Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl, Mathias; Vassilenko, Konstantin S.

doi:10.1093/nar/gki012

Cited by 1,150 publications

(307 citation statements)

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“…tRNA sequences were obtained from the tRNA sequence database [23]. Theoretical RNase digestion products of E. coli tRNA TyrII were calculated using the Mongo Oligo Mass Calculator (http//www-medstat.med.utah.edu/massspec/mongo.htm).…”

Section: Discussionmentioning

confidence: 99%

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

Durairaj

Limbach

2008

Analytica Chimica Acta

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A protocol that utilizes matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and N-cyclohexyl-N′-β-(4-methylmorpholinium)ethylcarbodiimide (CMC) derivatization to detect the post-transcriptionally modified nucleoside, pseudouridine, in RNA has been optimized for RNase digests. Because pseudouridine is mass-silent (i.e. the mass of pseudouridine is the same as the mass of uridine), after CMC derivatization and alkaline treatment, all pseudouridine residues exhibit a mass shift of 252 Da that allows its presence to be easily detected by mass spectrometry. This protocol is illustrated by the direct MALDI-MS identification of pseudouridines within Escherichia coli tRNA TyrII starting from microgram amounts of sample. During this optimization study, it was discovered that the post-transcriptionally modified nucleoside 2-methylthio-N 6 -isopentenyladenosine, which is present in bacterial tRNAs, also retains a CMC unit after derivatization and incubation with base. Thus, care must be exercised when applying this MALDIbased CMC-derivatization approach for pseudouridine detection to samples containing transfer RNAs to minimize the misidentification of pseudouridine.

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Section: Discussionmentioning

confidence: 99%

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

Durairaj

Limbach

2008

Analytica Chimica Acta

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“…First, we used tRNA fMet from the E. coli thiI mutant strain as the substrate, since the nucleotide sequence of the tRNA is almost identical to that of tRNA fMet from T. thermophilus. At the unmodified nucleoside level, the differences are that the U50 of E. coli tRNA is C50 in T. thermophilus (25) (Fig. 2A (a and b)) and that the tRNA from the thiI mutant has no s 4 U (26).…”

Section: For Ns0821mentioning

confidence: 99%

Temperature-dependent Biosynthesis of 2-Thioribothymidine of Thermus thermophilus tRNA

Shigi

Suzuki

Terada

et al. 2006

Journal of Biological Chemistry

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2-Thioribothymidine (s 2 T) is a modified nucleoside of U, specifically found at position 54 of tRNAs from extreme thermophilic microorganisms. The function of the 2-thiocarbonyl group of s 2 T54 is thermostabilization of the three-dimensional structure of tRNA; however, its biosynthesis has not been clarified until now. Using an in vivo tRNA labeling experiment, we demonstrate that the sulfur atom of s 2 T in tRNA is derived from cysteine or sulfate. We attempted to reconstitute 2-thiolation of s 2 T in vitro, using a cell extract of Thermus thermophilus. Specific 2-thiolation of ribothymidine, at position 54, was observed in vitro, in the presence of ATP. Using this assay, we found a strong temperature dependence of the 2-thiolation reaction in vitro as well as expression of 2-thiolation enzymes in vivo. These results suggest that the variable content of s 2 T in vivo at different temperatures may be explained by the above characteristics of the enzymes responsible for the 2-thiolation reaction. Furthermore, we found that another posttranscriptionally modified nucleoside, 1-methyladenosine at position 58, is required for the efficient 2-thiolation of ribothymidine 54 both in vivo and in vitro.Post-transcriptional modification is a characteristic feature of RNA molecules. In transfer RNA, post-transcriptional modification plays various roles that are required for the translation process, including fidelity control of codon recognition, reading frame maintenance, and stabilization of the tertiary tRNA structure (1).2-thioribothymidine (s 2 T) 2 is a 2-thiolated derivative of 5-methyluridine (ribothymidine (rT)), located at position 54 of Thermus thermophilus tRNA (2), and has been shown to stabilize tRNA structure in a high temperature environment (3). In the extreme thermophilic eubacteria, Thermus thermophilus (4), and the archaea, Pyrococcus furiosus (5), the 2-thiolation level of rT54 in tRNA increases with cultivation temperature; the melting temperature (T m ) of the tRNA increases concomitantly with incremental increases in s 2 T content. These findings indicate that 2-thiolation of rT54 is responsible for the thermostability of thermophile tRNA at a variety of cultivation temperatures, thereby ensuring the adaptation of the protein synthesis machinery to specific thermal environments.However, the body of knowledge regarding s 2 T biosynthesis is limited. First, the enzymes responsible for the tRNA modification and the genes involved in the 2-thiolation reaction have not been identified to date. Previously, we demonstrated that the tRNA structural elements required for 2-thiolation are the conserved bases in the TC loop and the structure created by those bases (6). In this report, we investigated the sulfur donor for s 2 T biosynthesis in vivo. We also examined the 2-thiolation reaction in vitro, in order to characterize the temperature dependence of this reaction, and considered the contribution of neighboring nucleoside modifications to the efficiency of 2-thiolation of rT54, both in vivo and in vitro. ...

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“…18), with exception of the mammalian mitochondrial enzyme (19 or domains of life) and bacterial tRNA Tyr species (20). In bacterial-type SerRS, the N-terminal domain forms an antiparallel ␣-helical coiled-coil structure (3,16), whereas in the methanogenic-type counterpart it is significantly larger and composed of a six-stranded antiparallel ␤-sheet capped by a bundle of three helices (H1, H2, and H4) with up-down topology and an additional short helix (H3) that runs almost perpendicular to helix H4 (21) (see Fig.…”

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confidence: 99%

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

Jarić

Bilokapić

Lesjak

et al. 2009

Journal of Biological Chemistry

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The aminoacyl-tRNA synthetases (aaRSs) 2 catalyze the activation of cognate amino acids and their transfer to the 3Ј-end of corresponding tRNA molecules. The aaRSs are a highly conserved family of enzymes comprised of two distinct structural groups referred to as classes I and II (1-3), with a notable exception of LysRS representatives, which belong to both classes (4). Although the catalytic mechanisms of various aaRSs are broadly similar (5), each enzyme has developed a high specificity in recognizing its cognate amino acid and tRNA, which is pivotal for accurate translation of the genetic code (1). The discrimination of the amino acids is based on recognizing the differences in the size and charge of the molecules (6). The specificity of tRNA selection depends on a set of identity determinants that are mostly located at two distal extremities: the anticodon loop and the amino acid accepting stem. In a few instances, identity elements are also found in the D-arm, T-arm, and variable loop. They can either act as positive determinants that enhance aminoacylation or negative ones that prevent aminoacylation. The recognition of tRNAs by synthetases can also be affected by the modification of particular nucleotides (7,8). AaRSs show divergent strategies for tRNA recognition. Most notably, class I and class II aaRSs (including pyrrolysyl-tRNA synthetase, see Ref. 9) approach tRNAs from the minor and major groove sides of the acceptor stem, respectively (10). Although the majority of determinants are in direct contact with cognate synthetases (8), the aminoacylation fidelity is controlled by kinetic differences more than by binding affinities (11).Seryl-tRNA synthetases (SerRSs), which catalyze the aminoacylation of several tRNA Ser isoacceptors and tRNA Sec with serine, can be divided into two structurally different groups: bacterial-type SerRSs function in a variety of archaeal, bacterial, and eukaryotic organisms, whereas the methanogenic-type was found only in methanogenic archaea (12, 13). Furthermore, based on sequence comparison (14, 15) and x-ray analyses, two subgroups of bacterial-type SerRSs were identified: one consists of the enzymes from bacterial sources, best represented by those from Thermus thermophilus (16) and Escherichia coli (3), and an archaeal/eukaryal-type, structurally related to SerRS from archaeon Pyrococcus horikoshii (17).All SerRSs are functional homodimers with a C-terminal active site domain typical for class II aaRSs and an N-terminal domain that is responsible for binding of the long

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Compilation of tRNA sequences and sequences of tRNA genes

Cited by 1,150 publications

References 459 publications

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

Temperature-dependent Biosynthesis of 2-Thioribothymidine of Thermus thermophilus tRNA

Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition

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