Insights into Genome Recoding from the Mechanism of a Classic +1-frameshifting TRNA

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Jan 13

PMID 33436566

Citations 20

Authors

Howard Gamper

Haixing Li

Isao Masuda

D Miklos Robkis

Thomas Christian

Adam B Conn

Gregor Blaha

E James Petersson

Ruben L Gonzalez Jr

Ya-Ming Hou

Affiliations

Soon will be listed here.

Abstract

While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.

Citing Articles

Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.

Nakano Y, Gamper H, McGuigan H, Maharjan S, Li J, Sun Z Nat Commun. 2025; 16(1):1047.

PMID: 39865096 PMC: 11770116. DOI: 10.1038/s41467-025-56348-1.

A tRNA modification pattern that facilitates interpretation of the genetic code.

Masuda I, Hou Y Front Microbiol. 2024; 15:1415100.

PMID: 38933027 PMC: 11199890. DOI: 10.3389/fmicb.2024.1415100.

Mechanisms and Delivery of tRNA Therapeutics.

Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm S, Heinemann I Chem Rev. 2024; 124(12):7976-8008.

PMID: 38801719 PMC: 11212642. DOI: 10.1021/acs.chemrev.4c00142.

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.

Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H Chem Rev. 2024; 124(10):6444-6500.

PMID: 38688034 PMC: 11122139. DOI: 10.1021/acs.chemrev.3c00894.

Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human.

Ren G, Gu X, Zhang L, Gong S, Song S, Chen S Nucleic Acids Res. 2024; 52(5):2463-2479.

PMID: 38281188 PMC: 10954444. DOI: 10.1093/nar/gkae035.

References

Masuda I, Matsubara R, Christian T, Rojas E, Yadavalli S, Zhang L . tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance. Cell Syst. 2019; 8(4):302-314.e8. PMC: 6483872. DOI: 10.1016/j.cels.2019.03.008. View

Weiss R, Dunn D, Shuh M, Atkins J, GESTELAND R . E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. New Biol. 1989; 1(2):159-69. View

Munro J, Wasserman M, Altman R, Wang L, Blanchard S . Correlated conformational events in EF-G and the ribosome regulate translocation. Nat Struct Mol Biol. 2010; 17(12):1470-7. PMC: 2997181. DOI: 10.1038/nsmb.1925. View

Fagan C, Maehigashi T, Dunkle J, Miles S, Dunham C . Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA. 2014; 20(12):1944-54. PMC: 4238358. DOI: 10.1261/rna.046953.114. View

Datsenko K, Wanner B . One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000; 97(12):6640-5. PMC: 18686. DOI: 10.1073/pnas.120163297. View

Walker S, Fredrick K . Recognition and positioning of mRNA in the ribosome by tRNAs with expanded anticodons. J Mol Biol. 2006; 360(3):599-609. PMC: 2602952. DOI: 10.1016/j.jmb.2006.05.006. View

Liu G, Song G, Zhang D, Zhang D, Li Z, Lyu Z . EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat Struct Mol Biol. 2014; 21(9):817-24. DOI: 10.1038/nsmb.2869. View

Neumann H, Wang K, Davis L, Garcia-Alai M, Chin J . Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature. 2010; 464(7287):441-4. DOI: 10.1038/nature08817. View

Mohan S, Donohue J, Noller H . Molecular mechanics of 30S subunit head rotation. Proc Natl Acad Sci U S A. 2014; 111(37):13325-30. PMC: 4169957. DOI: 10.1073/pnas.1413731111. View

10.

Niu W, Schultz P, Guo J . An expanded genetic code in mammalian cells with a functional quadruplet codon. ACS Chem Biol. 2013; 8(7):1640-5. PMC: 4501474. DOI: 10.1021/cb4001662. View

11.

Studer S, Feinberg J, Joseph S . Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. J Mol Biol. 2003; 327(2):369-81. DOI: 10.1016/s0022-2836(03)00146-3. View

12.

Lee B, Kim S, Ko B, Yoo T . An efficient system for incorporation of unnatural amino acids in response to the four-base codon AGGA in Escherichia coli. Biochim Biophys Acta Gen Subj. 2017; 1861(11 Pt B):3016-3023. DOI: 10.1016/j.bbagen.2017.02.017. View

13.

Bronson J, Fei J, Hofman J, Gonzalez Jr R, Wiggins C . Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys J. 2009; 97(12):3196-205. PMC: 2793368. DOI: 10.1016/j.bpj.2009.09.031. View

14.

Aitken C, Marshall R, Puglisi J . An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J. 2007; 94(5):1826-35. PMC: 2242739. DOI: 10.1529/biophysj.107.117689. View

15.

Pulk A, Cate J . Control of ribosomal subunit rotation by elongation factor G. Science. 2013; 340(6140):1235970. PMC: 4274944. DOI: 10.1126/science.1235970. View

16.

Fei J, Richard A, Bronson J, Gonzalez Jr R . Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol. 2011; 18(9):1043-51. PMC: 3167956. DOI: 10.1038/nsmb.2098. View

17.

Bossi L, Roth J . Four-base codons ACCA, ACCU and ACCC are recognized by frameshift suppressor sufJ. Cell. 1981; 25(2):489-96. DOI: 10.1016/0092-8674(81)90067-2. View

18.

Chatterjee A, Lajoie M, Xiao H, Church G, Schultz P . A bacterial strain with a unique quadruplet codon specifying non-native amino acids. Chembiochem. 2014; 15(12):1782-6. DOI: 10.1002/cbic.201402104. View

19.

Kim H, Liu F, Fei J, Bustamante C, Gonzalez Jr R, Tinoco Jr I . A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation. Proc Natl Acad Sci U S A. 2014; 111(15):5538-43. PMC: 3992627. DOI: 10.1073/pnas.1403457111. View

20.

Gamper H, Masuda I, Frenkel-Morgenstern M, Hou Y . The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts. Int J Mol Sci. 2015; 16(7):14866-83. PMC: 4519876. DOI: 10.3390/ijms160714866. View