Home LiteratureArticle Details
PMID: 8516288 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

On the directional specificity of ribosome frameshifting at a "hungry" codon.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 90 ·No. 12 ·1993-06-15 ·Pages 5469-73

Lindsley D, Gallant J

Abstract

Limitation for aminoacyl-tRNA promotes ribosome frameshifting at certain sites. We have previously demonstrated ribosome frameshifting to the right (3') at an AAG site in one context, and to the left (5') at an AAG site in a different context. Here, we demonstrate that the "rightwing" context is largely specific for frameshifting to the right, and the "leftwing" context is largely specific for frameshifting to the left. Analysis of these context rules, and the conversion of a sequence that promotes leftward frameshifting to one that promotes rightward frameshifting, demonstrated here, permits us to define a minimal heptanucleotide sequence sufficient for shiftiness in each direction at an AAG codon whose lysyl-tRNA is in short supply.

Related Genes
gag lacZ pol
MeSH Terms
Amino Acid Sequence Base Sequence Codon/genetics Escherichia coli/enzymology,genetics Frameshift Mutation Gene Deletion Genes, Bacterial Kinetics Molecular Sequence Data Oligodeoxyribonucleotides RNA, Transfer, Amino Acyl/genetics Ribosomes/metabolism beta-Galactosidase/biosynthesis,genetics
Chemicals
Codon Oligodeoxyribonucleotides RNA, Transfer, Amino Acyl beta-Galactosidase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lindsley D
Department of Genetics, University of Washington, Seattle 98195.
Gallant J
References (69)
69 references, click to expand
  1. E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent.
    New Biol. 1989 Nov;1(2):159-69 PMID: 2562219
  2. The CDC25 protein of Saccharomyces cerevisiae promotes exchange of guanine nucleotides bound to ras.
    Mol Cell Biol. 1991 May;11(5):2641-6 PMID: 2017169
  3. Pheromone response elements are necessary and sufficient for basal and pheromone-induced transcription of the FUS1 gene of Saccharomyces cerevisiae.
    Mol Cell Biol. 1991 Jun;11(6):2952-61 PMID: 1903837
  4. Frameshifting in gene 10 of bacteriophage T7.
    J Bacteriol. 1991 Nov;173(21):6998-7003 PMID: 1938901
  5. FUS3 represses CLN1 and CLN2 and in concert with KSS1 promotes signal transduction.
    Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9392-6 PMID: 1946350
  6. The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting.
    Proc Natl Acad Sci U S A. 1990 May;87(10):3713-7 PMID: 2187190
  7. The where, what and how of ribosomal frameshifting in retroviral protein synthesis.
    Trends Biochem Sci. 1990 May;15(5):186-90 PMID: 2193436
  8. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site.
    Cell. 1990 Jul 27;62(2):339-52 PMID: 2164889
  9. Ribosome gymnastics--degree of difficulty 9.5, style 10.0.
    Cell. 1990 Aug 10;62(3):413-23 PMID: 2199062
  10. Rapid intracellular alkalinization of Saccharomyces cerevisiae MATa cells in response to alpha-factor requires the CDC25 gene product.
    Cell Signal. 1989;1(6):577-86 PMID: 2561949
  11. Low activity of -galactosidase in frameshift mutants of Escherichia coli.
    Proc Natl Acad Sci U S A. 1972 May;69(5):1192-5 PMID: 4556457
  12. Mutations affecting sexual conjugation and related processes in Saccharomyces cerevisiae. II. Genetic analysis of nonmating mutants.
    Genetics. 1974 Feb;76(2):273-88 PMID: 4595644
  13. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  14. Sterile host yeasts (SHY): a eukaryotic system of biological containment for recombinant DNA experiments.
    Gene. 1979 Dec;8(1):17-24 PMID: 395030
  15. Signal transduction during pheromone response in yeast.
    Annu Rev Cell Biol. 1991;7:699-728 PMID: 1667085
  16. Analysis of bacteriophage T7 gene 10A and frameshifted 10B proteins.
    Gene Expr. 1991 May;1(2):127-36 PMID: 1820210
  17. Signal transduction in yeast mating: receptors, transcription factors, and the kinase connection.
    Trends Genet. 1991 Nov-Dec;7(11-12):393-8 PMID: 1668192
  18. Signal transduction in Saccharomyces cerevisiae requires tyrosine and threonine phosphorylation of FUS3 and KSS1.
    Genes Dev. 1992 Jul;6(7):1280-92 PMID: 1628831
  19. Constitutive mutants of the protein kinase STE11 activate the yeast pheromone response pathway in the absence of the G protein.
    Genes Dev. 1992 Jul;6(7):1293-304 PMID: 1628832
  20. Order of action of components in the yeast pheromone response pathway revealed with a dominant allele of the STE11 kinase and the multiple phosphorylation of the STE7 kinase.
    Genes Dev. 1992 Jul;6(7):1305-18 PMID: 1628833
  21. Pheromone response in yeast.
    Annu Rev Biochem. 1992;61:1097-129 PMID: 1323233
  22. Context rules of rightward overlapping reading.
    New Biol. 1992 May;4(5):520-6 PMID: 1515416
  23. Frameshifting is required for production of the transposase encoded by insertion sequence 1.
    Proc Natl Acad Sci U S A. 1989 Jun;86(12):4609-13 PMID: 2543983
  24. The yeast STE12 protein binds to the DNA sequence mediating pheromone induction.
    Proc Natl Acad Sci U S A. 1989 Aug;86(15):5703-7 PMID: 2668945
  25. How 'hidden' reading frames are expressed.
    Trends Biochem Sci. 1989 May;14(5):165-7 PMID: 2773038
  26. In vitro reconstitution of cdc25 regulated S. cerevisiae adenylyl cyclase and its kinetic properties.
    EMBO J. 1990 Mar;9(3):641-51 PMID: 2155776
  27. Regulation of the yeast pheromone response pathway by G protein subunits.
    EMBO J. 1990 Mar;9(3):691-6 PMID: 2107073
  28. Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme.
    Proc Natl Acad Sci U S A. 1990 Apr;87(7):2516-20 PMID: 2181440
  29. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame.
    Nucleic Acids Res. 1990 Apr 11;18(7):1725-9 PMID: 2186364
  30. Mutants of Saccharomyces cerevisiae unresponsive to cell division control by polypeptide mating hormone.
    J Cell Biol. 1980 Jun;85(3):811-22 PMID: 6993497
  31. Two differentially regulated mRNAs with different 5' ends encode secreted with intracellular forms of yeast invertase.
    Cell. 1982 Jan;28(1):145-54 PMID: 7039847
  32. Transformation of intact yeast cells treated with alkali cations.
    J Bacteriol. 1983 Jan;153(1):163-8 PMID: 6336730
  33. Control of cell division in Saccharomyces cerevisiae mutants defective in adenylate cyclase and cAMP-dependent protein kinase.
    Exp Cell Res. 1983 Jun;146(1):151-61 PMID: 6305691
  34. Identification of the structural gene and nonsense alleles for adenylate cyclase in Saccharomyces cerevisiae.
    J Bacteriol. 1984 Jan;157(1):277-82 PMID: 6360999
  35. A comprehensive set of sequence analysis programs for the VAX.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95 PMID: 6546423
  36. Identification and comparison of two sequence elements that confer cell-type specific transcription in yeast.
    Nature. 1985 Apr 18-24;314(6012):598-603 PMID: 3887184
  37. Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2.
    Proc Natl Acad Sci U S A. 1985 Jun;82(11):3616-20 PMID: 3889910
  38. Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting.
    Science. 1985 Dec 13;230(4731):1237-42 PMID: 2416054
  39. Frameshift suppression in aminoacyl-tRNA limited cells.
    Genetics. 1986 Apr;112(4):727-39 PMID: 3514372
  40. Characterization of ribosomal frameshift events by protein sequence analysis.
    J Biol Chem. 1986 Jun 5;261(16):7491-500 PMID: 3711097
  41. tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding.
    Proc Natl Acad Sci U S A. 1986 Jul;83(14):5062-6 PMID: 2425361
  42. Random-clone strategy for genomic restriction mapping in yeast.
    Proc Natl Acad Sci U S A. 1986 Oct;83(20):7826-30 PMID: 3463999
  43. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway.
    Cell. 1987 Mar 13;48(5):789-99 PMID: 3545497
  44. Regulation of mating in the cell cycle of Saccharomyces cerevisiae.
    J Cell Biol. 1977 Nov;75(2 Pt 1):355-65 PMID: 400872
  45. CDC25: a component of the RAS-adenylate cyclase pathway in Saccharomyces cerevisiae.
    Science. 1987 Mar 6;235(4793):1218-21 PMID: 3547648
  46. Translational frameshifting: where will it stop?
    Cell. 1987 Jul 3;50(1):1-2 PMID: 3297347
  47. Saccharomyces cerevisiae mutants unresponsive to alpha-factor pheromone: alpha-factor binding and extragenic suppression.
    Mol Cell Biol. 1987 Apr;7(4):1311-9 PMID: 3037311
  48. A yeast operator overlaps an upstream activation site.
    Cell. 1987 Jul 31;50(3):369-77 PMID: 3301002
  49. GPA1, a haploid-specific essential gene, encodes a yeast homolog of mammalian G protein which may be involved in mating factor signal transduction.
    Cell. 1987 Sep 25;50(7):1011-9 PMID: 3113739
  50. The activation of adenylate cyclase by guanyl nucleotides in Saccharomyces cerevisiae is controlled by the CDC25 start gene product.
    Mol Cell Biol. 1987 Oct;7(10):3857-61 PMID: 3119992
  51. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli.
    Gene. 1987;57(2-3):267-72 PMID: 3319781
  52. An efficient ribosomal frame-shifting signal in the polymerase-encoding region of the coronavirus IBV.
    EMBO J. 1987 Dec 1;6(12):3779-85 PMID: 3428275
  53. a1 protein alters the DNA binding specificity of alpha 2 repressor.
    Cell. 1988 Mar 25;52(6):875-82 PMID: 3127056
  54. Yeast STE7, STE11, and STE12 genes are required for expression of cell-type-specific genes.
    Mol Cell Biol. 1988 Feb;8(2):551-6 PMID: 3280969
  55. Clones from two different genomic regions complement the cdc25 start mutation of Saccharomyces cerevisiae.
    Curr Genet. 1986;10(9):643-6 PMID: 3329039
  56. Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting.
    Cold Spring Harb Symp Quant Biol. 1987;52:687-93 PMID: 3135981
  57. Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon.
    Proc Natl Acad Sci U S A. 1988 Sep;85(18):6816-20 PMID: 2842793
  58. How eukaryotic transcriptional activators work.
    Nature. 1988 Oct 20;335(6192):683-9 PMID: 3050531
  59. Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region.
    Cell. 1988 Nov 4;55(3):447-58 PMID: 2846182
  60. On the mechanism of ribosomal frameshifting at hungry codons.
    J Mol Biol. 1988 Sep 20;203(2):403-10 PMID: 3199440
  61. HIV expression strategies: ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems.
    Cell. 1988 Dec 23;55(6):1159-69 PMID: 3060262
  62. The STE4 and STE18 genes of yeast encode potential beta and gamma subunits of the mating factor receptor-coupled G protein.
    Cell. 1989 Feb 10;56(3):467-77 PMID: 2536595
  63. Constitutive mutants in the yeast pheromone response: ordered function of the gene products.
    Cell. 1989 Feb 10;56(3):479-86 PMID: 2644047
  64. Role of STE genes in the mating factor signaling pathway mediated by GPA1 in Saccharomyces cerevisiae.
    Mol Cell Biol. 1988 Sep;8(9):3777-83 PMID: 3065623
  65. 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
  66. RNA pseudoknots: translational frameshifting and readthrough on viral RNAs.
    Virus Genes. 1990 Jul;4(2):121-36 PMID: 2402881
  67. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  68. Identification of a gene necessary for cell cycle arrest by a negative growth factor of yeast: FAR1 is an inhibitor of a G1 cyclin, CLN2.
    Cell. 1990 Nov 30;63(5):999-1011 PMID: 2147873
  69. Mapping yeast genes.
    Methods Enzymol. 1991;194:38-57 PMID: 2005798
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.90.12.5469
Published
1993-06-15
Pages
5469-73
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC46742
Subset
IM
Grants
NIGMS NIH HHS · GM13626 · United States
External Links
PubMed source DOI: 10.1073/pnas.90.12.5469 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: [email protected]

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