Characterization of mutations that are synthetic lethal with pol3-13, a mutated allele of DNA polymerase delta in Saccharomyces cerevisiae

Current Genetics

Volumn 43, Issue 5, 2003, Pages 337-350

  Chanet, Roland ^a   Heude, Martine ^a  

^a INSTITUT CURIE   (France)

Author keywords

DNA polymerase delta; DNA repair; Recombination; Synthetic lethal mutations

Indexed keywords

CYCLIC AMP; DNA DIRECTED DNA POLYMERASE DELTA; NUCLEOPORIN; RAS PROTEIN;

ALLELE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA REPAIR; DNA REPLICATION; ENZYME ACTIVE SITE; FUNGAL STRAIN; FUNGUS MUTATION; GENE DELETION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE MUTATION; GENETIC CODE; GENETIC RECOMBINATION; GENETIC SCREENING; GENETIC STABILITY; GENETIC TRANSCRIPTION; HEAT SENSITIVITY; HOMOLOGOUS RECOMBINATION; NONHUMAN; NUCLEAR PORE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN METABOLISM; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

CHROMOSOME MAPPING; DNA MUTATIONAL ANALYSIS; DNA POLYMERASE III; DNA REPAIR; FUNGAL PROTEINS; MUTATION; PLASMIDS; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; UBIQUITIN;

FUNGI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0042475409     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-003-0407-2     Document Type: Article

References (81)

1. Bender A, Pringle JR (1991) Use of a screen for synthetic lethal and multicopy suppressor mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol 11:1295-1305
2. Bennett CB, Lewis LK, Karthikeyan G, Lobachev KS, Jin YH, Sterling JF, Snipe JR, Resnick MA (2001) Genes required for ionizing radiation resistance in yeast. Nat Genet 29:426-434
3. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115-132
4. Budd ME, Campbell JL (1995) DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae. Mol Cell Biol 15:2173-2179
5. Clark AB, Valle F, Drotschmann K, Gary RK, Kunkel TA (2000) Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes. J Biol Chem 275:36498-36501
6. Cooper TG (2002) Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev 26:223-238
7. Costanzo V, Avvedimento EV, Gottesman ME, Gautier J, Grieco D (1999) Protein kinase A is required for chromosomal DNA replication. Curr Biol 9:903-906
8. Datta A, Schmeits JL, Amin NS, Lau PJ, Myung K, Kolodner RD (2000) Checkpoint-dependent activation of mutagenic repair in Saccharomyces cerevisiae pol3-01 mutants. Mol Cell 6:593-603
9. Davis AP, Symington LS (2001) The yeast recombinational repair protein Rad59 interacts with Rad52 and stimulates single-strand annealing. Genetics 159:515-525
10. Diede SJ, Gottschling DE (1999) Telomerase-mediated telomere addition in vivo requires DNA primase and DNA polymerases alpha and delta. Cell 99:723-733
11. Eissenberg JC, Ayyagari R, Gomes XV, Burgers PM (1997) Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase delta and DNA polymerase epsilon. Mol Cell Biol 17:6367-6378
12. Evans SK, Lundblad V (1999) Est1 and Cdc13 as comediators of telomerase access. Science 286:117-120
13. Fuss I, Linn S (2001) Human DNA polymerase epsilon colocalizes with PCNA and DNA replication late, but not early in S phase. J Biol Chem 10:10
14. Gailus-Durner V, Xie J, Chintamaneni C, Vershon AK (1996) Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene. Mol Cell Biol 16:2777-2786
15. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147
16. Gerik KJ, Li X, Pautz A, Burgers PM (1998) Characterization of the two small subunits of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem 273:19747-19755
17. Gietz RD, Sugino A (1988) New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527-534
18. Giot L, Simon M, Dubois C, Faye G (1995) Suppressors of thermosensitive mutations in the DNA polymerase delta gene of Saccharomyces cerevisiae. Mol Gen Genet 246:212-222
19. Giot L, Chanet R, Simon M, Facca C, Faye G (1997) Involvement of the yeast DNA polymerase delta in DNA repair in vivo. Genetics 146:1239-1251
20. Gromoller A, Lehming N (2000a) Srb7p is a physical and physiological target of Tup1p. EMBO J 19:6845-6852
21. Gromoller A, Lehming N (2000b) Srb7p is essential for the activation of a subset of genes. FEBS Lett 484:48-54
22. Habraken Y, Sung P, Prakash L, Prakash S (1996) Binding of insertion/deletion DNA mismatches by the heterodimer of yeast mismatch repair proteins MSH2 and MSH3. Curr Biol 6:1185-1187
23. Hishida T, Ohno T, Iwasaki H, Shinagawa H (2002) Saccharomyces cerevisiae MGS1 is essential in strains deficient in the RAD6-dependent DNA damage tolerance pathway. EMBO J 21:2019-2029
24. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang, L, Wolting, C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
25. Hochstrasser M (1996) Ubiquitin-dependent protein degradation. Annu Rev Genet 30:405-439
26. Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419:135-141
27. Holmes AM, Haber JE (1999) Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell 96:415-424
28. Hopfner KP, Craig L, Moncalian G, Zinkel RA, Usui T, Owen BA, Karcher A, Henderson B, Bodmer JL, McMurray CT, Carney JP, Petrini JH, Tainer JA (2002) The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature 418:562-566
29. Huang M, Elledge SJ (1997) Identification of RNR4, encoding a second essential small subunit of ribonucleotide reductase in Saccharomyces cerevisiae. Mol Cell Biol 17:6105-6113
30. Huang, ME, Calignon A de, Nicolas A, Galibert F (2000) POL32, a subunit of the Saccharomyces cerevisiae DNA polymerase delta, defines a link between DNA replication and the mutagenic bypass repair pathway. Curr Genet 38:178-187
31. Hubscher U, Maga G, Spadari S (2002) Eukaryotic DNA polymerases. Annu Rev Biochem 71:133-163
32. Hwang LH, Murray AW (1997) A novel yeast screen for mitotic arrest mutants identifies DOC1, a new gene involved in cyclin proteolysis. Mol Biol Cell 8:1877-1887
33. Jin YH, Obert R, Burgers PM, Kunkel TA, Resnick MA, Gordenin DA (2001) The 3′ → 5′ exonuclease of DNA polymerase delta can substitute for the 5′ flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability. Proc Natl Acad Sci USA 98:5122-5127
34. Kaplun L, Ivantsiv Y, Kornitzer D, Raveh D (2000) Functions of the DNA damage response pathway target Ho endonuclease of yeast for degradation via the ubiquitin-26S proteasome system. Proc Natl Acad Sci USA 97:10077-10082
35. Karthikeyan R, Vonarx EJ, Straffon AF, Simon M, Faye G, Kunz BA (2000) Evidence from mutational specificity studies that yeast DNA polymerases delta and epsilon replicate different DNA strands at an intracellular replication fork. J Mol Biol 299:405-419
36. Kokoska RJ, Stefanovic L, DeMai J, Petes TD (2000) Increased rates of genomic deletions generated by mutations in the yeast gene encoding DNA polymerase delta or by decreases in the cellular levels of DNA polymerase delta. Mol Cell Biol 20:7490-7504
37. Kumar A, Cheung KH, Ross-Macdonald P, Coelho PS, Miller P, Snyder M (2000) TRIPLES: a database of gene function in Saccharomyces cerevisiae. Nucleic Acids Res 28:81-84
38. Lauder S, Bankmann M, Guzder SN, Sung P, Prakash L, Prakash S (1996) Dual requirement for the yeast MMS19 gene in DNA repair and RNA polymerase II transcription. Mol Cell Biol 16:6783-6793
39. Lawrence CW, Hinkle DC (1996) DNA polymerase zeta and the control of DNA damage induced mutagenesis in eukaryotes. Cancer Surv 28:21-31
40. Liberi G, Chiolo I, Pellicioli A, Lopes M, Plevani P, Muzi-Falconi M, Foiani M (2000) Srs2 DNA helicase is involved in checkpoint response and its regulation requires a functional Mec1-dependent pathway and Cdk1 activity. EMBO J 19:5027-5038
41. Liefshitz B, Steinlauf R, Friedl A, Eckardt-Schupp F, Kupiec M (1998) Genetic interactions between mutants of the 'error-prone' repair group of Saccharomyces cerevisiae and their effect on recombination and mutagenesis. Mutat Res 407:135-145
42. Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA, Resnick MA (2000) Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J 19:3822-3830
43. Lombaerts M, Tijsterman M, Verhage RA, Brouwer J (1997) Saccharomyces cerevisiae mms19 mutants are deficient in transcription-coupled and global nucleotide excision repair. Nucleic Acids Res 25:3974-3979
44. Loo S, Laurenson P, Foss M, Dillin A, Rine J (1995) Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics 141:889-902
45. Lopes M, Cotta-Ramusino C, Pellicioli A, Liberi G, Plevani P, Muzi-Falconi M, Newlon CS, Foiani M (2001) The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412:557-561
46. Lu Z, Cyr DM (1998) The conserved carboxyl terminus and zinc finger-like domain of the co-chaperone Ydj1 assist Hsp70 in protein folding. J Biol Chem 273:5970-5978
47. Marelli M, Aitchison JD, Wozniak RW (1998) Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p. J Cell Biol 143:1813-1830
48. Masutani C, Kusumoto R, Yamada A, Dohmae N, Yokoi M, Yuasa M, Araki M, Iwai S, Takio K, Hanaoka F (1999) The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature 399:700-704
49. Matsuura A, Anraku Y (1993) Characterization of the MKS1 gene, a new negative regulator of the Ras-cyclic AMP pathway in Saccharomyces cerevisiae. Mol Gen Genet 238:6-16
50. Miled C, Mann C, Faye G (2001) Xbp1-mediated repression of CLB gene expression contributes to the modifications of yeast cell morphology and cell cycle seen during nitrogen-limited growth. Mol Cell Biol 21:3714-3724
51. Muchowski PJ, Schaffar G, Sittler A, Wanker EE, Hayer-Hartl MK, Hartl FU (2000) Hsp70 and Hsp40 chaperones can inhibit self-assembly of polyglutamine proteins into amyloid-like fibrils. Proc Natl Acad Sci USA 97:7841-7846
52. Mullen JR, Kaliraman V, Ibrahim SS, Brill SJ (2001) Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae. Genetics 157:103-118
53. Navas TA, Zhou Z, Elledge SJ (1995) DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell 80:29-39
54. Prakash L, Prakash S (1979) Three additional genes involved in pyrimidine dimer removal in Saccharomyces cerevisiae: RAD7, RAD14 and MMS19. Mol Gen Genet 176:351-359
55. Qi H, Zakian VA (2000) The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein. Genes Dev 14:1777-1788
56. Reed SH, Akiyama M, Stillman B, Friedberg EC (1999) Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev 13:3052-3058
57. Rhode PR, Elsasser S, Campbell JL (1992) Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol Cell Biol 12:1064-1077
58. Rose MD, Novick P, Thomas JH, Botstein D, Fink GR (1987) A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60:237-243
59. Schiestl RH, Gietz RD (1989) High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet 16:339-346
60. Sherman F (1991) Getting started with yeast. Methods Enzymol 194:339-346
61. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27
62. Simon M, Giot L, Faye G (1993) A random mutagenesis procedure: application to the POL3 gene of Saccharomyces cerevisiae. Gene 127:139-144
63. Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC (1996) A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell 84:265-275
64. Siniossoglou S, Santos-Rosa H, Rappsilber J, Mann M, Hurt E (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17:6449-6464
65. Sokolsky T, Alani E (2000) EXO1 and MSH6 are high-copy suppressors of conditional mutations in the MSH2 mismatch repair gene of Saccharomyces cerevisiae. Genetics 155:589-599
66. Stagljar I, Hubscher U, Barberis A (1999) Activation of DNA replication in yeast by recruitment of the RNA polymerase II transcription complex. Biol Chem 380:525-530
67. Stearns T, Botstein D (1988) Unlinked noncomplementation: isolation of new conditional-lethal mutations in each of the tubulin genes of Saccharomyces cerevisiae. Genetics 119:249-260
68. Struhl K, Stinchcomb DT, Scherer S, Davis RW (1979) High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc Natl Acad Sci USA 76:1035-1039
69. Teixeira MT, Dujon B, Fabre E (2002) Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae. J Mol Biol 321:551-561
70. Tercero JA, Diffley JF (2001) Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412:553-557
71. Toczyski DP, Galgoczy DJ, Hartwell LH (1997) CDC5 and CKII control adaptation to the yeast DNA damage checkpoint. Cell 90:1097-1106
72. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364-2368
73. Torres-Ramos CA, Prakash S, Prakash L (1997) Requirement of yeast DNA polymerase delta in post-replicational repair of UV-damaged DNA. J Biol Chem 272:25445-25448
74. Tran HT, Gordenin DA, Resnick MA (1999) The 3′ → 5′ exonucleases of DNA polymerases delta and epsilon and the 5′ → 3′ exonuclease Exo1 have major roles in postreplication mutation avoidance in Saccharomyces cerevisiae. Mol Cell Biol 19:2000-2007
75. Vitale G, Fabre E, Hurt EC (1996) NBP35 encodes an essential and evolutionary conserved protein in Saccharomyces cerevisiae with homology to a superfamily of bacterial ATPases. Gene 178:97-106
76. Ward MP, Garrett S (1994) Suppression of a yeast cyclic AMP-dependent protein kinase defect by overexpression of SOK1, a yeast gene exhibiting sequence similarity to a developmentally regulated mouse gene. Mol Cell Biol 14:5619-5627
77. Wilson TE, Lieber MR (1999) Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway. J Biol Chem 274:23599-23609
78. Winzeler EA, et al (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906
79. Yang SS, Yeh E, Salmon ED, Bloom K (1997) Identification of a mid-anaphase checkpoint in budding yeast. J Cell Biol 136:345-354
80. Zachariae W, Nasmyth K (1999) Whose end is destruction: cell division and the anaphase-promoting complex. Genes Dev 13:2039-2058
81. Zhao X, Chabes A, Domkin V, Thelander L, Rothstein R (2001) The ribonucleotide reductase inhibitor Sml1 is a new target of the Mec1/Rad53 kinase cascade during growth and in response to DNA damage. EMBO J 20:3544-3553