Home LiteratureArticle Details
PMID: 17000775 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.

Molecular and cellular biology ·Vol. 26 ·No. 23 ·2006-12-00 ·Pages 8992-9002

Rakauskaite R, Dinman JD

Abstract

Information must be shared and functions coordinated among the spatially distinct functional centers of the ribosome. To address these issues, a yeast-based genetic system enabling generation of stable strains expressing only mutant forms of rRNA was devised. The B1a bridge (helix 38) has been implicated in the subtle modulation of numerous ribosomal functions. Base-specific mutations were introduced into helix 38 at sites affecting the B1a bridge and where it contacts the aminoacyl-tRNA (aa-tRNA) D-loop. Both sets of mutants promoted increased affinities for aa-tRNA but had different effects in their responses to two A-site-specific drugs and on suppression nonsense codons. Structural analyses revealed an arc of nucleotides in 25S rRNA that link the B1a bridge, the peptidyltransferase center, the GTPase-associated center, and the sarcin/ricin loop. We propose that a series of regularly spaced "hinge bases" provide fulcrums around which rigid helices can reorient themselves depending on the occupancy status of the A-site.

MeSH Terms
Base Sequence Codon, Nonsense Escherichia coli/genetics Models, Molecular Mutation Nucleic Acid Conformation Peptidyl Transferases/chemistry,metabolism Plasmids/metabolism RNA, Bacterial/genetics RNA, Fungal/genetics RNA, Ribosomal/chemistry,genetics,metabolism RNA, Transfer/genetics,metabolism RNA, Transfer, Amino Acyl/metabolism Ribosomes/chemistry,genetics,metabolism Saccharomyces cerevisiae/genetics Structure-Activity Relationship
Chemicals
Codon, Nonsense RNA, Bacterial RNA, Fungal RNA, Ribosomal RNA, Transfer, Amino Acyl RNA, ribosomal, 25S RNA, Transfer Peptidyl Transferases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Rakauskaite Rasa
Department of Cell Biology and Molecular Genetics, University of Maryland, 2135 Microbiology Building, College Park, MD 20742, USA.
Dinman Jonathan D
References (42)
42 references, click to expand
  1. Selection of tRNA by the ribosome requires a transition from an open to a closed form.
    Cell. 2002 Nov 27;111(5):721-32 PMID: 12464183
  2. Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae.
    Mol Cell Biol. 2001 Dec;21(24):8264-75 PMID: 11713264
  3. Locking and unlocking of ribosomal motions.
    Cell. 2003 Jul 11;114(1):123-34 PMID: 12859903
  4. Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.
    J Mol Biol. 2003 Jul 25;330(5):1061-75 PMID: 12860128
  5. The economics of ribosome biosynthesis in yeast.
    Trends Biochem Sci. 1999 Nov;24(11):437-40 PMID: 10542411
  6. An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae.
    RNA. 2003 Aug;9(8):1019-24 PMID: 12869712
  7. X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
    Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8682-7 PMID: 12853578
  8. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
    Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9319-23 PMID: 12878726
  9. Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex.
    Mol Cell. 2003 Aug;12(2):321-8 PMID: 14536072
  10. Ribosomal RNA kink-turn motif--a flexible molecular hinge.
    J Biomol Struct Dyn. 2004 Oct;22(2):183-94 PMID: 15317479
  11. Creating ribosomes with an all-RNA 30S subunit P site.
    Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43 PMID: 15308780
  12. Evidence against a direct role for the Upf proteins in frameshifting or nonsense codon readthrough.
    RNA. 2004 Nov;10(11):1721-9 PMID: 15388879
  13. Inhibitors of protein biosynthesis. II. Mode of action of anisomycin.
    J Biol Chem. 1967 Jul 10;242(13):3226-33 PMID: 6027796
  14. Two chromosomal genes required for killing expression in killer strains of Saccharomyces cerevisiae.
    Genetics. 1976 Mar 25;82(3):429-42 PMID: 773743
  15. Electron microscopic heteroduplex analysis of "killer" double-stranded RNA species from yeast.
    Proc Natl Acad Sci U S A. 1978 Sep;75(9):4224-8 PMID: 360211
  16. Transformation of intact yeast cells treated with alkali cations.
    J Bacteriol. 1983 Jan;153(1):163-8 PMID: 6336730
  17. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension.
    Methods Enzymol. 1988;164:481-9 PMID: 2468070
  18. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation.
    Cell. 1989 Sep 8;58(5):857-67 PMID: 2673535
  19. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I.
    Proc Natl Acad Sci U S A. 1991 May 1;88(9):3962-6 PMID: 2023944
  20. An approach for isolation of mutants defective in 35S ribosomal RNA synthesis in Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7026-30 PMID: 1871118
  21. Multifunctional yeast high-copy-number shuttle vectors.
    Gene. 1992 Jan 2;110(1):119-22 PMID: 1544568
  22. Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation.
    J Virol. 1992 Jun;66(6):3669-76 PMID: 1583726
  23. Development and application of an in vivo system to study yeast ribosomal RNA biogenesis and function.
    Yeast. 1995 Feb;11(2):145-56 PMID: 7732724
  24. Interpretation of binding curves obtained with high receptor concentrations: practical aid for computer analysis.
    Mol Pharmacol. 1995 Jun;47(6):1197-203 PMID: 7603460
  25. A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae.
    Yeast. 1997 Jul;13(9):837-48 PMID: 9234672
  26. Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae.
    J Cell Biol. 1998 Oct 5;143(1):23-34 PMID: 9763418
  27. Systematic analysis of bicistronic reporter assay data.
    Nucleic Acids Res. 2004;32(20):e160 PMID: 15561995
  28. Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
    J Mol Biol. 2005 May 27;349(1):47-59 PMID: 15876367
  29. Structural insights into translational fidelity.
    Annu Rev Biochem. 2005;74:129-77 PMID: 15952884
  30. The conserved A-site finger of the 23S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway?
    J Mol Biol. 2005 Oct 14;353(1):116-23 PMID: 16165153
  31. Simulating movement of tRNA into the ribosome during decoding.
    Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15854-9 PMID: 16249344
  32. Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis.
    Mol Cell Biol. 2005 Dec;25(24):10863-74 PMID: 16314511
  33. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.
    Structure. 2006 May;14(5):825-35 PMID: 16698544
  34. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
    Mol Cell. 2006 May 19;22(4):533-43 PMID: 16713583
  35. Identification of an RNA-protein bridge spanning the ribosomal subunit interface.
    Science. 1999 Sep 24;285(5436):2133-6 PMID: 10497132
  36. Relationship between internucleotide linkage geometry and the stability of RNA.
    RNA. 1999 Oct;5(10):1308-25 PMID: 10573122
  37. A ratchet-like inter-subunit reorganization of the ribosome during translocation.
    Nature. 2000 Jul 20;406(6793):318-22 PMID: 10917535
  38. Complete deletion of yeast chromosomal rDNA repeats and integration of a new rDNA repeat: use of rDNA deletion strains for functional analysis of rDNA promoter elements in vivo.
    Nucleic Acids Res. 2000 Sep 15;28(18):3524-34 PMID: 10982872
  39. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.
    Nature. 2000 Sep 21;407(6802):340-8 PMID: 11014183
  40. Genetic interaction between yeast Saccharomyces cerevisiae release factors and the decoding region of 18 S rRNA.
    J Mol Biol. 2001 Jan 26;305(4):715-27 PMID: 11162087
  41. Crystal structure of the ribosome at 5.5 A resolution.
    Science. 2001 May 4;292(5518):883-96 PMID: 11283358
  42. Peptidyl-tRNA regulates the GTPase activity of translation factors.
    Cell. 2003 Jul 11;114(1):113-22 PMID: 12859902
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.01311-06
Published
2006-12-00
Epub
2006-00-25
Pages
8992-9002
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC1636827
Subset
IM
Grants
NIGMS NIH HHS · R01 GM058859 · United States
NIGMS NIH HHS · GM 58859 · United States
External Links
PubMed source DOI: 10.1128/MCB.01311-06 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