Differentiating Between Near- and Non-cognate Codons in Saccharomyces Cerevisiae

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2007 Jun 15

PMID 17565370

Citations 42

Authors

Ewan P Plant

Phuc Nguyen

Jonathan R Russ

Yvette R Pittman

Thai Nguyen

Jack T Quesinberry

Terri Goss Kinzy

Jonathan D Dinman

Affiliations

Soon will be listed here.

Abstract

Background: Decoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10(-3) - 10(-4)) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking.

Methodology/principal Findings: Misreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bgamma promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Balpha, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center.

Conclusions/significance: It is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human diseases. This study suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons in the ribosomal decoding center. An aminoglycoside and a ribosomal factor can be used to distinguish between near-cognate and non-cognate interactions.

Citing Articles

Phosphorylation of P-stalk proteins defines the ribosomal state for interaction with auxiliary protein factors.

Filipek K, Blanchet S, Molestak E, Zaciura M, Wu C, Horbowicz-Drozdzal P EMBO Rep. 2024; 25(12):5478-5506.

PMID: 39468350 PMC: 11624264. DOI: 10.1038/s44319-024-00297-1.

On the response of elongating ribosomes to forces opposing translocation.

Moore P Biophys J. 2024; 123(18):3010-3023.

PMID: 38845199 PMC: 11427781. DOI: 10.1016/j.bpj.2024.05.032.

Loss of Conserved rRNA Modifications in the Peptidyl Transferase Center Leads to Diminished Protein Synthesis and Cell Growth in Budding Yeast.

Leppik M, Pomerants L, Poldes A, Mihkelson P, Remme J, Tamm T Int J Mol Sci. 2024; 25(10).

PMID: 38791231 PMC: 11121408. DOI: 10.3390/ijms25105194.

Human T-cell leukemia virus type 1 uses a specific tRNA isodecoder to prime reverse transcription.

Syu Y, Hatterschide J, Budding C, Tang Y, Musier-Forsyth K RNA. 2024; 30(8):967-976.

PMID: 38684316 PMC: 11251516. DOI: 10.1261/rna.080006.124.

Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation.

Sterrett M, Cureton L, Cohen L, van Hoof A, Khoshnevis S, Fasken M bioRxiv. 2023; .

PMID: 37904946 PMC: 10614903. DOI: 10.1101/2023.10.18.562946.

References

Tumer N, Parikh B, Li P, Dinman J . The pokeweed antiviral protein specifically inhibits Ty1-directed +1 ribosomal frameshifting and retrotransposition in Saccharomyces cerevisiae. J Virol. 1998; 72(2):1036-42. PMC: 124575. DOI: 10.1128/JVI.72.2.1036-1042.1998. View

Hani J, Feldmann H . tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 1998; 26(3):689-96. PMC: 147333. DOI: 10.1093/nar/26.3.689. View

Bouadloun F, Donner D, Kurland C . Codon-specific missense errors in vivo. EMBO J. 1983; 2(8):1351-6. PMC: 555282. DOI: 10.1002/j.1460-2075.1983.tb01591.x. View

Carter A, Clemons W, Brodersen D, Morgan-Warren R, Wimberly B, Ramakrishnan V . Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000; 407(6802):340-8. DOI: 10.1038/35030019. View

Ogle J, Brodersen D, Clemons Jr W, Tarry M, Carter A, Ramakrishnan V . Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 2001; 292(5518):897-902. DOI: 10.1126/science.1060612. View

Andersen G, Valente L, Pedersen L, Kinzy T, Nyborg J . Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex. Nat Struct Biol. 2001; 8(6):531-4. DOI: 10.1038/88598. View

Meskauskas A, Dinman J . Ribosomal protein L5 helps anchor peptidyl-tRNA to the P-site in Saccharomyces cerevisiae. RNA. 2001; 7(8):1084-96. PMC: 1307509. DOI: 10.1017/s1355838201001480. View

Andersen G, Pedersen L, Valente L, Chatterjee I, Kinzy T, Kjeldgaard M . Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha. Mol Cell. 2000; 6(5):1261-6. DOI: 10.1016/s1097-2765(00)00122-2. View

Ogle J, Murphy F, Tarry M, Ramakrishnan V . Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell. 2002; 111(5):721-32. DOI: 10.1016/s0092-8674(02)01086-3. View

10.

Anand M, Chakraburtty K, Marton M, Hinnebusch A, Kinzy T . Functional interactions between yeast translation eukaryotic elongation factor (eEF) 1A and eEF3. J Biol Chem. 2002; 278(9):6985-91. DOI: 10.1074/jbc.M209224200. View

11.

Stansfield I, Jones K, Herbert P, Lewendon A, Shaw W, Tuite M . Missense translation errors in Saccharomyces cerevisiae. J Mol Biol. 1998; 282(1):13-24. DOI: 10.1006/jmbi.1998.1976. View

12.

Carr-Schmid A, Valente L, Loik V, Williams T, Starita L, Kinzy T . Mutations in elongation factor 1beta, a guanine nucleotide exchange factor, enhance translational fidelity. Mol Cell Biol. 1999; 19(8):5257-66. PMC: 84369. DOI: 10.1128/MCB.19.8.5257. View

13.

Carr-Schmid A, Durko N, Cavallius J, Merrick W, Kinzy T . Mutations in a GTP-binding motif of eukaryotic elongation factor 1A reduce both translational fidelity and the requirement for nucleotide exchange. J Biol Chem. 1999; 274(42):30297-302. DOI: 10.1074/jbc.274.42.30297. View

14.

Jacobs J, Dinman J . Systematic analysis of bicistronic reporter assay data. Nucleic Acids Res. 2004; 32(20):e160. PMC: 534638. DOI: 10.1093/nar/gnh157. View

15.

Rodnina M, Gromadski K, Kothe U, Wieden H . Recognition and selection of tRNA in translation. FEBS Lett. 2005; 579(4):938-42. DOI: 10.1016/j.febslet.2004.11.048. View

16.

Salas-Marco J, Bedwell D . Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol. 2005; 348(4):801-15. DOI: 10.1016/j.jmb.2005.03.025. View

17.

Ogle J, Ramakrishnan V . Structural insights into translational fidelity. Annu Rev Biochem. 2005; 74:129-77. DOI: 10.1146/annurev.biochem.74.061903.155440. View

18.

Lim V, Curran J, Garber M . Ribosomal elongation cycle: energetic, kinetic and stereochemical aspects. J Mol Biol. 2005; 351(3):470-80. DOI: 10.1016/j.jmb.2005.06.019. View

19.

Cochella L, Green R . Fidelity in protein synthesis. Curr Biol. 2005; 15(14):R536-40. DOI: 10.1016/j.cub.2005.07.018. View

20.

Gromadski K, Daviter T, Rodnina M . A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell. 2006; 21(3):369-77. DOI: 10.1016/j.molcel.2005.12.018. View