Decoding with the A:I wobble pair is inefficient - PubMed (original) (raw)
Decoding with the A:I wobble pair is inefficient
J F Curran. Nucleic Acids Res. 1995.
Free PMC article
Abstract
tRNAs with inosine (I) in the first position read three codons ending in U, C and A. However, A-ending codons read with I are rarely used. In Escherichia coli, CGA/U/C are all read solely by tRNAICGArg. CGU and CGC are very common codons, but CGA is very rare. Three independent in vivo assays show that translation of CGA is relatively inefficient. In the first, nine tandem CGA cause a strong rho-mediated polar effect on expression of a lacZ reporter gene. The inhibition is made more extreme by a mutation in ribosomal protein S12 (rpsL), which indicates that ribosomal binding by tRNAICGArg is slow and/or unstable in the CGA cluster. The second assay, in which codons are substituted for the regulatory UGA of the RF2 frameshift, confirms that aa-tRNA selection is slow and/or unstable at CGA. In the third assay, CGA is found to be a poor 5' context for amber suppression, which suggests that an A:I base pair in the P site can interfere with translation of a codon in the A site. Two possible errors, frameshifting and premature termination by RF2, are not significant causes for inefficiency at CGA. It is concluded that the A:I pair destabilizes codon:anticodon complexes during two successive ribosomal cycles, and it is suggested that these properties contribute to the rare usage of codons read with the A:I base pair.
Similar articles
- Analyses of frameshifting at UUU-pyrimidine sites.
Schwartz R, Curran JF. Schwartz R, et al. Nucleic Acids Res. 1997 May 15;25(10):2005-11. doi: 10.1093/nar/25.10.2005. Nucleic Acids Res. 1997. PMID: 9115369 Free PMC article. - A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy FV 4th, Ranganathan SV, Sarachan KL, Agris PF. Vangaveti S, et al. J Mol Biol. 2020 Feb 14;432(4):913-929. doi: 10.1016/j.jmb.2019.12.016. Epub 2020 Jan 14. J Mol Biol. 2020. PMID: 31945376 Free PMC article. - Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs.
Licznar P, Mejlhede N, Prère MF, Wills N, Gesteland RF, Atkins JF, Fayet O. Licznar P, et al. EMBO J. 2003 Sep 15;22(18):4770-8. doi: 10.1093/emboj/cdg465. EMBO J. 2003. PMID: 12970189 Free PMC article. - Bacterial wobble modifications of NNA-decoding tRNAs.
Nilsson EM, Alexander RW. Nilsson EM, et al. IUBMB Life. 2019 Aug;71(8):1158-1166. doi: 10.1002/iub.2120. Epub 2019 Jul 8. IUBMB Life. 2019. PMID: 31283100 Free PMC article. Review. - tRNA's wobble decoding of the genome: 40 years of modification.
Agris PF, Vendeix FA, Graham WD. Agris PF, et al. J Mol Biol. 2007 Feb 9;366(1):1-13. doi: 10.1016/j.jmb.2006.11.046. Epub 2006 Nov 15. J Mol Biol. 2007. PMID: 17187822 Review.
Cited by
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.
Aguilar Rangel M, Stein K, Frydman J. Aguilar Rangel M, et al. Sci Adv. 2024 Oct 18;10(42):eado0738. doi: 10.1126/sciadv.ado0738. Epub 2024 Oct 18. Sci Adv. 2024. PMID: 39423268 Free PMC article. - tRNA Modifications and Dysregulation: Implications for Brain Diseases.
Lv X, Zhang R, Li S, Jin X. Lv X, et al. Brain Sci. 2024 Jun 25;14(7):633. doi: 10.3390/brainsci14070633. Brain Sci. 2024. PMID: 39061374 Free PMC article. Review. - yaaJ, the tRNA-Specific Adenosine Deaminase, Is Dispensable in Bacillus subtilis.
Soma A, Kubota A, Tomoe D, Ikeuchi Y, Kawamura F, Arimoto H, Shiwa Y, Kanesaki Y, Nanamiya H, Yoshikawa H, Suzuki T, Sekine Y. Soma A, et al. Genes (Basel). 2023 Jul 25;14(8):1515. doi: 10.3390/genes14081515. Genes (Basel). 2023. PMID: 37628567 Free PMC article. - Context-based sensing of orthosomycin antibiotics by the translating ribosome.
Mangano K, Marks J, Klepacki D, Saha CK, Atkinson GC, Vázquez-Laslop N, Mankin AS. Mangano K, et al. Nat Chem Biol. 2022 Nov;18(11):1277-1286. doi: 10.1038/s41589-022-01138-9. Epub 2022 Sep 22. Nat Chem Biol. 2022. PMID: 36138139 Free PMC article. - A synonymous mutation in IGF-1 impacts the transcription and translation process of gene expression.
Wang SY, Cheng YY, Liu SC, Xu YX, Gao Y, Wang CL, Wang ZG, Feng TQ, Lu GH, Song J, Xia PJ, Hao LL. Wang SY, et al. Mol Ther Nucleic Acids. 2021 Aug 19;26:1446-1465. doi: 10.1016/j.omtn.2021.08.007. eCollection 2021 Dec 3. Mol Ther Nucleic Acids. 2021. PMID: 34938600 Free PMC article.
References
- Proc Natl Acad Sci U S A. 1965 Nov;54(5):1378-85 - PubMed
- Nucleic Acids Res. 1986 Aug 26;14(16):6661-79 - PubMed
- J Mol Biol. 1966 Aug;19(2):548-55 - PubMed
- Nat New Biol. 1971 Dec 29;234(52):261-4 - PubMed
- Proc Natl Acad Sci U S A. 1986 Sep;83(17):6538-42 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials