Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation
Language English Country Great Britain, England Media electronic
Document type Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
Grant support
R35 GM134931
NIGMS NIH HHS - United States
F31 HL152650
NHLBI NIH HHS - United States
R01 AI139202
NIAID NIH HHS - United States
R35 GM127094
NIGMS NIH HHS - United States
R01 GM106105
NIGMS NIH HHS - United States
R01 GM107465
NIGMS NIH HHS - United States
PubMed
34330903
PubMed Central
PMC8324841
DOI
10.1038/s41467-021-24911-1
PII: 10.1038/s41467-021-24911-1
Knihovny.cz E-resources
- MeSH
- Biocatalysis MeSH
- Cryoelectron Microscopy MeSH
- Peptide Chain Elongation, Translational genetics MeSH
- Peptide Elongation Factor G chemistry genetics metabolism MeSH
- Escherichia coli genetics metabolism MeSH
- Nucleic Acid Conformation MeSH
- Protein Conformation MeSH
- RNA, Messenger chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- Frameshifting, Ribosomal genetics MeSH
- Escherichia coli Proteins chemistry genetics metabolism MeSH
- Ribosomes genetics metabolism ultrastructure MeSH
- RNA, Ribosomal, 16S chemistry genetics metabolism MeSH
- RNA, Transfer chemistry genetics metabolism MeSH
- tRNA Methyltransferases genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Names of Substances
- Peptide Elongation Factor G MeSH
- RNA, Messenger MeSH
- Escherichia coli Proteins MeSH
- RNA, Ribosomal, 16S MeSH
- RNA, Transfer MeSH
- TrmD protein, E coli MeSH Browser
- tRNA Methyltransferases MeSH
Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
Central European Institute of Technology Masaryk University Brno Czech Republic
Department of Biochemistry and Molecular Biology Thomas Jefferson University Philadelphia PA USA
See more in PubMed
Frank J, Agrawal RK. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 2000;406:318–322. doi: 10.1038/35018597. PubMed DOI
Cornish PV, Ermolenko DN, Noller HF, Ha T. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell. 2008;30:578–588. doi: 10.1016/j.molcel.2008.05.004. PubMed DOI PMC
Noller HF, Lancaster L, Zhou J, Mohan S. The ribosome moves: RNA mechanics and translocation. Nat. Struct. Mol. Biol. 2017;24:1021–1027. doi: 10.1038/nsmb.3505. PubMed DOI PMC
Dinman JD. Control of gene expression by translational recoding. Adv. Protein Chem. Struct. Biol. 2012;86:129–149. doi: 10.1016/B978-0-12-386497-0.00004-9. PubMed DOI PMC
Craigen WJ, Caskey CT. Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature. 1986;322:273–275. doi: 10.1038/322273a0. PubMed DOI
Donly BC, Edgar CD, Adamski FM, Tate WP. Frameshift autoregulation in the gene for Escherichia coli release factor 2: partly functional mutants result in frameshift enhancement. Nucleic Acids Res. 1990;18:6517–6522. doi: 10.1093/nar/18.22.6517. PubMed DOI PMC
Rom E, Kahana C. Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. Proc. Natl Acad. Sci. USA. 1994;91:3959–3963. doi: 10.1073/pnas.91.9.3959. PubMed DOI PMC
Saffert P, Adamla F, Schieweck R, Atkins JF, Ignatova Z. An expanded CAG repeat in huntingtin causes +1 frameshifting. J. Biol. Chem. 2016;291:18505–18513. doi: 10.1074/jbc.M116.744326. PubMed DOI PMC
Wolf AS, Grayhack EJ. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA. 2015;21:935–945. doi: 10.1261/rna.049080.114. PubMed DOI PMC
Simms CL, Yan LL, Qiu JK, Zaher HS. Ribosome collisions result in +1 frameshifting in the absence of no-go decay. Cell Rep. 2019;28:1679–1689 e1674. doi: 10.1016/j.celrep.2019.07.046. PubMed DOI PMC
Chen Y, et al. Controlling the replication of a genomically recoded HIV-1 with a functional quadruplet codon in mammalian cells. ACS Synth. Biol. 2018;7:1612–1617. doi: 10.1021/acssynbio.8b00096. PubMed DOI PMC
Yourno J, Tanemura S. Restoration of in-phase translation by an unlinked suppressor of a frameshift mutation in Salmonella typhimurium. Nature. 1970;225:422–426. doi: 10.1038/225422a0. PubMed DOI
Sundararajan A, Michaud WA, Qian Q, Stahl G, Farabaugh PJ. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol. Cell. 1999;4:1005–1015. doi: 10.1016/S1097-2765(00)80229-4. PubMed DOI
O’Connor M. Imbalance of tRNA(Pro) isoacceptors induces +1 frameshifting at near-cognate codons. Nucleic Acids Res. 2002;30:759–765. doi: 10.1093/nar/30.3.759. PubMed DOI PMC
Urbonavicius J, Qian Q, Durand JM, Hagervall TG, Bjork GR. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 2001;20:4863–4873. doi: 10.1093/emboj/20.17.4863. PubMed DOI PMC
Waas WF, Druzina Z, Hanan M, Schimmel P. Role of a tRNA base modification and its precursors in frameshifting in eukaryotes. J. Biol. Chem. 2007;282:26026–26034. doi: 10.1074/jbc.M703391200. PubMed DOI
Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM. The UGG isoacceptor of tRNAPro is naturally prone to frameshifts. Int. J. Mol. Sci. 2015;16:14866–14883. doi: 10.3390/ijms160714866. PubMed DOI PMC
Gamper H, et al. Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat. Commun. 2021;12:328. doi: 10.1038/s41467-020-20373-z. PubMed DOI PMC
Sroga GE, Nemoto F, Kuchino Y, Bjork GR. Insertion (sufB) in the anticodon loop or base substitution (sufC) in the anticodon stem of tRNA(Pro)2 from Salmonella typhimurium induces suppression of frameshift mutations. Nucleic Acids Res. 1992;20:3463–3469. doi: 10.1093/nar/20.13.3463. PubMed DOI PMC
Bossi L, Roth JR. Four-base codons ACCA, ACCU and ACCC are recognized by frameshift suppressor sufJ. Cell. 1981;25:489–496. doi: 10.1016/0092-8674(81)90067-2. PubMed DOI
Bossi L, Smith DM. Suppressor sufJ: a novel type of tRNA mutant that induces translational frameshifting. Proc. Natl Acad. Sci. USA. 1984;81:6105–6109. doi: 10.1073/pnas.81.19.6105. PubMed DOI PMC
Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM. Maintenance of protein synthesis reading frame by EF-P and m(1)G37-tRNA. Nat. Commun. 2015;6:7226. doi: 10.1038/ncomms8226. PubMed DOI PMC
Jorgensen F, Kurland CG. Processivity errors of gene expression in Escherichia coli. J. Mol. Biol. 1990;215:511–521. doi: 10.1016/S0022-2836(05)80164-0. PubMed DOI
Nasvall SJ, Chen P, Bjork GR. The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. RNA. 2004;10:1662–1673. doi: 10.1261/rna.7106404. PubMed DOI PMC
Cummins CM, Donahue TF, Culbertson MR. Nucleotide sequence of the SUF2 frameshift suppressor gene of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA. 1982;79:3565–3569. doi: 10.1073/pnas.79.11.3565. PubMed DOI PMC
Prather NE, Murgola EJ, Mims BH. Nucleotide insertion in the anticodon loop of a glycine transfer RNA causes missense suppression. Proc. Natl Acad. Sci. USA. 1981;78:7408–7411. doi: 10.1073/pnas.78.12.7408. PubMed DOI PMC
Moore B, Persson BC, Nelson CC, Gesteland RF, Atkins JF. Quadruplet codons: implications for code expansion and the specification of translation step size. J. Mol. Biol. 2000;298:195–209. doi: 10.1006/jmbi.2000.3658. PubMed DOI
Qian Q, et al. A new model for phenotypic suppression of frameshift mutations by mutant tRNAs. Mol. Cell. 1998;1:471–482. doi: 10.1016/S1097-2765(00)80048-9. PubMed DOI
Jager G, Nilsson K, Bjork GR. The phenotype of many independently isolated +1 frameshift suppressor mutants supports a pivotal role of the P-site in reading frame maintenance. PLoS ONE. 2013;8:e60246. doi: 10.1371/journal.pone.0060246. PubMed DOI PMC
Farabaugh PJ. Translational frameshifting: implications for the mechanism of translational frame maintenance. Prog. Nucleic Acid Res. Mol. Biol. 2000;64:131–170. doi: 10.1016/S0079-6603(00)64004-7. PubMed DOI
Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA. 2014;20:1944–1954. doi: 10.1261/rna.046953.114. PubMed DOI PMC
Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops. Proc. Natl Acad. Sci. USA. 2014;111:12740–12745. doi: 10.1073/pnas.1409436111. PubMed DOI PMC
Dunham CM, et al. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA. 2007;13:817–823. doi: 10.1261/rna.367307. PubMed DOI PMC
Atkins JF, Bjork GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol. Mol. Biol. Rev. 2009;73:178–210. doi: 10.1128/MMBR.00010-08. PubMed DOI PMC
Zhang J, Pavlov MY, Ehrenberg M. Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions. Nucleic Acids Res. 2018;46:1362–1374. doi: 10.1093/nar/gkx1256. PubMed DOI PMC
Wohlgemuth I, Pohl C, Rodnina MV. Optimization of speed and accuracy of decoding in translation. EMBO J. 2010;29:3701–3709. doi: 10.1038/emboj.2010.229. PubMed DOI PMC
Ogle JM, Carter AP, Ramakrishnan V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci. 2003;28:259–266. doi: 10.1016/S0968-0004(03)00066-5. PubMed DOI
Loveland AB, Demo G, Grigorieff N, Korostelev AA. Ensemble cryo-EM elucidates the mechanism of translation fidelity. Nature. 2017;546:113–117. doi: 10.1038/nature22397. PubMed DOI PMC
Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. A new understanding of the decoding principle on the ribosome. Nature. 2012;484:256–259. doi: 10.1038/nature10913. PubMed DOI
Selmer M, et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science. 2006;313:1935–1942. doi: 10.1126/science.1131127. PubMed DOI
Loveland, A. B., Demo, G. & Korostelev, A. A. Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading. Nature, 10.1038/s41586-020-2447-x (2020). PubMed PMC
Moazed D, Noller HF. Intermediate states in the movement of transfer RNA in the ribosome. Nature. 1989;342:142–148. doi: 10.1038/342142a0. PubMed DOI
Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc. Natl Acad. Sci. USA. 2013;110:20994–20999. doi: 10.1073/pnas.1311423110. PubMed DOI PMC
Chen J, Tsai A, O’Leary SE, Petrov A, Puglisi JD. Unraveling the dynamics of ribosome translocation. Curr. Opin. Struct. Biol. 2012;22:804–814. doi: 10.1016/j.sbi.2012.09.004. PubMed DOI PMC
Ermolenko DN, Noller HF. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat. Struct. Mol. Biol. 2011;18:457–462. doi: 10.1038/nsmb.2011. PubMed DOI PMC
Gao YG, et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science. 2009;326:694–699. doi: 10.1126/science.1179709. PubMed DOI PMC
Ramrath DJ, et al. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc. Natl Acad. Sci. USA. 2013;110:20964–20969. doi: 10.1073/pnas.1320387110. PubMed DOI PMC
Zhou J, Lancaster L, Donohue JP, Noller HF. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science. 2013;340:1236086. doi: 10.1126/science.1236086. PubMed DOI PMC
Ling C, Ermolenko DN. Structural insights into ribosome translocation. Wiley Interdiscip. Rev. RNA. 2016;7:620–636. doi: 10.1002/wrna.1354. PubMed DOI PMC
Guo Z, Noller HF. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Proc. Natl Acad. Sci. USA. 2012;109:20391–20394. doi: 10.1073/pnas.1218999109. PubMed DOI PMC
Ratje AH, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 2010;468:713–716. doi: 10.1038/nature09547. PubMed DOI PMC
Pulk A, Cate JH. Control of ribosomal subunit rotation by elongation factor G. Science. 2013;340:1235970. doi: 10.1126/science.1235970. PubMed DOI PMC
Tourigny DS, Fernandez IS, Kelley AC, Ramakrishnan V. Elongation factor G bound to the ribosome in an intermediate state of translocation. Science. 2013;340:1235490. doi: 10.1126/science.1235490. PubMed DOI PMC
Li, W. et al. Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G. Sci Adv 1, 10.1126/sciadv.1500169 (2015). PubMed PMC
Liu G, et al. EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat. Struct. Mol. Biol. 2014;21:817–824. doi: 10.1038/nsmb.2869. PubMed DOI
Savelsbergh A, Matassova NB, Rodnina MV, Wintermeyer W. Role of domains 4 and 5 in elongation factor G functions on the ribosome. J. Mol. Biol. 2000;300:951–961. doi: 10.1006/jmbi.2000.3886. PubMed DOI
Zhou J, Lancaster L, Donohue JP, Noller HF. Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state. Proc. Natl Acad. Sci. USA. 2019;116:7813–7818. doi: 10.1073/pnas.1901310116. PubMed DOI PMC
Hoffer, E. et al. Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. Elife9, 10.7554/eLife.51898 (2020). PubMed PMC
Hong S, et al. Mechanism of tRNA-mediated +1 ribosomal frameshifting. Proc. Natl Acad. Sci. USA. 2018;115:11226–11231. doi: 10.1073/pnas.1809319115. PubMed DOI PMC
Carbone, C. E. et al. Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Preprint at bioRxiv, 10.1101/2021.05.31.446434 (2021). PubMed PMC
Liu C, et al. Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase. J. Mol. Biol. 2007;367:1063–1078. doi: 10.1016/j.jmb.2007.01.050. PubMed DOI PMC
Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 2012;9:671–675. doi: 10.1038/nmeth.2089. PubMed DOI PMC
Svidritskiy E, Korostelev AA. Conformational control of translation termination on the 70S ribosome. Structure. 2018;26:821–828 e823. doi: 10.1016/j.str.2018.04.001. PubMed DOI PMC
Svidritskiy, E., Demo, G., Loveland, A. B., Xu, C. & Korostelev, A. A. Extensive ribosome and RF2 rearrangements during translation termination. Elife8, 10.7554/eLife.46850 (2019). PubMed PMC
Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996;116:71–76. doi: 10.1006/jsbi.1996.0013. PubMed DOI
Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. Elife7, 10.7554/eLife.35383 (2018). PubMed PMC
Grigorieff N. Frealign: an exploratory tool for single-particle Cryo-EM. Methods Enzymol. 2016;579:191–226. doi: 10.1016/bs.mie.2016.04.013. PubMed DOI PMC
Demo, G. et al. Mechanism of ribosome rescue by ArfA and RF2. Elife6, 10.7554/eLife.23687 (2017). PubMed PMC
Cardone G, Heymann JB, Steven AC. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 2013;184:226–236. doi: 10.1016/j.jsb.2013.08.002. PubMed DOI PMC
Tang G, et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 2007;157:38–46. doi: 10.1016/j.jsb.2006.05.009. PubMed DOI
Pettersen EF, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 2004;25:1605–1612. doi: 10.1002/jcc.20084. PubMed DOI
Korostelev A, Bertram R, Chapman MS. Simulated-annealing real-space refinement as a tool in model building. Acta Crystallogr. D. Biol. Crystallogr. 2002;58:761–767. doi: 10.1107/S0907444902003402. PubMed DOI
Adams PD, et al. The Phenix software for automated determination of macromolecular structures. Methods. 2011;55:94–106. doi: 10.1016/j.ymeth.2011.07.005. PubMed DOI PMC
Chen VB, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. Biol. Crystallogr. 2010;66:12–21. doi: 10.1107/S0907444909042073. PubMed DOI PMC
Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP