Dbp7p, a putative ATP-dependent RNA helicase from Saccharomyces cerevisiae, is required for 60S ribosomal subunit assembly

RNA

Volumn 4, Issue 5, 1998, Pages 566-581

  Daugeron, Marie Claire ^a   Linder, Patrick ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

DEAD box protein; Pre rRNA processing; Ribosome biogenesis; Yeast

Indexed keywords

ADENOSINE TRIPHOSPHATE; RNA HELICASE;

ARTICLE; ENZYME ACTIVITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; RIBOSOME; SACCHAROMYCES CEREVISIAE;

AMINO ACID SEQUENCE; CELL NUCLEOLUS; CLONING, MOLECULAR; DEAD-BOX RNA HELICASES; MOLECULAR SEQUENCE DATA; MUTATION; OPEN READING FRAMES; RIBOSOMES; RNA HELICASES; RNA NUCLEOTIDYLTRANSFERASES; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 5.8S; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 0031957283     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298980190     Document Type: Article

References (75)

1. Abou Elela S, Igel H, Ares M Jr. 1996. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell 85:115-124.
2. 3 is linked. RNA 2:63-73.
3. Appel RD, Bairoch A, Hochstrasser DF. 1994. A new generation of information retrieval tools for biologists: The example of the Ex-PASy WWW server. Trends Biochem Sci 19:258-260.
4. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. 1994. Saccharomyces cerevisiae. In: Current protocols in molecular biology. New York: John Wiley & Sons, Inc. pp 13.0.1-13.14.17.
5. Beltrame M, Tollervey D. 1995. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J 14:4350-4356.
6. Bergès T, Petfalski E, Tollervey D, Hurt EC. 1994. Synthetic lethality with fibrillarin identifies NOP77p, a nucleolar protein required for pre-rRNA processing and modification. EMBO J 13:3136-3148.
7. Burgess SM, Guthrie C. 1993. Beat the clock: Paradigms for NTPases in the maintenance of biological fidelity. Trends Biochem Sci 18:381-384.
8. Cantor CR, Schimmel PR. 1980. The conformation of biological macromolecules. In: Biophysical chemistry, part I. San Francisco: W.H. Freeman, pp 287-288.
9. Church GM, Gilbert W. 1984. Genomic sequencing. Proc Natl Acad Sci USA 81:1991-1995.
10. de la Cruz J, Kressler D, Tollervey D, Linder P. 1998. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J 17:1128-1140.
11. Deshmukh M, Tsay YF, Paulovich AG, Woolford JL Jr. 1993. Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits. Mol Cell Biol 13:2835-2845.
12. Eichler DC, Craig N. 1994. Processing of eukaryotic ribosomal RNA. Prog Nucleic Acids Res Mol Biol 49:197-239.
13. Eisinger DP, Dick FA, Trumpower BL 1997. Qrs1p, a 60S ribosomal subunit protein, is required for joining of 40S and 60S subunits. Mol Cell Biol 17:5136-5145.
14. Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. 1993. DbpA: A DEAD box protein specifically activated by 23S rRNA. EMBO J 12:3619-3626.
15. Gietz D, St. Jean A, Woods RA, Schiestl RH. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res 20:1425.
16. Gietz RD, Sugino A. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527-534.
17. Guthrie C, Nashimoto H, Nomura M. 1969. Structure and function of E. coli ribosomes, VIII. Cold-sensitive mutants defective in ribosome assembly. Proc Natl Acad Sci USA 63:384-391.
18. Henry Y, Wood H, Morrissey JP, Petfalski E, Kearsey S, 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.
19. Hirling H, Scheffner M, Restle T, Stahl H. 1989. RNA helicase activity associated with the human p68 protein. Nature 339:562-564.
20. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
21. Hong B, Brockenbrough JS, Wu P, Aris JP. 1997. Nop2p is required for pre-rRNA processing and 60S ribosome subunit synthesis in yeast. Mol Cell Biol 17:378-388.
22. Jacobs Anderson JS, Parker R. 1996. RNA turnover: The helicase story unwinds. Curr Biol 6:780-782.
23. Kaiser C, Michaelis S, Mitchell A. 1994. In: Methods in yeast genetics: A Cold Spring Harbor Laboratory course manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
24. Kang HA, Hershey JW. 1994. Effect of initiation factor eIF-5A depletion on protein synthesis and proliferation of Saccharomyces cerevisiae. J Biol Chem 269:3934-3940.
25. Kim SH, Smith J, Claude A, Lin RJ. 1992. The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase. EMBO J 11:2319-2326.
26. Klootwijk J, Planta RJ. 1989. Isolation and characterization of yeast ribosomal RNA precursors and preribosomes. Methods Enzymol 180:96-109.
27. Kressler D, de la Cruz J, Rojo M, Linder P. 1997. Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 17:7283-7294.
28. Kressler D, de la Cruz J, Rojo M, Linder P. 1998. Dbp6p is an essential putative ATP-dependent RNA helicase required for 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae. Mol Cell Biol 18:1855-1865.
29. Kruiswijk T, Planta RJ, Krop JM. 1978. The course of the assembly of ribosomal subunits in yeast. Biochim Biophys Acta 517:378-389.
30. Lafontaine D, Vandenhaute J, Tollervey D. 1995. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes & Dev 9:2470-2481.
31. Li HV, Zagorski J, Fournier MJ. 1990. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 10:1145-1152.
32. Liang L, Diehl-Jones W, Lasko P. 1994. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development 120:1201-1211.
33. Liang WQ, Clark JA, Fournier MJ. 1997. The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein. Mol Cell Biol 17:4124-4132.
34. Liang WQ, Fournier MJ. 1997. Synthesis of functional eukaryotic ribosomal RNAs in trans: Development of a novel in vivo rDNA system for dissecting ribosome biogenesis. Proc Natl Acad Sci USA 94:2864-2868.
35. Linder P, Lasko PF, Ashburner M, Leroy P, Nielsen PJ, Nishi K, Schnier J, Slonimski PP. 1989. Birth of the D-E-A-D box. Nature 337:121-122.
36. Margossian SP, Butow RA. 1996. RNA turnover and the control of mitochondrial gene expression. Trends Biochem Sci 21:392-396.
37. Mélèse T, Xue Z. 1995. The nucleolus: An organelle formed by the act of building a ribosome. Curr Opin Cell Biol 7:319-324.
38. Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D. 1997. The exosome; a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell 91:457-466.
39. Mitchell P, Petfalski E, Tollervey D. 1996. The 3′ end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes & Dev 10:502-513.
40. Moritz M, Paulovitch AG, Tsay FY, Woolford JL Jr. 1990. Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly. J Cell Biol 111:2261-2274.
41. Moritz M, Pulaski BA, Woolford JL Jr. 1991. Assembly of 60S ribosomal subunits is perturbed in temperature-sensitive yeast mutants defective in ribosomal protein L16. Mol Cell Biol 11:5681-5692.
42. Morrissey JP, Tollervey D. 1993. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol 13:2469-2477.
43. O'Day CL, Chavanikamannil F, Abelson J. 1996a. 18S rRNA processing requires the RNA helicase-like protein Rrp3. Nucleic Acids Res 24:3201-3207.
44. O'Day CL, Dalbadie-McFarland G, Abelson J. 1996b. The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J Biol Chem 271:33261-33267.
45. Pause A, Méthot N, Sonenberg N. 1993. The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis. Mol Cell Biol 13:6789-6798.
46. Pause A, Sonenberg N. 1993. Helicases and RNA unwinding in translation. Curr Opin Struct Biol 3:953-959.
47. Pringle JR, Adams AEM, Drubin DG, Haarer BK. 1991. Immunofluorescence methods for yeast. In: Guthrie C, Fink GR, eds. Guide to yeast genetics and molecular biology. San Diego: Academic Press, Inc. pp 565-602.
48. Ripmaster TL, Vaughn GP, Woolford JL Jr. 1992. A putative ATP-dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly. Proc Natl Acad Sci USA 89:11131-11135.
49. Robbins J, Dilsworth SM, Laskey RA, Dingwall C. 1991. Two inter-dependent basic domains in nucleoplasmin nuclear targeting sequence: Identification of a class of bipartite nuclear targeting sequence. Cell 64:615-623.
50. Rotenberg MO, Moritz M, Woolford JL Jr. 1988. Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes. Genes & Dev 2:160-172.
51. Rothstein RJ. 1983. One-step gene disruption in yeast. Methods Enzymol 101:202-211.
52. Rozen F, Edery I, Meerovitch K, Dever TE, Merrick WC, Sonenberg N. 1990. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol Cell Biol 10:1134-1144.
53. Rymond BC, Rosbash M. 1992. Yeast pre-mRNA splicing. In: Jones EW, Pringle JR, Broach JR, eds. The molecular and cellular biology of the yeast Saccharomyces: Gene expression. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 143-192.
54. Sachs AB, Davis RW. 1990. Translation initiation and ribosomal biogenesis: Involvement of a putative rRNA helicase and RPL46. Science 247:1077-1079.
55. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
56. Schmid SR, Linder P. 1992. D-E-A-D protein family of putative RNA helicases. Mol Microbiol 6:283-292.
57. Schwer B, Guthrie C. 1991. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349:494-499.
58. Sun C, Woolford JJL 1994. The yeast NOP4 gene product is an essential nucleolar protein required for pre-rRNA processing and accumulation of 60S ribosomal subunits. EMBO J 13:3127-3135.
59. Tai PC, Kessler DP, Ingraham J. 1969. Cold-sensitive mutations in Salmonella typhimurium which affect ribosome synthesis. J Bacteriol 97:1298-1304.
60. Thomas BJ, Rothstein R. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619-630.
61. Tollervey D. 1987. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J 6:4169-4175.
62. Tollervey D. 1996. Trans-acting factors in ribosome synthesis. Exp Cell Res 229:226-232.
63. Tollervey D, Kiss T. 1997. Function and synthesis of small nucleolar RNAs. Curr Opin Cell Biol 9:337-342.
64. Tollervey D, Lehtonen H, Carmo-Fonseca M, Hurt EC. 1991. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J 10:573-583.
65. Trapman J, Retèl J, Planta RJ. 1975. Ribosomal precursor particles from yeast. Exp Cell Res 90:95-104.
66. van Nues RW, Venema J, Rientjes JMJ, Dirks-Mulder A, Raué HA. 1995. Processing of eukaryotic pre-rRNA: The role of the transcribed spacers. Biochem Cell Biol 73:789-801.
67. Venema J, Bousquet-Antonelli C, Gelugne JP, Caizergues-Ferrer M, Tollervey D. 1997a. Rok1p is a putative RNA helicase required for rRNA processing. Mol Cell Biol 17:3398-3407.
68. Venema J, Planta RJ, Raué HA. 1997b. In vivo mutational analysis of ribosomal RNA in Saccharomyces cerevisiae. In: Martin R, ed. Protein synthesis: Methods and protocols. Totowa, New Jersey: Humana Press. Forthcoming.
69. Venema J, Tollervey D. 1995. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast 11:1629-1650.
70. Venema J, Tollervey D. 1996. RRPS is required for formation of both 18S and 5.8S rRNA in yeast. EMBO J 15:5701-5714.
71. Vilardell J, Warner JR. 1997. Ribosomal protein L32 of Saccharomyces cerevisiae influences both the splicing of its own transcript and the processing of rRNA. Mol Cell Biol 17:1959-1965.
72. Wach A, Brachat A, Alberti-Segui C, Rebischung C, Philippsen P. 1997. Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae. Yeast 13:1065-1075.
73. Weaver PL, Sun C, Chang TH. 1997. Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3. Mol Cell Biol 17:1354-1365.
74. Woolford JL Jr, Warner JR. 1991. The ribosome and its synthesis. In: Broach JR, Pringle JR, Jones EW, ed. The molecular and cellular biology of the yeast Saccharomyces: Genome dynamics, protein synthesis, and energetics. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 587-626.
75. Zanchin NIT, Roberts P, DeSilva A, Sherman F, Goldfarb DS. 1997. Saccharomyces cerevisiae Nip7p is required for efficient 60S ribosome subunit biogenesis. Mol Cell Biol 17:5001-5015.