Systematic identification, classification, and characterization of the open reading frames which encode novel helicase-related proteins in Saccharomyces cerevisiae by gene disruption and Northern analysis

Yeast

Volumn 15, Issue 3, 1999, Pages 219-253

  Shiratori, Akiko ^a,b   Shibata, Takehiko ^a,b   Arisawa, Mikio ^c   Hanaoka, Fumio ^a,d   Murakami, Yasufumi ^a   Eki, Toshihiko ^a  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b SAITAMA UNIVERSITY   (Japan)

^c NIPPON ROCHE RESEARCH CENTER   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

Atpase; Essential gene; Expression profile; Functional genomics; Gene disruption; Gene family; Heat shock; Helicase; Phylogenetic analysis; Saccharomyces cerevisiae; Slow growth phenotype; Systematic analysis; Transcriptional activation; Ybr245c; Ydl03lw; Ydl070w; Ydl084w; Ydr291w; Ydr332w; Ydr334w; Yer176w; Yfr038w; Ygl064c; Ygl15oc; Yhr031c; Yir002c; Ykl017c; Ykl078w; Ylr247c; Ylr276c; Ylr419w; Ymr128w; Ynl218w; Yol095c; Yor304w

Indexed keywords

FUNGAL PROTEIN; HELICASE; MESSENGER RNA;

ARTICLE; FUNGUS GROWTH; GENE DISRUPTION; NONHUMAN; NORTHERN BLOTTING; NUCLEIC ACID SYNTHESIS; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; TEMPERATURE; TRANSACTIVATION;

AMINO ACID SEQUENCE; BLOTTING, NORTHERN; CONSERVED SEQUENCE; DATABASES, FACTUAL; DNA HELICASES; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; GENES, ESSENTIAL; GENES, FUNGAL; HEAT-SHOCK RESPONSE; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; OPEN READING FRAMES; PHENOTYPE; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; TEMPERATURE;

FUNGI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0032942212     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0061(199902)15:3<219::AID-YEA349>3.0.CO;2-3     Document Type: Article

References (149)

1. Aasland, R., Gibson, T. J. and Stewart, A. F. (1995). The PHD finger: implications for chromatin-mediated transcriptional regulation. Trend Biochem. Sci. 20, 56-59.
2. Aasland, R., Stewart, A. F. and Gibson, T. (1996). The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem. Sci. 21, 87-88.
3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Anderson, J. S. J. and Parker, R. P. (1998). The 3′ to 5′ degradation of yeast mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J. 17, 1497-1506.
5. Arenas, J. E. and Abelson, J. N. (1997). Prp43: an RNA helicase-like factor involved in spliceosome disassembly. Proc. Natl Acad. Sci. USA 94, 11,798-11,802.
6. Auble, D. T., Wang, D., Post, K. W. and Hahn, S. (1997). Molecular analysis of the SNF2/SWI2 protein family member MOT1, an ATP-driven enzyme that dissociates TATA-binding protein from DNA. Mol. Cell. Biol. 17, 4842-4851.
7. Bairoch, A. (1993). The PROSITE dictionary of sites and patterns in proteins, its current status. Nucl. Acids Res. 21, 3097-3103.
8. Baganz, F., Hayes, A., Marren, D., Gardner, D. C. J. and Oliver, S. G. (1997). Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13, 1563-1573.
9. Baker, T. A. and Bell, S. P. (1998). Polymerases and the replisome: machines within machines. Cell 92, 295-305.
10. Bang, D. D., Timmermans, V., Verhage, R., Zeeman, A. M., van de Putte, P. and Brouwer, J. (1995). Regulation of the Saccharomyces cerevisiae DNA repair gene RAD16. Nucl. Acids Res. 23, 1679-1685.
11. Barta, I. and Iggo, R. (1995). Autoregulation of expression of the yeast Dbp2p 'DEAD-box' protein is mediated by sequences in the conserved DBP2 intron. EMBO J. 14, 3800-3808.
12. Baumeister, W., Walz, J., Zuhl, F. and Seemuller, E. (1998). The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367-380.
13. Bean, D. W. and Matson, S. W. (1997). Identification of the gene encoding scHell, a DNA helicase from Saccharomyces cerevisiae. Yeast 13, 1465-1475.
14. Biswas, S. B., Chen, P. H. and Biswas, E. E. (1997). Purification and characterization of DNA polymerase α-associated replication protein A-dependent yeast DNA helicase A. Biochemistry 36, 13,270-13,276.
15. Brandriss, M. C. and Falvey, D. A. (1992). Proline biosynthesis in Saccharomyces cerevisiae: analysis of the PRO3 gene, which encodes delta 1-pyrroline-5-carboxylate reductase. J. Bacteriol. 74, 3782-3788. [Erratum J. Bacteriol. 174, 5176.]
16. Budd, M. E. and Campbell, J. L. (1995). A yeast gene required for DNA replication encodes a protein with homology to DNA helicases. Proc. Natl Acad. Sci. USA 92, 7642-7646.
17. Chang, R.-Y., Weaver, P. L., Liu, Z. and Chang, T.-H. (1997). Requirement of the DEAD-box protein Ded1p for messenger RNA translation. Science 275, 1468-1471.
18. Chang, T. H., Arenas, J. and Abelson, J. (1990). Identification of five putative yeast RNA helicase genes. Proc. Natl Acad. Sci. USA 87, 1571-1575.
19. Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S. and Botstein, D. (1998). SGD: Saccharomyces Genome Database. Nucl. Acids Res. 26, 73-79.
20. Chia, L. L. and McLaughlin, C. (1979). The half-life of mRNA in Saccharomyces cerevisiae. Mol. Gen. Genet. 170, 137-144.
21. Chong, J. P., Thommes, P. and Blow, J. J. (1996). The role of MCM/P1 proteins in the licensing of DNA replication. Trends Biochem. Sci. 21, 102-106.
22. Chua, P. and Roeder, G. S. (1995). Bdfl, a yeast chromosomal protein required for sporulation. Mol. Cell. Biol. 15, 3685-3696.
23. Clark, M. W., Zhong, W. W., Keng, T., Storms, R. K., Barton, A., Kaback, D. B. and Bussey, H. (1992). Identification of a Saccharomyces cerevisiae homolog of the SNF2 transcriptional regulator in the DNA sequence of an 8·6 kb region in the LTE1-CYS1 interval of the left arm of chromosome I. Yeast 8, 133-145.
24. Coissac, E., Maillier, E., Robineau, S. and Netter, P. (1996). Sequence of a 39,411 bp DNA fragment covering the left end of chromosome VII of Saccharomyces cerevisiae. Yeast 12, 1555-1562.
25. Cole, G. M., Schild, D. and Mortimer, R. K. (1989). Two DNA repair and recombination genes in Saccharomyces cerevisiae, RAD52 and RAD54, are induced during meiosis. Mol. Cell. Biol. 9, 3101-3104.
26. Company, M., Arenas, J. and Abelson, J. (1991). Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature 349, 487-493.
27. Confalonieri, F. and Duguet, M. (1995). A 200-amino acid ATPase module in search of a basic function. Bioessays 17, 639-650.
28. Coster, F., Van Dyck, L., Jonniaux, J. L., Purnelle, B. and Goffeau, A. (1995). The sequence of a 13·5 kb DNA segment from the left arm of yeast chromosome XIV reveals MER1: RAP1; a new putative member of the DNA replication complex and a new putative serine/threonine phosphatase gene. Yeast 11, 85-91.
29. Craig, E. A. (1992). The heat-shock response of Saccharomyces cerevisiae. In Jones, E., Pringle, J. R. and Broach, J. R. (Eds), Molecular Biology of the Yeast Saccharomyces: Gene Expression. Cold Spring Harbor Laboratory Press, New York, pp. 501-537.
30. Cullmann, G., Fien, K., Kobayashi, R. and Stillman, B. (1995). Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol. Cell Biol. 15, 4661-4671.
31. 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.
32. Daugeron, M. C. and Linder, P. (1998). Dbp7p, a putative ATP-dependent RNA helicase from Saccharomyces cerevisiae, is required for 60S ribosomal subunit assembly. RNA 4, 566-581.
33. Decottignies, A. and Goffeau, A. (1997). Complete inventory of the yeast ABC proteins. Nature Genet. 15, 137-145.
34. DeRisi, J. L., Iyer, V. R. and Brown, P. O. (1997). Exploring the metabolic and genetic control of gene expression on a genome scale. Science 278, 680-686.
35. Dhawale, S. S. and Lane, A. C. (1993). Compilation of sequence-specific DNA binding proteins implicated in transcriptional control in fungi. Nucl. Acids Res. 21, 5537-5546.
36. DiDomenico, B. J., Bugaisky, G. E. and Lindquist, S. (1982). Heat shock and recovery are mediated by different translational mechanisms. Proc. Natl Acad. Sci. USA 79, 6181-6185.
37. Eisen, J. A., Sweden, K. S. and Hanawalt, P. C. (1995). Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucl. Acids Res. 23, 2715-2723.
38. Eki, T., Naitou, M., Hagiwara, H., Abe, M. et al. (1996). Fifteen open reading frames in a 30·8 kb region of the right arm of chromosome VI from Saccharomyces cerevisiae. Yeast 12, 177-190.
39. Elledge, S. J., Zhou, Z., Allen, J. B. and Navas, T. A. (1993). DNA damage and cell cycle regulation of ribonucleotide reductase. Bioessays 15, 333-339.
40. Elledge, S. J. (1996). Cell cycle checkpoints: preventing an identity crisis. Science 274, 1664-1672.
41. Ellis, N. A., Gorden, J., Ye, T.-Z., Straughen, J., Ciocci, S., Lennon, D. J., Proytcheva, M., Alhadeff, B. and German, J. (1995). The Bloom's syndrome gene product is homologous to RecQ helicases. Cell 83, 655-666.
42. Ellis, N. A. (1997). DNA helicases in inherited human disorders. Curr. Opin. Genet. Dev. 7, 354-363.
43. 65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev. 11, 1864-1872.
44. Fraser, R. A., Rossignol, M., Heard, D. J., Egly, J. M. and Chambon, P. (1997). SUG1, a putative transcriptional mediator and subunit of the PA700 proteasome regulatory complex, is a DNA helicase. J. Biol. Chem. 272, 7122-7126.
45. Friedberg, E. C., Siede, W. and Cooper, A. J. (1991). Cellular responses to DNA damage in yeast. In Jones, E., Pringle, J. R. and Broach, J. R. (Eds), Molecular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis and Energetics. Cold Spring Harbor Laboratory Press, New York, pp. 147-192.
46. 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, 277-282.
47. Gerring, S. L., Spencer, F. and Hieter, P. (1990). The CHL 1 (CTF 1) gene product of Saccharomyces cerevisiae is important for chromosome transmission and normal cell cycle progression in G2/M. EMBO J 9, 4347-4358.
48. Gibbons, R. J., Picketts, D. J., Villard, L. and Higgs, D. R. (1995). Mutations in a putative global transcriptional regulator cause X-linked mental retardation with α-thalassemia (ATR-X syndrome). Cell 80, 837-845.
49. Gietz, R. D., Schiestl, R. H., Willems, A. R. and Woods, R. A. (1995). Studies on the transformation of intact yeast cells by LiAc/SS-DNA/PEG procedure. Yeast 11, 355-360.
50. Goffeau, A. et al. 1997). The yeast genome directory. Nature 387 (Suppl.), 5-105.
51. Gorbalenya, A. E. and Koonin, E. V. (1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Biol. 3, 419-429.
52. Grant, P. A., Duggan, L., Cote, J., Roberts, S. M., Brownell, J. E., Candau, R., Ohba, R., Owen-Hughes, T., Allis, C. D., Winston, F., Berger, S. L. and Workman, J. L. (1997). Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histories: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640-1650.
53. Guzder, S. N., Sung, P., Bailly, V., Prakash, L. and Prakash, S. (1994). RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature 369, 578-581.
54. Guzder, S. N., Habraken, Y., Sung, P., Prakash, L. and Prakash, S. (1996). RAD26, the yeast homolog of human Cockayne's syndrome group B gene, encodes a DNA-dependent ATPase. J. Biol. Chem. 271, 18,314-18,317.
55. Hampsey, M. (1997). A review of phenotypes in Saccharomyces cerevisiae. Yeast 13, 1099-1133.
56. Henikoff, S., Greene, E. A., Pietrokovski, S., Bork, P., Attwood, T. K. and Hood, L. (1997). Gene families: the taxonomy of protein paralogs and chimeras. Science 278, 609-614.
57. Hodges, P. E., Payne, W. E. and Garrels, J. I. (1998). The Yeast Protein Database: a curated proteome database for Saccharomyces cerevisiae. Nucl. Acids Res. 26, 68-72.
58. Hofmann, K. and Stoffel, W. (1993). TMBASE - A database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler 374, 166.
59. Hunter, T. and Plowman, G. D. (1997). The protein kinases of budding yeast: six score and more. Trend. Biochem. Sci. 22, 18-22.
60. Ishimi, Y. (1997). A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex. J. Biol. Chem. 272, 24,508-24,513.
61. Jacobson, A. and Peltz, S. W. (1996). Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Ann. Rev. Biochem. 65, 693-739.
62. James, C. M., Indge, K. J. and Oliver, S. G. (1995). DNA sequence analysis of a 35 kb segment from Saccharomyces cerevisiae chromosome VII reveals 19 open reading frames including RAD54, ACE1CUP2, PMR1, RCK1, AMS1 and CAL1/CDC43. Yeast 11, 1413-1419.
63. Jamieson, D. J. and Beggs, J. D. (1991). A suppressor of yeast spp81ldedI mutations encodes a very similar putative ATP-dependent RNA helicase. Mol. Microbiol. 5, 805-812.
64. Jeanmougin, F., Wurtz, J.-M., Le Douarin, B., Chanbon, P. and Losson, R. (1997). The bromodomain revisited. Trends Biochem. Sci. 22, 151-153.
65. Johnson, R. E., Prakash, S. and Prakash, L. (1994). Yeast DNA repair protein RAD5 that promotes instability of simple repetitive sequences is a DNA-dependent ATPase. J. Biol. Chem. 269, 28,259-28,262.
66. Kadonaga, J. T. (1998). Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell 92, 307-313.
67. Kaiser, C., Michaelis, S. and Mitchell, A. (Eds) (1994). Methods in Yeast Genetics, 1994 edn. Cold Spring Harbor Press, New York.
68. Karow, J. K., Chakraverty, R. K. and Hickson, I. D. (1997). The Bloom's syndrome gene product is a 3′-5′ DNA helicase. J. Biol. Chem. 272, 30,611-30,614.
69. Kim, S. H., Smith, J., Claude, A. and Lin, R. J. (1992). The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase. EMBO J. 11, 2319-2326.
70. Kitada, K., Yamaguchi, E. and Arisawa, M. (1995). Cloning of the Candida glabrata TRP1 and HIS3 genes, and construction of their disruptant strains by sequential integrative transformation. Gene 165, 203-206.
71. Klein, H. L. (1997). RDH54, a RAD54 homologue in Saccharomyces cerevisiae, is required for mitotic diploid-specific recombination and repair and for meiosis. Genetics 147, 1533-1543.
72. Kogoma, T., Cadwell, G. W., Barnard, K. G. and Asai, T. (1996). The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair. J. Bacteriol. 178, 1258-1264.
73. Koonin, E. V. (1992). A new group of putative RNA helicases. Trend. Biochem. Sci. 17, 495-497.
74. Koonin, E. V. (1993a). A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. Nucl. Acids Res. 21, 2541-2547.
75. Koonin, E. V. (1993b). A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif. J. Mol. Biol. 229, 1165-1174.
76. Koonin, E. V. and Rudd, K. E. (1996). Two domains of superfamily I helicases may exist as separate proteins. Protein Science 5, 178-180.
77. Kouprina, N., Kroll, E., Kirillov, A., Bannikov, V., Zakharyev, V. and Larionov, V. (1994). CHL12, a gene essential for the fidelity of chromosome transmission in the yeast Saccharomyces cerevisiae. Genetics 138, 1067-1079.
78. Kressler, D., de la Cruz, J., Rojo, M. and Linder, P. (1997). Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 7283-7294.
79. Kressler, D., de la Cruz, J., Rojo, M. and Linder, P. (1998). Dbp6p is an essential putative ATP-dependent RNA helicase required for 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 1855-1865.
80. Lahaye, A., Stahl, H., Thines-Sempoux, D. and Foury, F. (1991). PIF1: a DNA helicase in yeast mitochondria. EMBO J 10, 997-1007.
81. Laurent, B. C., Yang, X. and Carlson, M. (1992). An essential Saccharomyces cerevisiae gene homologous to SNF2 encodes a helicase-related protein in a new family. Mol. Cell. Biol. 12, 1893-1902.
82. Laurent, B. C., Treich, I. and Carlson, M. (1993). The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev. 7, 583-591.
83. Lee, C. G., Chang, K. A., Kuroda, M. I. and Hurwitz, J. (1997). The NTPase/helicase activities of Drosophila maleless, an essential factor in dosage compensation. EMBO J. 16, 2671-2681.
84. Li, X. and Burgers, P. M. (1994). Molecular cloning and expression of the Saccharomyces cerevisiae RFC3 gene, an essential component of replication factor C. Proc. Natl Acad. Sci. USA 91, 868-872.
85. Liang, S., Hitomi, M., Hu, Y. H., Liu, Y. and Tartakoff, A. M. (1996). A DEAD-box-family protein is required for nucleocytoplasmic transport of yeast mRNA. Mol. Cell. Biol. 16, 5139-5146.
86. Liang, W. Q., Clark, J. A. and Fournier, M. J. (1997). The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein. Mol. Cell. Biol. 17, 4124-4132.
87. Linder, P. and Slonimski, P. P. (1989). An essential yeast protein, encoded by duplicated genes TIF1 and TIF2 and homologous to the mammalian translation initiation factor eIF-4A, can suppress a mitochondrial missense mutation. Proc. Natl Acad. Sci. USA 86, 2286-2290.
88. Lindquist, S. (1981). Regulation of protein synthesis during heat shock. Nature 293, 311-314.
89. Lohman, T. M. and Bjornson, K. P. (1996). Mechanisms of helicase-catalyzed DNA unwinding. Ann. Rev. Biochem. 65, 169-214.
90. Louis, E. J. (1995). The chromosome ends of Saccharomyces cerevisiae. Yeast 11, 1553-1573.
91. Lu, J., Mullen, J. R., Brill, S. J., Kleff, S., Romeo, A. M. and Sternglanz, R. (1996a). Human homologues of yeast helicase. Nature 383, 678-679.
92. Lu, J., Kobayashi, R. and Brill, S. J. (1996b). Characterization of a high mobility group 1/2 homolog in yeast. J. Biol. Chem. 271, 33,678-33,685.
93. Lussier, M., White, A.-M., Sheraton, J., di Paolo, T., Treadwell, J. et al. (1997). Large scale identification of genes involved in cell surface biogenesis and architecture in Saccharomyces cerevisiae. Genetics 147, 435-450.
94. Makino, Y., Yamano, K., Kanemaki, M., Morikawa, K., Kishimoto, T., Shimabara, N., Tanaka, K. and Tamura, T. (1997). SUG1, a component of the 26S proteasome, is an ATPase stimulated by specific RNAs. J. Biol. Chem. 272, 23,201-23,205.
95. Marians, K. J. (1997). Helicase structures: a new twist on DNA unwinding. Structure 5, 1129-1134.
96. Martegani, E., Vanoni, M., Mauri, I., Rudoni, S., Saliola, M. and Alberghina, L. (1997). Identification of a gene encoding a putative RNA-helicase, homologous to SKI2, in chromosome VII of Saccharomyces cerevisiae. Yeast 13, 391-397.
97. Matson, S. W. and Kaiser-Rogers, K. A. (1990). DNA helicases. Ann. Rev. Biochem. 59, 289-329.
98. Mewes, H. W., Albermann, K., Bahr, M., Frishman, D., Gleissner, A., Hani, J., Heumann, K., Kleine, K., Maierl, A., Oliver, S. G., Pfeiffer, F. and Zollner, A. (1997). Overview of the yeast genome. Nature 387 (Suppl.), 7-65.
99. Mewes, H. W., Hani, J., Pfeiffer, F. and Frishman, D. (1998). MIPS: a database for protein sequences and complete genomes. Nucl. Acids Res. 26, 33-37.
100. Mitchell, P. A. (1994). Control of meiotic gene expression in Saccharomyces cerevisiae. Microbiol. Rev. 58, 56-70.
101. Naitou, M., Hagiwara, H., Hanaoka, F., Eki, T. and Murakami, Y. (1997). Expression profiles of transcripts from 126 open reading frames in the entire chromosome VI of Saccharomyces cerevisiae by systematic Northern analyses. Yeast 13, 1275-1290.
102. Nakai, K. and Kanehisa, M. (1992). A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14, 897-911.
103. Noble, S. M. and Guthrie, C. (1996). Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 143, 67-80.
104. O'Day, C. L., Chavanikamannil, F. and Abelson, J. (1996a). 18S rRNA processing requires the RNA helicase-like protein Rrp3. Nucl. Acids Res. 24, 3201-3207.
105. O'Day, C. L., Dalbadie-McFarland, G. and Abelson, J. (1996b). The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J. Biol. Chem. 271, 33,261-33,267.
106. Page, R. D. M. (1996). TREEVIEW: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12, 357-358.
107. Petukhova, G., Stratton, S. and Sung, P. (1998). Catalysis of homologus DNA pairing by yeast Rad51 and Rad54 proteins. Nature 393, 91-94.
108. Razin, M. J. and Kadonaga, J. T. (1997). SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions? Cell 88, 737-740.
109. Rieger, K.-J., Kaniak, A., Cooppée, J.-Y., Alijinovic, G., Baudin-Baillieu, A., Orlowska, R., Groudinsky, O., Di Rago, J.-P. and Slonimski, P. P. (1997). Large-scale phenotypic analysis - the pilot project on yeast chromosome III. Yeast 13, 1547-1562.
110. Ripmaster, T. L., Vaughn, G. P. and Woolford, J. L., Jr (1992). A putative ATP-dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly. Proc. Natl Acad. Sci. USA 89, 11,131-11,135.
111. Robbins, J., Dilworth, S. M., Laskey, R. A. and Dingwall, C. (1991). Two interdependent basic domains in nucleoplasmin nuclear targeting sequence: identification of a class of bipartite nuclear targeting sequence. Cell 64, 615-623.
112. Rong, L. and Klein, H. L. (1993). Purification and characterization of the SRS2 DNA helicase of the yeast Saccharomyces cerevisiae. J. Biol. Chem. 268, 1252-1259.
113. Raymond, B. C. and Rosbash, M. (1992). Yeast pre-mRNA splicing. In Jones, E., Pringle, J. R. and Broach, J. R. (Eds), Molecular Biology of the Yeast Saccharomyces: Gene Expression. Cold Spring Harbor Laboratory Press, New York, pp. 143-192.
114. Sachs, A. B. and Davis, R. W. (1990). Translation initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46. Science 247, 1077-1079.
115. Sarén, A. M., Laamanen, P., Lejarcegui, J. B. and Paulin, L. (1997). The sequence of a 36·7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs. Yeast 13, 65-71.
116. Schild, D., Glassner, B. J., Mortimer, R. K., Carlson, M. and Laurent, B. C. (1992). Identification of RAD16, a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. Yeast 8, 385-395.
117. Schmid, S. R. and Linder, P. (1991). Translation initiation factor 4A from Saccharomyces cerevisiae: analysis of residues conserved in the D-E-A-D family of RNA helicases. Mol. Cell. Biol. 11, 3463-3471.
118. Schmid, S. R. and Linder, P. (1992). D-E-A-D protein family of putative RNA helicases. Mol. Microbiol. 6, 283-291.
119. Schnall, R., Mannhaupt, G., Stucka, R., Tauer, R., Ehnle, S., Schwarzlose, C., Vetter, I. and Feldman, H. (1994). Identification of a set of yeast genes coding for a novel family of putative ATPases with high similarity to constituents of the 26S proteasome complex. Yeast 10, 1141-1155.
120. Schwer, B. and Guthrie, C. (1991). PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349, 494-499.
121. Schwer, B. and Gross, C. H. (1998). Prp22, a DExH-box RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 17, 2086-2094.
122. Seraphin, B., Simon, M., Boulet, A. and Faye, G. (1989). Mitochondrial splicing requires a protein from a novel helicase family. Nature 337, 84-87.
123. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagiocco, F., Wilm, M., Vorm, O., Mortensen, P., Shevchenko, A., Boucherie, H. and Mann, M. (1996). Linking genome and proteome by mass spectrometry - large scale identification of yeast proteins from 2-dimensional gels. Proc. Natl Acad. Sci. USA 93, 14,440-14,445.
124. Sinclair, D. A. and Guarante, L. (1997). Extrachromosomal rDNA circles - a cause of aging in yeast. Cell 91, 1033-1042.
125. Sinclair, D. A., Mills, K. and Guarente, L. (1997). Accelerated aging and nucleolar fragmentation in yeast sgs1 mutants. Science 277, 1313-1316.
126. Staley, J. P. and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315-326.
127. Steinmetz, E. J. and Brow, D. A. (1996). Repression of gene expression by an exogenous sequence element acting in concert with a heterogenous nuclear ribonucleoprotein-like protein. Nrd1, and the putative helicase Sen1. Mol. Cell. Biol. 16, 6993-7003.
128. Stepien, P. P., Margossian, S. P., Landsman, D. and Butow, R. A. (1992). The yeast nuclear gene suv3 affecting mitochondrial post-transcriptional processes encodes a putative ATP-dependent RNA helicase. Proc. Natl Acad. Sci. USA 89, 6813-6817.
129. Strahl-Bolsinger, S. and Tanner, W. (1993). A yeast gene encoding a putative RNA helicase of the "DEAD"-box family. Yeast 9, 429-432.
130. Strauss, E. J. and Guthrie, C. (1994). PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro. Nucl. Acids Res. 22, 3187-3193.
131. Sun, Z. W. and Hampsey, M. (1996). Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo. Mol. Cell. Biol. 16, 1557-1566.
132. Sung, P., Prakash, L., Matson, S. W. and Prakash, S. (1987). RAD3 protein of Saccharomyces cerevisiae is a DNA helicase. Proc. Natl Acad. Sci. USA 84, 8951-8955.
133. Suzuki, N., Shimamoto, A., Imamura, O., Kuromitsu, J., Kitao, S., Goto, M. and Furuichi, Y. (1997). DNA helicase activity in Werner's syndrome gene product synthesized in a baculovirus system. Nucl. Acids Res. 25, 2973-2987.
134. Takeuchi, K., Kawashima, A., Nagafuchi, A. and Tsukita, S. (1994). Structural diversity of band 4.1 superfamily members. J. Cell Sci. 107, 1921-1928.
135. Tanaka, K., Matsumoto, K. and Toh-e, A. (1988). Dual regulation of the expression of the polyubiquitin gene by cyclic AMP and heat shock in yeast. EMBO J. 7, 495-502.
136. Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
137. + RNA export. EMBO J. 17, 2651-2662.
138. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E., Jr. Hieter, P., Vogelstein, B. and Kinzler, K. W. (1997). Characterization of the yeast transcriptome. Cell 88, 243-251.
139. Venema, J., Bousquet-Antonelli, C. Gelugne, J. P., Caizergues-Ferrer, M. and Tollervey, D. (1997). Rok1p is a putative RNA helicase required for rRNA processing. Mol. Cell. Biol. 17, 3398-3407.
140. Wang, Y., Wagner, J. D. O. and Guthrie, C. (1998). The DEAH-box splicing factor Prp16 unwinds RNA duplexes in vitro. Curr. Biol. 8, 441-451.
141. Weaver, P. L., Sun, C. and Chang, T. H. (1997). Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3. Mol. Cell. Biol. 17, 1354-1365.
142. Weeda, G., Rossignol, M., Fraser, R. A., Winkler, G. S., Vermeulen, W., van't Veer, L. J., Ma. L., Hoeijmakers, J. H. J. and Egly, J.-M. (1997). The XPB subunit of repair/transcription factor TFIIH directly interacts with SUG1, a subunit of the 26S proteasome and putative transcription factor. Nucl. Acids Res. 25, 2274-2283.
143. Wickner, R. B. (1996). Double-stranded RNA viruses of Saccharomyces cerevisiae. Microbiol. Rev. 60, 250-265.
144. Wodicka, L., Dong, H., Mittmann, M., Ho, M.-H. and Lockhart, D. L. (1997). Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotech. 15, 1359-1367.
145. Wolfe, K. H. and Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
146. Woodage, T., Basrai, M. A., Baxenvanis, A. D., Hieter, P. and Collins, F. S. (1997). Characterization of the CHD family of proteins. Proc. Natl Acad. Sci. USA 94, 11,471-11,477.
147. Worley, K. C., Wiese, B. A. and Smith, R. F. (1995). BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res. 5, 173-184.
148. Yu, C.-E., Oshima, J., Fu, Y.-H., Wijsman, E. M., Hisama, F., Alisch, R., Matthews, S., Nakura, J., Miki, T. et al. (1996). Positional cloning of the Werner's syndrome gene. Science 272, 258-262.
149. Zhang, Z. and Buchman, A. R. (1997). Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Mol. Cell. Biol. 17, 5461-5472.