1932

Abstract

Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biochem-071921-122857
2022-06-21
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/biochem/91/1/annurev-biochem-071921-122857.html?itemId=/content/journals/10.1146/annurev-biochem-071921-122857&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Spirin AS. 1969. A model of the functioning ribosome: locking and unlocking of the ribosome subparticles. Cold Spring Harb. Symp. Quant. Biol. 34:197–207
    [Google Scholar]
  2. 2.
    Frank J, Agrawal RK. 2000. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406:318–22
    [Google Scholar]
  3. 3.
    Ratje AH, Loerke J, Mikolajka A, Brunner M, Hildebrand PW et al. 2010. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature 468:713–16
    [Google Scholar]
  4. 4.
    Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A et al. 2005. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310:827–34
    [Google Scholar]
  5. 5.
    Cornish PV, Ermolenko DN, Noller HF, Ha T. 2008. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell 30:578–88
    [Google Scholar]
  6. 6.
    Wasserman MR, Alejo JL, Altman RB, Blanchard SC. 2016. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation. Nat. Struct. Mol. Biol. 23:333–41
    [Google Scholar]
  7. 7.
    Guo Z, Noller HF. 2012. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. PNAS 109:20391–94
    [Google Scholar]
  8. 8.
    Ermolenko DN, Noller HF. 2011. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat. Struct. Mol. Biol. 18:457–62
    [Google Scholar]
  9. 9.
    Blanchard SC, Kim HD, Gonzalez RL Jr., Puglisi JD, Chu S. 2004. tRNA dynamics on the ribosome during translation. PNAS 101:12893–98
    [Google Scholar]
  10. 10.
    Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J. 2020. Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo–electron microscopy. RNA 26:2017–30
    [Google Scholar]
  11. 11.
    Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. 2016. Large-scale movements of IF3 and tRNA during bacterial translation initiation. Cell 167:133–44.e13
    [Google Scholar]
  12. 12.
    Ogle JM, Brodersen DE, Clemons WM Jr., Tarry MJ, Carter AP, Ramakrishnan V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897–902
    [Google Scholar]
  13. 13.
    Ogle JM, Ramakrishnan V. 2005. Structural insights into translational fidelity. Annu. Rev. Biochem. 74:129–77
    [Google Scholar]
  14. 14.
    Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. 2012. A new understanding of the decoding principle on the ribosome. Nature 484:256–59
    [Google Scholar]
  15. 15.
    Korostelev A, Ermolenko DN, Noller HF. 2008. Structural dynamics of the ribosome. Curr. Opin. Chem. Biol. 12:674–83
    [Google Scholar]
  16. 16.
    Frank J, Gonzalez RL Jr. 2010. Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu. Rev. Biochem. 79:381–412
    [Google Scholar]
  17. 17.
    Blanchard SC. 2009. Single-molecule observations of ribosome function. Curr. Opin. Struct. Biol. 19:103–9
    [Google Scholar]
  18. 18.
    Behrmann E, Loerke J, Budkevich TV, Yamamoto K, Schmidt A et al. 2015. Structural snapshots of actively translating human ribosomes. Cell 161:845–57
    [Google Scholar]
  19. 19.
    Ma J, Campbell A, Karlin S. 2002. Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J. Bacteriol. 184:5733–45
    [Google Scholar]
  20. 20.
    O'Connor M, Gregory ST, Rajbhandary UL, Dahlberg AE. 2001. Altered discrimination of start codons and initiator tRNAs by mutant initiation factor 3. RNA 7:969–78
    [Google Scholar]
  21. 21.
    Gualerzi CO, Pon CL. 2015. Initiation of mRNA translation in bacteria: structural and dynamic aspects. Cell. Mol. Life Sci. 72:4341–67
    [Google Scholar]
  22. 22.
    Milon P, Rodnina MV. 2012. Kinetic control of translation initiation in bacteria. Crit. Rev. Biochem. Mol. Biol. 47:334–48
    [Google Scholar]
  23. 23.
    Shine J, Dalgarno L. 1974. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. PNAS 71:1342–46
    [Google Scholar]
  24. 24.
    Steitz JA, Jakes K. 1975. How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. PNAS 72:4734–38
    [Google Scholar]
  25. 25.
    Kaminishi T, Wilson DN, Takemoto C, Harms JM, Kawazoe M et al. 2007. A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction. Structure 15:289–97
    [Google Scholar]
  26. 26.
    Korostelev A, Trakhanov S, Asahara H, Laurberg M, Lancaster L, Noller HF. 2007. Interactions and dynamics of the Shine–Dalgarno helix in the 70S ribosome. PNAS 104:16840–43
    [Google Scholar]
  27. 27.
    Ringquist S, Jones T, Snyder EE, Gibson T, Boni I, Gold L. 1995. High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites. Biochemistry 34:3640–48
    [Google Scholar]
  28. 28.
    Antoun A, Pavlov MY, Lovmar M, Ehrenberg M. 2006. How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis. Mol. Cell 23:183–93
    [Google Scholar]
  29. 29.
    Simonetti A, Marzi S, Myasnikov AG, Fabbretti A, Yusupov M et al. 2008. Structure of the 30S translation initiation complex. Nature 455:416–20
    [Google Scholar]
  30. 30.
    Julian P, Milon P, Agirrezabala X, Lasso G, Gil D et al. 2011. The cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli. PLOS Biol 9:e1001095
    [Google Scholar]
  31. 31.
    Carter AP, Clemons WM Jr., Brodersen DE, Morgan-Warren RJ, Hartsch T et al. 2001. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291:498–501
    [Google Scholar]
  32. 32.
    Wu XQ, RajBhandary UL. 1997. Effect of the amino acid attached to Escherichia coli initiator tRNA on its affinity for the initiation factor IF2 and on the IF2 dependence of its binding to the ribosome. J. Biol. Chem. 272:1891–95
    [Google Scholar]
  33. 33.
    Hartz D, Binkley J, Hollingsworth T, Gold L. 1990. Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3. Genes Dev 4:1790–800
    [Google Scholar]
  34. 34.
    Petrelli D, LaTeana A, Garofalo C, Spurio R, Pon CL, Gualerzi CO. 2001. Translation initiation factor IF3: two domains, five functions, one mechanism?. EMBO J 20:4560–69
    [Google Scholar]
  35. 35.
    Elvekrog MM, Gonzalez RL Jr. 2013. Conformational selection of translation initiation factor 3 signals proper substrate selection. Nat. Struct. Mol. Biol. 20:628–33
    [Google Scholar]
  36. 36.
    Grunberg-Manago M, Dessen P, Pantaloni D, Godefroy-Colburn T, Wolfe AD, Dondon J. 1975. Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes. J. Mol. Biol. 94:461–78
    [Google Scholar]
  37. 37.
    Grigoriadou C, Marzi S, Pan D, Gualerzi CO, Cooperman BS. 2007. The translational fidelity function of IF3 during transition from the 30 S initiation complex to the 70 S initiation complex. J. Mol. Biol. 373:551–61
    [Google Scholar]
  38. 38.
    Freier SM, Kierzek R, Caruthers MH, Neilson T, Turner DH. 1986. Free energy contributions of G·U and other terminal mismatches to helix stability. Biochemistry 25:3209–13
    [Google Scholar]
  39. 39.
    Caban K, Gonzalez RL Jr. 2015. The emerging role of rectified thermal fluctuations in initiator aa-tRNA- and start codon selection during translation initiation. Biochimie 114:30–38
    [Google Scholar]
  40. 40.
    Korostelev A, Trakhanov S, Laurberg M, Noller HF. 2006. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126:1065–77
    [Google Scholar]
  41. 41.
    Lancaster L, Noller HF. 2005. Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNA. Mol. Cell 20:623–32
    [Google Scholar]
  42. 42.
    Ling C, Ermolenko DN. 2015. Initiation factor 2 stabilizes the ribosome in a semirotated conformation. PNAS 112:15874–79
    [Google Scholar]
  43. 43.
    Kaledhonkar S, Fu Z, Caban K, Li W, Chen B et al. 2019. Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature 570:400–4
    [Google Scholar]
  44. 44.
    Sprink T, Ramrath DJ, Yamamoto H, Yamamoto K, Loerke J et al. 2016. Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Sci. Adv. 2:e1501502
    [Google Scholar]
  45. 45.
    Roy B, Liu Q, Shoji S, Fredrick K. 2018. IF2 and unique features of initiator tRNAfMet help establish the translational reading frame. RNA Biol 15:604–13
    [Google Scholar]
  46. 46.
    Milon P, Konevega AL, Gualerzi CO, Rodnina MV. 2008. Kinetic checkpoint at a late step in translation initiation. Mol. Cell 30:712–20
    [Google Scholar]
  47. 47.
    Wintermeyer W, Gualerzi C. 1983. Effect of Escherichia coli initiation factors on the kinetics of N-AcPhe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study. Biochemistry 22:690–94
    [Google Scholar]
  48. 48.
    Milon P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV. 2012. Real-time assembly landscape of bacterial 30S translation initiation complex. Nat. Struct. Mol. Biol. 19:609–15
    [Google Scholar]
  49. 49.
    Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. 2016. Modular assembly of the bacterial large ribosomal subunit. Cell 167:1610–22.e15
    [Google Scholar]
  50. 50.
    Hinnebusch AG, Lorsch JR. 2012. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb. Perspect. Biol. 4:a011544
    [Google Scholar]
  51. 51.
    Jackson RJ, Hellen CU, Pestova TV. 2010. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11:113–27
    [Google Scholar]
  52. 52.
    Aylett CH, Boehringer D, Erzberger JP, Schaefer T, Ban N. 2015. Structure of a yeast 40S–eIF1–eIF1A–eIF3–eIF3j initiation complex. Nat. Struct. Mol. Biol. 22:269–71
    [Google Scholar]
  53. 53.
    Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. 2020. Structural insights into the mammalian late-stage initiation complexes. Cell Rep 31:107497
    [Google Scholar]
  54. 54.
    Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A et al. 2015. Conformational differences between open and closed states of the eukaryotic translation initiation complex. Mol. Cell 59:399–412
    [Google Scholar]
  55. 55.
    Hussain T, Llacer JL, Fernandez IS, Munoz A, Martin-Marcos P et al. 2014. Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Cell 159:597–607
    [Google Scholar]
  56. 56.
    Wang J, Johnson AG, Lapointe CP, Choi J, Prabhakar A et al. 2019. eIF5B gates the transition from translation initiation to elongation. Nature 573:605–8
    [Google Scholar]
  57. 57.
    Fernandez IS, Bai XC, Hussain T, Kelley AC, Lorsch JR et al. 2013. Molecular architecture of a eukaryotic translational initiation complex. Science 342:1240585
    [Google Scholar]
  58. 58.
    Pavlov MY, Ehrenberg M. 2018. Substrate-induced formation of ribosomal decoding center for accurate and rapid genetic code translation. Annu. Rev. Biophys. 47:525–48
    [Google Scholar]
  59. 59.
    Rodnina MV, Fischer N, Maracci C, Stark H. 2017. Ribosome dynamics during decoding. Philos. Trans. R. Soc. B 372:20160182
    [Google Scholar]
  60. 60.
    Ling C, Ermolenko DN. 2016. Structural insights into ribosome translocation. WIREs RNA 7:620–36
    [Google Scholar]
  61. 61.
    Noller HF, Lancaster L, Zhou J, Mohan S. 2017. The ribosome moves: RNA mechanics and translocation. Nat. Struct. Mol. Biol. 24:1021–27
    [Google Scholar]
  62. 62.
    Voorhees RM, Ramakrishnan V. 2013. Structural basis of the translational elongation cycle. Annu. Rev. Biochem. 82:203–36
    [Google Scholar]
  63. 63.
    Prabhakar A, Puglisi EV, Puglisi JD. 2019. Single-molecule fluorescence applied to translation. Cold Spring Harb. Perspect. Biol. 11:a032714
    [Google Scholar]
  64. 64.
    Rodnina MV, Peske F, Peng BZ, Belardinelli R, Wintermeyer W. 2019. Converting GTP hydrolysis into motion: versatile translational elongation factor G. Biol. Chem. 401:131–42
    [Google Scholar]
  65. 65.
    Wohlgemuth I, Pohl C, Rodnina MV. 2010. Optimization of speed and accuracy of decoding in translation. EMBO J 29:3701–9
    [Google Scholar]
  66. 66.
    Hopfield JJ. 1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. PNAS 71:4135–39
    [Google Scholar]
  67. 67.
    Thompson RC, Stone PJ. 1977. Proofreading of the codon-anticodon interaction on ribosomes. PNAS 74:198–202
    [Google Scholar]
  68. 68.
    Pape T, Wintermeyer W, Rodnina M. 1999. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J 18:3800–7
    [Google Scholar]
  69. 69.
    Zhang J, Ieong KW, Johansson M, Ehrenberg M. 2015. Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. PNAS 112:9602–7
    [Google Scholar]
  70. 70.
    Ieong KW, Uzun U, Selmer M, Ehrenberg M. 2016. Two proofreading steps amplify the accuracy of genetic code translation. PNAS 113:13744–49
    [Google Scholar]
  71. 71.
    Kothe U, Rodnina MV. 2006. Delayed release of inorganic phosphate from elongation factor Tu following GTP hydrolysis on the ribosome. Biochemistry 45:12767–74
    [Google Scholar]
  72. 72.
    Geggier P, Dave R, Feldman MB, Terry DS, Altman RB et al. 2010. Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. J. Mol. Biol. 399:576–95
    [Google Scholar]
  73. 73.
    Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD 2004. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11:1008–14
    [Google Scholar]
  74. 74.
    Gonzalez RL Jr., Chu S, Puglisi JD. 2007. Thiostrepton inhibition of tRNA delivery to the ribosome. RNA 13:2091–97
    [Google Scholar]
  75. 75.
    Liu W, Chen C, Kavaliauskas D, Knudsen CR, Goldman YE, Cooperman BS. 2015. EF-Tu dynamics during pre-translocation complex formation: EF-Tu·GDP exits the ribosome via two different pathways. Nucleic Acids Res 43:9519–28
    [Google Scholar]
  76. 76.
    Polekhina G, Thirup S, Kjeldgaard M, Nissen P, Lippmann C, Nyborg J. 1996. Helix unwinding in the effector region of elongation factor EF-Tu-GDP. Structure 4:1141–51
    [Google Scholar]
  77. 77.
    Noel JK, Whitford PC. 2016. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nat. Commun. 7:13314
    [Google Scholar]
  78. 78.
    Sanbonmatsu KY, Joseph S, Tung CS 2005. Simulating movement of tRNA into the ribosome during decoding. PNAS 102:15854–59
    [Google Scholar]
  79. 79.
    Warias M, Grubmuller H, Bock LV. 2020. tRNA dissociation from EF-Tu after GTP hydrolysis: primary steps and antibiotic inhibition. Biophys. J. 118:151–61
    [Google Scholar]
  80. 80.
    Loveland AB, Demo G, Grigorieff N, Korostelev AA. 2017. Ensemble cryo-EM elucidates the mechanism of translation fidelity. Nature 546:113–17
    [Google Scholar]
  81. 81.
    Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S et al. 2018. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Nucleic Acids Res 46:5861–74
    [Google Scholar]
  82. 82.
    Loveland AB, Demo G, Korostelev AA. 2020. Cryo-EM of elongating ribosome with EF-Tu·GTP elucidates tRNA proofreading. Nature 584:640–45
    [Google Scholar]
  83. 83.
    Voorhees RM, Schmeing TM, Kelley AC, Ramakrishnan V. 2010. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330:835–38
    [Google Scholar]
  84. 84.
    Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. 2010. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA 16:1196–204
    [Google Scholar]
  85. 85.
    Choi J, O'Loughlin S, Atkins JF, Puglisi JD. 2020. The energy landscape of −1 ribosomal frameshifting. Sci. Adv. 6:eaax6969
    [Google Scholar]
  86. 86.
    Gamper H, Li H, Masuda I, Robkis DM, Christian T et al. 2021. Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat. Commun. 12:328
    [Google Scholar]
  87. 87.
    Li W, Liu Z, Koripella RK, Langlois R, Sanyal S, Frank J. 2015. Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G. Sci. Adv. 1:1500169
    [Google Scholar]
  88. 88.
    Lin J, Gagnon MG, Bulkley D, Steitz TA. 2015. Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell 160:219–27
    [Google Scholar]
  89. 89.
    Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. 2013. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. PNAS 110:20994–99
    [Google Scholar]
  90. 90.
    Zhou J, Lancaster L, Donohue JP, Noller HF. 2013. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science 340:1236086
    [Google Scholar]
  91. 91.
    Ramrath DJ, Lancaster L, Sprink T, Mielke T, Loerke J et al. 2013. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. PNAS 110:20964–69
    [Google Scholar]
  92. 92.
    Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V. 2009. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326:694–99
    [Google Scholar]
  93. 93.
    Rundlet EJ, Holm M, Schacherl M, Natchiar SK, Altman RB et al. 2021. Structural basis of early translocation events on the ribosome. Nature 595:741–45
    [Google Scholar]
  94. 94.
    Petrychenko V, Peng B-Z, Schwarzer ACAP, Peske F, Rodnina MV, Fischer N. 2021. Structural mechanism of GTPase-powered ribosome-tRNA movement. Nat. Commun. 12:5933
    [Google Scholar]
  95. 95.
    Demo G, Gamper HB, Loveland AB, Masuda I, Carbone CE et al. 2021. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat. Commun. 12:4644
    [Google Scholar]
  96. 96.
    Holtkamp W, Cunha CE, Peske F, Konevega AL, Wintermeyer W, Rodnina MV. 2014. GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits. EMBO J 33:1073–85
    [Google Scholar]
  97. 97.
    Carbone CE, Loveland AB, Gamper HB Jr., Hou YM, Demo G, Korostelev AA. 2021. Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Nat. Commun. 12:7236
    [Google Scholar]
  98. 98.
    Moazed D, Noller HF. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342:142–48
    [Google Scholar]
  99. 99.
    Agirrezabala X, Lei J, Brunelle JL, Ortiz-Meoz RF, Green R, Frank J. 2008. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell 32:190–97
    [Google Scholar]
  100. 100.
    Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H. 2010. Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature 466:329–33
    [Google Scholar]
  101. 101.
    Abeyrathne PD, Koh CS, Grant T, Grigorieff N, Korostelev AA. 2016. Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. eLife 5:e14874
    [Google Scholar]
  102. 102.
    Zhou J, Lancaster L, Donohue JP, Noller HF. 2019. Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state. PNAS 116:7813–18
    [Google Scholar]
  103. 103.
    Gavrilova LP, Kostiashkina OE, Koteliansky VE, Rutkevitch NM, Spirin AS. 1976. Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol. 101:537–52
    [Google Scholar]
  104. 104.
    Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W. 1997. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385:37–41
    [Google Scholar]
  105. 105.
    Katunin VI, Savelsbergh A, Rodnina MV, Wintermeyer W. 2002. Coupling of GTP hydrolysis by elongation factor G to translocation and factor recycling on the ribosome. Biochemistry 41:12806–12
    [Google Scholar]
  106. 106.
    Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD 2013. Coordinated conformational and compositional dynamics drive ribosome translocation. Nat. Struct. Mol. Biol. 20:718–27
    [Google Scholar]
  107. 107.
    Salsi E, Farah E, Ermolenko DN 2016. EF-G activation by phosphate analogs. J. Mol. Biol. 428:2248–58
    [Google Scholar]
  108. 108.
    Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. 2016. Decoding mammalian ribosome-mRNA states by translational GTPase complexes. Cell 167:1229–40.e15
    [Google Scholar]
  109. 109.
    Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T et al. 2018. tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis. Cell Rep 25:2676–88.e7
    [Google Scholar]
  110. 110.
    Korostelev AA. 2011. Structural aspects of translation termination on the ribosome. RNA 17:1409–21
    [Google Scholar]
  111. 111.
    Rodnina MV. 2018. Translation in prokaryotes. Cold Spring Harb. Perspect. Biol. 10:a032664
    [Google Scholar]
  112. 112.
    Shin DH, Brandsen J, Jancarik J, Yokota H, Kim R, Kim SH 2004. Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome. J. Mol. Biol. 341:227–39
    [Google Scholar]
  113. 113.
    Vestergaard B, Van LB, Andersen GR, Nyborg J, Buckingham RH, Kjeldgaard M. 2001. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol. Cell 8:1375–82
    [Google Scholar]
  114. 114.
    Demo G, Svidritskiy E, Madireddy R, Diaz-Avalos R, Grant T et al. 2017. Mechanism of ribosome rescue by ArfA and RF2. eLife 6:e23687
    [Google Scholar]
  115. 115.
    James NR, Brown A, Gordiyenko Y, Ramakrishnan V. 2016. Translational termination without a stop codon. Science 354:1437–40
    [Google Scholar]
  116. 116.
    Svidritskiy E, Korostelev AA. 2018. Conformational control of translation termination on the 70S ribosome. Structure 26:821–28
    [Google Scholar]
  117. 117.
    Trappl K, Joseph S 2016. Ribosome induces a closed to open conformational change in release factor 1. J. Mol. Biol. 428:1333–44
    [Google Scholar]
  118. 118.
    Fu Z, Indrisiunaite G, Kaledhonkar S, Shah B, Sun M et al. 2019. The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat. Commun. 10:2579
    [Google Scholar]
  119. 119.
    Adio S, Sharma H, Senyushkina T, Karki P, Maracci C et al. 2018. Dynamics of ribosomes and release factors during translation termination in E. coli. eLife 7:e34252
    [Google Scholar]
  120. 120.
    Mikuni O, Ito K, Moffat J, Matsumura K, McCaughan K et al. 1994. Identification of the prfC gene, which encodes peptide-chain-release factor 3 of Escherichia coli. PNAS 91:5798–802
    [Google Scholar]
  121. 121.
    Grentzmann G, Brechemier-Baey D, Heurgue V, Mora L, Buckingham RH. 1994. Localization and characterization of the gene encoding release factor RF3 in Escherichia coli. PNAS 91:5848–52
    [Google Scholar]
  122. 122.
    Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF. 2007. Observation of intersubunit movement of the ribosome in solution using FRET. J. Mol. Biol. 370:530–40
    [Google Scholar]
  123. 123.
    Gao H, Zhou Z, Rawat U, Huang C, Bouakaz L et al. 2007. RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129:929–41
    [Google Scholar]
  124. 124.
    Korostelev A, Zhu J, Asahara H, Noller HF. 2010. Recognition of the amber UAG stop codon by release factor RF1. EMBO J 29:2577–85
    [Google Scholar]
  125. 125.
    Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. 2019. Extensive ribosome and RF2 rearrangements during translation termination. eLife 8:e46850
    [Google Scholar]
  126. 126.
    Graf M, Huter P, Maracci C, Peterek M, Rodnina MV, Wilson DN. 2018. Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1. Nat. Commun. 9:3053
    [Google Scholar]
  127. 127.
    Fu Z, Kaledhonkar S, Borg A, Sun M, Chen B et al. 2016. Key intermediates in ribosome recycling visualized by time-resolved cryoelectron microscopy. Structure 24:2092–101
    [Google Scholar]
  128. 128.
    Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V. 2015. Structural basis for stop codon recognition in eukaryotes. Nature 524:493–96
    [Google Scholar]
  129. 129.
    Poole ES, Brown CM, Tate WP. 1995. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J 14:151–58
    [Google Scholar]
  130. 130.
    Brown CM, Stockwell PA, Trotman CN, Tate WP. 1990. Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res 18:6339–45
    [Google Scholar]
  131. 131.
    Jungreis I, Lin MF, Spokony R, Chan CS, Negre N et al. 2011. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res 21:2096–113
    [Google Scholar]
  132. 132.
    des Georges A, Hashem Y, Unbehaun A, Grassucci RA, Taylor D et al. 2014. Structure of the mammalian ribosomal pre-termination complex associated with eRF1·eRF3·GDPNP. Nucleic Acids Res 42:3409–18
    [Google Scholar]
  133. 133.
    Preis A, Heuer A, Barrio-Garcia C, Hauser A, Eyler DE et al. 2014. Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. Cell Rep 8:59–65
    [Google Scholar]
  134. 134.
    Pisarev AV, Skabkin MA, Pisareva VP, Skabkina OV, Rakotondrafara AM et al. 2010. The role of ABCE1 in eukaryotic posttermination ribosomal recycling. Mol. Cell 37:196–210
    [Google Scholar]
  135. 135.
    Desai BJ, Gonzalez RL Jr. 2020. Multiplexed genomic encoding of non-canonical amino acids for labeling large complexes. Nat. Chem. Biol. 16:1129–35
    [Google Scholar]
  136. 136.
    Zhong ED, Bepler T, Berger B, Davis JH. 2021. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18:176–85
    [Google Scholar]
  137. 137.
    Schmitt E, Coureux PD, Kazan R, Bourgeois G, Lazennec-Schurdevin C, Mechulam Y. 2020. Recent advances in archaeal translation initiation. Front. Microbiol. 11:584152
    [Google Scholar]
  138. 138.
    Nurenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kotter P et al. 2020. Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex. EMBO J 39:e103788
    [Google Scholar]
  139. 139.
    Ranjan N, Pochopien AA, Chih-Chien Wu C, Beckert B, Blanchet S et al. 2021. Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation. EMBO J 40:e106449
    [Google Scholar]
  140. 140.
    Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM et al. 2020. Structure of a human 48S translational initiation complex. Science 369:1220–27
    [Google Scholar]
  141. 141.
    Aibara S, Singh V, Modelska A, Amunts A. 2020. Structural basis of mitochondrial translation. eLife 9:e58362
    [Google Scholar]
  142. 142.
    Kummer E, Ban N. 2020. Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1. EMBO J 39:e104820
    [Google Scholar]
  143. 143.
    Koripella RK, Sharma MR, Bhargava K, Datta PP, Kaushal PS et al. 2020. Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Nat. Commun. 11:3830
    [Google Scholar]
  144. 144.
    Irastortza-Olaziregi M, Amster-Choder O. 2020. Coupled transcription-translation in prokaryotes: an old couple with new surprises. Front. Microbiol. 11:624830
    [Google Scholar]
  145. 145.
    Tesina P, Heckel E, Cheng J, Fromont-Racine M, Buschauer R et al. 2019. Structure of the 80S ribosome–Xrn1 nuclease complex. Nat. Struct. Mol. Biol. 26:275–80
    [Google Scholar]
  146. 146.
    Matsuo Y, Tesina P, Nakajima S, Mizuno M, Endo A et al. 2020. RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nat. Struct. Mol. Biol. 27:323–32
    [Google Scholar]
  147. 147.
    Demo G, Rasouly A, Vasilyev N, Svetlov V, Loveland AB et al. 2017. Structure of RNA polymerase bound to ribosomal 30S subunit. eLife 6:e28560
    [Google Scholar]
  148. 148.
    O'Reilly FJ, Xue L, Graziadei A, Sinn L, Lenz S et al. 2020. In-cell architecture of an actively transcribing-translating expressome. Science 369:554–57
    [Google Scholar]
  149. 149.
    Tegunov D, Xue L, Dienemann C, Cramer P, Mahamid J. 2021. Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat. Methods 18:186–93
    [Google Scholar]
  150. 150.
    Lucas BA, Himes BA, Xue L, Grant T, Mahamid J, Grigorieff N. 2021. Locating macromolecular assemblies in cells by 2D template matching with cisTEM. eLife 10:e68946
    [Google Scholar]
  151. 151.
    Adio S, Senyushkina T, Peske F, Fischer N, Wintermeyer W, Rodnina MV. 2015. Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome. Nat. Commun. 6:7442
    [Google Scholar]
/content/journals/10.1146/annurev-biochem-071921-122857
Loading
/content/journals/10.1146/annurev-biochem-071921-122857
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error