Dim2p, a KH-domain protein required for small ribosomal subunit synthesis

RNA

Volumn 10, Issue 4, 2004, Pages 645-656

  Vanrobays, Emmanuel ^a,b   Gélugne, Jean Paul ^b   Caizergues Ferrer, Michéle ^b   Lafontaine, Denis L J ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b Université Paul Sabatier   (France)

Author keywords

KH domain; Nucleolus; Pre rRNA processing; Ribosome synthesis

Indexed keywords

DNA DIRECTED RNA POLYMERASE; KH DOMAIN PROTEIN; METHYLTRANSFERASE; PROTEIN; PROTEIN DIM2P; RIBOSOME PROTEIN; RIBOSOME RNA; RNA 18S; SMALL SUBUNIT RIBOSOMAL RNA; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; BIOGENESIS; COMPLEX FORMATION; DEMETHYLATION; GENETIC CONSERVATION; GROWTH REGULATION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; PROTEOMICS; RIBOSOME SUBUNIT; RNA CLEAVAGE; RNA PROCESSING; RNA SYNTHESIS;

CELL NUCLEOLUS; CYTOPLASM; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL, 18S; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; YEASTS;

EID: 1642447091     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5162204     Document Type: Article

References (57)

1. Adinolfi, S., Bagni, C., Castiglione Morelli, M.A., Fraternali, F., Musco, G., and Pastore, A. 1999. Novel RNA-binding motif: The KH module. Biopolymers 51: 153-164.
2. Allmang, C., Mitchell, P., Petfalski, E., and Tollervey, D. 2000. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28: 1684-1691.
3. Burd, C.G. and Dreyfuss, G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265: 615-621.
4. Chan, H.Y., Brogna, S., and O'Kane, C.J. 2001. Dribble, the Drosophila KRR1p homologue, is involved in rRNA processing. Mol. Biol. Cell. 12: 1409-1419.
5. Chen, W., Bucaria, J., Band, D.A., Sutton, A., and Sternglanz, R. 2003. Enp1, a yeast protein associated with U3 and U14 snoRNAs, is required for pre-rRNA processing and 40S subunit synthesis. Nucleic Acids Res. 31: 690-699.
6. De Boulle, K., Verkerk, A.J., Reyniers, E., Vits, L., Hendrickx, J., Van Roy, B., Van den Bos, F., de Graaff, E., Oostra, B.A., and Willems, P.J. 1993. A point mutation in the FMR-1 gene associated with fragile X mental retardation. Nat. Genet. 3: 31-35.
7. Dragon, F., Gallagher, J.E., Compagnone-Post, P.A., Mitchell, B.M., Porwancher, K.A., Wehner, K.A., Wormsley, S., Settlage, R.E., Shabanowitz, J., Osheim, Y., et al. 2002. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417: 967-970.
8. Fatica, A. and Tollervey, D. 2002. Making ribosomes. Curr. Opin. Cell Biol. 14: 313-318.
9. Fatica, A., Oeffinger, M., Dlakic, M., and Tollervey, D. 2003. Nob1p is required for cleavage of the 3′ end of 18S rRNA. Mol. Cell. Biol. 23: 1798-1807.
10. Gadal, O., Strauss, D., Braspenning, J., Hoepfner, D., Petfalski, E., Philippsen, P., Tollervey, D., and Hurt, E. 2001. A nuclear AAA-type ATPase (Rix7p) is required for biogenesis and nuclear export of 60S ribosomal subunits. EMBO J. 20: 3695-3704.
11. Gadal, O., Strauss, D., Petfalski, E., Gleizes, P.E., Gas, N., Tollervey, D., and Hurt, E. 2002. Rlp7p is associated with 60S preribosomes, restricted to the granular component of the nucleolus, and required for pre-rRNA processing. J. Cell. Biol. 157: 941-951.
12. Ganot, P., Caizergues-Ferrer, M., and Kiss, T. 1997. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 11: 941-956.
13. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
14. Gelperin, D., Horton, L., Beckman, J., Hensold, J., and Lemmon, S.K. 2001. Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40S ribosome biogenesis in yeast. RNA 7: 1268-1283.
15. Gibson, T.J., Rice, P.M., Thompson, J.D., and Heringa, J. 1993a. KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism. Trends Biochem. Sci. 18: 331-333.
16. Gibson, T.J., Thompson, J.D., and Heringa, J. 1993b. The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. FEBS Lett. 324: 361-366.
17. Grandi, P., Rybin, V., Bassler, J., Petfalski, E., Strauss, D., Marzioch, M., Schafer, T., Kuster, B., Tschochner, H., Tollervey, D., et al. 2002. 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Mol. Cell 10: 105-115.
18. Grava, S., Dumoulin, P., Madania, A., Tarassov, I., and Winsor, B. 2000. Functional analysis of six genes from chromosomes XIV and XV of Saccharomyces cerevisiae reveals YOR145c as an essential gene and YNL059c/ARP5 as a strain-dependent essential gene encoding nuclear proteins. Yeast 16: 1025-1033.
19. Grishin, N.V. 2001. KH domain: One motif, two folds. Nucleic Acids Res. 29: 638-643.
20. Henry, Y., Wood, H., Morrissey, J.P., Petfalski, E., Kearsey, S., and Tollervey, D. 1994. The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J. 13: 2452-2463.
21. Herman, P.K. 2002. Stationary phase in yeast. Curr. Opin. Microbiol. 5: 602-607.
22. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
23. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31: 370-377.
24. Irie, K., Tadauchi, T., Takizawa, P.A., Vale, R.D., Matsumoto, K., and Herskowitz, I. 2002. The Khd1 protein, which has three KH RNA-binding motifs, is required for proper localization of ASH1 mRNA in yeast. EMBO J. 21: 1158-1167.
25. Kiledjian, M., Wang, X., and Liebhaber, S.A. 1995. Identification of two KH domain proteins in the α-globin mRNP stability complex. EMBO J. 14: 4357-4364.
26. Kiss, T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145-148.
27. Kong, J., Ji, X., and Liebhaber, S.A. 2003. The KH-domain protein α CP has a direct role in mRNA stabilization independent of its cognate binding site. Mol. Cell Biol. 23: 1125-1134.
28. Kressler, D., Linder, P., and de la Cruz, J. 1999. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 19: 7897-7912.
29. Lafontaine, D.L.J. 2004. Eukaryotic ribosome synthesis. In Protein synthesis and ribosome structure (ed. K. Nierhaus). Wiley-InterScience (in press).
30. Lafontaine, D.L.J. and Tollervey, D. 2001. The function and synthesis of ribosomes. Nat. Rev. Mol. Cell. Biol. 2: 514-520.
31. Lafontaine, D., Vandenhaute, J., and Tollervey, D. 1995. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev. 9: 2470-2481.
32. Lafontaine, D.L.J., Preiss, T., and Tollervey, D. 1998. Yeast 18S rRNA dimethylase Dim1p: A quality control mechanism in ribosome synthesis? Mol. Cell. Biol. 18: 2360-2370.
33. Liu, P.C. and Thiele, D.J. 2001. Novel stress-responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis. Mol. Biol. Cell. 12: 3644-3657.
34. Milkereit, P., Gadal, O., Podtelejnikov, A., Trumtel, S., Gas, N., Petfalski, E., Tollervey, D., Mann, M., Hurt, E., and Tschochner, H. 2001. Maturation and intranuclear transport of pre-ribosomes requires noc proteins. Cell 105: 499-509.
35. Oldenburg, K.R., Vo, K.T., Michaelis, S., and Paddon, C. 1997. Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 25: 451-452.
36. Oleynikov, Y. and Singer, R.H. 2003. Real-time visualization of ZBP1 association with β-actin mRNA during transcription and localization. Curr. Biol. 13: 199-207.
37. Ostareck-Lederer, A., Ostareck, D.H., and Hentze, M.W. 1998. Cytoplasmic regulatory functions of the KH-domain proteins hnRNPs K and E1/E2. Trends Biochem. Sci. 23: 409-411.
38. Peng, W.T., Robinson, M.D., Mnaimneh, S., Krogan, N.J., Cagney, G., Morris, Q., Davierwala, A.P., Grigull, J., Yang, X., Zhang, W., et al. 2003. A panoramic view of yeast noncoding RNA processing. Cell 113: 919-933.
39. Raue, H.A. 2003. Pre-ribosomal RNA processing and assembly in Saccharomyces cerevisiae. In The nucleolus (ed. M.O. Olson). http://www.eurekah.com.
40. Sasaki, T., Toh, E.A., and Kikuchi, Y. 2000. Yeast Krr1p physically and functionally interacts with a novel essential Kri1p, and both proteins are required for 40S ribosome biogenesis in the nucleolus. Mol. Cell. Biol. 20: 7971-7979.
41. Schafer, T., Strauss, D., Petfalski, E., Tollervey, D., and Hurt, E. 2003. The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes. EMBO J. 22: 1370-1380.
42. Senapin, S., Clark-Walker, G.D., Chen, X.J., Seraphin, B., and Daugeron, M.C. 2003. RRP20, a component of the 90S preribosome, is required for pre-18S rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res. 31: 2524-2533.
43. Siomi, H., Matunis, M.J., Michael, W.M., and Dreyfuss, G. 1993. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res. 21: 1193-1198.
44. Siomi, H., Choi, M., Siomi, M.C., Nussbaum, R.L., and Dreyfuss, G. 1994. Essential role for KH domains in RNA binding: Impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome. Cell 77: 33-39.
45. Tabb, A.L., Utsugi, T., Wooten-Kee, C.R., Sasaki, T., Edling, S.A., Gump, W., Kikuchi, Y., and Ellis, S.R. 2001. Genes encoding ribosomal proteins Rps0A/B of Saccharomyces cerevisiae interact with TOM1 mutants defective in ribosome synthesis. Genetics 157: 1107-1116.
46. Tollervey, D. 1987. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J. 6: 4169-4175.
47. Tollervey, D., Lehtonen, H., Carmo-Fonseca, M., and Hurt, E.C. 1991. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 10: 573-583.
48. Tone, Y. and Toh, E.A. 2002. Nob1p is required for biogenesis of the 26S proteasome and degraded upon its maturation in Saccharomyces cerevisiae. Genes Dev. 16: 3142-3157.
49. Tone, Y., Tanahashi, N., Tanaka, K., Fujimuro, M., Yokosawa, H., and Toh-e, A. 2000. Nob1p, a new essential protein, associates with the 26S proteasome of growing Saccharomyces cerevisiae cells. Gene 243: 37-45.
50. Trapman, J., Retel, J., and Planta, R.J. 1975. Ribosomal precursor particles from yeast. Exp. Cell. Res. 90: 95-104.
51. Tschochner, H. and Hurt, E. 2003. Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell. Biol. 13: 255-263.
52. Udem, S.A. and Warner, J.R. 1973. The cytoplasmic maturation of a ribosomal precursor ribonucleic acid in yeast. J. Biol. Chem. 248: 1412-1416.
53. Vanrobays, E., Gleizes, P.E., Bousquet-Antonelli, C., Noaillac-Depeyre, J., Caizergues-Ferrer, M., and Gelugne, J.P. 2001. Processing of 20S pre-rRNA to 18S ribosomal RNA in yeast requires Rrp10p, an essential non-ribosomal cytoplasmic protein. EMBO J. 20: 4204-4213.
54. Vanrobays, E., Gelugne, J.P., Gleizes, P.E. and Caizergues-Ferrer, M. 2003. Late Cytoplasmic maturation of the small ribosomal subunit requires RIO proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 23: 2083-2095.
55. Vazquez, A., Flammini, A., Maritan, A., and Vespignani, A. 2003. Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21: 697-700.
56. Venema, J. and Tollervey, D. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Ann. Rev. Genet. 33: 261-311.
57. Wegierski, T., Billy, E., Nasr, F., and Filipowicz, W. 2001. Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast. RNA 7: 1254-1267.