Contribution of domain structure to the RNA 3′ end processing and degradation functions of the nuclear exosome subunit Rrp6p

RNA

Volumn 9, Issue 9, 2003, Pages 1098-1107

  Phillips, Seasson ^a   Butler, J Scott ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

Exosome; Riboexonuclease; RNA processing; Rrp6p

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; EXONUCLEASE; GLUTATHIONE TRANSFERASE; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; MESSENGER RNA PRECURSOR; POLYADENYLATED RNA; PROTEIN RRP6P; RIBONUCLEASE III; RIBOSOME RNA; RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; ENZYME ASSAY; ENZYME PURIFICATION; ENZYME SUBUNIT; ESCHERICHIA COLI; EXOSOME; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN LOCALIZATION; RNA DEGRADATION; RNA PROCESSING; RNA SYNTHESIS; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANIMALS; CELL NUCLEUS; EXORIBONUCLEASES; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROTEIN STRUCTURE, TERTIARY; RNA; RNA PRECURSORS; SCHIZOSACCHAROMYCES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0042834089     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5560903     Document Type: Article

References (33)

1. Allmang, C., Kufel, J., Chanfreau, G., Mitchell, P., Petfalski, E., and Tollervey, D. 1999a. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18: 5399-5410.
2. Allmang, C., Petfalski, E., Podtelejnikov, A., Mann, M., Tollervey, D., and Mitchell, P. 1999b. The yeast exosome and human PM-Scl are related complexes of 3′ → 5′ exonucleases. Genes & Dev. 13: 2148-2158.
3. Allmang, C., Mitchell, P., Petfalski, E., and Tollervey, D. 2000. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28: 1684-1691.
4. Anderson, J.S.J. and Parker, R.P. 1998. The 3prime to 5prime 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. Araki, Y., Takahashi, S., Kobayashi, T., Kajiho, H., Hoshino, S., and Katada, T. 2001. Ski7p G protein interacts with the exosome and the Ski complex for 3′-to-5′ mRNA decay in yeast. EMBO J. 20: 4684-4693.
6. Beese, L.S. and Steitz, T.A. 1991. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism. EMBO J. 10: 25-33.
7. Beese, L.S., Friedman, J.M., and Steitz, T.A. 1993. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochemistry 32: 14095-14101.
8. Bousquet-Antonelli, C., Presutti, C., and Tollervey, D. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102: 765-775.
9. Briggs, M.W., Burkard, K.T., and Butler, J.S. 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.
10. Brown, J.T., Bai, X., and Johnson, A.W. 2000. The yeast antiviral proteins Ski2p, Ski3p, and Ski8p exist as a complex in vivo. RNA 6: 449-457.
11. Burkard, K.T. and Butler, J.S. 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. Chen, C.Y., Gherzi, R., Ong, S.E., Chan, E.L., Raijmakers, R., Pruijn, G.J., Stoecklin, G., Moroni, C., Mann, M., and Karin, M. 2001. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107: 451-464.
14. Derbyshire, V., Grindley, N.D., and Joyce, C.M. 1991. The 3′-5′ exonuclease of DNA polymerase I of Escherichia coli: Contribution of each amino acid at the active site to the reaction. EMBO J. 10: 17-24.
15. Fatica, A., Morlando, M., and Bozzoni, I. 2000. Yeast snoRNA accumulation relies on a cleavage-dependent/polyadenylation-independent 3′-processing apparatus. EMBO J. 19: 6218-6229.
16. Frischmeyer, P.A., van Hoof, A., O'Donnell, K., Guerrerio, A.L., Parker, R., and Dietz, H.C. 2002. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295: 2258-2261.
17. Hilleren, P., McCarthy, T., Roshbash, M., Parker, P., and Jensen, T.H. 2001. Quality control of mRNA 3′-end processing requires the nuclear exosome. Nature 413: 538-542.
18. Kunkel, T.A., Bebenek, K., and McClary, J. 1991. Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol. 204: 125-139.
19. Liu, Z., Macias, M.J., Bottomley, M.J., Stier, G., Linge, J.P., Nilges, M., Bork, P., and Sattler, M. 1999. The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Structure Fold Des. 7: 1557-1566.
20. Mian, I.S. 1997. Comparative sequence analysis of ribonucleases HII, III, II, PH and D. Nucleic Acids Res. 25: 3187-3195.
21. Mitchell, P. and Tollervey, D. 2000. Musing on the structural organization of the exosome complex. Nat. Struct. Biol. 7: 843-846.
22. Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M., and Tollervey, D. 1997. The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′ → 5′ exoribonucleases. Cell 91: 457-466.
23. Morozov, V., Mushegian, A.R., Koonin, E.V., and Bork, P. 1997. A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. Trends Biochem. Sci. 22: 417-418.
24. Moser, M., Holley, W., Chatterjee, A., and Mian, I. 1997. The proof-reading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res. 25: 5110-5118.
25. Mukherjee, D., Gao, M., O'Connor, J.P., Raijmakers, R., Pruijn, G., Lutz, C.S., and Wilusz, J. 2002. The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO J. 21: 165-174.
26. Orr-Weaver, T.L., Szostak, J.W., and Rothstein, R.J. 1983. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol. 101: 228-245.
27. Patel, D. and Butler, J.S. 1992. Conditional defect in mRNA 3′ end processing caused by a mutation in the gene for poly(A) polymerase. Mol. Cell. Biol. 12: 3297-3304.
28. 2+-mediated cleavage. J. Biol. Chem. 277: 5982-5987.
29. van Hoof, A. and Parker, R. 1999. The exosome: A proteasome for RNA? Cell 99: 347-350.
30. van Hoof, A., Lennertz, P., and Parker, R. 2000. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20: 441-452.
31. van Hoof, A., Frischmeyer, P.A., Dietz, H.C., and Parker, R. 2002. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295: 2262-2264.
32. Venema, J. and Tollervey, D. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Annu. Rev. Genet. 33: 261-311.
33. Widner, W.R. and Wickner, R.B. 1993. Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol. Cell. Biol. 13: 4331-4341.