1,073
Views
7
CrossRef citations to date
0
Altmetric
Point of View

A close-up view of codon selection in eukaryotic initiation

, ORCID Icon &
Pages 815-819 | Received 30 Jan 2017, Accepted 14 Mar 2017, Published online: 21 Apr 2017

References

  • Shine J, Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A 1974; 71:1342-6; PMID:4598299; https://doi.org/10.1073/pnas.71.4.1342
  • Hinnebusch AG. The scanning mechanism of eukaryotic translation initiation. Annu Rev Biochem 2014; 83:779-812; PMID:24499181; https://doi.org/10.1146/annurev-biochem-060713-035802
  • Llácer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V. Conformational differences between open and closed states of the eukaryotic translation initiation complex. Mol Cell 2015; 59:399-412; PMID:26212456; https://doi.org/10.1016/j.molcel.2015.06.033
  • Hussain T, Llácer JL, Fernández IS, Munoz A, Martin-Marcos P, Savva CG, Lorsch JR, Hinnebusch AG, Ramakrishnan V. Structural changes enable start codon recognition by the eukaryotic translation initiation complex. Cell 2014; 159:597-607; PMID:25417110; https://doi.org/10.1016/j.cell.2014.10.001
  • Brandsdal BO, Osterberg F, Almlöf M, Feierberg I, Luzhkov VB, Åqvist J. Free energy calculations and ligand binding. Adv Protein Chem 2003; 66:123-58; PMID:14631818; https://doi.org/10.1016/S0065-3233(03)66004-3
  • Zwanzig RW. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 1954; 22:2099; https://doi.org/10.1063/1.1740409
  • Lind C, Åqvist J. Principles of start codon recognition in eukaryotic translation initiation. Nucleic Acids Res 2016; 44:8425-32; PMID:27280974; https://doi.org/10.1093/nar/gkw534
  • Kolitz SE, Takacs JE, Lorsch JR. Kinetic and thermodynamic analysis of the role of start codon/anticodon base pairing during eukaryotic translation initiation. RNA 2009; 15:138-52; PMID:19029312; https://doi.org/10.1261/rna.1318509
  • Peabody DS. Translation initiation at non-AUG triplets in mammalian cells. J Biol Chem 1989; 264:5031-5; PMID:2538469.
  • Satpati P, Sund J, Åqvist J. Structure-based energetics of mRNA decoding on the ribosome. Biochemistry 2014; 53:1714-22; PMID:24564511; https://doi.org/10.1021/bi5000355
  • Sund J, Andér M, Åqvist J. Principles of stop-codon reading on the ribosome. Nature 2010; 465:947-50; PMID:20512119; https://doi.org/10.1038/nature09082
  • Lind C, Sund J, Åqvist J. Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons. Nat Commun 2013; 4:2940; PMID:24352605; https://doi.org/10.1038/ncomms3940
  • Björk GR, Ericson JU, Gustafsson CE, Hagervall TG, Jönsson YH, Wikström PM. Transfer RNA modification. Annu Rev Biochem 1987; 56:263-87; PMID:3304135; https://doi.org/10.1146/annurev.bi.56.070187.001403
  • Grosjean H, de Crécy-Lagard V, Marck C. Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes. FEBS Lett 2010; 584:252-64; PMID:19931533; https://doi.org/10.1016/j.febslet.2009.11.052
  • Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. Sequence and organization of the human mitochondrial genome. Nature 1981; 290:457-65; PMID:7219534; https://doi.org/10.1038/290457a0
  • Osawa S, Jukes TH, Watanabe K, Muto A. Recent evidence for evolution of the genetic code. Microbiol Rev 1992; 56:229-64; PMID:1579111.
  • Jukes TH, Osawa S. Evolutionary changes in the genetic code. Comp Biochem Physiol, B 1993; 106:489-94; PMID:8281749; https://doi.org/10.1016/0300-9629(93)90243-W
  • Elzanowski AA, Ostell J. The genetic codes. National Center for Biotechnology Information; 2016 Nov 18 [accessed 2017 Jan 30]. https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi.
  • Starck SR, Jiang V, Pavon-Eternod M, Prasad S, McCarthy B, Pan T, Shastri N. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science 2012; 336:1719-23; PMID:22745432; https://doi.org/10.1126/science.1220270
  • Starck SR, Ow Y, Jiang V, Tokuyama M, Rivera M, Qi X, Roberts RW, Shastri N. A distinct translation initiation mechanism generates cryptic peptides for immune surveillance. PLoS One 2008; 3:e3460; PMID:18941630; https://doi.org/10.1371/journal.pone.0003460
  • Starck SR, Shastri N. Nowhere to hide: Unconventional translation yields cryptic peptides for immune surveillance. Immunological Rev 2016; 272:8-16; PMID:27319338; https://doi.org/10.1111/imr.12434
  • Donahue TF, Cigan AM. Genetic selection for mutations that reduce or abolish ribosomal recognition of the HIS4 translational initiator region. Mol Cell Biol 1988; 8:2955-63; PMID:3043200; https://doi.org/10.1128/MCB.8.7.2955
  • Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 1986; 44:283-92; PMID:3943125; https://doi.org/10.1016/0092-8674(86)90762-2
  • Desjardins P, Morais R. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J Mol Evol 1991; 32:153-61; PMID:1706782; https://doi.org/10.1007/BF02515387
  • Bragg WL. The structure of some crystals as indicated by their diffraction of X-rays. Proc R Soc A 1913; 89:248-77; https://doi.org/10.1098/rspa.1913.0083
  • Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, et al. Trendspotting in the protein data bank. FEBS Lett 2013; 587:1036-45; PMID:23337870; https://doi.org/10.1016/j.febslet.2012.12.029
  • Johansson M, Ieong K-W, Trobro S, Strazewski P, Åqvist J, Pavlov MY, Ehrenberg M. pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc Natl Acad Sci U S A 2011; 108:79-84; PMID:21169502; https://doi.org/10.1073/pnas.1012612107
  • Zhang J, Ieong K-W, Johansson M, Ehrenberg M. Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Proc Natl Acad Sci U S A 2015; 112:9602-7; PMID:26195797; https://doi.org/10.1073/pnas.1506823112
  • Gromadski KB, Rodnina MV. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell 2004; 13:191-200; PMID:14759365; https://doi.org/10.1016/S1097-2765(04)00005-X
  • Gromadski KB, Daviter T, Rodnina MV. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell 2006; 21:369-77; PMID:16455492; https://doi.org/10.1016/j.molcel.2005.12.018
  • Kuhlenkoetter S, Wintermeyer W, Rodnina MV. Different substrate-dependent transition states in the active site of the ribosome. Nature 2011; 476:351-4; PMID:21804565; https://doi.org/10.1038/nature10247
  • Trobro S, Åqvist J. Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A 2005; 102:12395-400; PMID:16116099; https://doi.org/10.1073/pnas.0504043102
  • Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, et al. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 2016; 540:80-5; PMID:27842381; https://doi.org/10.1038/nature20560
  • Sanbonmatsu KY, Joseph S, Tung C-S. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A 2005; 102:15854-9; PMID:16249344; https://doi.org/10.1073/pnas.0503456102
  • Allner O, Nilsson L. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA 2011; 17:2177-88; PMID:22028366; https://doi.org/10.1261/rna.029231.111
  • Satpati P, Bauer P, Åqvist J. Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome. Chem Eur J 2014; 20:10271-5; PMID:25043149; https://doi.org/10.1002/chem.201404016
  • Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 2014; 426:3201-13; PMID:24813122; https://doi.org/10.1016/j.jmb.2014.04.029
  • Wallin G, Åqvist J. The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci U S A 2010; 107:1888-93; PMID:20080677; https://doi.org/10.1073/pnas.0914192107
  • Sharma PK, Xiang Y, Kato M, Warshel A. What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry 2005; 44:11307-14; PMID:16114867; https://doi.org/10.1021/bi0509806
  • Świderek K, Martí S, Tuñón I, Moliner V, Bertrán J. Peptide bond formation mechanism catalyzed by ribosome. J Am Chem Soc 2015; 137:12024-34; PMID:26325003; https://doi.org/10.1021/jacs.5b05916
  • Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmüller H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol 2013; 20:1390-6; PMID:24186064; https://doi.org/10.1038/nsmb.2690
  • Nguyen K, Whitford PC. Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocation. Nat Commun 2016; 7:10586; PMID:26838673; https://doi.org/10.1038/ncomms10586
  • Kazemi M, Himo F, Åqvist J. Peptide release on the ribosome involves substrate-assisted base catalysis. ACS Catalysis 2016; 6:8432-8439; https://doi.org/10.1021/acscatal.6b02842
  • Trobro S, Åqvist J. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol Cell 2007; 27:758-66; PMID:17803940; https://doi.org/10.1016/j.molcel.2007.06.032
  • Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum mechanical study on the mechanism of peptide release in the ribosome. J Phys Chem B 2013; 117:3503-15; PMID:23442058; https://doi.org/10.1021/jp3110248
  • Kapp LD, Kolitz SE, Lorsch JR. Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation. RNA 2006; 12:751-64; PMID:16565414; https://doi.org/10.1261/rna.2263906
  • Kozak M. Role of ATP in binding and migration of 40S ribosomal subunits. Cell 1980; 22:459-67; PMID:7448869; https://doi.org/10.1016/0092-8674(80)90356-6

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.