Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast

A competitive growth assay has been used to identify yeast genes involved in the repair of UV- or MMS-induced DNA damage. A collection of 2,827 yeast strains was analyzed in which each strain has a single ORF replaced with a cassette containing two unique sequence tags, allowing for its detection by hybridization to a high-density oligonucleotide array. The hybridization data identify a high percentage of the deletion strains present in the collection that were previously characterized as being sensitive to the DNA-damaging agents. The assay, and subsequent analysis, has been used to identify six genes not formerly known to be involved in the damage response, whose deletion renders the yeast sensitive to UV or MMS treatment. The recently identified genes include three uncharacterized ORFs, as well as genes that encode protein products implicated in ubiquitination, gene silencing, and transport across the mitochondrial membrane. Epistatsis analysis of four of the genes was performed to determine the DNA damage repair pathways in which the protein products function.

[1]  F. Sherman,et al.  Micromanipulation and dissection of asci. , 1991, Methods in enzymology.

[2]  T. Ito,et al.  Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[4]  G. Sprague,,et al.  Assay of yeast mating reaction. , 1991, Methods in enzymology.

[5]  J. Diffley,et al.  Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint , 2001, Nature.

[6]  A. Carr,et al.  Rad18 is required for DNA repair and checkpoint responses in fission yeast. , 1999, Molecular biology of the cell.

[7]  C. Lawrence.  The RAD6 DNA repair pathway in Saccharomyces cerevisiae: What does it do, and how does it do it? , 1994, BioEssays : news and reviews in molecular, cellular and developmental biology.

[8]  H. Feldmann,et al.  Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S protease complex , 1994, Yeast.

[9]  P. Kaufman,et al.  Role of Saccharomyces cerevisiae chromatin assembly factor-I in repair of ultraviolet radiation damage in vivo. , 1999, Genetics.

[10]  J. Saffi,et al.  Importance of the Sgs1 helicase activity in DNA repair of Saccharomyces cerevisiae , 2000, Current Genetics.

[11]  Peer Bork,et al.  A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[12]  M. Fuller,et al.  Transcription of meiotic cell cycle and terminal differentiation genes depends on a conserved chromatin associated protein, whose nuclear localisation is regulated. , 2000, Development.

[13]  D. Botstein,et al.  Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression , 1991, The Journal of cell biology.

[14]  I. Ota,et al.  A Proteolytic Pathway That Recognizes Ubiquitin as a Degradation Signal (*) , 1995, The Journal of Biological Chemistry.

[15]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[16]  S. Jentsch,et al.  Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MATα2 repressor , 1993, Cell.

[17]  M. Bauer,et al.  The role of the TIM8–13 complex in the import of Tim23 into mitochondria , 2000, EMBO Journal.

[18]  H. Feiler,et al.  The higher plant Arabidopsis thaliana encodes a functional CDC48 homologue which is highly expressed in dividing and expanding cells. , 1995, The EMBO journal.

[19]  W. Xiao,et al.  The repair of DNA methylation damage in Saccharomyces cerevisiae , 1996, Current Genetics.

[20]  Alexander Varshavsky,et al.  In vivo degradation of a transcriptional regulator: The yeast α2 repressor , 1990, Cell.

[21]  P. Chambon,et al.  Chicken oviduct progesterone receptor: Location of specific regions of high-affinity binding in cloned DNA fragments of hormone-responsive genes , 1982, Cell.

[22]  T. Reiner,et al.  Ubiquitin Metabolism Affects Cellular Response to Volatile Anesthetics in Yeast , 1999, Molecular and Cellular Biology.

[23]  M. Resnick,et al.  Genes required for ionizing radiation resistance in yeast , 2001, Nature Genetics.

[24]  J. Heitman,et al.  Sphingolipids Signal Heat Stress-induced Ubiquitin-dependent Proteolysis* , 2000, The Journal of Biological Chemistry.

[25]  L. Samson,et al.  Saccharomyces cerevisiae 3‐methyladenine DNA glycosylase has homology to the AlkA glycosylase of E. coli and is induced in response to DNA alkylation damage. , 1990, The EMBO journal.

[26]  C. Koehler,et al.  Different import pathways through the mitochondrial intermembrane space for inner membrane proteins , 1999, The EMBO journal.

[27]  F. Fabre,et al.  Homologous recombination is responsible for cell death in the absence of the Sgs1 and Srs2 helicases , 2000, Nature Genetics.

[28]  R. Sikorski,et al.  A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.

[29]  D. M. Livingston,et al.  Effects of controlled RAD52 expression on repair and recombination in Saccharomyces cerevisiae , 1991, Molecular and cellular biology.

[30]  P. Philippsen,et al.  Heterologous HIS3 Marker and GFP Reporter Modules for PCR‐Targeting in Saccharomyces cerevisiae , 1997, Yeast.

[31]  D. Gottschling,et al.  The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae , 1997, Molecular and cellular biology.

[32]  A. Varshavsky,et al.  Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin‐mediated proteolysis in Saccharomyces cerevisiae. , 1996, The EMBO journal.

[33]  J. Sterling,et al.  Yeast and human genes that affect the Escherichia coli SOS response. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[34]  D. Murdock,et al.  Mitochondria and dystonia: the movement disorder connection? , 1999, Proceedings of the National Academy of Sciences of the United States of America.