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Research Paper

Naturally occurring dual recognition of tRNAHis substrates with and without a universal identity element

, , , , , , & show all
Pages 1275-1285 | Received 15 Jan 2019, Accepted 14 May 2019, Published online: 16 Jun 2019

References

  • Carter CW Jr. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu Rev Biochem. 1993;62:715–748.
  • McClain WH. Transfer RNA identity. Faseb J. 1993;7:72–78.
  • Giege R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 1998;26:5017–5035.
  • Ardell DH. Computational analysis of tRNA identity. FEBS Lett. 2010;584:325–333.
  • Burbaum JJ, Schimmel P. Structural relationships and the classification of aminoacyl-tRNA synthetases. J Biol Chem. 1991;266:16965–16968.
  • Giege R. The early history of tRNA recognition by aminoacyl-tRNA synthetases. J Biosci. 2006;31:477–488.
  • Lee YH, Chang CP, Cheng YJ, et al. Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase. Cell Mol Life Sci. 2017;74:2663–2677.
  • Natsoulis G, Hilger F, Fink GR. The HTS1 gene encodes both the cytoplasmic and mitochondrial histidine tRNA synthetases of S. cerevisiae. Cell. 1986;46:235–243.
  • Chatton B, Walter P, Ebel JP, et al. The yeast VAS1 gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. J Biol Chem. 1988;263:52–57.
  • Chang KJ, Wang CC. Translation initiation from a naturally occurring non-AUG codon in Saccharomyces cerevisiae. J Biol Chem. 2004;279:13778–13785.
  • Tang HL, Yeh LS, Chen NK, et al. Translation of a yeast mitochondrial tRNA synthetase initiated at redundant non-AUG codons. J Biol Chem. 2004;279:49656–49663.
  • Juhling F, Morl M, Hartmann RK, et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2009;37:D159–D162.
  • Orellana O, Cooley L, Soll D. The additional guanylate at the 5ʹ terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Mol Cell Biol. 1986;6:525–529.
  • Cooley L, Appel B, Soll D. Post-transcriptional nucleotide addition is responsible for the formation of the 5ʹ terminus of histidine tRNA. Proc Natl Acad Sci U S A. 1982;79:6475–6479.
  • Gu W, Jackman JE, Lohan AJ, et al. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5ʹ end of tRNAHis. Genes Dev. 2003;17:2889–2901.
  • Abad MG, Rao BS, Jackman JE. Template-dependent 3ʹ-5ʹ nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. Proc Natl Acad Sci U S A. 2010;107:674–679.
  • Rao BS, Mohammad F, Gray MW, et al. Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii. Nucleic Acids Res. 2013;41:1885–1894.
  • Rao BS, Jackman JE. Life without post-transcriptional addition of G-1: two alternatives for tRNAHis identity in Eukarya. RNA. 2015;21:243–253.
  • Wang C, Sobral BW, Williams KP. Loss of a universal tRNA feature. J Bacteriol. 2007;189:1954–1962.
  • Nameki N, Asahara H, Shimizu M, et al. Identity elements of Saccharomyces cerevisiae tRNA(His). Nucleic Acids Res. 1995;23:389–394.
  • Gu W, Hurto RL, Hopper AK, et al. Depletion of Saccharomyces cerevisiae tRNAHis guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m5C. Mol Cell Biol. 2005;25:8191–8201.
  • Chiu WC, Chang CP, Wen WL, et al. Schizosaccharomyces pombe possesses two paralogous valyl-tRNA synthetase genes of mitochondrial origin. Mol Biol Evol. 2010;27:1415–1424.
  • Preston MA, Phizicky EM. The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase. RNA. 2010;16:1068–1077.
  • Sakurai M, Ohtsuki T, Watanabe K. Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm. Nucleic Acids Res. 2005;33:1653–1661.
  • Su D, Lieberman A, Lang BF, et al. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res. 2011;39:4866–4874.
  • Jackman JE, Gott JM, Gray MW. Doing it in reverse: 3ʹ-to-5ʹ polymerization by the Thg1 superfamily. RNA. 2012;18:886–899.
  • Himeno H, Hasegawa T, Ueda T, et al. Role of the extra G-C pair at the end of the acceptor stem of tRNA(His) in aminoacylation. Nucleic Acids Res. 1989;17:7855–7863.
  • Choi H, Gabriel K, Schneider J, et al. Recognition of acceptor-stem structure of tRNA(Asp) by Escherichia coli aspartyl-tRNA synthetase. RNA. 2003;9:386–393.
  • Brennan T, Sundaralingam M. Structlre of transfer RNA molecules containing the long variable loop. Nucleic Acids Res. 1976;3:3235–3250.
  • Rudinger J, Felden B, Florentz C, et al. Strategy for RNA recognition by yeast histidyl-tRNA synthetase. Bioorg Med Chem. 1997;5:1001–1009.
  • Heinemann IU, Nakamura A, O’Donoghue P, et al. tRNAHis-guanylyltransferase establishes tRNAHis identity. Nucleic Acids Res. 2012;40:333–344.
  • Placido A, Sieber F, Gobert A, et al. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res. 2010;38:7711–7717.
  • Long Y, Abad MG, Olson ED, et al. Identification of distinct biological functions for four 3ʹ-5ʹ RNA polymerases. Nucleic Acids Res. 2016;44:8395–8406.
  • Chang CP, Lin G, Chen SJ, et al. Promoting the formation of an active synthetase/tRNA complex by a nonspecific tRNA-binding domain. J Biol Chem. 2008;283:30699–30706.
  • Chang KJ, Lin G, Men LC, et al. Redundancy of non-AUG initiators. A clever mechanism to enhance the efficiency of translation in yeast. J Biol Chem. 2006;281:7775–7783.
  • Boeke JD, Trueheart J, Natsoulis G, et al. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 1987;154:164–175.
  • King MP, Attardi G. Post-transcriptional regulation of the steady-state levels of mitochondrial tRNAs in HeLa cells. J Biol Chem. 1993;268:10228–10237.
  • Janssen BD, Diner EJ, Hayes CS. Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis. Methods Mol Biol. 2012;905:291–309.
  • Francklyn C, Schimmel P (1990) Enzymatic aminoacylation of an eight-base-pair microhelix with histidine. Proc Nat Acad Sci USA, 87, 8655–8659.
  • Fersht AR, Ashford JS, Bruton CJ, et al. Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl-tRNA synthetases. Biochemistry. 1975;14:1–4.
  • Chang CY, Chien CI, Chang CP, et al. A WHEP domain regulates the dynamic structure and activity of Caenorhabditis elegans Glycyl-tRNA synthetase. J Biol Chem. 2016;291:16567–16575.
  • Ladror US, Egan DA, Snyder SW, et al. Domain structure analysis of elongation factor-3 from Saccharomyces cerevisiae by limited proteolysis and differential scanning calorimetry. Protein Sci. 1998;7:2595–2601.

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