A role for tRNAHis guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5′-tRNA editing

RNA

Volumn 17, Issue 4, 2011, Pages 613-623

  Abad, Maria G ^a   Long, Yicheng ^a   Willcox, Allison ^a   Gott, Jonatha M ^b   Gray, Michael W ^c   Jackman, Jane E ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

^c DALHOUSIE UNIVERSITY   (Canada)

Author keywords

3 5 ; G 1 addition; Polymerase; RNA editing; tRNA repair; tRNAHis

Indexed keywords

ENZYME; PROTEIN; RNA; TRANSFER RNA; TRANSFER RNA HISTIDYLGUANYLYLTRANSFERASE 1; TRANSFER RNA HISTIDYLGUANYLYLTRANSFERASE 1 LIKE PROTEIN; TRANSFERASE; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMOEBOZOA; ANIMAL CELL; ARTICLE; CATALYSIS; CELL CYCLE G1 PHASE; CHEMICAL ANALYSIS; CONTROLLED STUDY; CYTOPLASM; DICTYOSTELIUM DISCOIDEUM; ENZYME ACTIVITY; EUKARYOTE; GENE DUPLICATION; IN VITRO STUDY; MITOCHONDRION; MOULD; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PURIFICATION; RNA EDITING; RNA REPAIR; STRUCTURAL GENE;

AMINO ACID SEQUENCE; CATALYSIS; DICTYOSTELIUM; MOLECULAR SEQUENCE DATA; NUCLEOTIDYLTRANSFERASES; RNA EDITING; RNA, TRANSFER, AMINO ACYL; SEQUENCE ALIGNMENT;

AMOEBOZOA; DICTYOSTELIUM DISCOIDEUM; EUKARYOTA;

EID: 79952998913     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2517111     Document Type: Article

References (34)

1. Abad MG, Rao BS, Jackman JE. 2010. Template-dependent 3′-5′ nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. Proc Natl Acad Sci 107: 674-679.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
3. Bullerwell CE, Gray MW. 2005. In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. J Biol Chem 280: 2463-2470.
4. Claros MG. 1995. MitoProt, a Macintosh application for studying mitochondrial proteins. Comput Appl Biosci 11: 441-447.
5. Claros MG, Vincens P. 1996. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786. (Pubitemid 26379380)
6. Cooley L, Appel B, Soll D. 1982. Post-transcriptional nucleotide addition is responsible for the formation of the 5′ terminus of histidine tRNA. Proc Natl Acad Sci 79: 6475-6479. (Pubitemid 13207517)
7. Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881-10890.
8. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, et al. 2005. The genome of the social amoeba Dictyostelium discoideum. Nature 435: 43-57. (Pubitemid 40655903)
9. Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, et al. 2009. dictyBase - a Dictyostelium bioinformatics resource update. Nucleic Acids Res 37: D515-D519.
10. Gott JM, Somerlot BH, Gray MW. 2010. Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 16: 482-488.
11. Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM. 2003. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5′ end of tRNAHis. Genes Dev 17: 2889-2901. (Pubitemid 37523154)
12. Gu W, Hurto RL, Hopper AK, Grayhack EJ, Phizicky EM. 2005. Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Mol Cell Biol 25: 8191-8201.
13. Heinemann IU, O'Donoghue P, Madinger C, Benner J, Randau L, Noren CJ, Soll D. 2009. The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. Proc Natl Acad Sci 106: 21103-21108.
14. Heinemann IU, Randau L, Tomko RJ Jr, Soll D. 2010. 3′-5′ tRNAHis guanylyltransferase in bacteria. FEBS Lett 584: 3567-3572.
15. Hyde SJ, Eckenroth BE, Smith BA, Eberley WA, Heintz NH, Jackman JE, Doublie S. 2010. tRNAHis guanylyltransferase (THG1), a unique 3′-5′ nucleotidyl transferase, shares unexpected structural homology with canonical 5′-3′ DNA polymerases. Proc Natl Acad Sci 107: 20305-20310.
16. -1 to the 5′ end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases. RNA 12: 1007-1014.
17. -1 addition. Proc Natl Acad Sci 103: 8640-8645.
18. -1 addition and substrate recognition by tRNA(His) guanylyltransferase. Biochemistry 47: 4817-4825.
19. Laforest MJ, Roewer I, Lang BF. 1997. Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine. Nucleic Acids Res 25: 626-632.
20. Laforest MJ, Bullerwell CE, Forget L, Lang BF. 2004. Origin, evolution, and mechanism of 5′ tRNA editing in chytridiomycete fungi. RNA 10: 1191-1199. (Pubitemid 38989005)
21. Lonergan KM, Gray MW. 1993a. Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 259: 812-816. (Pubitemid 23066310)
22. Lonergan KM, Gray MW. 1993b. Predicted editing of additional transfer RNAs in Acanthamoeba castellanii mitochondria. Nucleic Acids Res 21: 4402. doi: 10.1093/nar/21.18.4402. (Pubitemid 23279044)
23. Morl M, Lizano E, Willkomm DK, Hartmann RK. 2005. Production of RNAs with homogeneous 5′ and 3′ ends. In Handbook of RNA biochemistry (ed. RK Hartmann, A Schon, E Westhof), pp. 22-35. Wiley-VCH, Wenheim, Germany.
24. Nameki N, Asahara H, Shimizu M, Okada N, Himeno H. 1995. Identity elements of Saccharomyces cerevisiae tRNA(His). Nucleic Acids Res 23: 389-394.
25. Ogawa S, Yoshino R, Angata K, Iwamoto M, Pi M, Kuroe K, Matsuo K, Morio T, Urushihara H, Yanagisawa K, et al. 2000. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol Gen Genet 263: 514-519.
26. Orellana O, Cooley L, Soll D. 1986. The additional guanylate at the 5′ terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Mol Cell Biol 6: 525-529. (Pubitemid 16158127)
27. -1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase. RNA 16: 1068-1077.
28. Price DH, Gray MW. 1999a. Confirmation of predicted edits and demonstration of unpredicted edits in Acanthamoeba castellanii mitochondrial tRNAs. Curr Genet 35: 23-29. (Pubitemid 29137288)
29. Price DH, Gray MW. 1999b. A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA 5: 302-317. (Pubitemid 29079289)
30. Rao BS, Maris EL, Jackman JE. 2010. tRNA 5′-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea. Nucl Acids Res doi: 10.1093/nar/gkq976.
31. -1:C73 atomic groups by Escherichia coli histidyl-tRNA synthetase. J Am Chem Soc 126: 64-65.
32. Rudinger J, Florentz C, Giege 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.
33. Rudinger J, Felden B, Florentz C, Giege R. 1997. Strategy for RNA recognition by yeast histidyl-tRNA synthetase. Bioorg Med Chem 5: 1001-1009. (Pubitemid 27264826)
34. Schindel E. 2004. Editing of mitochondrial tRNAs in Polysphondylium pallidum. In Biochemistry and molecular biology. Dalhousie University, Halifax, Nova Scotia, Canada.