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The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

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Fu Z, Indrisiunaite G, Kaledhonkar S, Shah B, Sun M, Chen B, Grassucci RA, Ehrenberg M, Frank J
OpenAccess logo Nat Commun 10 2579 (2019)
Related entries: 6ore, 6osk, 6osq, 6ost, 6ot3, 6ouo

Cited: 27 times
EuropePMC logo PMID: 31189921

Abstract

When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.

Reviews citing this publication (12)

  1. Ribosome Rescue Pathways in Bacteria. Müller C, Crowe-McAuliffe C, Wilson DN. Front Microbiol 12 652980 (2021)
  2. The Structural Dynamics of Translation. Korostelev AA. Annu Rev Biochem 91 245-267 (2022)
  3. Understanding the invisible hands of sample preparation for cryo-EM. Weissenberger G, Henderikx RJM, Peters PJ. Nat Methods 18 463-471 (2021)
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Articles citing this publication (15)

  1. Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling. van der Stel AX, Gordon ER, Sengupta A, Martínez AK, Klepacki D, Perry TN, Herrero Del Valle A, Vázquez-Laslop N, Sachs MS, Cruz-Vera LR, Innis CA. Nat Commun 12 5340 (2021)
  2. Light-coupled cryo-plunger for time-resolved cryo-EM. Yoder N, Jalali-Yazdi F, Noreng S, Houser A, Baconguis I, Gouaux E. J Struct Biol 212 107624 (2020)
  3. A switch from α-helical to β-strand conformation during co-translational protein folding. Agirrezabala X, Samatova E, Macher M, Liutkute M, Maiti M, Gil-Carton D, Novacek J, Valle M, Rodnina MV. EMBO J 41 e109175 (2022)
  4. Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 toward Total Omnipotence. Abdalaal H, Pundir S, Ge X, Sanyal S, Näsvall J. Mol Biol Evol 37 2918-2930 (2020)
  5. GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors. Pundir S, Ge X, Sanyal S. J Biol Chem 296 100681 (2021)
  6. A simple flash and freeze system for cryogenic time-resolved electron microscopy. Bhattacharjee B, Rahman MM, Hibbs RE, Stowell MHB. Front Mol Biosci 10 1129225 (2023)
  7. Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria. Parajuli NP, Emmerich A, Mandava CS, Pavlov MY, Sanyal S. Nat Commun 14 918 (2023)
  8. Dynamics of release factor recycling during translation termination in bacteria. Prabhakar A, Pavlov MY, Zhang J, Indrisiunaite G, Wang J, Lawson MR, Ehrenberg M, Puglisi JD. Nucleic Acids Res 51 5774-5790 (2023)
  9. Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin. Parajuli NP, Mandava CS, Pavlov MY, Sanyal S. Nucleic Acids Res 49 6880-6892 (2021)
  10. Microsecond melting and revitrification of cryo samples with a correlative light-electron microscopy approach. Bongiovanni G, Harder OF, Drabbels M, Lorenz UJ. Front Mol Biosci 9 1044509 (2022)
  11. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue. Kurita D, Abo T, Himeno H. J Biol Chem 295 13326-13337 (2020)
  12. Overview of tRNA Modifications in Chloroplasts. Fages-Lartaud M, Hohmann-Marriott MF. Microorganisms 10 226 (2022)
  13. Rate-limiting hydrolysis in ribosomal release reactions revealed by ester activation. Bao L, Karpenko VV, Forster AC. J Biol Chem 298 102509 (2022)
  14. Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs. Smith AM, Costello MS, Kettring AH, Wingo RJ, Moore SD. Proc. Natl. Acad. Sci. U.S.A. 116 21769-21779 (2019)
  15. Salt-Specific Suppression of the Cold Denaturation of Thermophilic Multidomain Initiation Factor 2. Džupponová V, Tomášková N, Antošová A, Sedlák E, Žoldák G. Int J Mol Sci 24 6787 (2023)


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