Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid α-aminobutyrate

References

• Ibba M, Söll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem 2000; 69:617-50; https://doi.org/10.1146/annurev.biochem.69.1.617
   PubMed Web of Science ®Google Scholar
• Pauling L. The probability of errors in the process of synthesis of protein molecules. Basel (Switzerland): Birkhauser; 1957.
   Google Scholar
• Yadavalli SS, Ibba M. Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 2012; 86:1-43;
   PubMed Web of Science ®Google Scholar
• Mascarenhas AP, An S, Rosen AE, Martinis SA, Musier-Forsyth K. Fidelity Mechanisms of the Aminoacyl-tRNA Synthetases. In: Köhrer C, RajBhandary UL, editors. Protein Engineering: Nucleic Acids and Molecular Biology. Berlin Heidelberg (Germany): Springer-Verlag; 2009; 155-203.
   Google Scholar
• Ahel I, Korencic D, Ibba M, Söll D. Trans-editing of mischarged tRNAs. Proc Natl Acad Sci U S A 2003; 100:15422-7; https://doi.org/10.1073/pnas.2136934100
   PubMed Web of Science ®Google Scholar
• Beuning PJ, Musier-Forsyth K. Hydrolytic editing by a class II aminoacyl-tRNA synthetase. Proc Natl Acad Sci U S A 2000; 97:8916-20; https://doi.org/10.1073/pnas.97.16.8916
   PubMed Web of Science ®Google Scholar
• Ruan B, Söll D. The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNACys deacylase. J Biol Chem 2005; 280:25887-91; https://doi.org/10.1074/jbc.M502174200
   PubMed Web of Science ®Google Scholar
• Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Söll D. Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J Biol Chem 2002; 277:34743-8; https://doi.org/10.1074/jbc.M206928200
   PubMed Web of Science ®Google Scholar
• An S, Musier-Forsyth K. Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein. J Biol Chem 2004; 279:42359-62; https://doi.org/10.1074/jbc.C400304200
   PubMed Web of Science ®Google Scholar
• Beuning PJ, Musier-Forsyth K. Species-specific differences in amino acid editing by class II prolyl-tRNA synthetase. J Biol Chem 2001; 276:30779-85; https://doi.org/10.1074/jbc.M104761200
   PubMed Web of Science ®Google 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; 283:7128-34; https://doi.org/10.1074/jbc.M709902200
   PubMed Web of Science ®Google Scholar
• 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; https://doi.org/10.1074/jbc.M507550200
   PubMed Web of Science ®Google Scholar
• So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K. Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. J Biol Chem 2011; 286:31810-20; https://doi.org/10.1074/jbc.M111.232611
   PubMed Web of Science ®Google Scholar
• Vargas-Rodriguez O, Musier-Forsyth K. Exclusive use of trans-editing domains prevents proline mistranslation. J Biol Chem 2013; 288:14391-9; https://doi.org/10.1074/jbc.M113.467795
   PubMed Web of Science ®Google Scholar
• Das M, Vargas-Rodriguez O, Goto Y, Suga H, Musier-Forsyth K. Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation. Nucleic Acids Res 2014; 42:3943-53; https://doi.org/10.1093/nar/gkt1332
   PubMed Web of Science ®Google Scholar
• Liu Z, Vargas-Rodriguez O, Goto Y, Novoa EM, Ribas de Pouplana L, Suga H, Musier-Forsyth K. Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation. Proc Natl Acad Sci U S A 2015; 112:6027-32; https://doi.org/10.1073/pnas.1423664112
   PubMed Web of Science ®Google Scholar
• Cava F, Hidalgo A, Berenguer J. Thermus thermophilus as biological model. Extremophiles 2009; 13:213-31; https://doi.org/10.1007/s00792-009-0226-6
   PubMed Web of Science ®Google Scholar
• VerBerkmoes NC, Shah MB, Lankford PK, Pelletier DA, Strader MB, Tabb DL, McDonald WH, Barton JW, Hurst GB, Hauser L, et al. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res 2006; 5:287-98; https://doi.org/10.1021/pr0503230
   PubMed Web of Science ®Google Scholar
• Crepin T, Yaremchuk A, Tukalo M, Cusack S. Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure 2006; 14:1511-25; https://doi.org/10.1016/j.str.2006.08.007
   PubMed Web of Science ®Google Scholar
• Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, et al. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 2004; 22:55-61; https://doi.org/10.1038/nbt923
   PubMed Web of Science ®Google Scholar
• Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzator S, Park YM, Buso N, Lopez R. The EMBL-EBI bioinformatics web and programmatic tools framework. - Abstract - Europe PMC. Nucleic Acids Res 2015; 43:W580-W4; https://doi.org/10.1093/nar/gkv279
   PubMed Web of Science ®Google Scholar
• McWilliam H, Li W, Uludag M, Squizzato S, Park Ym, Buso N, Cowley AP, Lopez R. Analysis Tool Web Services from the EMBL-EBI. - Abstract - Europe PMC. Nucleic Acids Res 2013; 41:W597-W600; https://doi.org/10.1093/nar/gkt376
   PubMed Web of Science ®Google Scholar
• Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. - Abstract - Europe PMC. Trends in Genetics 2000; 16:276-7; https://doi.org/10.1016/S0168-9525(00)02024-2
   PubMed Web of Science ®Google Scholar
• Fotheringham IG, Grinter N, Pantaleone DP, Senkpeil RF, Taylor PP. Engineering of a novel biochemical pathway for the biosynthesis of L-2-aminobutyric acid in Escherichia coli K12. Bioorg Med Chem 1999; 7:2209-13; https://doi.org/10.1016/S0968-0896(99)00153-4
   PubMed Web of Science ®Google Scholar
• Zhang W, Gao C, Che B, Ma C, Zheng Z, Qin T, Xu P. Efficient bioconversion of l-threonine to 2-oxobutyrate using whole cells of Pseudomonas stutzeri SDM. Bioresour Technol 2012; 110:719-22; https://doi.org/10.1016/j.biortech.2012.01.123
   PubMed Web of Science ®Google Scholar
• Zhang K, Li H, Cho KM, Liao JC. Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine. Proc Natl Acad Sci U S A 2010; 107:6234-9; https://doi.org/10.1073/pnas.0912903107
   PubMed Web of Science ®Google Scholar
• Zhu L, Tao R, Wang Y, Jiang Y, Lin X, Yang Y, Zheng H, Jiang W, Yang S. Removal of L-alanine from the production of L-2-aminobutyric acid by introduction of alanine racemase and D-amino acid oxidase. Appl Microbiol Biotechnol 2011; 90:903-10; https://doi.org/10.1007/s00253-011-3127-4
   PubMed Web of Science ®Google Scholar
• Kumar S, Das M, Hadad CM, Musier-Forsyth K. Substrate specificity of bacterial prolyl-tRNA synthetase editing domain is controlled by a tunable hydrophobic pocket. J Biol Chem 2012; 287:3175-84; https://doi.org/10.1074/jbc.M111.313619
   PubMed Web of Science ®Google Scholar
• Wong FC, Beuning PJ, Nagan M, Shiba K, Musier-Forsyth K. Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing. Biochemistry 2002; 41:7108-15; https://doi.org/10.1021/bi012178j
   PubMed Web of Science ®Google Scholar
• Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 2015; 10:449-61; https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Bartholow TG, Sanford BL, Cao B, Schmit HL, Johnson JM, Meitzner J, Bhattacharyya S, Musier-Forsyth K, Hati S. Strictly conserved lysine of prolyl-tRNA Synthetase editing domain facilitates binding and positioning of misacylated tRNA(Pro.). Biochemistry 2014; 53:1059-68; https://doi.org/10.1021/bi401279r
   PubMed Web of Science ®Google Scholar
• Loftfield RB, Vanderjagt D. The frequency of errors in protein biosynthesis. Biochem J 1972; 128:1353-6; https://doi.org/10.1042/bj1281353
   PubMed Web of Science ®Google Scholar
• Splan KE, Musier-Forsyth K, Boniecki MT, Martinis SA. In vitro assays for the determination of aminoacyl-tRNA synthetase editing activity. Methods 2008; 44:119-28; https://doi.org/10.1016/j.ymeth.2007.10.009
   PubMed Web of Science ®Google Scholar
• Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009; 37:D93-7; https://doi.org/10.1093/nar/gkn787
   PubMed Web of Science ®Google Scholar
• Fersht AR, Dingwall C. Establishing the misacylation/deacylation of the tRNA pathway for the editing mechanism of prokaryotic and eukaryotic valyl-tRNA synthetases. Biochemistry 1979; 18:1238-45; https://doi.org/10.1021/bi00574a019
   PubMed Web of Science ®Google Scholar
• Doring V, Mootz HD, Nangle LA, Hendrickson TL, de Crecy-Lagard V, Schimmel P, Marlière P. Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 2001; 292:501-4; https://doi.org/10.1126/science.1057718
   PubMed Web of Science ®Google Scholar
• Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I. The physiological target for LeuRS translational quality control is norvaline. EMBO J 2014; 33:1639-53; https://doi.org/10.15252/embj.201488199
   PubMed Web of Science ®Google Scholar
• Jakubowski H. Quality control in tRNA charging. Wiley Interdiscip Rev RNA 2012; 3:295-10; https://doi.org/10.1002/wrna.122
   PubMed Web of Science ®Google Scholar
• Nangle LA, De Crecy Lagard V, Doring V, Schimmel P. Genetic code ambiguity. Cell viability related to the severity of editing defects in mutant tRNA synthetases. J Biol Chem 2002; 277:45729-33; https://doi.org/10.1074/jbc.M208093200
   PubMed Web of Science ®Google Scholar
• Bullwinkle T, Lazazzera B, Ibba M. Quality control and infiltration of translation by amino acids outside of the genetic code. Annu Rev Genet 2014; 48:149-66; https://doi.org/10.1146/annurev-genet-120213-092101
   PubMed Web of Science ®Google Scholar
• Bullwinkle TJ, Reynolds NM, Raina M, Moghal A, Matsa E, Rajkovic A, Kayadibi H, Fazlollahi F, Ryan C, Howitz N, et al. Oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code. Elife 2014; 3:1-16; https://doi.org/10.7554/eLife.02501
   Web of Science ®Google Scholar
• Peterson PJ, Fowden L. Purification, properties and comparative specificities of the enzyme prolyl-transfer ribonucleic acid synthetase from Phaseolus aureus and Polygonatum multiflorum. Biochem J 1965; 97:112-24; https://doi.org/10.1042/bj0970112
   PubMed Web of Science ®Google Scholar
• Norris RD. Substrate discrimination by prolyl-tRNA synthetase from various higher plants. Phytochemistry 1972; 11:2921-35; https://doi.org/10.1016/0031-9422(72)80082-7
   Web of Science ®Google Scholar
• Fowden L. Amino-acid Analogues and the Growth of Seedlings. J Exp Bot 1963; 14:387-98; https://doi.org/10.1093/jxb/14.3.387
   Web of Science ®Google Scholar
• Lee J, Joshi N, Pasini R, Dobson RC, Allison J, Leustek T. Inhibition of Arabidopsis growth by the allelopathic compound azetidine-2-carboxylate is due to the low amino acid specificity of cytosolic prolyl-tRNA synthetase. Plant J 2016; 88:236-46; https://doi.org/10.1111/tpj.13246
   PubMed Web of Science ®Google Scholar
• Yang H, Zheng G, Peng X, Qiang B, Yuan J. D-Amino acids and D-Tyr-tRNA(Tyr) deacylase: stereospecificity of the translation machine revisited. FEBS Lett 2003; 552:95-8; https://doi.org/10.1016/S0014-5793(03)00858-5
   PubMed Web of Science ®Google Scholar
• Jakubowski H, Fersht AR. Alternative pathways for editing non-cognate amino acids by aminoacyl-tRNA synthetases. Nucleic Acids Res 1981; 9:3105-17; https://doi.org/10.1093/nar/9.13.3105
   PubMed Web of Science ®Google Scholar
• Igloi GL, von der Haar F, Cramer F. Hydrolytic action of aminoacyl-tRNA synthetases from baker's yeast. “Chemical proofreading” of Thr-tRNAVal by valyl-tRNA synthetase studied with modified tRNAVal and amino acid analogues. Biochemistry 1977; 16:1696-702; https://doi.org/10.1021/bi00627a027
   PubMed Web of Science ®Google Scholar
• Nangle LA, Motta CM, Schimmel P. Global effects of mistranslation from an editing defect in mammalian cells. Chem Biol 2006; 13:1091-100; https://doi.org/10.1016/j.chembiol.2006.08.011
   PubMedGoogle Scholar
• LaRiviere FJ, Wolfson AD, Uhlenbeck OC. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 2001; 294:165-8; https://doi.org/10.1126/science.1064242
   PubMed Web of Science ®Google Scholar
• Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, Duke RE, Luo R, Walker RX, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails K, Goets AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell DR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Hsieh M-J, Cui G, Roe DR, Matthews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA. AMBER 12. 2012. San Francisco (CA): University of California, San Francisco; 2012.
   Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79:926-35; https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995). J Am Chem Soc 1996; 118:2309-; https://doi.org/10.1021/ja955032e
   Web of Science ®Google Scholar
• Cheatham TE, Kollman PA. Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem 2000; 51:435-71; https://doi.org/10.1146/annurev.physchem.51.1.435
   PubMed Web of Science ®Google Scholar
• York DM, Darden TA, Pedersen LG. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J Chem Phys 1993; 99:8345-8; https://doi.org/10.1063/1.465608
   Web of Science ®Google Scholar
• Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977; 23:327-41; https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers 1992; 32:523-35; https://doi.org/10.1002/bip.360320508
   PubMed Web of Science ®Google Scholar
• Sindhikara DJ, Kim S, Voter AF, Roitberg AE. Bad seeds sprout perilous dynamics: Stochastic thermostat induced trajectory synchronization in biomolecules. J Chem Theory Comput 2009; 5:1624-31; https://doi.org/10.1021/ct800573m
   PubMed Web of Science ®Google Scholar
• Uberuaga BP, Anghel M, Voter AF. Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. J Chem Phys 2004; 120:6363-74; https://doi.org/10.1063/1.1667473
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996; 14:33-8, 27–8; https://doi.org/10.1016/0263-7855(96)00018-5
   PubMed Web of Science ®Google Scholar
• DeLano WL. PyMOL molecular viewer: Updates and refinements. Abstracts of Papers of the American Chemical Society 2009; 238.
   Web of Science ®Google Scholar
• DeLano WL, Lam JW. PyMOL: A communications tool for computational models. Abstracts of Papers of the American Chemical Society 2005; 230:U1371-U2.
   Web of Science ®Google Scholar
• Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 2012; 4:17; https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 2009; 30:2785-91; https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010; 31:455-61;
   PubMed Web of Science ®Google Scholar
• Voss NR, Gerstein M. 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res 2010; 38:W555-62; https://doi.org/10.1093/nar/gkq395
   PubMed Web of Science ®Google Scholar
• Nordin BE, Schimmel P. Plasticity of recognition of the 3′-end of mischarged tRNA by class I aminoacyl-tRNA synthetases. J Biol Chem 2002; 277:20510-7; https://doi.org/10.1074/jbc.M202023200
   PubMed Web of Science ®Google Scholar
• Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72:248-54; https://doi.org/10.1016/0003-2697(76)90527-3
   PubMed Web of Science ®Google Scholar
• Fersht AR, Ashford JS, Bruton CJ, Jakes R, Koch GL, Hartley BS. Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl-tRNA synthetases. Biochemistry 1975; 14:1-4; https://doi.org/10.1021/bi00672a001
   PubMed Web of Science ®Google Scholar
• Liu H, Musier-Forsyth K. Escherichia coli proline tRNA synthetase is sensitive to changes in the core region of tRNA(Pro). Biochemistry 1994; 33:12708-14; https://doi.org/10.1021/bi00208a023
   PubMed Web of Science ®Google Scholar
• Ledoux S, Uhlenbeck OC. [3′-32P]-labeling tRNA with nucleotidyltransferase for assaying aminoacylation and peptide bond formation. Methods 2008; 44:74-80; https://doi.org/10.1016/j.ymeth.2007.08.001
   PubMed Web of Science ®Google Scholar
• Eliceiri CAS, Wayne SR, Kevin W. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 2012; 9:671-5; https://doi.org/10.1038/nmeth.2089
   PubMed Web of Science ®Google Scholar
• Goto Y, Katoh T, Suga H. Flexizymes for genetic code reprogramming. Nat Protoc 2011; 6:779-90; https://doi.org/10.1038/nprot.2011.331
   PubMed Web of Science ®Google Scholar
• Murakami H, Ohta A, Ashigai H, Suga H. A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat Methods 2006; 3:357; https://doi.org/10.1038/nmeth877
   PubMed Web of Science ®Google Scholar