C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids

Gaston, Kirk W.; Rubio, Mary Anne T.; Spears, Jessica L.; Pastar, Irena; Papavasiliou, F. Nina; Alfonzo, Juan D.

doi:10.1093/nar/gkm745

Cited by 22 publications

(19 citation statements)

References 46 publications

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“…3f–j) (m/z 269.09 at 20.8 min) resulting from deamination of position 34 by ADAT2/3, as previously described. However, inosine formation occurred independently of the methylation or editing status at position 32 as shown previously 7 . These data establish that formation of m 3 U is strictly dependent on prior base methylation of cytosine 32 while requiring the presence of both enzymes.…”

supporting

confidence: 73%

“…2a, b). Prior to this work we reported that although ADAT2/3 is mostly cytoplasmic, a portion of the enzyme is found in the nucleus 4,7 . Nuclear localization of ADAT2/3 can be explained by the mutual reliance upon both enzymes for activity.…”

mentioning

confidence: 84%

“…Downregulation of T. brucei tRNA adenosine to inosine deaminase (ADAT2/3) expression by RNAi leads to a decrease in both A-to-I editing at position 34 and C-to-U editing at position 32 of tRNA Thr AGU , suggesting that it is involved in both editing events 4 . However, ADAT2/3 could not catalyse C-to-U in vitro 7 , but since position 32 of eukaryotic tRNA Thr molecules is commonly modified to m 3 C (Extended Data Fig. 1) 8 , it raises the possibility that RNA editing may strictly target a methylated base, ultimately forming m 3 U (Fig.…”

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confidence: 99%

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Editing and methylation at a single site by functionally interdependent activities

Rubio

Gaston

McKenney

et al. 2017

Nature

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Nucleic acids undergo naturally occurring chemical modifications. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified1. Despite recent progress, the mechanism for the biosynthesis of most modifications is not fully understood, owing, in part, to the difficulty associated with reconstituting enzyme activity in vitro. Whereas some modifications can be efficiently formed with purified components, others may require more intricate pathways2. A model for modification interdependence, in which one modification is a prerequisite for another, potentially explains a major hindrance in reconstituting enzymatic activity in vitro3. This model was prompted by the earlier discovery of tRNA cytosine-to-uridine editing in eukaryotes, a reaction that has not been recapitulated in vitro and the mechanism of which remains unknown. Here we show that cytosine 32 in the anticodon loop of Trypanosoma brucei tRNAThr is methylated to 3-methylcytosine (m3C) as a pre-requisite for C-to-U deamination. Formation of m3C in vitro requires the presence of both the T. brucei m3C methyltransferase TRM140 and the deaminase ADAT2/3. Once formed, m3C is deaminated to 3-methyluridine (m3U) by the same set of enzymes. ADAT2/3 is a highly mutagenic enzyme4, but we also show that when co-expressed with the methyltransferase its mutagenicity is kept in check. This helps to explain how T. brucei escapes ‘wholesale deamination’5 of its genome while harbouring both enzymes in the nucleus. This observation has implications for the control of another mutagenic deaminase, human AID, and provides a rationale for its regulation.

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confidence: 73%

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confidence: 84%

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confidence: 99%

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Editing and methylation at a single site by functionally interdependent activities

Rubio

Gaston

McKenney

et al. 2017

Nature

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“…Even though all these pre‐tRNA Val chimeras were capable of being properly processed into mature tRNAs, these results also pointed towards the importance of the tRNA tertiary structure and that I34 modification in yeast and HeLa cells might occur at the precursor level and within the nuclear compartment. In contrast to these results, in Trypanosomatids, A34‐to‐I34 conversion was reported to occur in the cytosol [23]. Likewise, in vitro A34 deamination assays carried out with lysates from anucleated reticulocytes [5] or upon direct injection of the tRNA substrate into X. laevis cytosol [34] suggested that I34 modification could occur in the cytosol.…”

Section: Substrate Recognition By Adatsmentioning

confidence: 79%

A‐to‐I editing on tRNAs: Biochemical, biological and evolutionary implications

et al. 2014

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Edited by Wilhelm JustKeywords: Inosine Adenosine deaminase acting on tRNA Transfer RNA Deaminase Codon usage Evolution a b s t r a c t Inosine on transfer RNAs (tRNAs) are post-transcriptionally formed by a deamination mechanism of adenosines at positions 34, 37 and 57 of certain tRNAs. Despite its ubiquitous nature, the biological role of inosine in tRNAs remains poorly understood. Recent developments in the study of nucleotide modifications are beginning to indicate that the dynamics of such modifications are used in the control of specific genetic programs. Likewise, the essentiality of inosine-modified tRNAs in genome evolution and animal biology is becoming apparent. Here we review our current understanding on the role of inosine in tRNAs, the enzymes that catalyze the modification and the evolutionary link between such enzymes and other deaminases. Ó 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Inosine and inosine modification enzymesInosine is a non-canonical nucleoside found in all domains of life. Chemically, it is a guanosine analogue and it only differs from the latter by the lack of the N2 amino group. Inosine is rarely present in DNA but is often observed in different types of RNAs including double-stranded RNAs, tRNAs and viral RNAs [76,63,30]. In RNA, inosine is produced by the deamination of adenosine [31,5]. Generally, 2 groups of RNA adenosine deaminases exist: adenosine deaminases acting on messenger RNAs (ADARs) and adenosine deaminases acting on tRNAs (ADATs), the enzymes of each group being specific for specific modification sites [5,76,24,25].ADARs are present only in metazoans and, in vertebrates, three genes that encode for different ADAR proteins have been described. ADAR1 and ADAR2 are expressed in most tissues and their deamination activity has been confirmed. ADAR3 on the contrary is only expressed in the central nervous system and its function is currently unknown, as it lacks deamination activity [45]. As mentioned, ADARs deaminate adenosines in mRNAs to inosine. Since inosine (which is derived from adenosines), resembles guanosine, A-to-I editing on mRNAs can result in amino acid substitutions during translation, and alterations of splice sites during mRNA processing [76]. Additionally, ADARs can edit non-coding RNAs and have regulatory functions, for example, by affecting the biogenesis, processing and target selection of siRNAs and miRNAs [76].Inosine is found in tRNAs in all domains of life. It is present mainly at three positions on tRNAs: position 34, which is the first nucleotide of the anticodon (wobble-position), position 37 (following the anticodon), and position 57 (at the TWC-loop) (Fig. 1A). Interestingly, at position 34, inosine is the final modified base, while at positions 37 and 57 inosine is found in a methylated state (m 1 I37, m 1 I57 or m 1 Im57) [40,55]. Methyl-inosine 37 has only been found in eukaryotic tRNA Ala [30,40] and the modification involves two enzymatic reactions. First, A37 is deaminated to I3...

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“…This editing event is not necessary but is stimulating for a second deamination type of editing event taking place in the same tRNA, an A-to-I editing event in the wobble position 34 [232]. Interestingly, the C-to-U event appears to be a nuclear editing event whereas A-to-I editing takes place in the cytosol [233].…”

mentioning

confidence: 95%

When you can’t trust the DNA: RNA editing changes transcript sequences

Knoop¹

2010

Cell. Mol. Life Sci.

178

133

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RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.

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C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids

Cited by 22 publications

References 46 publications

Editing and methylation at a single site by functionally interdependent activities

Editing and methylation at a single site by functionally interdependent activities

A‐to‐I editing on tRNAs: Biochemical, biological and evolutionary implications

When you can’t trust the DNA: RNA editing changes transcript sequences

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