A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae

RNA

Volumn 16, Issue 9, 2010, Pages 1797-1808

  Kramer, Emily B ^a,b   Vallabhaneni, Haritha ^a,c   Mayer, Lauren M ^a   Farabaugh, Philip J ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

Aminoglycoside; Cognate; Dual luciferase; Eukaryotic translation; Mistranslation; Near cognate

Indexed keywords

HISTIDINE; LUCIFERASE; PAROMOMYCIN; STREPTOMYCIN; TRANSFER RNA; ARGININE TRANSFER RNA; CODON; LYSINE TRANSFER RNA;

ARTICLE; CODON; CONTROLLED STUDY; ESCHERICHIA COLI; GENE FREQUENCY; MISSENSE MUTATION; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; DRUG EFFECTS; GENETICS; METABOLISM; PROTEIN SYNTHESIS;

CODON; ESCHERICHIA COLI; MUTATION, MISSENSE; PAROMOMYCIN; PROTEIN BIOSYNTHESIS; RNA, TRANSFER, ARG; RNA, TRANSFER, LYS; SACCHAROMYCES CEREVISIAE;

EID: 77956019364     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2201210     Document Type: Article

References (49)

1. Alksne LE, Anthony RA, Liebman SW, Warner JR. 1993. An accuracy center in the ribosome conserved over 2 billion years. Proc Natl Acad Sci 90: 9538-9541.
2. Belcourt MF, Farabaugh PJ. 1990. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62: 339-352.
3. Benveniste R, Davies J. 1973. Structure-activity relationships among the aminoglycoside antibiotics: Role of hydroxyl and amino groups. Antimicrob Agents Chemother 4: 402-409.
4. Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH. 2007. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol 14: 727-732.
5. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132.
6. Branchini BR, Magyar RA, Murtiashaw MH, Anderson SM, Zimmer M. 1998. Site-directed mutagenesis of histidine 245 in firefly luciferase: A proposed model of the active site. Biochemistry 37: 15311-15319. (Pubitemid 28515991)
7. Branchini BR, Magyar RA, Murtiashaw MH, Anderson SM, Helgerson LC, Zimmer M. 1999. Site-directed mutagenesis of firefly luciferase active site amino acids: A proposed model for bioluminescence color. Biochemistry 38: 13223-13230.
8. Branchini BR, Murtiashaw MH, Magyar RA, Anderson SM. 2000. The role of lysine 529, a conserved residue of the acyl-adenylate-forming enzyme superfamily, in firefly luciferase. Biochemistry 39: 5433-5440.
9. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340-348.
10. Deluca M. 1976. Firefly luciferase. Adv Enzymol Relat Areas Mol Biol 44: 37-68.
11. Gromadski KB, Daviter T, Rodnina MV. 2006. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell 21: 369-377. (Pubitemid 43163532)
12. Grosjean H, DeHenau S, Crothers DM. 1978. On the physical basis for the ambiguity in genetic coding interactions. Proc Natl Acad Sci 75: 610-614.
13. Harger JW, Dinman JD. 2003. An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA 9: 1019-1024.
14. Hendrickson T, Schimmel P. 2003. Transfer RNA-dependent amino acid discrimination by aminoacyl-tRNA synthetases. In Translational mechanisms (ed. J Lapointe, L Brakier-Gingras), pp. 34-64. Kluwer Academic, New York.
15. Hopfield J. 1974. Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci 71: 4135-4139.
16. Ibba M, Soll D. 2000. Aminoacyl-tRNA synthesis. Annu Rev Biochem 69: 617-650.
17. Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrenceof the respective codons in its protein genes. J Mol Biol 146: 1-21.
18. Ikemura T. 1982. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. J Mol Biol 158: 573-597.
19. Ito H, Fukuda Y, Murata K, Kimura A. 1983. Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153: 163-168. (Pubitemid 13119852)
20. Katze JR, Basile B, McCloskey JA. 1982. Queuine, a modified base incorporated post-transcriptionally into eukaryotic transfer RNA: Wide distribution in nature. Science 216: 55-56.
21. Kawakami K, Shafer BK, Garfinkel DJ, Strathern JN, Nakamura Y. 1992. Ty element-induced temperature-sensitive mutations of Saccharomyces cerevisiae. Genetics 131: 821-832.
22. Kawakami K, Pande S, Faiola B, Moore D, Boeke J, Farabaugh P, Strathern J, Nakamura Y, Garfinkel D. 1993. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics 135: 309-320.
23. Kramer EB, Farabaugh PJ. 2007. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 13: 87-96.
24. Kurland C, Hughes D, Ehrenberg M. 1996. Limitations of translational accuracy. In Escherichia coli and Salmonella: Cellular and molecular biology (ed. FC Neidhardt et al.), Vol. 1, pp. 979-1004. ASM Press, Washington, DC.
25. Ninio J. 1975. Kinetic amplification of enzyme discrimination. Biochimie 57: 587-595.
26. Ogle JM, Ramakrishnan V. 2005. Structural insights into translational fidelity. Annu Rev Biochem 74: 129-177.
27. Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721-732.
28. Ogle JM, Carter AP, Ramakrishnan V. 2003. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28: 259-266.
29. Palmer E, Wilhelm JM, Sherman F. 1979. Phenotypic suppression of nonsense mutants in yeast by aminoglycoside antibiotics. Nature 277: 148-150.
30. Pande S, Vimaladithan A, Zhao H, Farabaugh PJ. 1995. Pulling the ribosome out of frame +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell Biol 15: 298-304. (Pubitemid 24379927)
31. Pape T, Wintermeyer W, Rodnina MV. 2000. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nat Struct Biol 7: 104-107.
32. Parker J. 1989. Errors and alternatives in reading the universal genetic code. Microbiol Rev 53: 273-298.
33. Parker J. 1992. Variations in reading the genetic code. In Transfer RNA in protein synthesis (ed. DL Hatfield et al.), pp. 23-85. CRC Press, Boca Raton, FL.
34. Percudani R, Pavesi A, Ottonello S. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol 268: 322-330.
35. Plant EP, Nguyen P, Russ JR, Pittman YR, Nguyen T, Quesinberry JT, Kinzy TG, Dinman JD. 2007. Differentiating between near- and noncognate codons in Saccharomyces cerevisiae. PLoS ONE 2: e517. doi: 10.1371/journal.pone.0000517.
36. Rakwalska M, Rospert S. 2004. The ribosome-bound chaperones RAC and Ssb1/2p are required for accurate translation in Saccharomyces cerevisiae. Mol Cell Biol 24: 9186-9197.
37. Recht MI, Douthwaite S, Puglisi JD. 1999. Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J 18: 3133-3138.
38. Rodnina MV, Gromadski KB, Kothe U, Wieden HJ. 2005. Recognition and selection of tRNA in translation. FEBS Lett 579: 938-942.
39. Salas-Marco J, Bedwell DM. 2005. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol 348: 801-815.
40. Schulman LH. 1991. Recognition of tRNAs by aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol 41: 23-87.
41. Singh A, Ursic D, Davies J. 1979. Phenotypic suppression and misreading in Saccharomyces cerevisiae. Nature 277: 146-148. (Pubitemid 9093810)
42. Soll D. 1990. The accuracy of aminoacylation - ensuring the fidelity of the genetic code. Experientia 46: 1089-1096.
43. Stansfield I, Jones KM, Herbert P, Lewendon A, Shaw WV, Tuite MF. 1998. Missense translation errors in Saccharomyces cerevisiae. J Mol Biol 282: 13-24.
44. Thompson R. 1988. EF-Tu provides an internal kinetic standard for translational accuracy. Trends Biochem Sci 13: 91-93.
45. Thompson RC, Stone PJ. 1977. Proofreading of the codon-anticodon interaction on ribosomes. Proc Natl Acad Sci 74: 198-202.
46. Uhlenbeck OC, Martin FH, Doty P. 1971. Self-complementary oligoribonucleotides: Effects of helix defects and guanylic acid-cytidylic acid base pairs. J Mol Biol 57: 217-229.
47. Ye L, Buck LM, Schaeffer HJ, Leach FR. 1997. Cloning and sequencing of a cDNA for firefly luciferase from Photuris pennsylvanica. Biochim Biophys Acta 1339: 39-52. (Pubitemid 27193311)
48. Youngman EM, He SL, Nikstad LJ, Green R. 2007. Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release. Mol Cell 28: 533-543.
49. Zaher HS, Green R. 2009. Quality control by the ribosome following peptide bond formation. Nature 457: 161-166.