Transcription factor Rpn4 promotes a complex antistress response in Saccharomyces cerevisiae cells exposed to methyl methanesulfonate

Molecular Biology

Volumn 48, Issue 1, 2014, Pages 141-149

  Spasskaya, D S ^a   Karpov, D S ^a   Mironov, A S ^a,b   Karpov, V L ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

Author keywords

DamID; DNA repair; methyl methanesulfonate; oxidative stress; Rpn4; Saccharomyces cerevisiae

Indexed keywords

EID: 84894628309     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893314010130     Document Type: Article

References (42)

1. Mannhaupt G., Schnall R., Karpov V., Vetter I., Feldmann H. 1999. Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett. 450, 27-34.
2. Kapranov A. B., Kuriatova M. V., Preobrazhenskaya O. V., Tiutiaeva V. V., Shtuka R., Feldmann H., Karpov V. L. 2001. Isolation and identification of PACE-binding protein Rpn4, a new transcription activator participating in regulation of 26S proteasome and other genes. Mol. Biol. (Moscow). 35(3), 356-364.
3. Cherry J. M., Hong E. L., Amundsen C., Balakrishnan R., Binkley G., Chan E. T., Christie K. R., Costanzo M. C., Dwight S. S., Engel S. R., Fisk D. G., Hirschman J. E., Hitz B. C., Karra K., Krieger C. J., Miyasato S. R., Nash R. S., Park J., Skrzypek M. S., Simison M., Weng S., Wong E. D. 2011. Saccharomyces genome database: The genomics resource of budding yeast. Nucleic Acids Res. 40, D700-D705.
4. Tallec B. L., Peyroche A. 2012. Using DNA damage sensitivity phenotypes to characterize mutations affecting proteasome function. Methods Mol. Biol. 832, 363-371.
5. Karpov D. S., Tutyaeva V. V., Karpov V. L. 2008. Mapping of yeast Rpn4p transactivation domains. FEBS Lett. 582, 3459-3464.
6. Jelinsky S. A., Estep P., Church G. M., Samson L. D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell Biol. 20, 8157-8167.
7. Fronza G., Gold B. 2004. The biological effects of N3-methyladenine. J. Cell Biochem. 91, 250-257.
8. Burgis N. E., Samson L. D. 2007. The protein degradation response of Saccharomyces cerevisiae to classical DNA-damaging agents. Chem. Res. Toxicol. 20, 1843-1853.
9. Rowe L. A., Degtyareva N., Doetsch P. W. 2008. DNA damage-induced reactive oxygen species (ROS) stress response in Saccharomyces cerevisiae. Free Radic. Biol. Med. 45, 1167-1177.
10. Kitanovic A., Walther T., Loret M. O., Holzwarth J., Kitanovic I., Bonowski F., van Bui N., Francois J. M., Wolfl S. 2009. Metabolic response to MMS-mediated DNA damage in Saccharomyces cerevisiae is dependent on the glucose concentration in the medium. FEMS Yeast Res. 9, 535-551.
11. Pirsel M., Bohr V. A. 1993. Methyl methanesulfonate adduct formation and repair in the DHFR gene and in mitochondrial DNA in hamster cells. Carcinogenesis. 14, 2105-2108.
12. Harbison C. T., Gordon D. B., Lee T. I., Rinaldi N. J., Macisaac K. D., Danford T. W., Hannett N. M., Tagne J. B., Reynolds D. B., Yoo J., Jennings E. G., Zeitlinger J., Pokholok D. K., Kellis M., Rolfe P. A., Takusagawa K. T., Lander E. S., Gifford D. K., Fraenkel E., Young R. A. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature. 431, 99-104.
13. Zhu Y., Xiao W. 2004. Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element. Nucleic Acids Res. 32, 5066-5075.
14. van Steensel B., Henikoff S. 2000. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nature Biotechnol. 18, 424-428.
15. Osipov S., Tutyaeva V., Preobrazhenskaya O., Karpov V. 2011. A rapid method for liquid β-galactosidase reporter assay in Saccharomyces cerevisiae. World J. Microbiol. Biotechnol. 27, 1255-1259.
16. Gietz D., St Jean A., Woods R. A., Schiestl R. H. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20, 1425.
17. Schmitt M. E., Brown T. A., Trumpower B. L. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18, 3091-3092.
18. Spasskaya D. S., Karpov D. S., Karpov V. L. 2011. Escherichia coli Dam methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4. Mol. Biol. (Moscow). 45(4), 591-599.
19. Ju D., Xie Y. 2004. Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent. J. Biol. Chem. 279, 23851-23854.
20. Looke M., Kristjuhan K., Kristjuhan A. 2011. Extraction of genomic DNA from yeasts for PCR-based applications. Biotechniques. 50, 325-328.
21. Hahn J. S., Neef D. W., Thiele D. J. 2006. A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor. Mol. Microbiol. 60, 240-251.
22. Liu Y., Xiao W. 1997. Bidirectional regulation of two DNA-damage-inducible genes, MAG1 and DDI1, from Saccharomyces cerevisiae. Mol. Microbiol. 23, 777-789.
23. Liu Y., Dai H., Xiao W. 1997. UAS (MAG1), a yeast cis-acting element that regulates the expression of MAG1 is located within the protein coding region of DDI1. Mol. Gen. Genet. 255, 533-542.
24. Xie Y., Varshavsky A. 2001. RPN4 is a ligand, substrate and transcriptional regulator of the 26S proteasome: A negative feedback circuit. Proc. Natl. Acad. Sci. U. S. A. 98, 3056-3061.
25. 2 sensing through oxidation of the Yap1 transcription factor. EMBO J. 19, 5157-5166.
26. Lee J., Godon C., Lagniel G., Spector D., Garin J., Labarre J., Toledano M. B. 1999. Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. J. Biol. Chem. 274, 16040-16046.
27. Lushchak V. I. 2010. Oxidative stress in yeast. Biochemistry (Moscow). 75, 281-296.
28. 2 or thiol-reactive chemicals elicits distinct adaptive gene responses. Free Radic. Biol. Med. 50, 1-13.
29. Kuge S., Jones N. 1994. YAP1 dependent activation of TRX2 is essential for the response of Saccharomyces cerevisiae to oxidative stress by hydroperoxides. EMBO J. 13, 655-664.
30. Rowe L. A., Degtyareva N., Doetsch P. W. 2012. Yap1: A DNA damage responder in Saccharomyces cerevisiae. Mech. Ageing Dev. 133, 147-156.
31. Salmon T. B., Evert B. A., Song B., Doetsch P. W. 2004. Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae. Nucleic Acids Res. 32, 3712-3723.
32. Haugen A. C., Kelley R., Collins J. B., Tucker C. J., Deng C., Afshari C. A., Brown J. M., Ideker T., van Houten B. 2004. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 5, R95.
33. Salin H., Fardeau V., Piccini E., Lelandais G., Tanty V., Lemoine S., Jacq C., Devaux F. 2008. Structure and properties of transcriptional networks driving selenite stress response in yeasts. BMC Genomics. 9, 333.
34. Owsianik G., Balzil L., Ghislain M. 2002. Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae. Mol. Microbiol. 43, 1295-1308.
35. Teixeira M. C., Dias P. J., Simoes T., Sa-Correia I. 2008. Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1. Biochem. Biophys. Res. Commun. 367, 249-255.
36. Venters B. J., Wachi S., Mavrich T. N., Andersen B. E., Jena P., Sinnamon A. J., Jain P., Rolleri N. S., Jiang C., Hemeryck-Walsh C., Pugh B. F. 2011. A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol. Cell. 41, 480-492.
37. Gasch A. P., Huang M., Metzner S., Botstein D., Elledge S. J., Brown P. O. 2001. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell. 12, 2987-3003.
38. Monteiro P. T., Mendes N. D., Teixeira M. C., d'Orey S., Tenreiro S., Mira N. P., Pais H., Francisco A. P., Carvalho A. M., Lourenco A. B., Sa-Correia I., Oliveira A. L., Freitas A. T. 2008. YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 36, D132-D136.
39. Nogae I., Johnston M. 1990. Isolation and characterization of the ZWF1 gene of Saccharomyces cerevisiae, encoding glucose-6-phosphate dehydrogenase. Gene. 96, 161-169.
40. Izawa S., Maeda K., Miki T., Mano J., Inoue Y., Kimura A. 1998. Importance of glucose-6-phosphate dehydrogenase in the adaptive response to hydrogen peroxide in Saccharomyces cerevisiae. Biochem. J. 330, 811-817.
41. Karpov D. S., Osivpov S. A., Preobrazhenskaya O. V., Karpov V. L. 2008. Rpn4p is a positive and negative transcriptional regulator of the ubiquitin-proteasome system. Mol. Biol. (Moscow). 42(3), 463-468.
42. Dias P. J., Teixeira M. C., Telo J. P., Sa-Correia I. 2010. Insights into the mechanisms of toxicity and tolerance to the agricultural fungicide mancozeb in yeast, as suggested by a chemogenomic approach. OMICS. 14, 211-227.