Structural basis of 3′ end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core

Molecular Cell

Volumn 20, Issue 3, 2005, Pages 473-481

  Lorentzen, Esben ^a   Conti, Elena ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE; EXORIBONUCLEASE; RIBONUCLEASE; RNA;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME DEGRADATION; ENZYME SUBSTRATE; MOLECULAR INTERACTION; MOLECULAR MECHANICS; NONHUMAN; RNA BINDING; RNA SEQUENCE; SULFOLOBUS SOLFATARICUS;

ARCHAEAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; MULTIENZYME COMPLEXES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASES; RNA STABILITY; RNA, ARCHAEAL; SUBSTRATE SPECIFICITY; SULFOLOBUS SOLFATARICUS;

SULFOLOBUS SOLFATARICUS;

EID: 27644496002     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.10.020     Document Type: Article

References (35)

1. C. Allmang, J. Kufel, G. Chanfreau, P. Mitchell, E. Petfalski, and D. Tollervey Functions of the exosome in rRNA, snoRNA and snRNA synthesis EMBO J. 18 1999 5399 5410
2. C. Allmang, E. Petfalski, A. Podtelejnikov, M. Mann, D. Tollervey, and P. Mitchell The yeast exosome and human PM-Scl are related complexes of 3′→5′ exonucleases Genes Dev. 13 1999 2148 2158
3. K.E. Baker, and R. Parker Nonsense-mediated mRNA decay: terminating erroneous gene expression Curr. Opin. Cell Biol. 16 2004 293 299
4. W. Baumeister, and A. Lupas The proteasome Curr. Opin. Struct. Biol. 7 1997 273 278
5. C. Bousquet-Antonelli, C. Presutti, and D. Tollervey Identification of a regulated pathway for nuclear pre-mRNA turnover Cell 102 2000 765 775
6. M.W. Briggs, K.T. Burkard, and J.S. Butler Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8S rRNA 3′ end formation J. Biol. Chem. 273 1998 13255 13263
7. J.A. Chekanova, R.J. Shaw, M.A. Wills, and D.A. Belostotsky Poly(A) tail-dependent exonuclease AtRrp41p from Arabidopsis thaliana rescues 5.8S rRNA processing and mRNA decay defects of the yeast ski6 mutant and is found in an exosome-sized complex in plant and yeast cells J. Biol. Chem. 275 2000 33158 33166
8. C.Y. Chen, R. Gherzi, S.E. Ong, E.L. Chan, R. Raijmakers, G.J. Pruijn, G. Stoecklin, C. Moroni, M. Mann, and M. Karin AU binding proteins recruit the exosome to degrade ARE-containing mRNAs Cell 107 2001 451 464
9. CCP4 (Collaborative Computational Project, Number 4) The CCP4 Suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
10. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
11. A.M. Estevez, T. Kempf, and C. Clayton The exosome of Trypanosoma brucei EMBO J. 20 2001 3831 3839
12. E. Evguenieva-Hackenberg, P. Walter, E. Hochleitner, F. Lottspeich, and G. Klug An exosome-like complex in Sulfolobus solfataricus EMBO Rep. 4 2003 889 893
13. D. Forler, T. Kocher, M. Rode, M. Gentzel, E. Izaurralde, and M. Wilm An efficient protein complex purification method for functional proteomics in higher eukaryotes Nat. Biotechnol. 21 2003 89 92
14. L.S. Harlow, A. Kadziola, K.F. Jensen, and S. Larsen Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding Protein Sci. 13 2004 668 677
15. P. Hilleren, T. McCarthy, M. Rosbash, R. Parker, and T.H. Jensen Quality control of mRNA 3′-end processing is linked to the nuclear exosome Nature 413 2001 538 542
16. A. Jarrige, D. Brechemier-Baey, N. Mathy, O. Duche, and C. Portier Mutational analysis of polynucleotide phosphorylase from Escherichia coli J. Mol. Biol. 321 2002 397 409
17. W. Kabsch Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. Appl. Crystallogr. 26 1993 795 800
18. E.V. Koonin, Y.I. Wolf, and L. Aravind Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach Genome Res. 11 2001 240 252
19. J. LaCava, J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey RNA degradation by the exosome is promoted by a nuclear polyadenylation complex Cell 121 2005 713 724
20. H. Li, A.D. Robertson, and J.H. Jensen The determinants of carboxyl pKa values in turkey ovomucoid third domain Proteins 55 2004 689 704
21. E. Lorentzen, P. Walter, S. Fribourg, E. Evguenieva-Hackenberg, G. Klug, and E. Conti The archaeal exosome core is a hexameric ring structure with three catalytic subunits Nat. Struct. Mol. Biol. 12 2005 575 581
22. A.S. Mildvan Mechanisms of signaling and related enzymes Proteins 29 1997 401 416
23. P. Mitchell, E. Petfalski, and D. Tollervey The 3′ end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism Genes Dev. 10 1996 502 513
24. P. Mitchell, E. Petfalski, A. Shevchenko, M. Mann, and D. Tollervey The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases Cell 91 1997 457 466
25. D. Mukherjee, M. Gao, J.P. O'Connor, R. Raijmakers, G. Pruijn, C.S. Lutz, and J. Wilusz The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements EMBO J. 21 2002 165 174
26. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D53 1997 240 255
27. R. Raijmakers, W.V. Egberts, W.J. van Venrooij, and G.J. Pruijn Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring J. Mol. Biol. 323 2002 653 663
28. C. Spickler, and G.A. Mackie Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure J. Bacteriol. 182 2000 2422 2427
29. M.F. Symmons, G.H. Jones, and B.F. Luisi A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation Struct. Fold. Des. 8 2000 1215 1226
30. M.F. Symmons, M.G. Williams, B.F. Luisi, G.H. Jones, and A.J. Carpousis Running rings around RNA: a superfamily of phosphate-dependent RNases Trends Biochem. Sci. 27 2002 11 18
31. S. Vanacova, J. Wolf, G. Martin, D. Blank, S. Dettwiler, A. Friedlein, H. Langen, G. Keith, and W. Keller A new yeast poly(A) polymerase complex involved in RNA quality control PLoS Biol. 3 2005 e189 10.1371/journal.pbio.0030189
32. A. van Hoof, and R. Parker The exosome: a proteasome for RNA? Cell 99 1999 347 350
33. A. van Hoof, P. Lennertz, and R. Parker Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs Mol. Cell. Biol. 20 2000 441 452
34. A. van Hoof, P.A. Frischmeyer, H.C. Dietz, and R. Parker Exosome-mediated recognition and degradation of mRNAs lacking a termination codon Science 295 2002 2262 2264
35. F. Wyers, M. Rougemaille, G. Badis, J.C. Rousselle, M.E. Dufour, J. Boulay, B. Regnault, F. Devaux, A. Namane, and B. Seraphin Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase Cell 121 2005 725 737