Genomes and Genes
transfer rna aminoacylation
Summary: The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.
- Fukunaga R, Yokoyama S. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nat Struct Mol Biol. 2005;12:915-22 pubmed..One conformation is the canonical 'aminoacylation state.' The other conformation seems to be the 'intermediate state,' where the misaminoacylated 3' end has partially relocated to the editing domain. ..
- Ling J, So B, Yadavalli S, Roy H, Shoji S, Fredrick K, et al. Resampling and editing of mischarged tRNA prior to translation elongation. Mol Cell. 2009;33:654-60 pubmed publisher..Resampling of mischarged tRNAs was shown to increase the accuracy of translation over ten fold during in vitro protein synthesis, supporting the presence of an additional quality control step prior to translation elongation. ..
- An S, Musier Forsyth K. Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. J Biol Chem. 2005;280:34465-72 pubmed publisher..These results suggest that the specificity of trans-editing by YbaK is ensured through formation of a novel ProRS.YbaK.tRNA complex...
- Park H, Hohn M, Umehara T, Guo L, Osborne E, Benner J, et al. Expanding the genetic code of Escherichia coli with phosphoserine. Science. 2011;333:1151-4 pubmed publisher..This system has general utility in protein engineering, molecular biology, and disease research. ..
- Tardif K, Liu M, Vitseva O, Hou Y, Horowitz J. Misacylation and editing by Escherichia coli valyl-tRNA synthetase: evidence for two tRNA binding sites. Biochemistry. 2001;40:8118-25 pubmed..Gel-mobility-shift experiments to characterize the interaction of tRNA(Val) with the enzyme provide evidence for two tRNA binding sites on ValRS. ..
- Wiltrout E, Goodenbour J, Frechin M, Pan T. Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:10494-506 pubmed publisher..Our results indicate that the yeast MetRS is responsible for extensive misacylation of non-methionyl tRNAs, and mismethionylation also occurs in this evolutionary branch. ..
- Zhou X, Ruan Z, Huang Q, Tan M, Wang E. Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote. Nucleic Acids Res. 2013;41:302-14 pubmed publisher..This study has provided the first comprehensive elucidation of the translational fidelity control mechanism of eukaryotic ThrRS. ..
- Nomanbhoy T, Hendrickson T, Schimmel P. Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis. Mol Cell. 1999;4:519-28 pubmed..These results illustrate a remarkable capacity for a specific tRNA to enhance amino acid fine structure recognition by triggering a unimolecular translocation event. ..
- Wang C, Sobral B, Williams K. Loss of a universal tRNA feature. J Bacteriol. 2007;189:1954-62 pubmed..The altered tRNA charging system may have affected other tRNA charging systems in these bacteria; for example, a site in tRNA(Glu) sequences was found to covary with tRNA(His) among alphaproteobacteria...
- Hu Q, Huang Q, Wang E. Crucial role of the C-terminal domain of Mycobacterium tuberculosis leucyl-tRNA synthetase in aminoacylation and editing. Nucleic Acids Res. 2013;41:1859-72 pubmed publisher..This system for the investigation of the interactions between MtbLeuRS and tRNA(Leu) provides a platform for the development of novel antitubercular drugs. ..
- Martin F, Eriani G, Eiler S, Moras D, Dirheimer G, Gangloff J. Overproduction and purification of native and queuine-lacking Escherichia coli tRNA(Asp). Role of the wobble base in tRNA(Asp) acylation. J Mol Biol. 1993;234:965-74 pubmed..coli, where only one contact is thought to occur at position 34. ..
- McClain W, Schneider J, Gabriel K. Distinctive acceptor-end structure and other determinants of Escherichia coli tRNAPro identity. Nucleic Acids Res. 1994;22:522-9 pubmed..The results speak for the importance of a distinctive conformation in the acceptor-stem helix of tRNAPro for aminoacylation by the prolyl-tRNA synthetase. The anticodon also contributes to tRNAPro identity but is not necessary in vivo. ..
- Yan W, Tan M, Eriani G, Wang E. Leucine-specific domain modulates the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nucleic Acids Res. 2013;41:4988-98 pubmed publisher..The present work provides a novel framework of co-evolution between LeuRS and its cognate tRNA through LSD. ..
- Dale T, Fahlman R, Olejniczak M, Uhlenbeck O. Specificity of the ribosomal A site for aminoacyl-tRNAs. Nucleic Acids Res. 2009;37:1202-10 pubmed publisher..We propose that uniform aa-tRNA binding to the A site may be a consequence of a conformational change in the ribosome, induced by the presence of the appropriate combination of contributions from the anticodon, amino acid and tRNA body. ..
- Park S, Schimmel P, Kim S. Aminoacyl tRNA synthetases and their connections to disease. Proc Natl Acad Sci U S A. 2008;105:11043-9 pubmed publisher..Although much has been uncovered in recent years, many novel functions, disease connections, and interpathway connections of tRNA synthetases have yet to be worked out. ..
- Itoh Y, Sekine S, Kuroishi C, Terada T, Shirouzu M, Kuramitsu S, et al. Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. RNA Biol. 2008;5:169-77 pubmed..Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel. ..
- Johansson M, Esberg A, Huang B, Bjork G, Byström A. Eukaryotic wobble uridine modifications promote a functionally redundant decoding system. Mol Cell Biol. 2008;28:3301-12 pubmed publisher..Moreover, the observation that the mcm(5)U(34)- and some ncm(5)U(34)-containing tRNAs efficiently read G-ending codons challenges the notion that eukaryotes do not use U-G wobbling. ..
- Boniecki M, Vu M, Betha A, Martinis S. CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase. Proc Natl Acad Sci U S A. 2008;105:19223-8 pubmed publisher..Further investigation showed that a second tRNA-dependent activity prevented misacylation and is intrinsic to the active site for aminoacylation. ..
- Turk R, Chumachenko N, Yarus M. Multiple translational products from a five-nucleotide ribozyme. Proc Natl Acad Sci U S A. 2010;107:4585-9 pubmed publisher..Small size and minimal requirements for regiospecific translational activity strongly support the hypothesis that minuscule RNA enzymes participated in early forms of translation. ..
- Li R, Guan M. Human mitochondrial leucyl-tRNA synthetase corrects mitochondrial dysfunctions due to the tRNALeu(UUR) A3243G mutation, associated with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like symptoms and diabetes. Mol Cell Biol. 2010;30:2147-54 pubmed publisher..These findings provide new insights into the molecular mechanism of maternally inherited diseases and a step toward therapeutic interventions for these disorders...
- Pan T. Adaptive translation as a mechanism of stress response and adaptation. Annu Rev Genet. 2013;47:121-37 pubmed publisher..This review describes the occurrence of, the translation mechanisms for, and the functional hypotheses on regulated synthesis of mutant proteins. ..
- Zhou X, Du D, Tan M, Lei H, Ruan L, Eriani G, et al. Role of tRNA amino acid-accepting end in aminoacylation and its quality control. Nucleic Acids Res. 2011;39:8857-68 pubmed publisher..Collectively, the data show how protein synthesis quality is controlled by the CCA?? homogeneity of tRNAs. ..
- Yadavalli S, Ibba M. Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res. 2013;41:1104-12 pubmed publisher..However, minor changes in the defunct editing domain of the Mycoplasma enzyme were sufficient to restore E. coli growth, indicating that translational accuracy is an evolutionarily selectable trait. ..
- Fersht A, Kaethner M. Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing. Biochemistry. 1976;15:3342-6 pubmed..The hyperspecificity of the enzyme is based on discriminating between the two competing substrates twice: once against the undesired substrate in the synthetic step, and once against the desired substrate in the destructive step. ..
- Wolfson A, Pleiss J, Uhlenbeck O. A new assay for tRNA aminoacylation kinetics. RNA. 1998;4:1019-23 pubmed
- Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol. 2005;12:923-30 pubmed..The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA-3' end dynamics associated successively with aminoacylation, post-transfer editing and product release. ..
- Dale T, Uhlenbeck O. Binding of misacylated tRNAs to the ribosomal A site. RNA. 2005;11:1610-5 pubmed
- Wang L, Brock A, Herberich B, Schultz P. Expanding the genetic code of Escherichia coli. Science. 2001;292:498-500 pubmed..This approach should provide a general method for increasing the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids. ..
- Fukunaga J, Yokogawa T, Ohno S, Nishikawa K. Misacylation of yeast amber suppressor tRNA(Tyr) by E. coli lysyl-tRNA synthetase and its effective repression by genetic engineering of the tRNA sequence. J Biochem. 2006;139:689-96 pubmed..This "optimized" tRNA together with our mutant TyrRS should serve as an efficient and faithful tool for site-specific incorporation of unnatural amino acids into proteins in a protein-synthesizing system in vitro or in vivo. ..
- Ferrer E. Spotlight on targeting aminoacyl-tRNA synthetases for the treatment of fungal infections. Drug News Perspect. 2006;19:347-8 pubmed..Aminoacyl-tRNA synthetases, crucial for protein synthesis, represent a new target for the treatment of different infectious diseases. ..
- Rodin S, Rodin A. Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. DNA Cell Biol. 2006;25:617-26 pubmed..The principle of evolutionary continuity suggests that their protein successors also arose on complementary strands. Our analyses support this hypothesis. ..
- Delarue M. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA. 2007;13:161-9 pubmed
- Nureki O, Vassylyev D, Tateno M, Shimada A, Nakama T, Fukai S, et al. Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science. 1998;280:578-82 pubmed
- Giege R. The early history of tRNA recognition by aminoacyl-tRNA synthetases. J Biosci. 2006;31:477-88 pubmed
- Liu C, Gamper H, Shtivelband S, Hauenstein S, Perona J, Hou Y. Kinetic quality control of anticodon recognition by a eukaryotic aminoacyl-tRNA synthetase. J Mol Biol. 2007;367:1063-78 pubmed..This kinetic quality control reflects an evolutionary adaptation of some tRNA synthetases to improve the anticodon specificity of tRNA aminoacylation from bacteria to humans, possibly to accommodate concomitant changes in codon usage. ..
- Kawakami T, Murakami H, Suga H. Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem Biol. 2008;15:32-42 pubmed publisher..This platform technology offers a convenient tool for the construction of N-methyl-peptide libraries, potentially leading to the discovery of therapeutic peptides. ..
- Weygand Durasevic I, Schwob E, Soll D. Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA. Proc Natl Acad Sci U S A. 1993;90:2010-4 pubmed..Thus, the stability of the noncognate complex may be the basis for mischarging in vivo. ..
- Zhang C, Perona J, Ryu K, Francklyn C, Hou Y. Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases. J Mol Biol. 2006;361:300-11 pubmed..These results emphasize that the distinct mechanistic signatures of class I versus class II tRNA synthetases ensure rapid turnover of aminoacyl-tRNAs during protein synthesis. ..
- Dock Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, et al. Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell. 2000;103:877-84 pubmed..As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation. ..
- Fahlman R, Dale T, Uhlenbeck O. Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites. Mol Cell. 2004;16:799-805 pubmed
- Schulman L, Pelka H. Anticodon switching changes the identity of methionine and valine transfer RNAs. Science. 1988;242:765-8 pubmed..These results indicate that the anticodon contains sufficient information to distinguish methionine and valine tRNAs with high fidelity. ..
- Jakubowski H. Quality control in tRNA charging -- editing of homocysteine. Acta Biochim Pol. 2011;58:149-63 pubmed..Excessive homocysteine thiolactone synthesis in hyperhomocysteinemia caused by genetic or nutritional deficiencies is linked to human vascular and neurological diseases. ..
- McClain W. Surprising contribution to aminoacylation and translation of non-Watson-Crick pairs in tRNA. Proc Natl Acad Sci U S A. 2006;103:4570-5 pubmed..The statistical preservation of the six mutant mispair sites across tRNA(Gly) in many organisms points to a fundamental structure-function signature within tRNA(Gly) with possible analogous missions in other RNAs. ..
- Netzer N, Goodenbour J, David A, Dittmar K, Jones R, Schneider J, et al. Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature. 2009;462:522-6 pubmed publisher..In demonstrating an unexpected conditional aspect of decoding mRNA, our findings illustrate the importance of considering alternative iterations of the genetic code. ..
- McGuire A, Mangroo D. Cex1p is a novel cytoplasmic component of the Saccharomyces cerevisiae nuclear tRNA export machinery. EMBO J. 2007;26:288-300 pubmed..cerevisiae. They also suggest that Cex1p collects aminoacyl-tRNAs from the nuclear export receptors at the cytoplasmic side of the nuclear pore complex, and transfers them to eEF-1A using a channelling mechanism. ..
- Hauenstein S, Hou Y, Perona J. The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity. J Biol Chem. 2008;283:21997-2006 pubmed publisher..tRNA(Cys) binding to SepRS also enhances the capacity of the enzyme to discriminate among amino acids, indicating the existence of functional connectivity between the tRNA and amino acid binding sites of the enzyme. ..
- Subtelny A, Hartman M, Szostak J. Ribosomal synthesis of N-methyl peptides. J Am Chem Soc. 2008;130:6131-6 pubmed publisher..Such libraries could be subjected to in vitro selection methods to identify drug-like, high-affinity ligands for protein targets of interest. ..
- Walker S, Fredrick K. Preparation and evaluation of acylated tRNAs. Methods. 2008;44:81-6 pubmed publisher..Here, methods to prepare aminoacyl-tRNA, N-acetyl-aminoacyl-tRNA, and fMet-tRNA(fMet) and to assess their homogeneity are described. Using these methods, acylated tRNAs of high homogeneity can be reliably obtained. ..