TRNA His-guanylyltransferase establishes tRNA His identity

Nucleic Acids Research

Volumn 40, Issue 1, 2012, Pages 333-344

  Heinemann, Ilka U ^a   Nakamura, Akiyoshi ^b   O'Donoghue, Patrick ^a   Eiler, Daniel ^a   Söll, Dieter ^a  

^a YALE UNIVERSITY   (United States)

^b HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

HISTIDINE TRANSFER RNA; HISTIDINE TRANSFER RNA GUANYLYLTRANSFERASE; INORGANIC PYROPHOSPHATASE; TETRAMER; TRANSFER RNA; TRANSFERASE; UNCLASSIFIED DRUG; ADENOSINE TRIPHOSPHATE; NUCLEOTIDYLTRANSFERASE; TRNA GUANYLYLTRANSFERASE;

ANTICODON; ARCHAEBACTERIUM; ARTICLE; CHEMICAL REACTION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; EUKARYOTE; GUANYLATION; HORIZONTAL GENE TRANSFER; HUMAN; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; RNA EDITING; RNA REPAIR; STRUCTURAL HOMOLOGY; YEAST; BACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ARCHAEA; EUKARYOTA;

ADENOSINE TRIPHOSPHATE; ANTICODON; ARCHAEA; BACTERIA; BASE SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEOTIDYLTRANSFERASES; PYROPHOSPHATASES; RNA EDITING; RNA, TRANSFER, HIS; YEASTS;

EID: 84855286097     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr696     Document Type: Article

References (47)

1. Giegé R., Sissler, M. and Florentz, C. (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res., 26, 5017-5035.
2. Himeno, H., Hasegawa, T., Ueda, T., Watanabe, K., Miura, K. and Shimizu, M. (1989) Role of the extra G-C pair at the end of the acceptor stem of tRNAHis in aminoacylation. Nucleic Acids Res., 17, 7855-7863. (Pubitemid 19251952)
3. Francklyn, C. and Schimmel, P. (1990) Enzymatic aminoacylation of an eight-base-pair microhelix with histidine. Proc. Natl Acad. Sci. USA, 87, 8655-8659.
4. Rudinger, J., Florentz, C. and Giegé R. (1994) Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context. Nucleic Acids Res., 22, 5031-5037.
5. Nameki, N., Asahara, H., Shimizu, M., Okada, N. and Himeno, H. (1995) Identity elements of Saccharomyces cerevisiae tRNAHis. Nucleic Acids Res., 23, 389-394.
6. Fromant, M., Plateau, P. and Blanquet, S. (2000) Function of the extra 50-phosphate carried by histidine tRNA. Biochemistry, 39, 4062-4067. (Pubitemid 30210383)
7. Connolly, S.A., Rosen, A.E., Musier-Forsyth, K. and Francklyn, C.S. (2004) G-1:C73 recognition by an arginine cluster in the active site of Escherichia coli histidyl-tRNA synthetase. Biochemistry, 43, 962-969. (Pubitemid 38141494)
8. Rosen, A.E., Brooks, B.S., Guth, E., Francklyn, C.S. and Musier-Forsyth, K. (2006) Evolutionary conservation of a functionally important backbone phosphate group critical for aminoacylation of histidine tRNAs. RNA, 12, 1315-1322. (Pubitemid 43990556)
9. Rosen, A.E. and Musier-Forsyth, K. (2004) Recognition of G-1:C73 atomic groups by Escherichia coli histidyl-tRNA synthetase. J. Am. Chem. Soc., 126, 64-65. (Pubitemid 38090340)
10. Orellana, O., Cooley, L. and Söll, D. (1986) The additional guanylate at the 50 terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Mol. Cell. Biol., 6, 525-529. (Pubitemid 16158127)
11. Burkard, U., Willis, I. and Söll, D. (1988) Processing of histidine transfer RNA precursors. Abnormal cleavage site for RNase P. J. Biol. Chem., 263, 2447-2451. (Pubitemid 18060310)
12. Brannvall, M., Fredrik Pettersson, B.M. and Kirsebom, L.A. (2002) The residue immediately upstream of the RNase P cleavage site is a positive determinant. Biochimie., 84, 693-703. (Pubitemid 35363454)
13. Ardell, D.H. and Andersson, S.G. (2006) TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res., 34, 893-904. (Pubitemid 43380673)
14. Wang, C., Sobral, B.W. and Williams, K.P. (2007) Loss of a universal tRNA feature. J. Bacteriol., 189, 1954-1962. (Pubitemid 46446159)
15. Yuan, J., Gogakos, T., Babina, A.M., Söll, D. and Randau, L. (2011) Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/ tRNAHis pair. Nucleic Acids Res., 39, 2286-2293.
16. Cooley, L., Appel, B. and Söll, D. (1982) Post-transcriptional nucleotide addition is responsible for the formation of the 50 terminus of histidine tRNA. Proc. Natl Acad. Sci. USA, 79, 6475-6479. (Pubitemid 13207517)
17. Williams, J.B., Cooley, L. and Söll, D. (1990) Enzymatic addition of guanylate to histidine transfer RNA. Methods Enzymol., 181, 451-462. (Pubitemid 20219715)
18. Pande, S., Jahn, D. and Söll, D. (1991) Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties. J. Biol. Chem., 266, 22826-22831. (Pubitemid 21908725)
19. Jahn, D. and Pande, S. (1991) Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. II. Catalytic mechanism. J. Biol. Chem., 266, 22832-22836. (Pubitemid 21908726)
20. Gu, W., Jackman, J.E., Lohan, A.J., Gray, M.W. and Phizicky, E.M. (2003) tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 50 end of tRNAHis. Genes Dev., 17, 2889-2901. (Pubitemid 37523154)
21. Heinemann, I.U., O'Donoghue, P., Madinger, C., Benner, J., Randau, L., Noren, C.J. and Söll, D. (2009) The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. Proc. Natl Acad. Sci. USA, 106, 21103-21108.
22. Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K. and Ohyama, K. (1992) Transfer RNA genes in the mitochondrial genome from a liverwort, Marchantia polymorpha: the absence of chloroplast-like tRNAs. Nucleic Acids Res., 20, 3773-3777.
23. Maré hal-Drouard, L., Kumar, R., Remacle, C. and Small, I. (1996) RNA editing of larch mitochondrial tRNAHis precursors is a prerequisite for processing. Nucleic Acids Res., 24, 3229-3234. (Pubitemid 26278565)
24. Unseld, M., Marienfeld, J.R., Brandt, P. and Brennicke, A. (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides. Nat. Genet., 15, 57-61.
25. Placido, A., Sieber, F., Gobert, A., Gallerani, R., Giegé , P. and Maré hal-Drouard, L. (2010) Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res., 38, 7711-7717.
26. Gu, W., Hurto, R.L., Hopper, A.K., Grayhack, E.J. and Phizicky, E.M. (2005) Depletion of Saccharomyces cerevisiae tRNAHis guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m5C. Mol. Cell. Biol., 25, 8191-8201. (Pubitemid 41263010)
27. Preston, M.A. and Phizicky, E.M. (2010) The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase. RNA, 16, 1068-1077.
28. Jackman, J.E. and Phizicky, E.M. (2006) tRNAHis guanylyltransferase adds G-1 to the 50 end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases. RNA, 12, 1007-1014. (Pubitemid 43788119)
29. Heinemann, I.U., Randau, L., Tomko, R.J. Jr and Söll, D. (2010) 30-50 tRNAHis guanylyltransferase in bacteria. FEBS Lett., 584, 3567-3572.
30. Rao, B.S., Maris, E.L. and Jackman, J.E. (2011) tRNA 50-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from bacteria and archaea. Nucleic Acids Res., 39, 1833-1842.
31. Li, Y. and Zhou, H. (2009) tRNAs as regulators in gene expression. Sci. China C Life Sci., 52, 245-252.
32. Dong, J., Qiu, H., Garcia-Barrio, M., Anderson, J. and Hinnebusch, A.G. (2000) Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain. Mol. Cell, 6, 269-279.
33. Mascarenhas, C., Edwards-Ingram, L.C., Zeef, L., Shenton, D., Ashe, M.P. and Grant, C.M. (2008) Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae. Mol. Biol. Cell., 19, 2995-3007.
34. Abad, M.G., Rao, B.S. and Jackman, J.E. (2010) Template-dependent 30-50 nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. Proc. Natl Acad. Sci. USA, 107, 674-679.
35. Francklyn, C., Shi, J.P. and Schimmel, P. (1992) Overlapping nucleotide determinants for specific aminoacylation of RNA microhelices. Science, 255, 1121-1125.
36. Crothers, D.M., Seno, T. and Söll, D. (1972) Is there a discriminator site in transfer RNA? Proc. Natl Acad. Sci. USA, 69, 3063-3067.
37. Jackman, J.E. and Phizicky, E.M. (2006) tRNAHis guanylyltransferase catalyzes a 30-50 polymerization reaction that is distinct from G-1 addition. Proc. Natl Acad. Sci. USA, 103, 8640-8645. (Pubitemid 43878073)
38. Hyde, S.J., Eckenroth, B.E., Smith, B.A., Eberley, W.A., Heintz, N.H., Jackman, J.E. and Doublié , S. (2010) tRNAHis guanylyltransferase (THG1), a unique 30-50 nucleotidyl transferase, shares unexpected structural homology with canonical 50-30 DNA polymerases. Proc. Natl Acad. Sci. USA, 107, 20305-20310.
39. Celesnik, H., Deana, A. and Belasco, J.G. (2007) Initiation of RNA decay in Escherichia coli by 50 pyrophosphate removal. Mol. Cell, 27, 79-90. (Pubitemid 46991386)
40. Deana, A., Celesnik, H. and Belasco, J.G. (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 50 pyrophosphate removal. Nature, 451, 355-358.
41. Abad, M.G., Long, Y., Willcox, A., Gott, J.M., Gray, M.W. and Jackman, J.E. (2011) A role for tRNAHis guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 50-tRNA editing. RNA, 17, 613-623.
42. Price, D.H. and Gray, M.W. (1999) A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA, 5, 302-317. (Pubitemid 29079289)
43. Bullerwell, C.E. and Gray, M.W. (2005) In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. J. Biol. Chem., 280, 2463-2470. (Pubitemid 40189346)
44. Perona, J.J. and Oza, J.P. (2010) Crystal structure of a reverse polymerase. Proc. Natl Acad. Sci. USA, 107, 20149-20150.
45. Anantharaman, V., Iyer, L.M. and Aravind, L. (2010) Presence of a classical RRM-fold palm domain in Thg1-type 30-50nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Biol. Direct., 5, 43.
46. Jackman, J.E. and Phizicky, E.M. (2008) Identification of critical residues for G-1 addition and substrate recognition by tRNAHis guanylyltransferase. Biochemistry, 47, 4817-4825. (Pubitemid 351555503)
47. Rice, T.S., Ding, M., Pederson, D.S. and Heintz, N.H. (2005) The highly conserved tRNAHis guanylyltransferase Thg1p interacts with the origin recognition complex and is required for the G2/M phase transition in the yeast Saccharomyces cerevisiae. Eukaryot. Cell., 4, 832-835. (Pubitemid 40600436)