Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid?
© Seligmann; licensee BioMed Central Ltd. 2010
Received: 12 February 2010
Accepted: 28 May 2010
Published: 28 May 2010
Accurate amino acid insertion during peptide elongation requires tRNAs loaded by cognate amino acids and that anticodons match codons. However, tRNA misloading does not necessarily cause misinsertions: misinsertion is avoided when anticodons mismatch codons coding for misloaded amino acids.
Presentation of the hypothesis
Occasional compensation of misacylation by codon-anticodon mismatch necessarily occurs. Putatively, occasional error compensation may be enhanced beyond the random combination of independent errors in tRNA loading and codon-anticodon interactions: tRNA misacylation might alter potentials for codon-anticodon mismatches, perhaps specifically increasing potentials for mismatching those codons coding for the misacylated non-cognate amino acid. This hypothetical phenomenon is called 'error coordination', in distinction from 'error compensation' that assumes independence between misacylation and mismatch.
Testing the hypothesis
Eventually, the hypothesis should be tested for each combination of amino acid misacylation and codon-anticodon mismatch, by comparing stabilities or frequencies of mismatched codon-anticodon duplexes formed by tRNAs loaded by their cognate amino acid with stabilities formed by that tRNA when misloaded with the amino acid coded by the mismatched codon. Competitive mismatching experiments between misloaded and correctly loaded tRNAs could also be useful, yet more sophisticated experiments.
Implications of the hypothesis
Detecting error coordination implies estimating error compensation, which also promotes protein synthesis accuracy. Hence even in the absence of evidence for error coordination, experiments would yield very useful insights into misacylation and mismatch processes. In case experiments consider post-transcriptional RNA modifications (especially at wobble positions), results on codon-anticodon mismatches would enable significant improvements and sophistications of secondary structure prediction softwares. Positive results would show that protein translation enhances accuracies of products, not of single steps in the production. Ancient translational machineries putatively optimized error coordination, especially before tRNA editing by tRNA synthetases evolved: few primitive, but functionally versatile tRNA species perhaps executed low accuracy translation. Systems artificially designed/selected for low complexity and high efficiency could make use of this property for anticodons with high levels of error compensation and coordination.
The two major groups of tRNA synthetases, class I and II, seem to minimize impacts of misinserted amino acids in protein sequences by tRNAs that were misloaded by these tRNA synthetases [1, 2]. Accurate loading of tRNA acceptor stems with cognate amino acids by tRNA synthetases is a crucial step in protein synthesis, and indeed misacylated (misloaded) tRNAs are frequently edited by tRNA synthetases , which sometimes even edit tRNAs at advanced stages in the translational pathway . Both pre- or post-transfer editing occur. These mechanisms are not exclusive and depend on catalytic sites other than the aminoacylation site [5, 6]. The complex editing functions of some tRNA synthetases probably originated from multifunctionality of ancient tRNA synthetases, at the origins of the genetic code and the translational machinery . Note that some mutations affecting editing associate with mitochondrial diseases .
Presentation of the hypothesis
Despite editing, misinsertion sometimes occurs. However, misinsertion is avoided if the misloaded tRNA's anticodon mismatches a codon coding for the misloaded amino acid, a phenomenon potentially meaningful for organisms. If mismatch is unaffected by misacylation, combinatorial probabilities predict their joint occurrence. This phenomenon is called here error compensation. The hypothesis suggested here is that misacylation affects mismatch potentials and hence joint occurrences of misacylations and mismatches do not match combinatorial probabilities, called error coordination. Error compensation is an unavoidable phenomenon whose potential effects are explored elsewhere. Here I focus on error coordination, which is a more readily testable phenomenon because it can be compared to a null hypothesis, that defined by error compensation, hence its detection implies estimating error compensation.
Another amino acid property potentially affecting error coordination is its charge. Charge differences between cognate and misloaded amino acid could affect the tRNA's electro-magnetic properties, including of its anticodon. Codon-anticodon interactions depend on electro-magnetic properties of the interacting atoms (hydrogen atoms with positive partial dipole moments interact with negative partial dipole moments of nitrogen or oxygen in the complementary base). Misacylations altering amino acid charges could affect codon-anticodon interactions: positive charges (arginine, histidine and lysine) might enhance positive partial dipole moments, decrease negative ones; the opposite would occur for negative charges (aspartic and glutamic acids). These effects would alter codon-anticodon duplex stabilities, including for mismatches. Such effects on anticodons are difficult to predict, because tRNA acceptor stems are not adjacent to anticodons. Charge effects on anticodon interactions may be buffered as well as enhanced by particular RNA sequences connecting amino acid and anticodon. Perhaps RNA rich in pyrimidines (which have high dipole moments) functions as conductor of effects of amino acid charge on anticodons. Softwares predicting dipole moments of proteins exist [17, 18], hence applications predicting similar properties for loaded tRNAs could be developed on similar principles.
Other amino acid properties might also affect codon-anticodon interactions. This suggests that experimental observations on effects of misacylations on mismatches should be made for all combinations of misacylations and codon-anticodon mismatches, because effects of swapping one amino acid with another may be unpredictable, as different amino acid properties may be relevant. As noted above, specific tRNA sequences may also influence. If this is the case, models predicting these influences would be particularly important for predicting error coordination, because tRNA sequences frequently vary between species and individuals, and it is unrealistic that experimental data will be produced for more than a few model species (most likely Escherichia coli and Homo sapiens).
Testing the hypothesis
The comparison between error compensation and coordination is interesting from an epistemological point of view. Error compensation is a trivial phenomenon that necessarily occurs. It can only be quantified and compared between different cases (anticodons, tRNAs, species etc...), so as to test for associations between that quantity and its assumed effects on protein metabolism and related phenomena at higher organismic levels (for different treatments, individuals, species, etc...). Error compensation is a case where a null hypothesis is in itself biologically interesting, similar to the neutral theory of evolution. Error coordination is more adequate in relation to designing classical manipulative experimental tests. It expects that misacylated tRNAs form more stable (or more frequently) mismatched codon-anticodon duplexes with codons coding for the misloaded amino acid than the same tRNA when it is correctly aminoacylated. This can be tested by comparing results from different, independent experiments. Experiments designed to estimate 'competition' between molecules can also be designed. For example, matching and mismatching codons are put in presence of either correctly or incorrectly loaded tRNAs, and duplex stabilities/frequencies of correctly matched and mismatched anticodons are compared (one way competition between codons). Mixing correctly and incorrectly loaded tRNAs with either matching or mismatching codons would estimate one way competition between correctly and incorrectly loaded tRNAs. Two-way competition (all 4 types of molecules are mixed and all duplex types quantified) could also be considered. Ideally, such experiments should be done for all combinations of codons, anticodons and amino acids.
Implications of the hypothesis
Recent observations suggest that ribosomes select against misacylated tRNAs . Error coordination could be a further mechanism ensuring translational accuracy despite misacylations and mismatches. The translational machinery (the genetic code's amino acid-codon-anticodon assignments, and properties of tRNAs and tRNA synthetases) might be optimized in relation to error coordination if error coordination is observed for a majority of amino acids in relation to either a given tRNA, anticodon, or codon.
Precisely estimating error coordination would imply producing data that include effects of posttranscriptional tRNA modifications [20–22], in particular at wobble positions [23, 24], on misacylation and on anticodon-codon interactions. The latter could be used to improve accuracies of RNA secondary structure predictions. Some codons, anticodons, tRNAs, or organisms may more coordinate errors than others. In the former case, selection enhances directly product accuracy, while in the latter it might minimize errors at each single step of the production process. These two types of selections might lead to very different types of genetic, epistatic and metabolic networks. They would probably associate with different types of evolutionary life history strategies (i.e., r- versus K-strategies). In some cases, low error rates in either misacylation or mismatch may result in more misinsertions than higher error rates at both steps, hence selection for error rates above minimal thresholds might occur.
Error compensation and coordination suggest that accurate translation has probabilistic properties. Design of artificial translational systems might take advantage of error compensation and coordination. Primordial systems at the origins of life perhaps used few versatile, yet accurate tRNAs (or tRNA-like molecules), thanks to high error compensation and coordination. Various editing mechanisms [25, 26] exist and evolved independently in each tRNA synthetase classes: class I, ValRS, IleRS, and LeuRS (editing presumably evolved in the common ancestor of these enzymes ); class II, ThrRS, AlaRS, ProRS, and PheRS . These probably evolved relatively late in the history of the translational machinery [28, 29]. Error compensation and coordination probably predates editing mechanisms for these amino acids. Editing mechanisms have not been detected for many tRNA synthetases, and their loss [30, 31] in those usually possessing editing capacities suggests that other mechanisms, such as error compensation and coordination, exist and prevent amino acid misinsertion also in modern organisms. Loss of editing functions might associate with increased usages of codons prone to error compensation and coordination, as well as alter tRNA structures if these affect error coordination. Error compensation and coordination are unlikely byproducts of a randomly evolving genetic code and the coevolving translational machinery. They promote translational accuracy in the absence and in addition to editing mechanisms.
I thank an anonymous reviewer for proposing the term 'error compensation', resulting in distinguishing error coordination and compensation.
- Cavalcanti ARO, Neto BD, Ferreira R: On the classes of aminoacyl-tRNA synthetases and the error minimization in the genetic code. J Theor Biol 2000, 204: 15-20. 10.1006/jtbi.2000.1082 10.1006/jtbi.2000.1082View ArticlePubMedGoogle Scholar
- Torabi N, Goodarzi H, Najafabadi HS: The case for an error minimizing set of coding amino acids. J Theor Biol 2007, 244: 737-744. 10.1016/j.jtbi.2006.09.021 10.1016/j.jtbi.2006.09.021View ArticlePubMedGoogle Scholar
- Ling JQ, Reynolds N, Ibba M: Aminoacyl-tRNA Synthesis and Translational Quality Control. Ann Rev Microbiol 2009, 63: 61-78. 10.1146/annurev.micro.091208.073210 10.1146/annurev.micro.091208.073210View ArticleGoogle Scholar
- Splan KE, Ignatov ME, Musier-Forsyth K: Transfer RNA modulates the editing mechanism used by class II prolyl-tRNA synthetase. J Biol Chem 2008, 283: 7128-7134. 10.1074/jbc.M709902200 10.1074/jbc.M709902200View ArticlePubMedGoogle Scholar
- Yadavalli SS, Musier-Forsyth K, Ibba M: The return of pretransfer editing in protein synthesis. Proc Nat Acad Scie USA 2008, 105: 19031-19032. 10.1073/pnas.0810781106 10.1073/pnas.0810781106View ArticleGoogle Scholar
- Martinis SA, Boniecki MT: The balance between pre- and post-transfer editing in tRNA synthetases. FEBS Letters 2010, 584: 455-459. 10.1016/j.febslet.2009.11.071 10.1016/j.febslet.2009.11.071View ArticlePubMedPubMed CentralGoogle Scholar
- Zhu B, Zhao MW, Eriani G, Wang ED: A present-day aminoacyl-tRNA synthetase with ancestral editing properties. RNA 2007, 13: 15-21. 10.1261/rna.228707 10.1261/rna.228707View ArticlePubMedPubMed CentralGoogle Scholar
- Zhou XL, Wang ED: Mitochondrial aminoacyl-tRNA synthetases related to human diseases. Progress Biochem & Biophys 2008, 35: 853-858.Google Scholar
- Yu CH, Liao JY, Zhou H, Qu LH: The rat mitochondrial Ori L encodes a novel small RNA resembling an ancestral tRNA. Biochem Biophys Res 2008, 372: 634-638. 10.1016/j.bbrc.2008.05.092 10.1016/j.bbrc.2008.05.092View ArticleGoogle Scholar
- Seligmann H, Amzallag GN: Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code. Naturwissenschaften 2002, 89: 542-551.PubMedGoogle Scholar
- Sonneborn TM: Evolving genes and proteins. Academic Press, New York; 1965.Google Scholar
- Woese CR: Order in the genetic code. Proc Natl Acad Sci USA 1965, 54: 71-75. 10.1073/pnas.54.1.71 10.1073/pnas.54.1.71View ArticlePubMedPubMed CentralGoogle Scholar
- Woese CR: On the evolution of the genetic code. Proc Natl Acad Sci USA 1965, 54: 1546-1552. 10.1073/pnas.54.6.1546 10.1073/pnas.54.6.1546View ArticlePubMedPubMed CentralGoogle Scholar
- Massey SE: A neutral origin for error minimization in the genetic code. J Mol Evol 2008, 67: 510-516. 10.1007/s00239-008-9167-4 10.1007/s00239-008-9167-4View ArticlePubMedGoogle Scholar
- Markham NR, Zuker M: DINAMelt web server for nucleic acid melting prediction. Nuc Acids Res 2005, 33: W577-W581. 10.1093/nar/gki591 10.1093/nar/gki591View ArticleGoogle Scholar
- Markham NR, Zuker M: UNAFold: software for nucleic acid folding and hybriziation. In Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology. Volume chapter 1. Edited by: Keith JM. Humana Press, Totowa, NJ; 2008:3-31. ISBN 978-1-603271-428-9;Google Scholar
- Felder CE, Prilusky J, Silman I, Sussman JL: A server database for dipole moments of proteins. Nuc Acids Res 2007, 35: W512-W521. 10.1093/nar/gkm307 10.1093/nar/gkm307View ArticleGoogle Scholar
- Kantardjiev AA, Atanasov BP: PHEMTO: protein pH-dependent electric moment tools. Nuc Acids Res 2009, 37: W422-W427. 10.1093/nar/gkp336 10.1093/nar/gkp336View ArticleGoogle Scholar
- Effraim PR, Wang JN, Englander MT, Avins J, Leyh TS, Gonzalez RL, Cornish VW: Natural amino acids do not require their native tRNAs for efficient selection by the ribosome. Nature Chem Biol 2009, 5: 947-953. 10.1038/nchembio.255 10.1038/nchembio.255View ArticleGoogle Scholar
- Björk GR, Ericson JU, Gustafsson CED, Hagervall TG, Jonsson YH, Wikstrom PM: Transfer RNA modification. Ann Rev Biochem 1987, 56: 263-285. 10.1146/annurev.bi.56.070187.001403 10.1146/annurev.bi.56.070187.001403View ArticlePubMedGoogle Scholar
- Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K: Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J 2002, 21: 6581-6589. 10.1093/emboj/cdf656 10.1093/emboj/cdf656View ArticlePubMedPubMed CentralGoogle Scholar
- Watanabe K: Role of modified Nucleosides in the translation function of tRNAs from extreme thermophilic bacteria and animal mitochondria. Bull Chem Soc Japan 2007, 80: 1253-1267. 10.1246/bcsj.80.1253 10.1246/bcsj.80.1253View ArticleGoogle Scholar
- Agris PF: Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Reports 2008, 9: 629-635. 10.1038/embor.2008.104 10.1038/embor.2008.104View ArticlePubMedPubMed CentralGoogle Scholar
- Vendeix FAP, Dziergowska A, Gustilo EM, Graham WD, Sproat B, Malkiewicz A, Agris PF: Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding. Biochemistry 2008, 47: 6117-6129. 10.1021/bi702356j 10.1021/bi702356jView ArticlePubMedGoogle Scholar
- Ahel I, Korencic D, Ibba M, Soll D: Trans-editing of mischarged tRNAs. Proc Nat Acad Sci USA 2003, 100: 15422-15427. 10.1073/pnas.2136934100 10.1073/pnas.2136934100View ArticlePubMedPubMed CentralGoogle Scholar
- Beebe K, Mock M, Merriman E, Schimmel P: Distinct domains of tRNA synthetase recognize the same base pair. Nature 2008, 451: 90-U14. 10.1038/nature06454 10.1038/nature06454View ArticlePubMedGoogle Scholar
- Safro MG, Moor NA: Codases: 50 Years After. Mol Biol 2009, 43: 211-222. 10.1134/S0026893309020046 10.1134/S0026893309020046View ArticleGoogle Scholar
- Schimmel P: Development of tRNA synthetases and connection to genetic code and disease. Prot Sci 2008, 17: 1643-1652. 10.1110/ps.037242.108 10.1110/ps.037242.108View ArticleGoogle Scholar
- Martinis SA, Boniecki MT: The balance between pre- and post-transfer editing in tRNA synthetases. Febs Letters 2010, 584: 455-459. 10.1016/j.febslet.2009.11.071 10.1016/j.febslet.2009.11.071View ArticlePubMedPubMed CentralGoogle Scholar
- Lue SW, Kelley SO: An aminoacyl-tRNA synthetase with a defunct editing site. Biochemistry 2005, 44: 3010-3016. 10.1021/bi047901v 10.1021/bi047901vView ArticlePubMedGoogle Scholar
- Roy H, Ling JQ, Alfonzo J, Ibba M: Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem 2005, 280: 38186-38192. 10.1074/jbc.M508281200 10.1074/jbc.M508281200View ArticlePubMedGoogle Scholar
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