Home LiteratureArticle Details
PMID: 19628622 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing.

RNA (New York, N.Y.) ·Vol. 15 ·No. 9 ·2009-09-00 ·Pages 1716-28

Liang XH, Liu Q, Fournier MJ

Abstract

The ribosome decoding center is rich in modified rRNA nucleotides and little is known about their effects. Here, we examine the consequences of systematically deleting eight pseudouridine and 2'-O-methylation modifications in the yeast decoding center. Loss of most modifications individually has no apparent effect on cell growth. However, deletions of 2-3 modifications in the A- and P-site regions can cause (1) reduced growth rates (approximately 15%-50% slower); (2) reduced amino acid incorporation rates (14%-24% slower); and (3) a significant deficiency in free small subunits. Negative and positive interference effects were observed, as well as strong positional influences. Notably, blocking formation of a hypermodified pseudouridine in the P region delays the onset of the final cleavage event in 18S rRNA formation ( approximately 60% slower), suggesting that modification at this site could have an important role in modulating ribosome synthesis.

MeSH Terms
Base Sequence Cell Proliferation Drug Resistance, Fungal/genetics Efficiency Models, Biological Models, Molecular Mutation/physiology Nucleic Acid Conformation Organisms, Genetically Modified Protein Biosynthesis/genetics RNA Precursors/genetics,metabolism RNA Processing, Post-Transcriptional/genetics,physiology RNA, Ribosomal/chemistry,genetics,metabolism RNA, Ribosomal, 18S/chemistry,genetics,metabolism Ribosomes/chemistry,genetics,metabolism Yeasts/genetics,metabolism
Chemicals
RNA Precursors RNA, Ribosomal RNA, Ribosomal, 18S
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Liang Xue-Hai
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA.
Liu Qing
Fournier Maurille J
References (48)
48 references, click to expand
  1. Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.
    Mol Cell Biol. 2008 May;28(10):3151-61 PMID: 18332120
  2. Mapping 2'-O-methyl groups in ribosomal RNA.
    Methods. 2001 Nov;25(3):374-82 PMID: 11860292
  3. Structure of the 70S ribosome complexed with mRNA and tRNA.
    Science. 2006 Sep 29;313(5795):1935-42 PMID: 16959973
  4. rRNA modifications and ribosome function.
    Trends Biochem Sci. 2002 Jul;27(7):344-51 PMID: 12114023
  5. Secondary methylation of yeast ribosomal precursor RNA.
    Eur J Biochem. 1977 May 2;75(1):311-8 PMID: 405217
  6. Identities and phylogenetic comparisons of posttranscriptional modifications in 16 S ribosomal RNA from Haloferax volcanii.
    J Biol Chem. 2000 Aug 11;275(32):24484-9 PMID: 10818097
  7. GCD2, a translational repressor of the GCN4 gene, has a general function in the initiation of protein synthesis in Saccharomyces cerevisiae.
    Mol Cell Biol. 1991 Jun;11(6):3203-16 PMID: 2038326
  8. Involvement of helix 34 of 16 S rRNA in decoding and translocation on the ribosome.
    J Biol Chem. 2006 Nov 17;281(46):35235-44 PMID: 16990269
  9. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography.
    Biochimie. 1995;77(1-2):142-4 PMID: 7599271
  10. U17/snR30 is a ubiquitous snoRNA with two conserved sequence motifs essential for 18S rRNA production.
    Mol Cell Biol. 2004 Feb;24(4):1769-78 PMID: 14749391
  11. A mutation allowing an mRNA secondary structure diminishes translation of Saccharomyces cerevisiae iso-1-cytochrome c.
    Mol Cell Biol. 1985 Aug;5(8):1839-46 PMID: 3018530
  12. Recognition of cognate transfer RNA by the 30S ribosomal subunit.
    Science. 2001 May 4;292(5518):897-902 PMID: 11340196
  13. Crystal structure of the ribosome at 5.5 A resolution.
    Science. 2001 May 4;292(5518):883-96 PMID: 11283358
  14. Ribosomal RNA processing and ribosome biogenesis in eukaryotes.
    IUBMB Life. 2004 Aug;56(8):457-65 PMID: 15545225
  15. 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
  16. Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.
    J Mol Biol. 2008 Feb 22;376(3):645-57 PMID: 18177894
  17. Structural insights into translational fidelity.
    Annu Rev Biochem. 2005;74:129-77 PMID: 15952884
  18. rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity.
    Mol Cell. 2007 Dec 28;28(6):965-77 PMID: 18158895
  19. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D158-62 PMID: 16381836
  20. The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.
    Mol Cell Biol. 2005 Dec;25(23):10352-64 PMID: 16287850
  21. Mutations in 16S ribosomal RNA disrupt antibiotic--RNA interactions.
    EMBO J. 1989 Apr;8(4):1213-6 PMID: 2472961
  22. 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
  23. Identifying effects of snoRNA-guided modifications on the synthesis and function of the yeast ribosome.
    Methods Enzymol. 2007;425:283-316 PMID: 17673089
  24. Plant snoRNA database.
    Nucleic Acids Res. 2003 Jan 1;31(1):432-5 PMID: 12520043
  25. The process of mRNA-tRNA translocation.
    Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19671-8 PMID: 18003906
  26. The bacterial ribosome as a target for antibiotics.
    Nat Rev Microbiol. 2005 Nov;3(11):870-81 PMID: 16261170
  27. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification.
    RNA. 2005 May;11(5):619-45 PMID: 15840815
  28. Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction.
    J Mol Biol. 1999 Feb 12;286(1):33-43 PMID: 9931247
  29. Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center.
    Mol Cell. 2003 Feb;11(2):425-35 PMID: 12620230
  30. Making ribosomes.
    Curr Opin Cell Biol. 2002 Jun;14(3):313-8 PMID: 12067653
  31. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA.
    Cell. 1997 May 16;89(4):565-73 PMID: 9160748
  32. 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
  33. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
    Mol Cell. 2008 Oct 24;32(2):292-9 PMID: 18951096
  34. Base pairing between U3 small nucleolar RNA and the 5' end of 18S rRNA is required for pre-rRNA processing.
    Mol Cell Biol. 1999 Sep;19(9):6012-9 PMID: 10454548
  35. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique.
    Biochemistry. 1993 Sep 21;32(37):9754-62 PMID: 8373778
  36. Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit.
    J Biol Chem. 2008 Sep 19;283(38):26026-36 PMID: 18611858
  37. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs.
    Cell. 1997 May 30;89(5):799-809 PMID: 9182768
  38. Biochemical characterization of the ribosomal decoding site.
    Biochimie. 2006 Aug;88(8):935-41 PMID: 16730404
  39. Identification of essential elements in U14 RNA of Saccharomyces cerevisiae.
    EMBO J. 1990 Dec;9(13):4503-9 PMID: 2265615
  40. Site-directed cross-linking of mRNA analogues to 16S ribosomal RNA; a complete scan of cross-links from all positions between '+1' and '+16' on the mRNA, downstream from the decoding site.
    Nucleic Acids Res. 1993 Jun 25;21(12):2853-9 PMID: 8392709
  41. Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid.
    Biochem J. 1978 Jan 1;169(1):71-7 PMID: 629754
  42. The U14 snoRNA is required for 2'-O-methylation of the pre-18S rRNA in Xenopus oocytes.
    RNA. 1998 Feb;4(2):195-204 PMID: 9570319
  43. The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast.
    J Mol Biol. 1994 Aug 19;241(3):492-7 PMID: 8064863
  44. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA.
    J Mol Biol. 1990 Jan 5;211(1):135-45 PMID: 2405162
  45. RNA-guided nucleotide modification of ribosomal and other RNAs.
    J Biol Chem. 2003 Jan 10;278(2):695-8 PMID: 12431975
  46. The helicase Has1p is required for snoRNA release from pre-rRNA.
    Mol Cell Biol. 2006 Oct;26(20):7437-50 PMID: 16908538
  47. Insights into the decoding mechanism from recent ribosome structures.
    Trends Biochem Sci. 2003 May;28(5):259-66 PMID: 12765838
  48. Structural dynamics of ribosomal RNA during decoding on the ribosome.
    Biochimie. 2002 Aug;84(8):745-54 PMID: 12457562
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.1724409
Published
2009-09-00
Epub
2009-00-23
Pages
1716-28
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC2743053
Subset
IM
Grants
NIGMS NIH HHS · R01 GM019351 · United States
NIGMS NIH HHS · GM19351 · United States
External Links
PubMed source DOI: 10.1261/rna.1724409 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