COMPLEX, JOURNAL OF BIOLOGICAL CHEMISTRY 270: 15037 (1995).
  • GUELIN, E, SEQUENCE OF THE AFG3 GENE ENCODING A NEW MEMBER OF THE FTSH/YME1/TMA SUBFAMILY OF THE AAA-PROTEIN FAMILY, YEAST 10: 1389 (1994).
  • HARRINGTON, A, MOL MICROBIOL 9: 545 (1993).
  • IRIE, K, THE YEAST MOT2 GENE ENCODES A PUTATIVE ZINC-FINGER PROTEIN THAT SERVES AS A GLOBAL NEGATIVE REGULATOR AFFECTING EXPRESSION OF SEVERAL CATEGORIES OF GENES, INCLUDING MATING-PHEROMONE-RESPONSIVE GENES, MOLECULAR AND CELLULAR BIOLOGY 14: 3150 (1994).
  • KIM, Y.J., CONTROL OF CELLULAR MORPHOGENESIS BY THE IPL2 BEM2 GTPASE-ACTIVATING PROTEIN - POSSIBLE ROLE OF PROTEIN-PHOSPHORYLATION, JOURNAL OF CELL BIOLOGY 127: 1381 (1994).
  • MASSELOT, M, METHIONINE BIOSYNTHESIS IN SACCHAROMYCES-CEREVISIAE .1. GENETIC-ANALYSIS OF AUXOTROPHIC MUTANTS, MOLECULAR & GENERAL GENETICS 139: 121 (1975).
  • MCEWEN, J.E., SEQUENCE AND CHROMOSOMAL LOCALIZATION OF 2 PET GENES REQUIRED FOR CYTOCHROME-C-OXIDASE ASSEMBLY IN SACCHAROMYCES-CEREVISIAE, CURRENT GENETICS 23: 9 (1993).
  • MCNEIL, J.B., CLONING AND MOLECULAR CHARACTERIZATION OF 3 GENES, INCLUDING 2 GENES ENCODING SERINE HYDROXYMETHYLTRANSFERASES, WHOSE INACTIVATION IS REQUIRED TO RENDER YEAST AUXOTROPHIC FOR GLYCINE, JOURNAL OF BIOLOGICAL CHEMISTRY 269: 9155 (1994).
  • MITCHELL, A.P., REGULATION OF GLUTAMINE-REPRESSIBLE GENE-PRODUCTS BY THE GLN3 FUNCTION IN SACCHAROMYCES-CEREVISIAE, MOLECULAR AND CELLULAR BIOLOGY 4: 2758 (1984).
  • MITCHELL, A.P., 3 REGULATORY SYSTEMS CONTROL PRODUCTION OF GLUTAMINE-SYNTHETASE IN SACCHAROMYCES-CEREVISIAE, MOLECULAR AND CELLULAR BIOLOGY 4: 2767 (1984).
  • MOEHLE, C.M., PROTEASE-B OF SACCHAROMYCES-CEREVISIAE - ISOLATION AND REGULATION OF THE PRB1 STRUCTURAL GENE, GENETICS 115: 255 (1987).
  • NAKAFUKU, M, ISOLATION OF A 2ND YEAST SACCHAROMYCES-CEREVISIAE GENE (GP A2) CODING FOR GUANINE NUCLEOTIDE-BINDING REGULATORY PROTEIN - STUDIES ON ITS STRUCTURE AND POSSIBLE FUNCTIONS, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 85: 1374 (1988).
  • NASS, G, GENETICS OF BORRELIDIN RESISTANT MUTANTS OF SACCHAROMYCES-CERIVISIAE AND PROPERTIES OF THEIR THREONYL-TRANSFER-RNA SYNTHETASE, MOLECULAR & GENERAL GENETICS 147: 39 (1976).
  • OHMEN, J.D., MOLECULAR-CLONING AND NUCLEOTIDE-SEQUENCE OF THE NUCLEAR PET122 GENE REQUIRED FOR EXPRESSION OF THE MITOCHONDRIAL COX3 GENE IN S-CEREVISIAE, NUCLEIC ACIDS RESEARCH 16: 10783 (1988).
  • OLIVER, S.G., THE COMPLETE DNA-SEQUENCE OF YEAST CHROMOSOME-III, NATURE 357: 38 (1992).
  • PRAKASH, S, INCREASED SPONTANEOUS MITOTIC SEGREGATION IN MMS-SENSITIVE MUTANTS OF SACCHAROMYCES-CEREVISIAE, GENETICS 87: 229 (1977).
  • SHINOHARA, A, RAD51 PROTEIN INVOLVED IN REPAIR AND RECOMBINATION IN SACCHAROMYCES-CEREVISIAE IS A RECA-LIKE PROTEIN, CELL 69: 457 (1992).
  • SMITH, V, GENETIC FOOTPRINTING - A GENOMIC STRATEGY FOR DETERMINING A GENES FUNCTION GIVEN ITS SEQUENCE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 92: 6479 (1995).
  • THIAGALINGAM, S, PAK1, A GENE THAT CAN REGULATE P53 ACTIVITY IN YEAST, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 92: 6062 (1995).
  • WERNERWASHBURNE, M, COMPLEX INTERACTIONS AMONG MEMBERS OF AN ESSENTIAL SUBFAMILY OF HSP70 GENES IN SACCHAROMYCES-CEREVISIAE, MOLECULAR AND CELLULAR BIOLOGY 7: 2568 (1987).


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
The Hermes Transposon of Musca domestica Is an Efficient Tool for the Mutagenesis of Schizosaccharomyces pombe.
A. G. Evertts, C. Plymire, N. L. Craig, and H. L. Levin (2007)
Genetics 177, 2519-2523
   Abstract »    Full Text »    PDF »
Appearances can be deceiving: phenotypes of knockout mice.
I. Barbaric, G. Miller, and T. N. Dear (2007)
Brief Funct Genomic Proteomic
   Abstract »    Full Text »    PDF »
Natural Transposon Mutagenesis of Clinical Isolates of Mycobacterium tuberculosis: How Many Genes Does a Pathogen Need?.
H. Yesilkaya, J. W. Dale, N. J. C. Strachan, and K. J. Forbes (2005)
J. Bacteriol. 187, 6726-6732
   Abstract »    Full Text »    PDF »
A modular minimal cell model: Purine and pyrimidine transport and metabolism.
M. Castellanos, D. B. Wilson, and M. L. Shuler (2004)
PNAS 101, 6681-6686
   Abstract »    Full Text »    PDF »
DEG: a database of essential genes.
R. Zhang, H.-Y. Ou, and C.-T. Zhang (2004)
Nucleic Acids Res. 32, D271-272
   Abstract »    Full Text »    PDF »
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
I. Famili, J. Forster, J. Nielsen, and B. O. Palsson (2003)
PNAS 100, 13134-13139
   Abstract »    Full Text »    PDF »
Evolution in Saccharomyces cerevisiae: Identification of Mutations Increasing Fitness in Laboratory Populations.
V. M. Blanc and J. Adams (2003)
Genetics 165, 975-983
   Abstract »    Full Text »    PDF »
Functional Genomics Reveals Relationships Between the Retrovirus-Like Ty1 Element and Its Host Saccharomyces cerevisiae.
J. L. Griffith, L. E. Coleman, A. S. Raymond, S. G. Goodson, W. S. Pittard, C. Tsui, and S. E. Devine (2003)
Genetics 164, 867-879
   Abstract »    Full Text »    PDF »
From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways.
S. Y. Gerdes, M. D. Scholle, M. D'Souza, A. Bernal, M. V. Baev, M. Farrell, O. V. Kurnasov, M. D. Daugherty, F. Mseeh, B. M. Polanuyer, et al. (2002)
J. Bacteriol. 184, 4555-4572
   Abstract »    Full Text »    PDF »
The fifth essential DNA polymerase phi in Saccharomyces cerevisiae is localized to the nucleolus and plays an important role in synthesis of rRNA.
K. Shimizu, Y. Kawasaki, S.-I. Hiraga, M. Tawaramoto, N. Nakashima, and A. Sugino (2002)
PNAS 99, 9133-9138
   Abstract »    Full Text »    PDF »
Evolutionary Rate in the Protein Interaction Network.
H. B. Fraser, A. E. Hirsh, L. M. Steinmetz, C. Scharfe, and M. W. Feldman (2002)
Science 296, 750-752
   Abstract »    Full Text »    PDF »
fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen.
D. S. Fay, S. Keenan, and M. Han (2002)
Genes & Dev. 16, 503-517
   Abstract »    Full Text »    PDF »
A genome-scale analysis for identification of genes required for growth or survival of Haemophilusinfluenzae.
B. J. Akerley, E. J. Rubin, V. L. Novick, K. Amaya, N. Judson, and J. J. Mekalanos (2002)
PNAS 99, 966-971
   Abstract »    Full Text »    PDF »
Multiple Regulators of Ty1 Transposition in Saccharomyces cerevisiae Have Conserved Roles in Genome Maintenance.
D. T. Scholes, M. Banerjee, B. Bowen, and M. J. Curcio (2001)
Genetics 159, 1449-1465
   Abstract »    Full Text »    PDF »
An active retrotransposon in Candida albicans.
N. J. Holton, T. J. D. Goodwin, M. I. Butler, and R. T. M. Poulter (2001)
Nucleic Acids Res. 29, 4014-4024
   Abstract »    Full Text »    PDF »
Direct Estimate of the Mutation Rate and the Distribution of Fitness Effects in the Yeast Saccharomyces cerevisiae.
D. M. Wloch, K. Szafraniec, R. H. Borts, and R. Korona (2001)
Genetics 159, 441-452
   Abstract »    Full Text »    PDF »
Quantitative target display: a method to screen yeast mutants conferring quantitative phenotypes by 'mutant DNA fingerprints'.
V. M. Sharma, R. Chopra, I. Ghosh, and K. Ganesan (2001)
Nucleic Acids Res. 29, e86
   Abstract »    Full Text »    PDF »
The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes.
A. Wagner (2001)
Mol. Biol. Evol. 18, 1283-1292
   Abstract »    Full Text »    PDF »
Genetic Footprinting in Bacteria.
R. S. Hare, S. S. Walker, T. E. Dorman, J. R. Greene, L.-M. Guzman, T. J. Kenney, M. C. Sulavik, K. Baradaran, C. Houseweart, H. Yu, et al. (2001)
J. Bacteriol. 183, 1694-1706
   Abstract »    Full Text »    PDF »
Point Mutations Identify a Conserved Region of the Saccharomyces cerevisiae AFR1 Gene That Is Essential for Both the Pheromone Signaling and Morphogenesis Functions.
C. R. DeMattei, C. P. Davis, and J. B. Konopka (2000)
Genetics 155, 43-55
   Abstract »    Full Text »
TRIPLES: a database of gene function in Saccharomyces cerevisiae.
A. Kumar, K.-H. Cheung, P. Ross-Macdonald, P. S. R. Coelho, P. Miller, and M. Snyder (2000)
Nucleic Acids Res. 28, 81-84
   Abstract »    Full Text »    PDF »
A Genetic Strategy to Eliminate Self-Activator Baits Prior to High-Throughput Yeast Two-Hybrid Screens.
A. J.M. Walhout and M. Vidal (1999)
Genome Res. 9, 1128-1134
   Abstract »    Full Text »
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis.
E. A. Winzeler, D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, et al. (1999)
Science 285, 901-906
   Abstract »    Full Text »
Proteins Connecting the Nuclear Pore Complex with the Nuclear Interior.
C. Strambio-de-Castillia, G. Blobel, and M. P. Rout (1999)
J. Cell Biol. 144, 839-855
   Abstract »    Full Text »    PDF »
Genomics and Antimicrobial Drug Discovery.
D. T. Moir, K. J. Shaw, R. S. Hare, and G. F. Vovis (1999)
Antimicrob. Agents Chemother. 43, 439-446
   Full Text »    PDF »
Parallel analysis of genetic selections using whole genome oligonucleotide arrays.
R. J. Cho, M. Fromont-Racine, L. Wodicka, B. Feierbach, T. Stearns, P. Legrain, D. J. Lockhart, and R. W. Davis (1998)
PNAS 95, 3752-3757
   Abstract »    Full Text »    PDF »
Nonhomologous End Joining during Restriction Enzyme-Mediated DNA Integration in Saccharomyces cerevisiae.
P. Manivasakam and R. H. Schiestl (1998)
Mol. Cell. Biol. 18, 1736-1745
   Abstract »    Full Text »    PDF »
Marginal fitness contributions of nonessential genes in yeast.
J. W. Thatcher, J. M. Shaw, and W. J. Dickinson (1998)
PNAS 95, 253-257
   Abstract »    Full Text »    PDF »
Yeast microarrays for genome wide parallel genetic and gene expression analysis.
D. A. Lashkari, J. L. DeRisi, J. H. McCusker, A. F. Namath, C. Gentile, S. Y. Hwang, P. O. Brown, and R. W. Davis (1997)
PNAS 94, 13057-13062
   Abstract »    Full Text »    PDF »
Whole genome analysis: Experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR.
D. A. Lashkari, J. H. McCusker, and R. W. Davis (1997)
PNAS 94, 8945-8947
   Abstract »    Full Text »    PDF »
Ubiquitous, heritable damage in cell populations that survive treatment with methotrexate.
M. Chow and H. Rubin (1997)
PNAS 94, 8773-8778
   Abstract »    Full Text »    PDF »
Small Open Reading Frames: Beautiful Needles in the Haystack.
M. A. Basrai, P. Hieter, and J. D. Boeke (1997)
Genome Res. 7, 768-771
   Full Text »    PDF »
High-resolution functional mapping of a cloned gene by genetic footprinting.
I. R. Singh, R. A. Crowley, and P. O. Brown (1997)
PNAS 94, 1304-1309
   Abstract »    Full Text »    PDF »
ABC50 Interacts with Eukaryotic Initiation Factor 2 and Associates with the Ribosome in an ATP-dependent Manner.
J. K. Tyzack, X. Wang, G. J. Belsham, and C. G. Proud (2000)
J. Biol. Chem. 275, 34131-34139
   Abstract »    Full Text »    PDF »
Yeast Genes Controlling Responses to Topogenic Signals in a Model Transmembrane Protein.
D. J. Tipper and C. A Harley (2002)
Mol. Biol. Cell 13, 1158-1174
   Abstract »    Full Text »    PDF »



To Advertise     Find Products


Science. ISSN 0036-8075 (print), 1095-9203 (online)