Chapter 10 Reconstitution of RNA Exosomes from Human and Saccharomyces cerevisiae. Cloning, Expression, Purification, and Activity Assays

Methods in Enzymology

Volumn 448, Issue , 2008, Pages 185-210

  Greimann, Jaclyn C ^a   Lima, Christopher D ^a  

^a NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; FUNGAL PROTEIN; HYBRID PROTEIN; PROTEIN SUBUNIT; RECOMBINANT PROTEIN; RNA; EXONUCLEASE; SACCHAROMYCES CEREVISIAE PROTEIN;

CELL INTERACTION; CELL NUCLEUS; EUKARYOTIC CELL; EXOSOME; HUMAN; HYDROLYSIS KINETICS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PURIFICATION; REVIEW; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; ANIMAL; ARTICLE; CHEMISTRY; ENZYME SPECIFICITY; GENE EXPRESSION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; SACCHAROMYCES CEREVISIAE;

ANIMALS; CLONING, MOLECULAR; EXONUCLEASES; EXOSOMES; GENE EXPRESSION; HUMANS; POLYMERASE CHAIN REACTION; RNA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUBSTRATE SPECIFICITY;

EID: 57749178666     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)02610-4     Document Type: Review

References (25)

1. Allmang C., Kufel J., Chanfreau G., Mitchell P., Petfalski E., and Tollervey D. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18 (1999) 5399-5410
2. Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., and Mitchell P. The yeast exosome and human PM-Scl are related complexes of 3′ to 5′-exonucleases. Genes Dev. 13 (1999) 2148-2158
3. Burkard K.T., and Butler J.S. A nuclear 3′ to 5′-exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell Biol. 20 (2000) 604-616
4. Buttner K., Wenig K., and Hopfner K.-P. Structural framework for the mechanism of Archaeal exosomes in RNA processing. Mol. Cell 20 (2005) 461-471
5. Carpousis A.J. The Escherichia coli RNA degradosome: Structure, function and relationship in other ribonucleolytic multienzyme complexes. Biochem. Soc. Trans. 30 (2002) 150-155
6. Cheng C., and Shuman S. Recombinogenic flap ligation pathway for intrinsic repair of topoisomerase IB-induced double-strand breaks. Mol. Cell Biol. 20 (2000) 8059-8068
7. Dziembowski A., Lorentzen E., Conti E., and Séraphin B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat. Struc. Molec. Biol. 14 (2007) 15-22
8. Evguenieva-Hackenberg E., Walter P., Hochleitner E., Lottspeich F., and Klug G. An exosome-like complex in Sulfolobus solfataricus. EMBO Rep. 4 (2003) 889-893
9. Graham A.C., Kiss D.L., and Andrulis E.D. Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci. Mol. Biol. Cell 17 (2006) 1399-1409
10. Heus H.A., and Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253 (1991) 191-194
11. Houseley J., LaCava J., and Tollervey D. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7 (2006) 529-539
12. Koonin E.V., Wolf Y.I., and Aravind L. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Gen. Res. 11 (2001) 240-252
13. Liu Q., Greimann J.C., and Lima C.D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127 (2006) 1223-1237
14. Liu Q., Greimann J.C., and Lima C.D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 131 (2007) 188-189
15. Lorentzen E., Walter P., Fribourg S., Evguenieva-Hackenberg E., Klug G., and Conti E. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct. Molec. Biol. 12 (2005) 575-581
16. Lorentzen E., and Conti E. Structural basis of 3′-end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol. Cell 20 (2005) 473-481
17. Lorentzen E., Dziembowski A., Lindner D., Seraphin B., and Conti E. RNA channelling by the archaeal exosome. EMBO Rep. 8 (2007) 470-476
18. Mitchell P., Petfalski E., and Tollervey D. The 3′-end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 10 (1996) 502-513
19. Mitchell P., Petfalski E., Shevchenko A., Mann M., and Tollervey D. The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′ to 5′-exoribonucleases. Cell 91 (1997) 457-466
20. Mossessova E., and Lima C.D. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell 5 (2000) 865-876
21. Raijmakers R., Schilders G., and Pruijn G.J. The exosome, a molecular machine for controlled RNA degradation in both nucleus and cytoplasm. Eur. J. Cell Biol. 83 (2004) 175-183
22. Schneider C., Anderson J.T., and Tollervey D. The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol. Cell 27 (2007) 324-331
23. Symmons M.F., Jones G.H., and Luisi B.F. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 8 (2000) 1215-1226
24. Wang Z., and Kiledjian M. Functional link between the mammalian exosome and mRNA decapping. Cell 107 (2001) 751-762
25. Wang H.-W., Wang J., Ding F., Callahan K., Bratkowski M.A., Butler J.S., Nogales E., and Ke A. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3′-end processing. Proc. Nat. Acad. Sci. USA 104 (2007) 16844-16849