The TRAMP complex shows tRNA editing activity in S. cerevisiae

Molecular Biology and Evolution

Volumn 29, Issue 5, 2012, Pages 1451-1459

  Dickinson, Helena ^a   Tretbar, Sandy ^a   Betat, Heike ^a   Mörl, Mario ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Enzyme promiscuity; Evolution; Nucleotidyltransferases; RNA editing

Indexed keywords

MULTIPROTEIN COMPLEX; RNA POLYMERASE; TRAMP4 COMPLEX; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVITY; EUKARYOTE EVOLUTION; NONHUMAN; POLYADENYLATION; PROTEIN ANALYSIS; REGULATORY RNA SEQUENCE; RNA BINDING; RNA DEGRADATION; RNA EDITING; RNA PURIFICATION; RNA TRANSCRIPTION; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIENZYME COMPLEXES; RNA EDITING; RNA NUCLEOTIDYLTRANSFERASES; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

SACCHAROMYCES CEREVISIAE;

EID: 84862894535     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr312     Document Type: Article

References (49)

1. Abad MG, Long Y, Willcox A, Gott JM, Gray MW, Jackman JE. 2011. A role for tRNA(His) guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5#-tRNA editing. RNA 17:613-623.
2. 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 U S A. 107:674-679.
3. Betat H, Rammelt C, Martin G, Mörl M. 2004. Exchange of regions between bacterial poly(A) polymerase and CCA adding enzyme generates altered specificities. Mol Cell. 15:389-398. (Pubitemid 39092755)
4. 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. (Pubitemid 40189346)
5. Cavalier-Smith T. 1997. Cell and genome coevolution: facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends Genet. 13:6-9. (Pubitemid 27062501)
6. Covello PS, Gray MW. 1993. On the evolution of RNA editing. Trends Genet. 9:265-268. (Pubitemid 23218831)
7. Egecioglu DE, Henras AK, Chanfreau GF. 2006. Contributions of Trf4pand Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12:26-32. (Pubitemid 43037450)
8. Engel SR, Balakrishnan R, Binkley G, et al. (21 co-authors). 2010. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 38:D433-D436.
9. Fechter P, Rudinger-Thirion J, Théobald-Dietrich A, Giegé R. 2000. Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features. Biochemistry 39:1725-1733. (Pubitemid 30108963)
10. Gaur RK, Hanne A, Conrad F, Kahle D, Krupp G. 1996. Differences in the interaction of Escherichia coli RNase P RNA with tRNAs containing a short or a long extra arm. RNA 2:674-681. (Pubitemid 26374219)
11. Gott JM, Somerlot BH, Gray MW. 2010. Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 16:482-488.
12. Houseley J, Tollervey D. 2006. Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep. 7:205-211.
13. Hunter S, Apweiler R, Attwood TK, et al. (37 co-authors). 2009. InterPro: the integrative protein signature database. Nucleic Acids Res. 37:D211-D215.
14. Inoue K, Mizuno T, Wada K, Hagiwara M. 2000. Novel RING finger proteins, Air1p and Air2p, interact with Hmt1p and inhibit the arginine methylation of Npl3p. J Biol Chem. 275:32793-32799.
15. Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. 2005. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics. 4:1265-1272. (Pubitemid 41448714)
16. Jackman JE, Phizicky EM. 2006. tRNAHis guanylyltransferase catalyzes a 3'-5' polymerization reaction that is distinct from G-1 addition. Proc Natl Acad Sci U S A. 103:8640-8645. (Pubitemid 43878073)
17. Jensen TH, Moore C. 2005. Reviving the exosome. Cell 121:660-662. (Pubitemid 40797586)
18. Jia H, Wang X, Liu F, Guenther UP, Srinivasan S, Anderson JT, Jankowsky E. 2011. The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. Cell 145:890-901.
19. Kadaba S, Krueger A, Trice T, Krecic AM, Hinnebusch AG, Anderson J. 2004. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev. 18:1227-1240. (Pubitemid 38720591)
20. Khersonsky O, Tawfik DS. 2010. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem. 79:471-505.
21. LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713-724. (Pubitemid 40797594)
22. Laforest M-J, Roewer I, Lang FB. 1997. Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine. Nucleic Acids Res. 25:626-632. (Pubitemid 27298247)
23. Lavrov DV, Brown WM, Boore JL. 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede lithobius forficatus. Proc Natl Acad Sci U S A. 97:13738-13742.
24. Leigh J, Lang BF. 2004. Mitochondrial 3' tRNA editing in the jakobid Seculamonas ecuadoriensis: a novel mechanism and implications for tRNA processing. RNA 10:615-621. (Pubitemid 38405940)
25. Liang S, Hitomi M, Hu YH, Liu Y, Tartakoff AM. 1996. A DEAD-boxfamily protein is required for nucleocytoplasmic transport of yeast mRNA. Mol Cell Biol. 16:5139-5146. (Pubitemid 26272167)
26. Lonergan KM, Gray MW. 1993a. Editing of Transfer RNAs in Acanthamoeba castellanii Mitochondria. Science 259:812-815.
27. Lonergan KM, Gray MW. 1993b. Predicted editing of additional transfer RNAs in Acanthamoeba castellanii mitochondria. Nucleic Acids Res. 21:4402. (Pubitemid 23279044)
28. Magrane M, Consortium U. 2011. UniProt knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009.
29. Martin G, Keller W. 2007. RNA-specific ribonucleotidyl transferases. RNA 13:1834-1849. (Pubitemid 350005209)
30. Müller SA, Kohajda T, Findeiß S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. 2010. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem. 398:2867-2881.
31. Price DH, Gray MW. 1999. A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA 5:302-317. (Pubitemid 29079289)
32. Rao BS, Maris EL, Jackman JE. 2011. tRNA 5'-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea. Nucleic Acids Res. 39:1833-1842.
33. Reichert A, Rothbauer U, Mörl M. 1998. Processing and editing of overlapping tRNAs in human mitochondria. J Biol Chem. 273:31977-31984. (Pubitemid 29177137)
34. Sadoff BU, Heath-Pagliuso S, Castano IB, Zhu Y, Kieff FS, Christman MF. 1995. Isolation of mutants of Saccharomyces cerevisiae requiring DNA topoisomerase I. Genetics 141:465-479.
35. Schürer H, Lang K, Schuster J, Mörl M. 2002. A universal method to produce in vitro transcripts with homogeneous 3' ends. Nucleic Acids Res. 30:e56.
36. Schuster J, Betat H, Mörl M. 2005. Is yeast on its way to evolving tRNA editing? EMBO Rep. 6:367-372. (Pubitemid 40561630)
37. Schuster J, Mörl M. 2004. Mitochondrial tRNA editing. In: Koehler CM, Bauer MF, editors. Mitochondrial function and biogenesis. Berlin (Germany): Springer. p. 81-96.
38. Simpson L, Thiemann OH, Savill NJ, Alfonzo JD, Maslov DA. 2000. Evolution of RNA editing in trypanosome mitochondria. Proc Natl Acad Sci U S A. 97:6986-6993. (Pubitemid 30431406)
39. Soderbom F, Svard SG, Kirsebom LA. 2005. RNase E cleavage in the 5' leader of a tRNA precursor. J Mol Biol. 352:22-27. (Pubitemid 41207438)
40. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26:148-153. (Pubitemid 28295271)
41. Tomita K, Ueda T, Watanabe K. 1996. RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr). Nucleic Acids Res. 24:4987-4991.
42. UniProt Consortium 2011. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39:D214-D219.
43. Vanacova S, Wolf J, Martin G, Blank D, Dettwiler S, Friedlein A, Langen H, Keith G, Keller W. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3:e189.
44. Wahle E. 1995. 3'-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta. 1261:183-194.
45. Wang X, Jia H, Jankowsky E, Anderson JT. 2008. Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. RNA 14:107-116.
46. Wyers F, Rougemaille M, Badis G, et al. (11 co-authors). 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725-737. (Pubitemid 40797595)
47. Yokobori S-i, Pääbo S. 1995a. Transfer RNA editing in land snail mitochondria. Proc Natl Acad Sci U S A. 92:10432-10435.
48. Yokobori S-i, Pääbo S. 1995b. tRNA editing in metazoans. Nature 377:490.
49. Yokobori S-i, Pääbo S. 1997. Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr. J Mol Biol. 265:95-99. (Pubitemid 27110647)