Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing

Nucleic Acids Research

Volumn 32, Issue 8, 2004, Pages 2441-2452

  Ursic, Doris ^a   Chinchilla, Karen ^a   Finkel, Jonathan S ^a   Culbertson, Michael R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; HELICASE; PROTEIN SEN1P; RIBONUCLEASE; RIBONUCLEASE III; RNA HELICASE; RNA POLYMERASE II; UNCLASSIFIED DRUG; FUNGAL PROTEIN; FUNGAL RNA; RNT1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SEN1 PROTEIN, FUNGUS; SMALL NUCLEAR RNA; U5 SMALL NUCLEAR RNA;

ARTICLE; CONTROLLED STUDY; DNA REPAIR; ENZYME ACTIVITY; FUNGAL STRAIN; FUNGUS GROWTH; GENE IDENTIFICATION; GENE MUTATION; GENETIC TRANSCRIPTION; GROWTH RATE; IMMUNOPRECIPITATION; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA HYBRIDIZATION; RNA PROCESSING; SACCHAROMYCES CEREVISIAE; CELL DIVISION; CYTOLOGY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; MACROMOLECULE; METABOLISM; MUTATION; PHYSIOLOGY; TWO HYBRID SYSTEM;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

CELL DIVISION; DNA HELICASES; DNA REPAIR; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; MACROMOLECULAR SUBSTANCES; MUTATION; RIBONUCLEASE III; RNA HELICASES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, FUNGAL; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 2342453900     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh561     Document Type: Article

References (42)

1. Gall,J.G., Bellini,M., Wu,Z and Murphy,C. (1999) Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes. Mol. Biol. Cell, 10, 4385-4402.
2. Myer,V.E. and Young,R.A. (1998) RNA polymerase II holoezyme and subcomplexes. J. Biol. Chem., 273, 27757-27760.
3. Corden,J.L. and Patturajan,M. (1997) A CTD function linking transcription to splicing. Trends Biochem. Sci., 22, 413-416.
4. Winey,M. and Culbertson,M.R. (1988) Mutations affecting the tRNA-splicing endonuclease activity of Saccharomyces cerevisiae. Genetics, 118, 609-617.
5. DeMarini,D.J., Winey,M., Ursic,D., Webb,F. and Culbertson,M.R. (1992) SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae. Mol. Cell. Biol., 12, 2154-2164.
6. Ursic,D., DeMarini,D.J. and Culbertson,M.R. (1995) Inactivation of the yeast Sen1 protein affects the localization of nucleolar proteins. Mol. Gen. Genet., 249, 571-584.
7. Ursic,D., Himmel,K.L., Gurley,K.A., Webb,F. and Culbertson,M.R. (1997) The yeast SEN1 gene is required for processing of diverse RNA classes. Nucleic Acids Res., 25, 4778-4785.
8. Rasmussen,T.P. and Culbertson,M.R. (1998) The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol. Cell. Biol., 18, 6885-6896.
9. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
10. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 123-124.
11. Walsh,E.R, Lamont,D.J., Beattie,K.A. and Stark,M.J.R. (2002) Novel interactions of Saccharomyces cerevisiae type 1 protein phosphatase identified by single-step affinity purification and mass spectroscopy. Biochemistry, 41, 2409-2420.
12. Fromont-Racine,M., Rain,J.-C. and Legrain,P. (1997) Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet., 16, 216-217.
13. Tomkinson,A.E., Bardwell,A.J., Bardwell,L., Tappe,N.J. and Friedberg,E.C. (1993) Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature, 362, 860-862.
14. Habraken,Y., Sung,P., Prakash,L. and Prakash,S. (1993) Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature, 366, 365-368.
15. Kim,H.-D., Choe,J. and Seo,Y.-S. (1999) The sen1+ gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase. Biochemistry, 38, 14697-14710.
16. Steinmetz,E.J., Conrad,N.K., Brow,D.A. and Cordon,J.,L. (2001) RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature, 413, 327-331.
17. Steinmetz,E.J. and Brow,D.A. (1998) Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc. Natl Acad. Sci. USA, 95, 6699-6704.
18. Chanfreau,G., Elela,S.A., Ares,M.J. and Guthrie,C. (1997) Alternative 3′-end processing of U5 snRNA by RNAse III. Genes Dev., 11, 2741-2751.
19. Elela,S.A. and Ares,M. (1998) Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyaderylated but functional U2 snRNA. EMBO J., 17, 3738-3746.
20. Chanfreau,G., Legrain,P. and Jacquier,A. (1998) Yeast RNase III as a key processing enzyme in small nucleolar RNA metabolism. J. Mol. Biol., 284, 975-988.
21. Allmang,A., Kufel,J., Chanfreau,G., Mitchell,P., Petfalski,E. and Tollervey,D. (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J., 18, 5399-5410.
22. Elela,S.A., Igel,H. and Ares,M. (1996) RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site, Cell, 85, 115-124.
23. Kufel,J., Dichtl,B. and Tollervey,D. (1999) Yeast Rnt1p is required for cleavage of the pre-ribosomal RNA in the 3′ETS but not the 5′ ETS. RNA, 5, 909-917.
24. West,M.L. and Corden,J.L. (1995) Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics, 140, 1223-1233.
25. James,P., Halladay,J. and Craig,E.A. (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics, 144, 1425-1436.
26. Ursic,D. and Culbertson,M.R. (1991) The yeast homolog to mouse Tcp1-1 affects micrombule-mediated processes. Mol. Cell. Biol., 11, 2629-2640.
27. Fields,S. and Song,O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
28. Czaplinski,K., Weng,Y., Hagan,K.W. and Peltz,S.W. (1995) Purification and characterization of the Upf1 protein: a factor involved in translation and mRNA degradation. RNA, 1, 610-623.
29. Lamontagne,B., Tremblay,A. and Elela,S.A. (2000) The N-terminal domain that distinguishes yeast from bacterial RNase III contains a dimerization signal required for efficient double-stranded RNA cleavage. Mol. Cell. Biol., 20, 1104-1115.
30. Patterson,B. and Guthrie,C. (1987) An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell, 5, 613-624.
31. Stevens,S.W., Ryan,D.E., Ge,H.Y., Moore,R.E., Young,M.K., Lee,T.D. and Abelson,J. (2002) Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell, 1, 31-44.
32. Van Hoof,A., Lennertz,P. and Parker,R. (2000) Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNAse MRP and RNase P RNAs in yeast. EMBO J., 19, 1357-1365.
33. Briggs,M.W., Burkard,K.T.D. and Butler,J.S. (1998) Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNAse MRP and RNase P RNAs in yeast. J. Biol. Chem., 273, 13255-13263.
34. van Gool,A.J., Verhage,R., Swagemakers,S.M., van de Putte,P., Brouwer,J., Troelstra,C., Bootsma,D. and Hoeijmakers,J.H. (1994) RAD26, the functional S.cerevisiae homolog of the Cockayne syndrome B gene ERCC6. EMBO J., 13, 5361-5369.
35. Prakash,S. and Prakash,L. (2000) Nucleotide excision repair in yeast. Mutat. Res., 451, 13-24.
36. Hoogstraten,D., Nigg,A.L., Heath,H., Mullenders,L.H., van Driel,R., Hoeijmakers,J.H., Vermeulen,W. and Houtsmuller,A.B. (2002) Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell, 10, 1163-1174.
37. Nagel,R. and Ares,M. (2000) Substrate recognition by a eukaryotic RNase III: the double-stranded RNA-binding domain of Rnt1p selectively binds RNA containing a 5′-AGNN-3′ tetraloop. RNA, 6, 1142-1156.
38. Moreira,M.C., Klur,S., Watanabe,M., Nemeth,A.H., Le Ber,I., Moniz,J.C., Tranchant,C., Aubourg,P., Tazir,M., Schols,L. et al. (2004) Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2. Nature Genet., 36, 225-227.
39. Balakin,A.G., Smith,L. and Fournier,M.J. (1996) The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell, 86, 823-834.
40. Allmang,C., Petfalski,E., Podtelejnikov,A., Mann,M., Tollervey,D. and Mitchell,P. (1999) The yeast exosome and human PM-Sc1 are related complexes of 3′ to 5′ exonucleases. Genes Dev., 13, 2148-2158.
41. Will,C.L. and Luhrmann,R. (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol., 13, 290-301.
42. Zhang,D., Abovich,N. and Rosbash,M. (2001) A biochemical function for the Sm complex. Mol. Cell, 7, 319-329.