The Yeast Carboxyl-Terminal Repeat Domain Kinase CTDK-I Is a Divergent Cyclin–Cyclin-Dependent Kinase Complex

REFERENCES

• Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–410.
   PubMed Web of Science ®Google Scholar
• Andreadis, A., Y.-P. Hsu, G. B. Kohlhaw, and P. Schimmel. 1982. Nucleotide sequence of yeast LEU2 shows 59 noncoding region has sequences cognate to leucine. Cell 31:319–325.
   PubMed Web of Science ®Google Scholar
• Åström, S. U., U. von Pawel-Rammingen, and A. S. Byström. 1993. The yeast initiator tRNAMet can act as an elongator tRNAMet in vivo. J. Mol. Biol. 233:43–58.
   PubMedGoogle Scholar
• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1994. Current protocols in molecular biology. John Wiley & Sons, Inc., New York.
   Google Scholar
• Bartolomei, M. S., N. F. Halden, C. R. Cullen, and J. L. Corden. 1988. Genetic analysis of the repetitive carboxyl-terminal domain of the largest subunit of mouse RNA polymerase II. Mol. Cell. Biol. 8:330–339.
   PubMed Web of Science ®Google Scholar
• Bennetzen, J. L., and B. D. Hall. 1982. Codon selection in yeast. J. Biol. Chem. 257:3026–3031.
   PubMed Web of Science ®Google Scholar
• Bullock, W. O., J. M. Fernandez, and J. M. Short. 1987. XL-1 Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galac-tosidase selection. BioTechniques 4:376–379.
   Google Scholar
• Cisek, L. J., and J. L. Corden. 1989. Phosphorylation of RNA polymerase by the murine homologue of the cell-cycle control protein cdc2. Nature (London) 339:679–684.
   PubMedGoogle Scholar
• Cisek, L. J., and J. L. Corden. 1991. Purification of protein kinases that phosphorylate the repetitive carboxyl-terminal domain of eukaryotic RNA polymerase II. Methods Enzymol. 200:301–325.
   PubMedGoogle Scholar
• Corden, J. L. 1990. Tails of RNA polymerase II. Trends Biochem. Sci. 15: 383–387.
   PubMed Web of Science ®Google Scholar
• Dahmus, M. E., and W. S. Dynan. 1992. Phosphorylation of RNA polymerase II as a transcriptional regulatory mechanism, p. 109–129. In K. Yamamoto, and S. McKnight (ed.), Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387–395.
   PubMed Web of Science ®Google Scholar
• Ducommun, B., P. Brambilla, and G. Draetta. 1991. Mutations at sites involved in Suc1 binding inactivate Cdc2. Mol. Cell. Biol. 11:6177–6184.
   PubMedGoogle Scholar
• Eckhardt, A. E., C. S. Timpte, J. L. Abernethy, Y. Zhao, and R. L. Hill. 1991. Porcine submaxillary mucin contains a cysteine-rich, carboxyl-terminal domain in addition to a highly repetitive, glycosylated domain. J. Biol. Chem. 266:9678–9686.
   PubMedGoogle Scholar
• Estruch, F., and M. Carlson. 1990. SNF6 encodes a nuclear protein that is required for expression of many genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:2544–2553.
   PubMed Web of Science ®Google Scholar
• Feaver, W. J., J. Q. Svejstrup, N. L. Henry, and R. D. Kornberg. 1994. Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK. Cell 79:1103–1109.
   PubMed Web of Science ®Google Scholar
• Gibson, T. J., J. D. Thompson, A. Blocker, and T. Kouzarides. 1994. Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Nucleic Acids Res. 22:946–952.
   PubMed Web of Science ®Google Scholar
• Glotzer, M., A. W. Murray, and M. W. Kirschner. 1991. Cyclin is degraded by the ubiquitin pathway. Nature (London) 349:132–138.
   PubMed Web of Science ®Google Scholar
• Greenleaf, A. L. 1993. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18:117–119.
   Google Scholar
• Guthrie, C., and J. Abelson. 1982. Organization and expression of tRNA genes in Saccharomyces cerevisiae, p. 487–528. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccha-romyces: metabolism and gene expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Hadwiger, J. A., C. Wittenberg, M. D. Mendenhall, and S. I. Reed. 1989. The Saccharomyces cerevisiae CKS1 gene, a homolog of the Schizosaccharomyces pombe suc11 gene, encodes a subunit of the Cdc28 protein kinase complex. Mol. Cell. Biol. 9:2034–2041.
   PubMedGoogle Scholar
• Hancock, K., and V. C. W. Tsang. 1983. India ink staining of proteins on nitrocellulose paper. Anal. Biochem. 133:157–162.
   PubMed Web of Science ®Google Scholar
• Harlow, E., and D. Lane. 1988. Antibodies: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915–10919.
   PubMed Web of Science ®Google Scholar
• Herrmann, C. H., and A. P. Rice. 1995. Lentivirus Tat proteins specifically associate with a cellular protein kinase, TAK, that hyperphosphorylates the carboxyl-terminal domain of the large subunit of RNA polymerase II: candidate for a Tat cofactor. J. Virol. 69:1612–1620.
   PubMed Web of Science ®Google Scholar
• Hibbs, M. L., B. J. Classon, I. D. Walker, I. F. C. McKenzie, and P. M. Hogarth. 1988. The structure of the murine Fc receptor for IgG. J. Immunol. 140:544–550.
   PubMedGoogle Scholar
• Holm, C., D. W. Meeks-Wagner, W. L. Fangman, and D. Botstein. 1986. A rapid, efficient method for isolating DNA from yeast. Gene 42:169–173.
   PubMed Web of Science ®Google Scholar
• Hunter, T., and J. Pines. 1994. Cyclins and cancer. II. Cyclin D and CDK inhibitors come of age. Cell 79:573–582.
   Google Scholar
• Hyunh, T., R. A. Young, and R. W. Davis. 1984. Constructing and screening cDNA libraries in lgt10 and lgt11, p. 49–78. In D. Glover (ed.), DNA cloning techniques: a practical approach. IRL Press, Oxford.
   Google Scholar
• Ingles, C. J., H. J. Himmelfarb, M. Shales, A. L. Greenleaf, and J. D. Friesen. 1984. Identification, molecular cloning, and mutagenesis of Saccharomyces cerevisiae RNA polymerase genes. Proc. Natl. Acad. Sci. USA 81:2157–2161.
   PubMed Web of Science ®Google Scholar
• Kaffman, A., I. Herskowitz, R. Tjian, and E. K. O'Shea. 1994. Phosphorylation of the transcription factor PHO4 by a cyclin-CDK complex, PHO80-PHO85. Science 263:1153–1156.
   PubMed Web of Science ®Google Scholar
• Kelly, J. L., A. L. Greenleaf, and I. R. Lehman. 1986. Isolation of the nuclear gene encoding a subunit of the yeast mitochondrial RNA polymerase. J. Biol. Chem. 261:10348–10351.
   PubMedGoogle Scholar
• Kim, Y. J., S. Bjorklund, Y. Li, M. H. Sayre, and R. D. Kornberg. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77:599–608.
   PubMed Web of Science ®Google Scholar
• Koleske, A. J., and R. A. Young. 1994. An RNA polymerase II holoenzyme responsive to activators. Nature (London) 368:466–469.
   PubMed Web of Science ®Google Scholar
• Kunkel, T. A. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82:488–492.
   PubMed Web of Science ®Google Scholar
• Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227:680–685.
   PubMed Web of Science ®Google Scholar
• Lahue, E. E., A. V. Smith, and T. L. Orr-Weaver. 1991. A novel cyclin gene from Drosophila complements CLN function in yeast. Genes Dev. 5:2166–2175.
   PubMedGoogle Scholar
• Lane, W. S., A. Galat, M. W. Harding, and S. L. Schreiber. 1991. Complete amino acid sequence of the FK506 and rapamycin binding protein, FKBP, isolated from calf thymus. J. Prot. Chem. 10:151–160.
   PubMedGoogle Scholar
• Lee, J. M., and A. L. Greenleaf. 1989. A protein kinase that phosphorylates the C-terminal repeat domain of the largest subunit of RNA polymerase II. Proc. Natl. Acad. Sci. USA 86:3624–3628.
   PubMed Web of Science ®Google Scholar
• Lee, J. M., and A. L. Greenleaf. 1991. CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expr. 1:149–167.
   PubMed Web of Science ®Google Scholar
• Lees, E. M., and E. Harlow. 1993. Sequences within the conserved cyclin box of human cyclin A are sufficient for binding to and activation of cdc2 kinase. Mol. Cell. Biol. 13:1194–1201.
   PubMed Web of Science ®Google Scholar
• Leopold, P., and P. H. O'Farrell. 1991. An evolutionarily conserved cyclin homolog from Drosophila rescues yeast deficient in G1 cyclins. Cell 66:1207–1216.
   PubMed Web of Science ®Google Scholar
• Lew, D. J., V. Dulic, and S. I. Reed. 1991. Isolation of three novel human cyclins by rescue of G1 cyclin (Cln) function in yeast. Cell 66:1197–1206.
   PubMed Web of Science ®Google Scholar
• Li, Y., and R. D. Kornberg. 1994. Interplay of positive and negative effectors in function of the C-terminal repeat domain of RNA polymerase II. Proc. Natl. Acad. Sci. USA 91:2362–2366.
   PubMedGoogle Scholar
• Liao, S. M., and R. A. Young. Personal communication.
   Google Scholar
• Liao, S.-M., J. Zhang, D. A. Jeffery, A. J. Koleske, C. M. Thompson, D. M. Chao, M. Viljoen, H. J. J. van Vuuren, and R. A. Young. 1995. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature (London) 374:193–196.
   PubMed Web of Science ®Google Scholar
• Lu, H., L. Zawel, L. Fisher, J. M. Egly, and D. Reinberg. 1992. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature (London) 358:641–645.
   PubMed Web of Science ®Google Scholar
• McKinney, J., and F. Cross. 1992. A switch-hitter at the start of the cell cycle. Curr. Biol. 2:421–423.
   PubMedGoogle Scholar
• Messing, J., B. Gronenborn, B. Müller-Hill, and P. H. Hofschneider. 1977. Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro. Proc. Natl. Acad. Sci. USA 74:3642–3646.
   PubMed Web of Science ®Google Scholar
• Nonet, M., D. Sweetser, and R. A. Young. 1987. Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell 50: 909–915.
   PubMedGoogle Scholar
• Nugent, J. H. A., C. E. Alfa, T. Young, and J. S. Hyams. 1991. Conserved structural motifs in cyclins identified by sequence analysis. J. Cell Sci. 99:669–674.
   PubMed Web of Science ®Google Scholar
• O'Brien, T., S. Hardin, A. Greenleaf, and J. T. Lis. 1994. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature (London) 370:75–77.
   PubMed Web of Science ®Google Scholar
• Parker, R. C., and B. Seed. 1980. Two-dimensional agarose gel electrophoresis ‘‘SeaPlaque’’ agarose dimension. Methods Enzymol. 65:358–363.
   PubMedGoogle Scholar
• Robbins, A., W. S. Dynan, A. L. Greenleaf, and R. Tjian. 1984. Affinity-purified antibody as a probe of RNA polymerase II subunit structure. J. Mol. Appl. Genet. 2:343–353.
   PubMedGoogle Scholar
• Rogers, S., R. Wells, and M. Rechsteiner. 1986. Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis. Science 234: 364–369.
   PubMed Web of Science ®Google Scholar
• Rose, M., P. Grisafi, and D. Botstein. 1984. Structure and function of the yeast URA3 gene: expression in Escherichia coli. Gene 29:113–124.
   PubMedGoogle Scholar
• Rose, M. D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Rothstein, R. J. 1983. One step gene disruption in yeast. Methods Enzymol. 101:202–211.
   PubMed Web of Science ®Google Scholar
• Roy, R., J. P. Adamczewski, T. Seroz, W. Vermeulen, J. Tassan, L. Schaeffer, E. A. Nigg, J. H. J. Hoeijmakers, and J. Egly. 1994. The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor. Cell 79: 1093–1101.
   PubMed Web of Science ®Google Scholar
• Rüther, U., and B. Müller-Hill. 1983. Easy identification of cDNA clones. EMBO J. 2:1791–1794.
   PubMedGoogle Scholar
• Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463–5467.
   PubMed Web of Science ®Google Scholar
• Sherman, F., G. R. Fink, and J. B. Hicks. 1986. Laboratory course manual for methods in yeast genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Short, J. M., J. M. Fernandez, J. A. Sorge, and A. Huse. 1988. lZAP: a bacteriophage l expression vector with in vivo excision properties. Nucleic Acids Res. 16:7583–7600.
   PubMed Web of Science ®Google Scholar
• Sikorski, R., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevi-siae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Struhl, K. 1985. Nucleotide sequence and transcriptional mapping of the yeast pet56-his3-ded1 gene region. Nucleic Acids Res. 13:8587–8601.
   PubMedGoogle Scholar
• Tamura, K., Y. Kanaoka, S. Jinno, A. Nagata, Y. Ogiso, K. Shimizu, T. Hayakawa, H. Nojima, and H. Okayama. 1993. Cyclin G: a new mammalian cyclin with homology to fission yeast Cig1. Oncogene 8:2113–2118.
   PubMed Web of Science ®Google Scholar
• Weeks, J. R., D. E. Coulter, and A. L. Greenleaf. 1982. Immunological studies of RNA polymerase II using antibodies to subunits of Drosophila and wheat germ enzyme. J. Biol. Chem. 257:5884–5892.
   PubMed Web of Science ®Google Scholar
• Weeks, J. R., S. E. Hardin, J. Shen, J. M. Lee, and A. L. Greenleaf. 1993. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7:2329–2344.
   PubMedGoogle Scholar
• Winter, E., and A. Varshavsky. 1989. A DNA binding protein that recognizes oligo(dA)-oligo(dT) tracts. EMBO J. 8:1867–1877.
   PubMed Web of Science ®Google Scholar
• Young, R. A. 1991. RNA polymerase II. Annu. Rev. Biochem. 60:689–715.
   PubMed Web of Science ®Google Scholar
• Zehring, W. A., J. M. Lee, J. R. Weeks, R. S. Jokerst, and A. L. Greenleaf. 1988. The C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription initiation in vitro. Proc. Natl. Acad. Sci. USA 85:3698–3702.
   PubMedGoogle Scholar