Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations

Genetics

Volumn 143, Issue 1, 1996, Pages 67-80

  Noble, Suzanne M ^a   Guthrie, Christine ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA HELICASE;

ALTERNATIVE RNA SPLICING; ARTICLE; COLD SENSITIVITY; GENETIC ANALYSIS; GENETIC SCREENING; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN CONFORMATION; RNA SPLICING; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE; SPLICEOSOME; TEMPERATURE SENSITIVE MUTANT; YEAST;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; COLD; CONSERVED SEQUENCE; DNA PRIMERS; EXONS; FUNGAL PROTEINS; GENES, FUNGAL; GENETIC COMPLEMENTATION TEST; GENOTYPE; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; OLIGODEOXYRIBONUCLEOTIDES; PHENOTYPE; RNA HELICASES; RNA NUCLEOTIDYLTRANSFERASES; RNA PRECURSORS; RNA SPLICING; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC;

EID: 0029871680     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (66)

1. ABOVICH, N., X C. LIAO and M. ROSBASH, 1994 The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8: 843-854.
2. BENNETT, M., and R. REED, 1993 Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Science 262: 105-108.
3. BLANTON, S., A. SRINVASAN and B. C. RYMOND, 1992 PRP38 encodes a yeast protein required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Mol. Cell. Biol. 12: 3939-3947.
4. BROSI, R., K. KRONING, S. E. BEHRENS, R. LÜHRMANN, and A. KRÄMER, 1993 Interaction of mammalian splicing factor SF3a with U2 snRNP and relation of its 60-kD subunit to yeast PRP9. Science 262: 102-105.
5. CHAMPION-ARNAUD, P., and R. REED, 1994 The prespliceosome components SAP 49 and SAP 145 interact in a complex implicated in tethering U2 snRNP to the branch site. Genes Dev. 8: 1974-1983.
6. CHIARA, M. D., P. CHAMPION-ARNAUD, M. BUVOLI, B. NADAL-GINARD and R. REED, 1994 Specific protein-protein interactions between the essential mammalian spliceosome-associated proteins SAP 61 and SAP 114. Proc. Natl. Acad. Sci. USA 91: 6403-6407.
7. COOPER, M., L. H. JOHNSTON and J. D. BEGGS, 1995 Identification and characterization of Uss1p (Sdb23p): a novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins. EMBO J. 14: 2066-2075.
8. COUTO, J. R., J. TAMM, R. PARKER and C. GUTHRIE, 1987 A transacting suppressor restores splicing of a yeast intron with a branch point mutation. Genes Dev. 1: 445-455.
9. COX, J. H., and H B. STRACK, 1971 Cold-sensitive mutants of bacteriophage lambda. Genetics 67: 5-17.
10. DAMMEL, C. S., and H. F. NOLLER, 1993 A cold-sensitive mutation in 16S rRNA provides evidence for helical switching in ribosome assembly. Genes Dev. 7: 660-670.
11. DAMMEL, C. S., and H. F. NOLLER, 1995 Suppression of a cold-sensitive mutation in 16S rRNA by overexpression of a novel ribosome-binding factor, RbfA. Genes Dev. 9: 626-637.
12. DANGEL, A. W., L. SHEN, A. R. MENDOZA, L. C. WU and C. Y. YU, 1995 Human helicase gene SKI2W in the HLA class III region exhibits striking structural similarities to the yeast antiviral gene SKI2 and to the human gene K1AA0052: emergence of a new gene family. Nucleic Acids Res. 23: 2120-2126.
13. DIEHL, B. E., and J. R. PRINGLE, 1991 Molecular analysis of Saccharomyces cerevisiae chromosome I: identification of additional transcribed regions and demonstration that some encode essential functions. Genetics 127: 287-298.
14. ELLEDGE, S. J., and R. W. DAVIS, 1988 A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae. Gene 70: 303-312.
15. FRANK, D., B. PATTERSON and C. GUTHRIE, 1992 Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol. Cell. Biol. 12: 5197-5205.
16. GORBALENYA, A. E., E. V KOONIN, A. P. DONCHENKO and V. M. BLINOV, 1989 Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17: 4713-4730.
17. GUTHRIE, C., 1991 Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science 253: 157-163.
18. GUTHRIE, C., and G. R. FINK, 1991 Guide to Yeast Genetics and Molecular Biology Academic Press, San Diego.
19. GUTHRIE, C., H. NASHIMOTO and M. NOMURA, 1969a Structure and function of E. coli ribosomes. 8. Cold-sensitive mutants defective in ribosome assembly. Proc. Natl. Acad. Sci. USA 63: 384-391.
20. GUTHRIE, C., H. NASHIMOTO and M. NOMURA, 1969b Studies on the assembly of ribosomes in vivo. Cold Spring Harbor Symp. Quant. Biol. 34: 69-75.
21. HARRIS, S. D., and J. R. PRINGLE, 1991 Genetic analysis of Saccharomyces cerevisiae chromosome I: on the role of mutagen specificity in delimiting the set of genes identifiable using temperature-sensitive-lethal mutations. Genetics 127: 279-285.
22. HARTWELL, L H., C. S. MCLAUGHLIN and J. R. WARNER, 1970 Identification of ten genes that control ribosome formation in yeast. Mol. Gen. Genet. 109: 42-56.
23. HARTWELL, L. H., R. K. MORTIMER, J. CULOTTI, and M. CULOTTI 1973 Genetic control of the cell division cycle in yeast. V. Genetic analysis of the mutants. Genetics 74: 267-286.
24. HERMANN, H., P. FABRIZIO, V. A. RAKER, K. FOULAKI, H. HORNIG et al., 1995 snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions. EMBO J. 14: 2076-2088.
25. JARVIK, J., and D. BOTSTEIN, 1975 Conditional-lethal mutations that suppress genetic defects in morphogenesis by altering structural proteins. Proc. Natl. Acad. Sci. USA 72: 2738-2742.
26. JOHNSON, A. W., and R. D. KOLODNER, 1995 Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control. Mol. Cell. Biol. 15: 2719-2727.
27. KAO, H. Y., and P. G. SILICIANO, 1992 The yeast homolog of the U1 snRNP protein 70K is encoded by the SNP1 gene. Nucleic Acids Res. 20: 4009-4013.
28. KONARSKA, M. M., P. J. GRABOWSKI, R. A. PADGETT and P. A. SHARP, 1985 Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 313: 552-557.
29. KRÄMER, A., P. LEGRAIN, F. MULHAUSER, K. GRÖNING, R. BROSI et al., 1994 Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae, the conserved zinc finger-like motif is functionally exchangeable in vivo. Nucleic Acids Res. 22: 5223-5228.
30. KRÄMER, A., F. MULHAUSER, C. WERSIG, K. GRÖNING and G. BILBE, 1995 Mammalian splicing factor SF320 represents a new member of the SURP family of proteins and is homologous to the essential splicing factor PRP21p of Saccharomyces cerevisiae. RNA 1: 260-272.
31. LARKIN, J. C., and J. J. WOOLFORD, 1983 Molecular cloning and analysis of the CRY1 gene: a yeast ribosomal protein gene. Nucleic Acids Res. 11: 403-420.
32. LAST, R. L., J. R. MADDOCK and J. L. WOOLFORD, JR., 1987 Evidence for related functions of the RNA genes of Saccharomyces cerevisiae. Genetics 117: 619-631.
33. LESSER, C. F., and C. GUTHRIE, 1993 Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 133: 851-863.
34. LIAO, X. C., J. TANG and M ROSBASH, 1993 An enhancer screen identifies a gene that encodes the yeast U1 snRNP A protein: implications for snRNP protein function in pre-mRNA splicing. Genes Dev. 7: 419-428.
35. LOCKHART, S. R., and B. C. RYMOND, 1994 Commitment of yeast pre-mRNA to the splicing pathway requires a novel U1 small nuclear ribonucleoprotein polypeptide, Prp39p. Mol. Cell. Biol. 14: 3623-3633.
36. MADHANI, H. D., and C. GUTHRIE, 1992 A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell 71: 803-817.
37. MADHANI, H. D., and C. GUTHRIE, 1994 Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28: 1-26.
38. MASISON, D. C., A. BLANC, J. C. RIBAS, K. CARROLL, N. SONENBERG et al., 1995 Decoying the cap-mRNA degradation system by a double-stranded RNA virus and poly(A)-mRNA surveillance by a yeast antiviral system. Mol. Cell. Biol. 15: 2763-2771.
39. MOIR, D , S. E. STEWART, B. C. OSMOND and D. BOTSTEIN, 1982 Cold-sensitive cell-division-cycle mutants of yeast: isolation, properties, and pseudoreversion studies. Genetics 100: 547-563.
40. MOORE, M. J., and P. A. SHARP, 1993 Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 365: 364-368.
41. MOORE, M. J., C. C. QUERY and P. A. SHARP, 1993 Splicing of precursors to mRNA by the spliceosome, pp. 303-358 in The RNA World, edited by R. F. GESTELAND and J. F. ATKINS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. MYSLINSKI, E., V. SEGAULT and C. BRANLANT, 1990 An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science 247: 1213-1216.
43. PATTERSON, B., and C. GUTHRIE, 1987 An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell 49: 613-624.
44. PATTERSON, B., and C. GUTHRIE, 1991 A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell 64: 181-187.
45. PATTON, J. G., E. B. PORRO, J. GALCERAN, P. TEMPST and B. NADALGINARD, 1993 Cloning and characterization of PSF, a novel pre-mRNA splicing factor. Genes Dev. 7: 393-406.
46. PIKIELNY, C. W., and M. ROSBASH, 1985 mRNA splicing efficiency in yeast and the contribution of nonconserved sequences. Cell 41: 119-126.
47. RIDLEY, S. P., S. S. SOMMER and R. B. WICKNER, 1984 Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN. Mol. Cell. Biol. 4: 761-770.
48. ROSBASH, M., P. K. HARRIS, J.J. WOOLFORD and J. L. TEEM, 1981 The effect of temperature-sensitive RNA mutants on the transcription products from cloned ribosomal protein genes of yeast. Cell 24: 679-686.
49. ROSE, M. D., P. NOVICK, J. H. THOMAS, D. BOTSTEIN and G. R. FINK, 1987 A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60: 237-243.
50. ROY, J., B. ZHENG, B. C. RYMOND and J. J. WOOLFORD, 1995 Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins. Mol. Cell. Biol. 15: 445-455.
51. RUSKIN, B., A. R. KRAINER, T. MANIATIS and M. R. GREEN, 1984 Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell 38: 317-331.
52. RYMOND, B., and M. ROSBASH, 1992 Yeast pre-mRNA splicing, pp. 143-192 in The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by E. W JONES, J. R. PRINGLE and J. R. BROACH. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. RYMOND, B. C., 1993 Convergent transcripts of the yeast PRP38-SMD1 locus encode two essential splicing factors, including the D1 core polypeptide of small nuclear ribonucleoprotein particles. Proc. Natl. Acad. Sci. USA 90: 848-852.
54. SAMBROOK, J., E. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
55. SCHMID, S. R., and P. LINDER, 1992 D-E-A-D protein family of putative RNA helicases. Mol. Microbiol. 6: 283-291.
56. SCOTTI, P. D., 1968 A new class of temperature conditional lethal mutants of bacteriophage T4D. Mutat. Res. 6: 1-14.
57. SÉRAPHIN, B., 1995 Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J. 14: 2089-2098.
58. SIKORSKI, R. S., and P. HIETER, 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
59. SMITH, V., and B. G. BARRELL, 1991 Cloning of a yeast U1 snRNP 70K protein homologue: functional conservation of an RNA-binding domain between humans and yeast. EMBO J. 10: 2627-2634.
60. STRAUSS, E. J., and C. GUTHRIE, 1991 A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family. Genes Dev. 5: 629-641.
61. TAI, P. C., D. P. KESSLER and J. INGRAHAM, 1969 Cold-sensitive mutations in Salmonella typhimurium which affect ribosome synthesis. J. Bacteriol. 97: 1298-1304.
62. TEEM, J. L., and M. ROSBASH, 1983 Expression of a beta-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast. Proc. Natl. Acad. Sci. USA 80: 4403-4407.
63. VIJAYRAGHAVAN, U., M. COMPANY and J. ABELSON, 1989 Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev. 3: 1206-1216.
64. WIDNER, W. R., and R. B. WICKNER, 1993 Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol. Cell. Biol. 13: 4331-4341.
65. ZAVANELLI, M. I., and M. J. ARES, 1991 Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element. Genes Dev. 5: 2521-2533.
66. ZAVANELLI, M. I. , J. S. BRITTON, A. H. IGEL and M. J. ARES, 1994 Mutations in an essential U2 small nuclear RNA structure cause cold-sensitive U2 small nuclear ribonucleoprotein function by favoring competing alternative U2 RNA structures. Mol. Cell. Biol. 14: 1689-1697.