Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

Abstract

Posttranscriptional modifications of transfer RNAs (tRNAs) are critical for all core aspects of tRNA function, such as folding, stability, and decoding. Most tRNA modifications were discovered in the 1970s; however, the near-complete description of the genes required to introduce the full set of modifications in both yeast and Escherichia coli is very recent. This led to a new appreciation of the key roles of tRNA modifications and tRNA modification enzymes as checkpoints for tRNA integrity and for integrating translation with other cellular functions such as transcription, primary metabolism, and stress resistance. A global survey of tRNA modification enzymes shows that the functional constraints that drive the presence of modifications are often conserved, but the solutions used to fulfill these constraints differ among different kingdoms, organisms, and species.

Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA

“…Although the positions and species of modifications in tRNAs are not comprehensively identified in full detail, research on tRNA biology suggests that tRNA modifications occur non-randomly at conserved positions, such as positions 34 and 37 in the anticodon-loop, and position 9 and 10 between acceptor-and D-stems. [16][17][18]28 To our knowledge, it has not been previously shown that there are modifications in the acceptor stem of mature tRNAs that disrupt Watson-Crick basepairing. In the TaqMan qRT-PCR of FL-PCR, the forward and RT/reverse primers were designed to be derived from the T-and D-arms of targeted mature tRNA, respectively, and the amplified cDNAs are quantified using the TaqMan probe targeting the SLadapter (Fig.…”

“…Over 100 post-transcriptional modifications are present in tRNAs, many of which play crucial roles in tRNA folding and function such as codon recognition. [16][17][18] Because many such modifications inhibit Watson-Crick base paring and thus arrest reverse-transcription, 19 standard qRT-PCR would produce severely biased results with underrepresentation of heavily-modified tRNAs. This modification issue is inevitable with any PCR-based technology used for the detection and quantification of RNA because there is no experimental methodology that removes all tRNA modifications.…”

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

“…Many of the covalent modifications within yeast (Saccharomyces cerevisiae) tRNAs have been identified and characterized through years of extensive research (Björk et al, 1987;Grosjean et al, 1997;Hopper and Phizicky, 2003;El Yacoubi et al, 2012;Machnicka et al, 2013). For this reason, the machine learning algorithm that HAMR uses to classify the type of modification occurring at each predicted site uses the substitution patterns from a yeast smRNA-seq data set at known tRNA modification sites as its training set (Ryvkin et al, 2013).…”

Overproduction, crystallization and preliminary X-ray crystallographic analysis ofEscherichia colitRNAN6-threonylcarbamoyladenosine dehydratase

“…Transfer RNAs (tRNAs) undergo various post-transcriptional modifications necessary for proper function during translation (reviewed by El Yacoubi et al, 2012). A well characterized alteration is the wobble modification, which includes 5-methoxycarbonylmethylation and 2-thiolation of U34.…”

“…N 6 -Threonylcarbamoyladenosine (t 6 A), N 6 -methylation and 2-methylthiolation at the A37 position of ANN-decoding tRNAs have also been well documented. All of these modifications were shown to stabilize the codon-anticodon interactions and to be necessary for precise decoding of translation (El Yacoubi et al, 2012;Schweizer et al, 1969;Murphy et al, 2004). Interestingly, Escherichia coli t 6 A has recently been shown to undergo further modification into a cyclic N 6 -threonylcarbamoyladenosine (ct 6 A) through an ATP-dependent dehydration reaction catalyzed by tRNA threonylcarbamoyladenosine dehydratase (TcdA; Miyauchi et al, 2013).…”