Editing and methylation at a single site by functionally interdependent activities

Nature

Volumn 542, Issue 7642, 2017, Pages 494-497

  Rubio, Mary Anne T ^a   Gaston, Kirk W ^a,b   McKenney, Katherine M ^a   Fleming, Ian M C ^a   Paris, Zdeněk ^a,c   Limbach, Patrick A ^b   Alfonzo, Juan D ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

^c UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DEAMINASE; METHYLTRANSFERASE; TRANSFER RNA; 3-METHYLCYTOSINE; ANTICODON; THREONINE TRANSFER RNA; URIDINE;

AMINO ACID; CHEMICAL ALTERATION; ENZYME ACTIVITY; EUKARYOTE; GENE EXPRESSION; METHYLATION; NUCLEIC ACID; RNA; SUGAR;

ARTICLE; DEAMINATION; IN VITRO STUDY; METHYLATION; MUTAGENICITY; NONHUMAN; PRIORITY JOURNAL; RNA EDITING; TRYPANOSOMA BRUCEI; ANALOGS AND DERIVATIVES; ANTICODON; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; TRYPANOSOMA BRUCEI BRUCEI;

EUKARYOTA; TRYPANOSOMA BRUCEI;

ANTICODON; BASE SEQUENCE; CYTOSINE; DEAMINATION; METHYLATION; METHYLTRANSFERASES; NUCLEOSIDE DEAMINASES; RNA EDITING; RNA, TRANSFER, THR; TRYPANOSOMA BRUCEI BRUCEI; URIDINE;

EID: 85016162683     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature21396     Document Type: Article

References (24)

1. Machnicka, M. A. et al. MODOMICS: a database of RNA modification pathways-2013 update. Nucleic Acids Res. 41, D262-D267 (2013).
2. Helm, M. & Alfonzo, J. D. Posttranscriptional RNA Modifications: playing metabolic games in a cells chemical Legoland. Chem. Biol. 21, 174-185 (2014).
3. Crain, P. F. et al. Modification of the universally unmodified uridine-33 in a mitochondria-imported edited tRNA and the role of the anticodon arm structure on editing efficiency. RNA 8, 752-761 (2002).
4. Rubio, M. A. et al. An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA. Proc. Natl Acad. Sci. USA 104, 7821-7826 (2007).
5. Carter, C. W. in Modification and Editing of RNA (eds Grosjean and Benne) 363-375 (ASM Press, 1998)
6. Randau, L. et al. A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science 324, 657-659 (2009).
7. Gaston, K. W. et al. C to U editing at position 32 of the anticodon loop precedes tRNA 5′ leader removal in trypanosomatids. Nucleic Acids Res. 35, 6740-6749 (2007).
8. Juhling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159-D162 (2009).
9. Spears, J. L., Gaston, K. W. & Alfonzo, J. D. Analysis of tRNA editing in native and synthetic substrates. Methods Mol. Biol. 718, 209-226 (2011).
10. Randerath, K., Chia, L. S., Gupta, R. C. & Randerath, E. Structural analysis of nonradioactive RNA by postlabeling: the primary structure of bakers yeast tRNA Leu/CUA. Biochem. Biophys. Res. Commun. 63, 157-163 (1975).
11. Fleming, I. M. et al. A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Sci. Rep. 6, 21438 (2016).
12. Ross, R., Cao, X., Yu, N. & Limbach, P. A. Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. Methods 107, 73-78 (2016).
13. Kapushoc, S. T., Alfonzo, J. D. & Simpson, L. Differential localization of nuclear-encoded tRNAs between the cytosol and mitochondrion in Leishmania tarentolae. RNA 8, 57-68 (2002).
14. Petersen-Mahrt, S. K., Harris, R. S. & Neuberger, M. S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418, 99-103 (2002).
15. Petersen-Mahrt, S. DNA deamination in immunity. Immunol. Rev. 203, 80-97 (2005).
16. Lonergan, K. M. & Gray, M. W. Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 259, 812-816 (1993).
17. Borner, G. V., Morl, M., Janke, A. & Paabo, S. RNA editing changes the identity of a mitochondrial tRNA in marsupials. EMBO J. 15, 5949-5957 (1996).
18. Morl, M., Dorner, M. & Paabo, S. C to U editing and modifications during the maturation of the mitochondrial tRNAAsp in marsupials. Nucleic Acids Res. 23, 3380-3384 (1995).
19. Alfonzo, J. D., Blanc, V., Estevez, A. M., Rubio, M. A. & Simpson, L. C to U editing of the anticodon of imported mitochondrial tRNATrp allows decoding of the UGA stop codon in Leishmania tarentolae. EMBO J. 18, 7056-7062 (1999).
20. Zhou, W., Karcher, D. & Bock, R. Identification of enzymes for adenosine-toinosine editing and discovery of cytidine-to-uridine editing in nucleusencoded transfer RNAs of Arabidopsis. Plant Physiol. 166, 1985-1997 (2014).
21. Rubio, M. A., Ragone, F. L., Gaston, K. W., Ibba, M. & Alfonzo, J. D. C to U editing stimulates A to I editing in the anticodon loop of a cytoplasmic threonyl tRNA in Trypanosoma brucei. J. Biol. Chem. 281, 115-120 (2006).
22. Teng, G. & Papavasiliou, F. N. Immunoglobulin somatic hypermutation. Annu. Rev. Genet. 41, 107-120 (2007).
23. Sample, P. J. et al. A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. Nucleic Acids Res. 43, 4262-4273 (2015).
24. Kapushoc, S. T., Alfonzo, J. D., Rubio, M. A. & Simpson, L. End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae. J. Biol. Chem. 275, 37907-37914 (2000).