Naf1p is a box H/ACA snoRNP assembly factor

RNA

Volumn 8, Issue 12, 2002, Pages 1502-1514

  Fatica, Alessandro ^a   Dlakić, Mensur ^b   Tollervey, David ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

ACA snoRNPs; Box H; snoRNP assembly

Indexed keywords

PROTEIN CBF5P; PROTEIN GAR1P; PROTEIN NAF1P; PROTEIN NHP2P; PROTEIN NOP10P; RNA POLYMERASE II; SMALL NUCLEOLAR RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG; CBF5 PROTEIN, S CEREVISIAE; FUNGAL PROTEIN; GAR1 PROTEIN, S CEREVISIAE; HYDROLYASE; MICROTUBULE ASSOCIATED PROTEIN; NAF1P PROTEIN, FUNGAL; NHP2 PROTEIN, S CEREVISIAE; NUCLEAR PROTEIN; RECOMBINANT PROTEIN; RIBOSOME RNA; RNA BINDING PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEOLAR RNA;

ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; RNA BINDING; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION; AMINO ACID SEQUENCE; BINDING SITE; BIOSYNTHESIS; CELL NUCLEUS; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN MOTIF; RNA PROCESSING; YEAST;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; CELL NUCLEUS; FUNGAL PROTEINS; HYDRO-LYASES; MICROTUBULE-ASSOCIATED PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; RECOMBINANT PROTEINS; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RIBONUCLEOPROTEINS, SMALL NUCLEOLAR; RNA POLYMERASE II; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL; RNA, SMALL NUCLEOLAR; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION, GENETIC; YEASTS;

EID: 0036916733     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (62)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
2. Bagni C, Lapeyre B. 1998. Gar1p binds to the small nucleolar RNAs snR10 and snR30 in vitro through a nontypical RNA binding element. J Biol Chem 273:10868-10873.
3. Barilla D, Lee BA, Proudfoot NJ. 2001. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 16:445-450.
4. Bousquet-Antonelli C, Presutti C, Tollervey D. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765-775.
5. Bowie JU, Luthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170.
6. Brahms H, Meheus L, de Brabandere V, Fischer U, Lührmann R. 2001. Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B′ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7:1531-1542.
7. Buhler D, Raker V, Lührmann R, Fischer U. 1999. Essential role for the tudor domain of SMN in spliceosomal U snRNP assembly: Implications for spinal muscular atrophy. Hum Mol Genet 8:2351-2357.
8. Chanfreau G, Legrain P, Jacquier A. 1998. Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J Mol Biol 248:975-988.
9. Charroux B, Pellizzoni L, Perkinson RA, Shevchenko A, Mann M, Dreyfuss G. 1999. Gemin3: A novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems. J Cell Biol 147:1181-1194.
10. Charroux B, Pellizzoni L, Perkinson RA, Yong J, Shevchenko A, Mann M, Dreyfuss G. 2000. Gemin4. A novel component of the SMN complex that is found in both gems and nucleoli. J Cell Biol 148:1177-1186.
11. Colley A, Beggs JD, Tollervey D, Lafontaine DL. 2000. Dhr1p, a putative DEAH-box RNA helicase, is associated with the box C+D snoRNP U3. Mol Cell Biol 20:7238-7246.
12. Conrad NK, Wilson SM, Steinmetz EJ, Patturajan M, Brow DA, Swanson MS, Corden JL. 2000. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154:557-571.
13. Dragon F, Pogacic V, Filipowicz W. 2000. In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAS. Mol Cell Biol 20:3037-3048.
14. Dunbar DA, Dragon F, Lee SJ, Baserga SJ. 2000. A nucleolar protein related to ribosomal protein L7 is required for an early step in large ribosomal subunit biogenesis. Proc Natl Acad Sci USA 97:13027-13032.
15. Fatica A, Cronshaw AD, Dlakiać M, Tollervey D. 2002. Ssf1p prevents premature processing of an early pre-60S ribosomal particle. Mol Cell 9:341-351.
16. Filipowicz W, Pogacic V. 2002. Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol 14:319-327.
17. Fischer U, Liu Q, Dreyfuss G. 1997. The SMN-SIP1 complex has an essential role in spliceosomal snRNP biogenesis. Cell 90:1023-1029.
18. Friesen WJ, Dreyfuss G. 2000. Specific sequences of the Sm and Sm-like (Lsm) proteins mediate their interaction with the spinal muscular atrophy disease gene product (SMN). J Biol Chem 275:26370-26375.
19. Friesen WJ, Paushkin S, Wyce A, Massenet S, Pesiridis GS, Van Duyne G, Rappsilber J, Mann M, Dreyfuss G. 2001. The methylosome, a 20S complex containing JBP1 and plCln, produces dimethylarginine-modified Sm proteins. Mol Cell Biol 21:8289-8300.
20. Girard JP, Lehtonen H, Caizergues-Ferrer M, Amalric F, Tollervey D, Lapeyre B. 1992. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J 11:673-682.
21. Grandi P, Doyl V, Hurt EC. 1993. Purification of NSP1 reveals complex formation with 'GLFG' nucleporins and a novel nuclear pore protein NIC96. EMBO J 12:3061-3071.
22. Gubitz AK, Mourelatos Z, Abel L, Rappsilber J, Mann M, Dreyfuss G. 2002. Gemin5, a novel WD repeat protein component of the SMN complex that binds Sm proteins. J Biol Chem 277:5631-5636.
23. Henras A, Dez C, Noaillac-Depeyre J, Henry Y, Caizergues-Ferrer M. 2001. Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p. Nucleic Acids Res 29:2733-2746.
24. Henras A, Henry Y, Bousquet-Antonelli C, Noaillac-Depeyre J, Gélugne J-P, Caizergues-Ferrer M. 1998. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J 17:7078-7090.
25. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
26. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactions. Proc Natl Acad Sci USA 98:4569-4574.
27. Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202.
28. Jones DT, Taylor WR, Thornton JM. 1992. A new approach to protein fold recognition. Nature 358:86-89.
29. Jones KW, Gorzynski K, Hales CM, Fischer U, Badbanchi F, Terns RM, Terns MP. 2001. Direct interaction of the spinal muscular atrophy disease protein SMN with the small nucleolar RNA-associated protein fibrillarin. J Biol Chem 276:38645-38651.
30. Kambach C, Walke S, Young R, Avis JM, de la Fortelle E, Raker VA, Lührmann R, Li J, Nagai K. 1999. Crystal structure of two Sm protein complexes and their implications for the assembly of the spliceosomal sn RNPs. Cell 5:375-387.
31. King TH, Decatur WA, Bertrand E, Maxwell ES, Fournier MJ. 2001. A well-connected and conserved nucleoplasmic helicase is required for production of box C/D and H/ACA snoRNAs and localization of snoRNP proteins. Mol Cell Biol 21:7731-7746.
32. Kiss T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109:145-148.
33. Kressler D, Linder P, delaCruz J. 1999. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 19:7897-7912.
34. Lafontaine D, Tollervey D. 1996. One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins. Nucleic Acids Res 24:3469-3472.
35. Lafontaine DLJ, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D. 1998. The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes & Dev 12:527-537.
36. Lafontaine DLJ, Tollervey D. 1999. Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA 5:455-467.
37. Lee JH, Cook JR, Pollack BP, Kinzy TG, Norris D, Pestka S. 2000. Hsp, the yeast homologue of human JBP1, is a protein methyl-transferase. Biochem Biophys Res Commun 274:105-111.
38. Meister G, Bühler D, Pillai R, Lottspeich F, Fischer U. 2001. A multiprotein complex mediates the ATP-dependent assembly of spliceosomal U snRNPs. Nat Cell Biol 3:945-949.
39. Milkereit P, Gadal O, Podtelejnikov A, Trumtel S, Gas N, Petfalski E, Tollervey D, Mann M, Hurt E, Tschochner H. 2001. Maturation and intranuclear transport of pre-ribosomes requires noc proteins. Cell 18:499-509.
40. Morlando M, Greco P, Dichtl B, Fatica A, Keller W, Bozzoni I. 2002. Functional analysis of yeast snoRNA and snRNA 3′-end formation mediated by uncoupling of cleavage and polyadenylation. Mol Cell Biol 22:1379-1389.
41. Morrissey JP, Tollervey D. 1993. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol 13:2469-2477.
42. Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448.
43. Pellizzoni L, Baccon J, Charroux B, Dreyfuss G. 2001a. The survival of motor neurons (SMN) protein interacts with the snoRNP proteins fibrillarin and GAR1. Curr Biol 11:1079-1088.
44. Pellizzoni L, Baccon J, Rappsilber J, Mann M, Dreyfuss G. 2002. Purification of native survival of motor neurons complexes and identification of Gemin6 as a novel component. J Biol Chem 277:7540-7545.
45. Pellizzoni L, Charroux B, Rappsilber J, Mann M, Dreyfuss G. 2001b. A functional interaction between the survival motor neuron complex and RNA polymerase II. J Cell Biol 152:75-85.
46. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol 17:1030-1032.
47. Saveanu C, Bienvenu D, Namane A, Gleizes P, Gas N, Jacquier A, Fromont-Racine M. 2001. Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J 20:6475-6484.
48. Selenko P, Sprangers R, Stier G, Buhler D, Fischer U, Sattler M. 2001. SMN tudor domain structure and its interaction with the Sm proteins. Nat Struct Biol 8:27-31.
49. Steinmetz EJ, Conrad NK, Brow DA, Corden JL. 2001. RNA-binding protein Nrd1 directs poly (A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413:327-331.
50. Terns MP, Terns RM. 2001. Macromolecular complexes: SMN - The master assembler. Curr Biol 11:862-864.
51. Tollervey D. 1987. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J 6:4169-4175.
52. Tollervey D, Kiss T. 1997. Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9:337-342.
53. Torchet C, Bousquet-Antonelli C, Milligan L, Thompson E, Kufel J, Tollervey D. 2002. Processing of 3′ extended read-through transcripts by the exosome can generate functional mRNAs. Mol Cell 9:1285-1296.
54. Upadhyaya AB, Lee SH, DeJong J. 1999. Identification of a general transcription factor TFIIAalpha/beta homolog selectively expressed in testis. J Biol Chem 274:18040-18044.
55. Veenstra GJ, Wolffe AP. 2001. Gene-selective developmental roles of general transcription factors. Trends Biochem Sci 26:665-671.
56. Venema J, Tollervey D. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Ann Rev Gen 33:261-311.
57. Watkins NJ, Gottschalk A, Neubauer G, Kastner B, Fabrizio P, Mann M, Lührmann R. 1998. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA 4:1549-1568.
58. Weinstein LB, Steitz JA. 1999. Guided tours: From precursor snoRNA to functional snoRNP. Curr Opin Cell Biol 11:378-384.
59. Wilson SM, Datar KV, Paddy MR, Swedlow JR, Swanson MS. 1994. Characterization of nuclear polyadenylated RNA-binding proteins in Saccharomyces cerevisiae. J Cell Biol 127:1173-1184.
60. Wootton JC, Federhen S. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554-571.
61. Yong J, Pellizzoni L, Dreyfuss G. 2002. Sequence-specific interaction of U1 snRNA with the SMN complex. EMBO J 21:1188-1196.
62. Yuryev A, Patturajan M, Litingtung Y, Joshi RV, Gentile C, Gebara M, Corden JL. 1996. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc Natl Acad Sci USA 93:6975-6980.