A novel plasmid-based microarray screen identifies suppressors of rrp6Δ in Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 27, Issue 3, 2007, Pages 1044-1055

  Abruzzi, Katharine ^a   Denome, Sylvia ^a   Olsen, Jens Raabjerg ^b   Assenholt, Jannie ^b   Haaning, Line Lindegaard ^b   Jensen, Torben Heick ^b   Rosbash, Michael ^a  

^a BRANDEIS UNIVERSITY   (United States)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; MESSENGER RNA; POLYADENYLATED RNA; PROTEIN LOS1P; PROTEIN NAB6; PROTEIN RRP6; RIBONUCLEOPROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CULTURE TECHNIQUE; DNA MICROARRAY; ENHANCER REGION; EXOSOME; FUNGAL GENE; FUNGAL STRAIN; FUNGUS GROWTH; GENE EXPRESSION; GENE IDENTIFICATION; GENE INTERACTION; GENE NUMBER; GENE OVEREXPRESSION; GENE REPRESSION; GENETIC SCREENING; LIQUID CULTURE; LOS1 GENE; MICROARRAY ANALYSIS; MICROARRAY ENHANCER SUPPRESSOR SCREENING; NAB6 GENE; NONHUMAN; PLASMID; PLATE SCREEN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN RNA BINDING; PROTEIN SYNTHESIS; RNA METABOLISM; RRP6 GENE; SACCHAROMYCES CEREVISIAE; SUPPRESSOR GENE; TEMPERATURE SENSITIVITY;

DOWN-REGULATION; EXORIBONUCLEASES; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, SUPPRESSOR; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; POLYADENYLATION; PROTEIN BINDING; RNA STABILITY; RNA, FUNGAL; RNA, MESSENGER; RNA, RIBOSOMAL; RNA, SMALL NUCLEOLAR; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUPPRESSION, GENETIC; TEMPERATURE;

SACCHAROMYCES CEREVISIAE;

EID: 33846562528     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.01299-06     Document Type: Article

References (46)

1. Allmang, C., J. Kufel, G. Chanfreau, P. Mitchell, E. Petfalski, and D. Tollervey. 1999. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18:5399-5410.
2. Allmang, C., P. Mitchell, E. Petfalski, and D. Tollervey. 2000. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28:1684-1691.
3. Allmang, C., E. Petfalski, A. Podtelenikov, M. Mann, D. Tollervey, and P. Mitchell. 1999. The yeast exosome and human PM-Scl are related complexes of 3′-5′ exonucleases. Genes Dev. 13:2148-2158.
4. Anderson, J. S., and R. P. Parker. 1998. The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J. 17:1497-1506.
5. Anderson, J. T., S. M. Wilson, K. V. Datar, and M. S. Swanson. 1993. NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability. Mol. Cell. Biol. 13:2730-2741.
6. Andrulis, E. D., J. Werner, A. Nazarian, H. Erdjument-Bromage, P. Tempst, and J. T. Lis. 2002. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420:837-841.
7. Arts, G. J., S. Kuersten, P. Romby, B. Ehresmann, and I. W. Mattaj. 1998. The role of exportin-t in selective nuclear export of mature tRNAs. EMBO J. 17:7430-7441.
8. Botstein, D., S. C. Falco, S. E. Stewart, M. Brennan, S. Scherer, D. T. Stinchcomb, K. Struhl, and R. W. Davis. 1979. Sterile host yeasts (SHY): a eukaryotic system of biological containment for recombinant DNA experiments. Gene 8:17-24.
9. Bousquet-Antonelli, C., C. Presutti, and D. Tollervey. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765-775.
10. Briggs, M. W., K. T. Burkard, and J. S. Butler. 1998. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3′ end formation. J. Biol. Chem. 273:13255- 13263.
11. Burkard, K. T., and J. S. Butler. 2000. A nuclear 3′-5′ exonuclease involved in mRNA degradation interacts with poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell. Biol. 20:604-616.
12. Butler, J. S. 2002. The yin and yang of the exosome. Trends Cell Biol. 12:90-96.
13. Colot, H. V., F. Stutz, and M. Rosbash. 1996. The yeast splicing factor MUD13 is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex. Genes Dev. 10:1699-1708.
14. Das, B., J. S. Butler, and F. Sherman. 2003. Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae. Mol. Cell. Biol. 23:5502-5515.
15. Das, B., S. Das, and F. Sherman. 2006. Mutant LYS2 mRNAs retained and degraded in the nucleus of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103:10871-10876.
16. Davis, C. A., and M. Ares, Jr. 2006. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103:3262-3267.
17. de la Cruz, J., D. Kressler, D. Tollervey, and P. Linder. 1998. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17:1128-1140.
18. Egecioglu, D. E., A. K. Henras, and G. F. Chanfreau. 2006. Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12:26-32.
19. Fatica, A., M. Morlando, and I. Bozzoni. 2000. Yeast snoRNA accumulation relies on a cleavage-dependent/polyadenylation-independent 3′-processing apparatus. EMBO J. 19:6218-6229.
20. Gentleman, R. C., V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, and J. Zhang. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
21. Grosshans, H., G. Simos, and E. Hurt. 2000. Transport of tRNA out of the nucleus-direct channeling to the ribosome? J. Struct. Biol 129:288-294.
22. Guthrie, C., and G. R. Fink. 1991. Guide to yeast genetics and molecular biology. Methods Enzymol. 194:389-398.
23. Hieronymus, H., M. C. Yu, and P. A. Silver. 2004. Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev. 18:2652-2662.
24. Hilleren, P., T. McCarthy, M. Rosbash, R. Parker, and T. H. Jensen. 2001. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413:538-542.
25. Jensen, T. H., J. Boulay, J. R. Olesen, J. Colin, M. Weyler, and D. Libri. 2004. Modulation of transcription affects mRNP quality. Mol. Cell 16:235-244.
26. Jensen, T. H., J. Boulay, M. Rosbash, and D. Libri. 2001. The DECD box putative ATPase Sub2p is an early mRNA export factor. Curr. Biol. 11:1711-1715.
27. Met in S. cerevisiae. Genes Dev. 18:1227-1240.
28. Kuai, L., B. Das, and F. Sherman. 2005. A nuclear degradation pathway controls the abundance of normal mRNAs in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102:13962-13967.
29. Kuai, L., F. Fang, J. S. Butler, and F. Sherman. 2004. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101:8581-8586.
30. LaCava, J., J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713-724.
31. Libri, D., K. Dower, J. Boulay, R. Thomsen, M. Rosbash, and T. H. Jensen. 2002. Interactions between mRNA export commitment, 3′-end quality control, and nuclear degradation. Mol. Cell. Biol. 22:8254-8266.
32. Midtgaard, S. F., J. Assenholt, A. T. Jonstrup, L. B. Van, T. H. Jensen, and D. E. Brodersen. 2006. Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc. Natl. Acad. Sci. USA 103:11898-11903.
33. Mitchell, P., E. Petfalski, R. Houalla, A. Podtelejnikov, M. Mann, and D. Tollervey. 2003. Rrp47p is an exosome-associated protein required for the 3′ processing of stable RNAs. Mol. Cell. Biol. 23:6982-6992.
34. Mitchell, P., and D. Tollervey. 2001. mRNA turnover. Curr. Opin. Cell Biol. 13:320-325.
35. Moreau, V., A. Madania, R. P. Martin, and B. Winson. 1996. The Saccharomyces cerevisiae actin-related protein Arp2 is involved in the actin cytoskeleton. J. Cell Biol. 134:117-132.
36. Petfalski, E., T. Dandekar, Y. Henry, and D. Tollervey. 1998. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol. Cell. Biol. 18:1181-1189.
37. Phillips, S., and J. S. Butler. 2003. Contribution of domain structure to the RNA 3′ end processing and degradation functions of the nuclear exosome subunit Rrp6p. RNA 9:1098-1107.
38. Puig, 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.
39. Russell, I., and D. Tollervey. 1995. Yeast Nop3p has structural and functional similarities to mammalian pre-mRNA binding proteins. Eur. J. Cell Biol. 66:293-301.
40. Samanta, M. P., and S. Liang. 2003. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc. Natl. Acad. Sci. USA 100:12579-12583.
41. Torchet, C., C. Bousquet-Antonelli, L. Milligan, E. Thompson, J. Kufel, and D. Tollervey. 2002. Processing of 3′-extended read-through transcripts by the exosome can generate functional mRNAs. Mol. Cell 9:1285-1296.
42. Vanacova, S., J. Wolf, G. Martin, D. Blank, S. Dettwiler, A. Friedlein, H. Langen, G. Keith, and W. Keller. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLOS Biol. 3:e189.
43. van Hoof, A., P. Lennertz, and R. Parker. 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.
44. van Hoof, A., P. Lennertz, and R. Parker. 2000. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 2:441-452.
45. Wyers, F., M. Rougemaille, G. Breard, J.-C. Rousselle, M.-E. Dufour, J. Boulay, F. Devaux, A. Namane, D. Libri, B. Séraphin, and A. Jacquier. 2005. Cryptic Pol II transcript degradation by nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725-737.
46. Zenklusen, D., P. Vinciguerra, J. C. Wyss, and F. Stutz. 2002. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol. Cell. Biol. 22:8241-8253.