Home LiteratureArticle Details
PMID: 9582098 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

RNA (New York, N.Y.) ·Vol. 4 ·No. 5 ·1998-05-00 ·Pages 566-81

Daugeron MC, Linder P

Abstract

Putative ATP-dependent RNA helicases are ubiquitous, highly conserved proteins that are found in most organisms and they are implicated in all aspects of cellular RNA metabolism. Here we present the functional characterization of the Dbp7 protein, a putative ATP-dependent RNA helicase of the DEAD-box protein family from Saccharomyces cerevisiae. The complete deletion of the DBP7 ORF causes a severe slow-growth phenotype. In addition, the absence of Dbp7p results in a reduced amount of 60S ribosomal subunits and an accumulation of halfmer polysomes. Subsequent analysis of pre-rRNA processing indicates that this 60S ribosomal subunit deficit is due to a strong decrease in the production of 27S and 7S precursor rRNAs, which leads to reduced levels of the mature 25S and 5.8S rRNAs. Noticeably, the overall decrease of the 27S pre-rRNA species is neither associated with the accumulation of preceding precursors nor with the emergence of abnormal processing intermediates, suggesting that these 27S pre-rRNA species are degraded rapidly in the absence of Dbp7p. Finally, an HA epitope-tagged Dbp7 protein is localized in the nucleolus. We propose that Dbp7p is involved in the assembly of the pre-ribosomal particle during the biogenesis of the 60S ribosomal subunit.

MeSH Terms
Amino Acid Sequence Cell Nucleolus/chemistry Cloning, Molecular DEAD-box RNA Helicases Molecular Sequence Data Mutation Open Reading Frames/genetics RNA Helicases RNA Nucleotidyltransferases/analysis,genetics,physiology RNA Precursors/genetics,metabolism RNA Processing, Post-Transcriptional/genetics RNA, Ribosomal/biosynthesis RNA, Ribosomal, 5.8S/biosynthesis Ribosomes/metabolism Saccharomyces cerevisiae/enzymology,genetics,growth & development Saccharomyces cerevisiae Proteins
Chemicals
RNA Precursors RNA, Ribosomal RNA, Ribosomal, 5.8S Saccharomyces cerevisiae Proteins RNA, ribosomal, 25S RNA Nucleotidyltransferases DBP7 protein, S cerevisiae DEAD-box RNA Helicases RNA Helicases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Daugeron M C
Département de Biochimie Médicale, Centre Médical Universitaire, Université de Genève, Geneva, Switzerland. marie-claire.daugeron@medecine.unige.ch
Linder P
References (67)
67 references, click to expand
  1. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3' end formation of 5.8S rRNA in Saccharomyces cerevisiae.
    EMBO J. 1998 Feb 16;17(4):1128-40 PMID: 9463390
  2. Dbp6p is an essential putative ATP-dependent RNA helicase required for 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae.
    Mol Cell Biol. 1998 Apr;18(4):1855-65 PMID: 9528757
  3. D-E-A-D protein family of putative RNA helicases.
    Mol Microbiol. 1992 Feb;6(3):283-91 PMID: 1552844
  4. Effect of initiation factor eIF-5A depletion on protein synthesis and proliferation of Saccharomyces cerevisiae.
    J Biol Chem. 1994 Feb 11;269(6):3934-40 PMID: 8307948
  5. The 5' end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site.
    EMBO J. 1994 May 15;13(10):2452-63 PMID: 7515008
  6. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities.
    Development. 1994 May;120(5):1201-11 PMID: 8026330
  7. The yeast NOP4 gene product is an essential nucleolar protein required for pre-rRNA processing and accumulation of 60S ribosomal subunits.
    EMBO J. 1994 Jul 1;13(13):3127-35 PMID: 8039505
  8. Synthetic lethality with fibrillarin identifies NOP77p, a nucleolar protein required for pre-rRNA processing and modification.
    EMBO J. 1994 Jul 1;13(13):3136-48 PMID: 8039506
  9. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server.
    Trends Biochem Sci. 1994 Jun;19(6):258-60 PMID: 8073505
  10. Processing of eukaryotic ribosomal RNA.
    Prog Nucleic Acid Res Mol Biol. 1994;49:197-239 PMID: 7863007
  11. The nucleolus: an organelle formed by the act of building a ribosome.
    Curr Opin Cell Biol. 1995 Jun;7(3):319-24 PMID: 7662360
  12. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis.
    EMBO J. 1995 Sep 1;14(17):4350-6 PMID: 7556076
  13. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast.
    Genes Dev. 1995 Oct 15;9(20):2470-81 PMID: 7590228
  14. Processing of the yeast pre-rRNA at sites A(2) and A(3) is linked.
    RNA. 1996 Jan;2(1):63-73 PMID: 8846297
  15. The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism.
    Genes Dev. 1996 Feb 15;10(4):502-13 PMID: 8600032
  16. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site.
    Cell. 1996 Apr 5;85(1):115-24 PMID: 8620530
  17. Processing of eukaryotic pre-rRNA: the role of the transcribed spacers.
    Biochem Cell Biol. 1995 Nov-Dec;73(11-12):789-801 PMID: 8721995
  18. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae.
    Yeast. 1995 Dec;11(16):1629-50 PMID: 8720068
  19. 18S rRNA processing requires the RNA helicase-like protein Rrp3.
    Nucleic Acids Res. 1996 Aug 15;24(16):3201-7 PMID: 8774901
  20. RNA turnover: the helicase story unwinds.
    Curr Biol. 1996 Jul 1;6(7):780-2 PMID: 8805288
  21. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast.
    EMBO J. 1996 Oct 15;15(20):5701-14 PMID: 8896463
  22. RNA turnover and the control of mitochondrial gene expression.
    Trends Biochem Sci. 1996 Oct;21(10):392-6 PMID: 8918194
  23. The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA.
    J Biol Chem. 1996 Dec 27;271(52):33261-7 PMID: 8969184
  24. Nop2p is required for pre-rRNA processing and 60S ribosome subunit synthesis in yeast.
    Mol Cell Biol. 1997 Jan;17(1):378-88 PMID: 8972218
  25. Trans-acting factors in ribosome synthesis.
    Exp Cell Res. 1996 Dec 15;229(2):226-32 PMID: 8986602
  26. Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3.
    Mol Cell Biol. 1997 Mar;17(3):1354-65 PMID: 9032262
  27. Ribosomal protein L32 of Saccharomyces cerevisiae influences both the splicing of its own transcript and the processing of rRNA.
    Mol Cell Biol. 1997 Apr;17(4):1959-65 PMID: 9121443
  28. Synthesis of functional eukaryotic ribosomal RNAs in trans: development of a novel in vivo rDNA system for dissecting ribosome biogenesis.
    Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2864-8 PMID: 9096312
  29. Rok1p is a putative RNA helicase required for rRNA processing.
    Mol Cell Biol. 1997 Jun;17(6):3398-407 PMID: 9154839
  30. Improved method for high efficiency transformation of intact yeast cells.
    Nucleic Acids Res. 1992 Mar 25;20(6):1425 PMID: 1561104
  31. The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase.
    EMBO J. 1992 Jun;11(6):2319-26 PMID: 1534753
  32. A putative ATP-dependent RNA helicase involved in Saccharomyces cerevisiae ribosome assembly.
    Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11131-5 PMID: 1454790
  33. Cold-sensitive mutations in Salmonella typhimurium which affect ribosome synthesis.
    J Bacteriol. 1969 Mar;97(3):1298-304 PMID: 4887510
  34. Structure and function of E. coli ribosomes. 8. Cold-sensitive mutants defective in ribosome assembly.
    Proc Natl Acad Sci U S A. 1969 Jun;63(2):384-91 PMID: 4895536
  35. Ribosomal precursor particles from yeast.
    Exp Cell Res. 1975 Jan;90(1):95-104 PMID: 1122947
  36. The course of the assembly of ribosomal subunits in yeast.
    Biochim Biophys Acta. 1978 Feb 16;517(2):378-89 PMID: 626744
  37. One-step gene disruption in yeast.
    Methods Enzymol. 1983;101:202-11 PMID: 6310324
  38. Genomic sequencing.
    Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991-5 PMID: 6326095
  39. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA.
    EMBO J. 1987 Dec 20;6(13):4169-75 PMID: 3327689
  40. Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes.
    Genes Dev. 1988 Feb;2(2):160-72 PMID: 3282992
  41. Birth of the D-E-A-D box.
    Nature. 1989 Jan 12;337(6203):121-2 PMID: 2563148
  42. Elevated recombination rates in transcriptionally active DNA.
    Cell. 1989 Feb 24;56(4):619-30 PMID: 2645056
  43. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites.
    Gene. 1988 Dec 30;74(2):527-34 PMID: 3073106
  44. RNA helicase activity associated with the human p68 protein.
    Nature. 1989 Jun 15;339(6225):562-4 PMID: 2471939
  45. Site-directed mutagenesis by overlap extension using the polymerase chain reaction.
    Gene. 1989 Apr 15;77(1):51-9 PMID: 2744487
  46. Isolation and characterization of yeast ribosomal RNA precursors and preribosomes.
    Methods Enzymol. 1989;180:96-109 PMID: 2693913
  47. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F.
    Mol Cell Biol. 1990 Mar;10(3):1134-44 PMID: 2304461
  48. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae.
    Mol Cell Biol. 1990 Mar;10(3):1145-52 PMID: 2406561
  49. Translation initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46.
    Science. 1990 Mar 2;247(4946):1077-9 PMID: 2408148
  50. Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly.
    J Cell Biol. 1990 Dec;111(6 Pt 1):2261-74 PMID: 2277060
  51. Two interdependent basic domains in nucleoplasmin nuclear targeting sequence: identification of a class of bipartite nuclear targeting sequence.
    Cell. 1991 Feb 8;64(3):615-23 PMID: 1991323
  52. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome.
    Nature. 1991 Feb 7;349(6309):494-9 PMID: 1825134
  53. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast.
    EMBO J. 1991 Mar;10(3):573-83 PMID: 1825809
  54. Immunofluorescence methods for yeast.
    Methods Enzymol. 1991;194:565-602 PMID: 2005809
  55. Assembly of 60S ribosomal subunits is perturbed in temperature-sensitive yeast mutants defective in ribosomal protein L16.
    Mol Cell Biol. 1991 Nov;11(11):5681-92 PMID: 1922070
  56. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis.
    Mol Cell Biol. 1993 Apr;13(4):2469-77 PMID: 8455623
  57. Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits.
    Mol Cell Biol. 1993 May;13(5):2835-45 PMID: 8474444
  58. 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. 1993 Nov;13(11):6789-98 PMID: 8413273
  59. DbpA: a DEAD box protein specifically activated by 23s rRNA.
    EMBO J. 1993 Sep;12(9):3619-26 PMID: 8253085
  60. Beat the clock: paradigms for NTPases in the maintenance of biological fidelity.
    Trends Biochem Sci. 1993 Oct;18(10):381-4 PMID: 8256287
  61. Function and synthesis of small nucleolar RNAs.
    Curr Opin Cell Biol. 1997 Jun;9(3):337-42 PMID: 9159079
  62. The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein.
    Mol Cell Biol. 1997 Jul;17(7):4124-32 PMID: 9199348
  63. Saccharomyces cerevisiae Nip7p is required for efficient 60S ribosome subunit biogenesis.
    Mol Cell Biol. 1997 Sep;17(9):5001-15 PMID: 9271378
  64. Qsr1p, a 60S ribosomal subunit protein, is required for joining of 40S and 60S subunits.
    Mol Cell Biol. 1997 Sep;17(9):5136-45 PMID: 9271391
  65. Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae.
    Yeast. 1997 Sep 15;13(11):1065-75 PMID: 9290211
  66. Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae.
    Mol Cell Biol. 1997 Dec;17(12):7283-94 PMID: 9372960
  67. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases.
    Cell. 1997 Nov 14;91(4):457-66 PMID: 9390555
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1355-8382
DOI
10.1017/s1355838298980190
Email
marie-claire.daugeron@medecine.unige.ch
Published
1998-05-00
Pages
566-81
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC1369640
Subset
IM
External Links
PubMed source DOI: 10.1017/s1355838298980190 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2