Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III

Molecular and Cellular Biology

Volumn 23, Issue 9, 2003, Pages 3329-3338

  Tan, Qian ^a   Prysak, Meredith H ^a   Woychik, Nancy A ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; RNA POLYMERASE II;

ARTICLE; CELL MUTANT; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SUBUNIT; EUKARYOTE; GENE MUTATION; GENETIC STRAIN; HIGH TEMPERATURE; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; REDUCTION;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; DNA-DIRECTED RNA POLYMERASES; FUNGAL PROTEINS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; PROTEIN SUBUNITS; RNA POLYMERASE I; RNA POLYMERASE II; RNA POLYMERASE III; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0037405790     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.23.9.3329-3338.2003     Document Type: Article

References (58)

1. Asturias, F. J., G. D. Meredith, C. L. Poglitsch, and R. D. Kornberg. 1997. Two conformations of RNA polymerase II revealed by electron crystallography. J. Mol. Biol. 272:536-540.
2. Awrey, D. E., R. G. Weilbaecher, S. A. Hemming, S. M. Orlicky, C. M. Kane, and A. M. Edwards. 1997. Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS J. Biol. Chem. 272:14747-14754.
3. Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154:164-175.
4. Burke, D., D. Dawson, and T. Stearns. 2000. Methods in yeast genetics. A Cold Spring Harbor Laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
5. Cho, E. J., M. S. Kobor, M. Kim, J. Greenblatt, and S. Buratowski. 2001. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15:3319-3329.
6. Choder, M., and R. A. Young. 1993. A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol. Cell. Biol. 13:6984-6991.
7. Cormack, B. P., and K. Struhl. 1992. The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells. Cell 69:685-696.
8. Craighead, J., W. Chang, and F. Asturias. 2002. Structure of yeast RNA polymerase II in solution. Implications for enzyme regulation and interaction with promoter DNA. Structure 10:1117-1125.
9. Cramer, P., D. A. Bushnell, J. Fu, A. L. Gnatt, B. Maier-Davis, N. E. Thompson, R. R. Burgess, A. M. Edwards, P. R. David, and R. D. Kornberg. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640-649.
10. Cramer, P., D. A. Bushnell, and R. D. Kornberg. 2001. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292:1863-1876.
11. Darst, S. A. 2001. Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11:155-162.
12. del Rio-Portilla, F., A. Gaskell, D. Gilbert, J. A. Ladias, and G. Wagner. 1999. Solution structure of the hRPABC14.4 subunit of human RNA polymerases. Nat. Struct. Biol. 6:1039-1042.
13. Dezelee, S., F. Wyers, A. Sentenac, and P. Fromageot. 1976. Two forms of RNA polymerase B in yeast. Proteolytic conversion in vitro of enzyme BI into BII. Eur. J. Biochem. 65:543-552.
14. Edwards, A. M., C. M. Kane, R. A. Young, and R. D. Kornberg. 1991. Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J. Biol. Chem. 266:71-75.
15. Gnatt, A. L., P. Cramer, J. Fu, D. A. Bushnell, and R. D. Kornberg. 2001. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 angstrom resolution. Science 292:1876-1882.
16. Ha, I., S. Roberts, E. Maldonado, X. Sun, L. U. Kim, M. Green, and D. Reinberg. 1993. Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 7:1021-1032.
17. Hampsey, M. 1997. A review of phenotypes in Saccharomyces cerevisiae. Yeast 13:1099-1133.
18. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
19. a. Hu, P., S. Wu, Y. Sun, C. C. Yuan, R. Kobayashi, M. P. Myers, and N. Hernandez. 2002. Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits. Mol. Cell. Biol. 22:8044-8055.
20. Ishiguro, A., Y. Nogi, K. Hisatake, M. Muramatsu, and A. Ishihama. 2000. The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol. Cell. Biol. 20:1263-1270.
21. James, P., J. Halladay, and E. A. Craig. 1996. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425-1436.
22. Jensen, G. J., G. Meredith, D. A. Bushnell, and R. D. Kornberg. 1998. Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7. EMBO J. 17:2353-2358.
23. Kayukawa, K., Y. Makino, S. Yogosawa, and T. Tamura. 1999. A serine residue in the N-terminal acidic region of rat RPB6, one of the common subunits of RNA polymerases, is exclusively phosphorylated by casein kinase II in vitro. Gene 234:139-147.
24. Kimura, M., H. Sakurai, and A. Ishihama. 2001. Intracellular contents and assembly states of all 12 subunits of the RNA polymerase II in the fission yeast Schizosaccharomyces pombe. Eur. J. Biochem. 268:612-619.
25. Kimura, M., H. Suzuki, and A. Ishihama. 2002. Formation of a carboxyterminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II. Mol. Cell. Biol. 22:1577-1588.
26. Kolodziej, P. A., N. Woychik, S. M. Liao, and R. A. Young. 1990. RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol. Cell. Biol. 10:1915-1920.
27. Lee, Y. C., S. Min, B. S. Gim, and Y. J. Kim. 1997. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol. Cell. Biol. 17:4622-4632.
28. Leuther, K. K., D. A. Bushnell, and R. D. Kornberg. 1996. Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation. Cell 85:773-779.
29. Liao, S. M., I. C. Taylor, R. E. Kingston, and R. A. Young. 1991. RNA polymerase II carboxy-terminal domain contributes to the response to multiple acidic activators in vitro. Genes Dev. 5:2431-2440.
30. Magill, C. P., S. P. Jackson, and S. D. Bell. 2001. Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J. Biol. Chem. 276:46693-46696.
31. Maillet, I., J. M. Buhler, A. Sentenac, and J. Labarre. 1999. Rpb4p is necessary for RNA polymerase II activity at high temperature. J. Biol. Chem. 274:22586-22590.
32. McKune, K., and N. A. Woychik. 1994. Functional substitution of an essential yeast RNA polymerase subunit by a highly conserved mammalian counterpart. Mol. Cell. Biol. 14:4155-4159.
33. Minakhin, L., S. Bhagat, A. Brunning, E. A. Campbell, S. A. Darst, R. H. Ebright, and K. Severinov. 2001. Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc. Natl. Acad. Sci. USA 98:892-897.
34. Miyao, T., J. D. Barnett, and N. A. Woychik. 2001. Deletion of the RNA polymerase subunit RPB4 acts as a global, not stress-specific, shut-off switch for RNA polymerase II transcription at high temperatures. J. Biol. Chem. 276:46408-46413.
35. Muhlrad, D., R. Hunter, and R. Parker. 1992. A rapid method for localized mutagenesis of yeast genes. Yeast 8:79-82.
36. Mukherjee, K., and D. Chatterji. 1997. Studies on the omega subunit of Escherichia coli RNA polymerase - its role in the recovery of denatured enzyme activity. Eur. J. Biochem. 247:884-889.
37. Murakami, K. S., S. Masuda, and S. A. Darst. 2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 angstrom resolution. Science 296:1280-1284.
38. Myers, L. C., and R. D. Kornberg. 2000. Mediator of transcriptional regulation. Annu. Rev. Biochem. 69:729-749.
39. Narlikar, G. J., H. Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475-487.
40. Nouraini, S., J. Archambault, and J. D. Friesen. 1996. Rpo26p, a subunit common to yeast RNA polymerases, is essential for the assembly of RNA polymerases I and II and for the stability of the largest subunits of these enzymes. Mol. Cell. Biol. 16:5985-5996.
41. Perbal, B. 1999. Nuclear localization of NOVH protein: a potential role for NOV in the regulation of gene expression. Mol. Pathol. 52:84-91.
42. Peyroche, G., E. Levillain, M. Siaut, I. Callebaut, P. Schultz, A. Sentenac, M. Riva, and C. Caries. 2002. The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits. Proc. Natl. Acad. Sci. USA 99:14670-14675.
43. Pulg, O., F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Seraphin. 2001. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218-229.
44. Rigaut, G., A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17:1030-1032.
45. Rubbi, L., S. Labarre-Mariotte, S. Chedin, and P. Thuriaux. 1999. Functional characterization of ABC10α, an essential polypeptide shared by all three forms of eukaryotic DNA-dependent RNA polymerases. J. Biol. Chem. 274:31485-31492.
46. Ruet, A., A. Sentenac, P. Fromageot, B. Winsor, and F. Lacroute. 1980. A mutation of the B220 subunit gene affects the structural and functional properties of yeast RNA polymerase B in vitro. J. Biol. Chem. 255:6450-6455.
47. Siaut, M., C. Zaros, E. Levivier, M. L. Ferri, M. Court, M. Werner, I. Callebaut, P. Thuriaux, A. Sentenac, and C. Conesa. 2003. An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol. Cell. Biol. 23:195-205.
48. Tan, Q., K. L. Linask, R. H. Ebright, and N. A. Woychik. 2000. Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 14:339-348.
49. Thompson, N. E., D. B. Aronson, and R. R. Burgess. 1990. Purification of eukaryotic RNA polymerase II by immunoaffinity chromatography. Elution of active enzyme with protein stabilizing agents from a polyol-responsive monoclonal antibody. J. Biol. Chem. 265:7069-7077.
50. Treco, D. A., and V. Lundblad. 1993. Preparation of yeast media, p. 13.1.1-13.1.7. In K. Janssen (ed.), Current protocols in molecular biology, vol. 2. Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., New York, N.Y.
51. Voutsina, A., M. Riva, C. Caries, and D. Alexandraki. 1999. Sequence divergence of the RNA polymerase shared subunit ABC14.5 (Rpb8) selectively affects RNA polymerase III assembly in Saccharomyces cerevisiae. Nucleic Acids Res. 27:1047-1055.
52. Warner, J. R., and C. Gorenstein. 1978. Yeast has a true stringent response. Nature 275:338-339.
53. Wootner, M., P. A. Wade, J. Bonner, and J. A. Jaehning. 1991. Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae. Mol. Cell. Biol. 11:4555-4560.
54. Woychik, N. A. 1998. Fractions to functions: RNA polymerase II thirty years later. Cold Spring Harbor Symp. Quant. Biol. 63:311-317.
55. Woychik, N. A., and R. A. Young. 1989. RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Mol. Cell. Biol. 9:2854-2859.
56. Zhang, G., E. A. Campbell, L. Minakhin, C. Richter, K. Severinov, and S. A. Darst. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 angstrom resolution. Cell 98:811-824.
57. Zhang, Y., and D. Reinberg. 2001. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 15:2343-2360.
58. Zhou, H., and K. A. Lee. 2001. An hsRPB4/7-dependent yeast assay for trans-activation by the EWS oncogene. Oncogene 20:1519-1524.