NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47

Nucleic Acids Research

Volumn 34, Issue 16, 2006, Pages 4593-4608

  Sekiguchi, Takeshi ^a   Hayano, Toshiya ^b   Yanagida, Mitsuaki ^b   Takahashi, Nobuhiro ^b   Nishimoto, Takeharu ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DEAD BOX PROTEIN; NUCLEAR PROTEIN; RIBOSOME RNA; RNA HELICASE; RNA PRECURSOR; SMALL INTERFERING RNA;

ANIMAL CELL; ARTICLE; BIOGENESIS; CELLULAR DISTRIBUTION; CONTROLLED STUDY; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MASS SPECTROMETRY; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RIBOSOME; RNA METABOLISM; RNA PROCESSING; RNA TRANSCRIPTION; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; CARRIER PROTEINS; CELL NUCLEOLUS; DEAD-BOX RNA HELICASES; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROTEIN BINDING; RIBOSOMES; RNA HELICASES; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL;

EID: 33750017647     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl603     Document Type: Article

References (51)

1. Granneman,S. and Baserga,S.J. (2004) Ribosome biogenesis: Of knobs and RNA processing. Exp. Cell Res., 296, 43-50.
2. Fromont-Racine,M., Senger,B., Saveanu,C. and Fasiolo,F. (2003) Ribosome assembly in eukaryotes. Gene, 313, 17-42.
3. Venema,J. and Tollervey,D. (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu. Rev. Genet., 33, 261-311.
4. Takahashi,N., Yanagida,M., Fujiyama,S., Hayano,T. and Isobe,T. (2003) Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells. Mass Spectrom Rev., 22, 287-317.
5. Nishimoto,T. (2000) Upstream and downstream of ran GTPase. Biol. Chem., 381, 397-405.
6. Sazer,S. and Dasso,M. (2000) The ran decathlon: Multiple roles of Ran. J. Cell Sci., 113, 1111-1118.
7. Shiomi,T., Fukushima,K., Suzuki,N., Nakashima,N., Noguchi,E. and Nishimoto,T. (1998) Human dis3p, which binds to either GTP- or GDP-Ran, complements Saccharomyces cerevisiae dis3. J. Biochem. (Tokyo), 123, 883-890.
8. Noguchi,E., Hayashi,N., Azuma,Y., Seki,T., Nakamura,M., Nakashima,N., Yanagida,M., He,X., Mueller,U., Sazer,S. et al. (1996) Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J., 15, 5595-5605.
9. Suzuki,N., Noguchi,E., Nakashima,N., Oki,M., Ohba,T., Tartakoff,A., Ohishi,M. and Nishimoto,T. (2001) The Saccharomyces cerevisiae small GTPase, Gsp1p/Ran, is involved in 3′ processing of 7S-to-5.8S rRNA and in degradation of the excised 5′-A0 fragment of 35S pre-rRNA, both of which are carried out by the exosome. Genetics, 158, 613-625.
10. Nakashima,N., Hayashi,N., Noguchi,E. and Nishimoto,T. (1996) Putative GTPase Gtr1p genetically interacts with the RanGTPase cycle in Saccharomyces cerevisiae. J. Cell Sci., 109, 2311-2318.
11. Nakashima,N., Noguchi,E. and Nishimoto,T. (1999) Saccharomyces cerevisiae putative G protein, Gtr1p, which forms complexes with itself and a novel protein designated as Gtr2p, negatively regulates the Ran/ Gsp1p G protein cycle through Gtr2p. Genetics, 152, 853-867.
12. Huang,J., Zhu,H., Haggarty,S.J., Spring,D.R., Hwang,H., Jin,F., Snyder,M. and Schreiber,S.L. (2004) Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc. Natl Acad. Sci. USA, 101, 16594-16599.
13. Dubouloz,F., Deloche,O., Wanke,V., Cameroni,E. and De Virgilio,C. (2005) The TOR and EGO protein complexes orchestrate microautophagy in yeast. Mol. Cell, 19, 15-26.
14. Todaka,Y., Wang,Y., Tashiro,K., Nakashima,N., Nishimoto,T. and Sekiguchi,T. (2005) Association of the GTP-binding protein Gtr1p with Rpc19p, a shared subunit of RNA polymerase I and III in yeast Saccharomyces cerevisiae. Genetics, 170, 1515-1524.
15. Sekiguchi,T., Todaka,Y., Wang,Y., Hirose,E., Nakashima,N. and Nishimoto,T. (2004) A novel human nucleolar protein, Nop132, binds to the G proteins, RRAG A/C/D. J. Biol. Chem., 279, 8343-8350.
16. Zanchin,N.I. and Goldfarb,D.S. (1999) Nip7p interacts with Nop8p, an essential nucleolar protein required for 60S ribosome biogenesis, and the exosome subunit Rrp43p. Mol. Cell Biol., 19, 1518-1525.
17. Zanchin,N.I., Roberts,P., DeSilva,A., Sherman,F. and Goldfarb,D.S. (1997) Saccharomyces cerevisiae Nip7p is required for efficient 60S ribosome subunit biogenesis. Mol. Cell Biol., 17, 5001-5015.
18. Hirose,E., Nakashima,N., Sekiguchi,T. and Nishimoto,T. (1998) RagA is a functional homologue of S. cerevisiae Gtr1p involved in the Ran/ Gsp1-GTPase pathway. J. Cell Sci., 111, 11-21.
19. Jinawath,N., Furukawa,Y. and Nakamura,Y. (2004) Identification of NOL8, a nucleolar protein containing an RNA recognition motif (RRM), which was overexpressed in diffuse-type gastric cancer. Cancer Sci., 95, 430-435.
20. de la Cruz,J., Kressler,D. and Linder,P. (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem. Sci., 24, 192-198.
21. Abdelhaleem,M., Maltais,L. and Wain,H. (2003) The human DDX and DHX gene families of putative RNA helicases. Genomics, 81, 618-622.
22. Sekiguchi,T., Hirose,E., Nakashima,N., Ii,M. and Nishimoto,T. (2001) Novel G proteins, Rag C and Rag D, interact with GTP-binding proteins, Rag A and Rag B. J. Biol. Chem., 276, 7246-7257.
23. Yanagida,M., Shimamoto,A., Nishikawa,K., Furuichi,Y., Isobe,T. and Takahashi,N. (2001) Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes. Proteomics, 1, 1390-1404.
24. Natsume,T., Yamauchi,Y., Nakayama,H., Shinkawa,T., Yanagida,M., Takahashi,N. and Isobe,T. (2002) A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics. Anal. Chem., 74, 4725-4733.
25. Sekiguchi,T., Nishimoto,T. and Hunter,T. (1999) Overexpression of D-type cyclins, E2F-1, SV40 large T antigen and HPV16 E7 rescue cell cycle arrest of tsBN462 cells caused by the CCG1/TAF(II)250 mutation. Oncogene, 18, 1797-1806.
26. Chien,C.T., Bartel,P.L., Sternglanz,R. and Fields,S. (1991) The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl Acad. Sci. USA, 88, 9578-9582.
27. Elbashir,S.M., Harborth,J., Lendeckel,W., Yalcin,A., Weber,K. and Tuschl,T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
28. Nishitani,H., Sugimoto,N., Roukos,V., Nakanishi,Y., Saijo,M., Obuse,C., Tsurimoto,T., Nakayama,K.I., Nakayama,K., Fujita,M. et al. (2006) Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis. EMBO J., 25, 1126-1136.
29. Sekiguchi,T., Miyata,T. and Nishimoto,T. (1988) Molecular cloning of the cDNA of human X chromosomal gene (CCG1) which complements the temperature-sensitive G1 mutants, tsBN462 and ts13, of the BHK cell line. EMBO J., 7, 1683-1687.
30. Hayano,T., Yanagida,M., Yamauchi,Y., Shinkawa,T., Isobe,T. and Takahashi,N. (2003) Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. J. Biol. Chem., 278, 34309-34319.
31. Dez,C., Froment,C., Noaillac-Depeyre,J., Monsarrat,B., Caizergues-Ferrer,M. and Henry,Y. (2004) Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification. Mol. Cell Biol., 24, 6324-6337.
32. Yanagida,M., Hayano,T., Yamauchi,Y., Shinkawa,T., Natsume,T., Isobe,T. and Takahashi,N. (2004) Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J. Biol. Chem., 279, 1607-1614.
33. Nachury,M.V., Ryder,U.W., Lamond,A.I. and Weis,K. (1998) Cloning and characterization of hSRP1 gamma, a tissue-specific nuclear transport factor. Proc. Natl Acad. Sci. USA, 95, 582-587.
34. Doorbar,J., Elston,R.C., Napthine,S., Raj,K., Medcalf,E., Jackson,D., Coleman,N., Griffin,H.M., Masterson,P., Stacey,S. et al. (2000) The E1E4 protein of human papillomavirus type 16 associates with a putative RNA helicase through sequences in its C terminus. J. Virol., 74, 10081-10095.
35. Andersen,J.S., Lyon,C.E., Fox,A.H., Leung,A.K., Lam,Y.W., Steen,H., Mann,M. and Lamond,A.I. (2002) Directed proteomic analysis of the human nucleolus. Curr. Biol., 12, 1-11.
36. Warner,J.R. (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci., 24, 437-440.
37. Andersen,J.S., Lam,Y.W., Leung,A.K., Ong,S.E., Lyon,C.E., Lamond,A.I. and Mann,M. (2005) Nucleolar proteome dynamics. Nature, 433, 77-83.
38. Marchler-Bauer,A., Anderson,J.B., Cherukuri,P.F., DeWeese-Scott,C., Geer,L.Y., Gwadz,M., He,S., Hurwitz,D.I., Jackson,J.D., Ke,Z. et al. (2005) CDD: A Conserved Domain Database for protein classification. Nucleic Acids Res., 33, D192-196.
39. Burkhard,P., Stetefeld,J. and Strelkov,S.V. (2001) Coiled coils: A highly versatile protein folding motif. Trends Cell Biol., 11, 82-88.
40. O'Day,C.L., Chavanikamannil,F. and Abelson,J. (1996) 18S rRNA processing requires the RNA helicase-like protein Rrp3. Nucleic Acids Res., 24, 3201-3207.
41. Fatica,A., Cronshaw,A.D., Dlakic,M. and Tollervey,D. (2002) Ssf1p prevents premature processing of an early pre-60S ribosomal particle. Mol. Cell, 9, 341-351.
42. Emery,B., de la Cruz,J., Rocak,S., Deloche,O. and Linder,P. (2004) Has1p, a member of the DEAD-box family, is required for 40S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Mol. Microbiol., 52, 141-158.
43. Grandori,C., Mac,J., Siebelt,F., Ayer,D.E. and Eisenman,R.N. (1996) Myc-Max heterodimers activate a DEAD box gene and interact with multiple E box-related sites in vivo. EMBO J., 15, 4344-4357.
44. Winzeler,E.A., Shoemaker,D.D., Astromoff,A., Liang,H., Anderson,K., Andre,B., Bangham,R., Benito,R., Boeke,J.D., Bussey,H. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
45. Thiry,M. and Lafontaine,D.L. (2005) Birth of a nucleolus: The evolution of nucleolar compartments. Trends Cell Biol., 15, 194-199.
46. Opresko,P.L., von Kobbe,C., Laine,J.P., Harrigan,J., Hickson,I.D. and Bohr,V.A. (2002) Telomere-binding protein TRF2 binds to and stimulates the Werner and Bloom syndrome helicases. J. Biol. Chem., 277, 41110-41119.
47. Lillard-Wetherell,K., Machwe,A., Langland,G.T., Combs,K.A., Behbehani,G.K., Schonberg,S.A., German,J., Turchi,J.J., Orren,D.K. and Groden,J. (2004) Association and regulation of the BLM helicase by the telomere proteins TRF1 and TRF2. Hum. Mol. Genet., 13, 1919-1932.
48. Tanner,N.K. and Linder,P. (2001) DExD/H box RNA helicases: From generic motors to specific dissociation functions. Mol. Cell, 8, 251-262.
49. de la Cruz,J., Lacombe,T., Deloche,O., Linder,P. and Kressler,D. (2004) The putative RNA helicase Dbp6p functionally interacts with Rpl3p, Nop8p and the novel trans-acting Factor Rsa3p during biogenesis of 60S ribosomal subunits in Saccharomyces cerevisiae. Genetics, 166, 1687-1699.
50. Daugeron,M.C., Kressler,D. and Linder,P. (2001) Dbp9p, a putative ATP-dependent RNA helicase involved in 60S-ribosomal-subunit biogenesis, functionally interacts with Dbp6p. RNA, 7, 1317-1334.
51. Rosado,I.V. and de la Cruz,J. (2004) Npa1p is an essential trans-acting factor required for an early step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae. RNA, 10, 1073-1083.