Transcript copy number of genes for DNA repair and translesion synthesis in yeast: Contribution of transcription rate and mRNA stability to the steady-state level of each mRNA along with growth in glucose-fermentative medium

DNA Repair

Volumn 4, Issue 4, 2005, Pages 469-478

  Michán, Carmen ^a   Monje Casas, Fernando ^a   Pueyo, Carmen ^a  

^a UNIVERSITY OF CÓRDOBA   (Spain)

Author keywords

Growth phase; mRNA decay; Quantitative RT PCR; Transcription rate

Indexed keywords

DNA DIRECTED DNA POLYMERASE ALPHA; GLUCOSE; MESSENGER RNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ARTICLE; CELL GROWTH; CELL PROLIFERATION; CONTROLLED STUDY; DNA REPAIR; FERMENTATION MEDIUM; GENE EXPRESSION; GENE NUMBER; GENETIC TRANSCRIPTION; HEAT SHOCK; MATHEMATICAL COMPUTING; NONHUMAN; NUTRIENT AVAILABILITY; PRIORITY JOURNAL; PROTEIN FUNCTION; QUANTITATIVE ANALYSIS; RNA DEGRADATION; RNA STABILITY; STEADY STATE; TRANSCRIPTION INITIATION; YEAST;

EID: 13844314659     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2004.12.001     Document Type: Article

References (51)

1. E.C. Friedberg DNA damage and repair Nature 421 2003 436 440
2. P.M. Girard, and S. Boiteux Repair of oxidized DNA bases in the yeast Saccharomyces cerevisiae Biochimie 79 1997 559 566
3. H.J. You, R.L. Swanson, and P.W. Doetsch Saccharomyces cerevisiae possesses two functional homologues of Escherichia coli endonuclease III Biochemistry 37 1998 6033 6040
4. L. Eide, M. Bjoras, M. Pirovano, I. Alseth, K.G. Berdal, and E. Seeberg Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli Proc. Natl. Acad. Sci. USA 93 1996 10735 10740
5. L. Augeri, Y.M. Lee, A.B. Barton, and P.W. Doetsch Purification, characterization, gene cloning, and expression of Saccharomyces cerevisiae redoxyendonuclease, a homolog of Escherichia coli endonuclease III Biochemistry 36 1997 721 729
6. H.J. You, R.L. Swanson, C. Harrington, A.H. Corbett, S. Jinks-Robertson, S. Senturker, S.S. Wallace, S. Boiteux, M. Dizdaroglu, and P.W. Doetsch Saccharomyces cerevisiaeNtg1p and Ntg2p: broad specificity N-glycosylases for the repair of oxidative DNA damage in the nucleus and mitochondria Biochemistry 38 1999 11298 11306
7. R.L. Swanson, N.J. Morey, P.W. Doetsch, and S. Jinks-Robertson Overlapping specificities of base excision repair, nucleotide excision repair, recombination, and translesion synthesis pathways for DNA base damage in Saccharomyces cerevisiae Mol. Cell. Biol. 19 1999 2929 2935
8. S. Senturker, P.A. van der Kemp, H.J. You, P.W. Doetsch, M. Dizdaroglu, and S. Boiteux Substrate specificities of the Ntg1 and Ntg2 proteins of Saccharomyces cerevisiae for oxidized DNA bases are not identical Nucl. Acids Res. 26 1998 5270 5276
9. I. Alseth, L. Eide, M. Pirovano, T. Rognes, E. Seeberg, and M. Bjoras The Saccharomyces cerevisiae homologues of endonuclease III from Escherichia coli, Ntg1 and Ntg2, are both required for efficient repair of spontaneous and induced oxidative DNA damage in yeast Mol. Cell. Biol. 19 1999 3779 3787
10. P.A. van der Kemp, D. Thomas, R. Barbey, R. de Oliveira, and S. Boiteux Cloning and expression in Escherichia coli of the OGG1 gene of Saccharomyces cerevisiae, which codes for a DNA glycosylase that excises 7,8-dihydro-8- oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine Proc. Natl. Acad. Sci. USA 93 1996 5197 5202
11. S. Boiteux, L. Gellon, and N. Guibourt Repair of 8-oxoguanine in Saccharomyces cerevisiae: interplay of DNA repair and replication mechanisms Free Radic. Biol. Med. 32 2002 1244 1253
12. S. Boiteux, and M. Guillet Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae DNA Repair (Amst.) 3 2004 1 12
13. S.C. Popoff, A.I. Spira, A.W. Johnson, and B. Demple Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV Proc. Natl. Acad. Sci. USA 87 1990 4193 4197
14. D. Ramotar, C. Kim, R. Lillis, and B. Demple Intracellular localization of the Apn1 DNA repair enzyme of Saccharomyces cerevisiae. Nuclear transport signals and biological role J. Biol. Chem. 268 1993 20533 20539
15. R. Vongsamphanh, P.K. Fortier, and D. Ramotar Pir1p mediates translocation of the yeast Apn1p endonuclease into the mitochondria to maintain genomic stability Mol. Cell. Biol. 21 2001 1647 1655
16. R.E. Johnson, C.A. Torres-Ramos, T. Izumi, S. Mitra, S. Prakash, and L. Prakash Identification of APN2, the Saccharomyces cerevisiae homolog of the major human AP endonuclease HAP1, and its role in the repair of abasic sites Genes Dev. 12 1998 3137 3143
17. B.D. Harfe, and S. Jinks-Robertson DNA mismatch repair and genetic instability Annu. Rev. Genet. 34 2000 359 399
18. C.W. Lawrence, and R.B. Christensen Ultraviolet-induced reversion of cyc1 alleles in radiation-sensitive strains of yeast. III. rev3 mutant strains Genetics 92 1979 397 408
19. H. Roche, R.D. Gietz, and B.A. Kunz Specificity of the yeast rev3Δ antimutator and REV3 dependency of the mutator resulting from a defect (rad1Δ) in nucleotide excision repair Genetics 137 1994 637 646
20. R.E. Johnson, S. Prakash, and L. Prakash Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Poleta Science 283 1999 1001 1004
21. Z. Wang Translesion synthesis by the UmuC family of DNA polymerases Mutat. Res. 486 2001 59 70
22. S. Prakash, and L. Prakash Translesion DNA synthesis in eukaryotes: a one- or two-polymerase affair Genes Dev. 16 2002 1872 1883
23. A.A. Roush, M. Suarez, E.C. Friedberg, M. Radman, and W. Siede Deletion of the Saccharomyces cerevisiae gene RAD30 encoding an Escherichia coli DinB homolog confers UV radiation sensitivity and altered mutability Mol. Gen. Genet. 257 1998 686 692
24. J.P. McDonald, A.S. Levine, and R. Woodgate The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free postreplication repair mechanism Genetics 147 1997 1557 1568
25. G. Mercier, Y. Denis, P. Marc, L. Picard, and M. Dutreix Transcriptional induction of repair genes during slowing of replication in irradiated Saccharomyces cerevisiae Mutat. Res. 487 2001 157 172
26. R.A. Bennett The Saccharomyces cerevisiae ETH1 gene, an inducible homolog of exonuclease III that provides resistance to DNA-damaging agents and limits spontaneous mutagenesis Mol. Cell. Biol. 19 1999 1800 1809
27. R.K. Singhal, D.C. Hinkle, and C.W. Lawrence The REV3 gene of Saccharomyces cerevisiae is transcriptionally regulated more like a repair gene than one encoding a DNA polymerase Mol. Gen. Genet. 236 1992 17 24
28. J. Jurado, M.J. Prieto-Álamo, J. Madrid-Rísquez, and C. Pueyo Absolute gene expression patterns of thioredoxin and glutaredoxin redox systems in mouse J. Biol. Chem. 278 2003 45546 45554
29. D. Burke, D. Dawson, and T. Stearns Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual 2000 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
30. M.A. Collar, S. Oliviero, Preparation of yeast RNA, Unit 13.12.1, in: Current Protocols in Molecular Biology, 1993.
31. M.J. Prieto-Álamo, J.M. Cabrera-Luque, and C. Pueyo Absolute quantitation of normal and ROS-induced patterns of gene expression: an in vivo real-time PCR study in mice Gene Exp. 11 2003 23 34
32. C. Pueyo, J. Jurado, M.J. Prieto-Álamo, F. Monje-Casas, and J. López-Barea Multiplex reverse transcription-polymerase chain reaction for determining transcriptional regulation of thioredoxin and glutaredoxin pathways Meth. Enzymol. 347 2002 441 451
33. S. Hohmann, and W.H. Mager Yeast Stress Responses 1997 Springer Verlag Heidelberg
34. F. Monje-Casas, C. Michán, and C. Pueyo Absolute transcript levels of thioredoxin- and glutathione-dependent redox systems in Saccharomyces cerevisiae: response to stress and modulation with growth Biochem. J. 383 2004 139 147
35. Y. Wang, C.L. Liu, J.D. Storey, R.J. Tibshirani, D. Herschlag, and P.O. Brown Precision and functional specificity in mRNA decay Proc. Natl. Acad. Sci. USA 99 2002 5860 5865
36. E. Boy-Marcotte, G. Lagniel, M. Perrot, F. Bussereau, A. Boudsocq, M. Jacquet, and J. Labarre The heat shock response in yeast: differential regulations and contributions of the Msn2p/Msn4p and Hsf1p regulons Mol. Microbiol. 33 1999 274 283
37. E. Boy-Marcotte, M. Perrot, F. Bussereau, H. Boucherie, and M. Jacquet Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclic AMP in Saccharomyces cerevisiae J. Bacteriol. 180 1998 1044 1052
38. A. Jimenez, D.J. Tipper, and J. Davies Mode of action of thiolutin, an inhibitor of macromolecular synthesis in Saccharomyces cerevisiae Antimicrob. Agents Chemother. 3 1973 729 738
39. D.J. Tipper Inhibition of yeast ribonucleic acid polymerases by thiolutin J. Bacteriol. 116 1973 245 256
40. J.V. Gray, G.A. Petsko, G.C. Johnston, D. Ringe, R.A. Singer, and M. Werner-Washburne Sleeping beauty: quiescence in Saccharomyces cerevisiae Microbiol. Mol. Biol. Rev. 68 2004 187 206
41. G. Jona, M. Choder, and O. Gileadi Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast Biochim. Biophys. Acta 1491 2000 37 48
42. M.J. Martinez, S. Roy, A.B. Archuletta, P.D. Wentzell, S. Santa Anna-Arriola, A.L. Rodriguez, A.D. Aragon, G.A. Quinones, C. Allen, and M. Werner-Washburne Genomic analysis of stationary phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes Mol. Biol. Cell 15 2004 5295 5305
43. B.A. Kunz, A.F. Straffon, and E.J. Vonarx DNA damage-induced mutation: tolerance via translesion synthesis Mutat. Res. 451 2000 169 185
44. R.E. Mitchel, and D.P. Morrison Inducible DNA-repair systems in yeast: competition for lesions Mutat. Res. 183 1987 149 159
45. E. Heidenreich, V. Holzmann, and H. Eisler Polymerase zeta dependency of increased adaptive mutation frequencies in nucleotide excision repair-deficient yeast strains DNA Repair (Amst.) 3 2004 395 402
46. E. Karathanasis, and T.E. Wilson Enhancement of Saccharomyces cerevisiae end-joining efficiency by cell growth stage but not by impairment of recombination Genetics 161 2002 1015 1027
47. J. García-Martínez, A. Aranda, and J.E. Pérez-Ortín Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms Mol. Cell 15 2004 303 313
48. Z. Yin, L. Hatton, and A.J. Brown Differential post-transcriptional regulation of yeast mRNAs in response to high and low glucose concentrations Mol. Microbiol. 35 2000 553 565
49. G.P. Cereghino, D.P. Atencio, M. Saghbini, J. Beiner, and I.E. Scheffler Glucose-dependent turnover of the mRNAs encoding succinate dehydrogenase peptides in Saccharomyces cerevisiae: sequence elements in the 5′ untranslated region of the Ip mRNA play a dominant role Mol. Biol. Cell 6 1995 1125 1143
50. S. Prieto, B.J. de la Cruz, and I.E. Scheffler Glucose-regulated turnover of mRNA and the influence of poly(A) tail length on half-life J. Biol. Chem. 275 2000 14155 14166
51. V. Iyer, and K. Struhl Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 93 1996 5208 5212