Identification of determinants for tRNA substrate recognition by<i>Escherichia coli</i>C/U34 2′-O-methyltransferase

Zhou, Mi; Long, Tao; Fang, Zhipeng; Zhou, Xiao‐Long; Liu, Ru-Juan; Wang, En‐Duo

doi:10.1080/15476286.2015.1050576

Cited by 33 publications

(44 citation statements)

References 53 publications

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“…Thus, the 5-carboxymethylaminomethyl group in cmnm 5 U34 is not involved in the recognition of tRNA by TrmL. Furthermore, the methylation of stem-loop RNA by TrmL [70] is consistent with the aforementioned proposed docking model of TrmL and tRNA [54]. …”

Section: Transfer Rna Recognition Mechanismmentioning

confidence: 53%

“…This model suggested a possibility of direct interaction between TrmL and ms 2 i 6 A37 in tRNA [54]. In 2015, it was reported that chemically synthesized stem-loop RNA containing Ψ32, i 6 A37 and Ψ39 was methylated by TrmL: the ribose methylation occurred at unmodified U34 [70]. Thus, the 5-carboxymethylaminomethyl group in cmnm 5 U34 is not involved in the recognition of tRNA by TrmL.…”

Section: Transfer Rna Recognition Mechanismmentioning

confidence: 99%

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Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

Hori

2017

Biomolecules

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The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’-O-methylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of anti-bacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered.

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Section: Transfer Rna Recognition Mechanismmentioning

confidence: 53%

Section: Transfer Rna Recognition Mechanismmentioning

confidence: 99%

Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

Hori

2017

Biomolecules

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“…Two SPOUT enzymes, TrmL (tRNA Um 34 /Cm 34 ) and RlmH (rRNA), are considered “minimalist” proteins where substrate binding is limited solely to the SPOUT domain and, in the case of TrmL, no other RNA-binding protein assists in binding [25,49–51]. TrmL acts as a homodimer to catalyze 2′-O-methylation at position 34 on two isoacceptors of tRNA Leu (anticodons: CAA and UAA), and like many RNA-binding enzymes, it uses positively charged residues for substrate recognition [50,51]. Interestingly, only three other SPOUT tRNA methyltransferases are found in bacteria (TrmH, TrmD, and TrmJ); all methylate many more different substrates than TrmL [50].…”

Section: The Diversity Of Rna Methylations Methyltransferases and Tmentioning

confidence: 99%

“…TrmL acts as a homodimer to catalyze 2′-O-methylation at position 34 on two isoacceptors of tRNA Leu (anticodons: CAA and UAA), and like many RNA-binding enzymes, it uses positively charged residues for substrate recognition [50,51]. Interestingly, only three other SPOUT tRNA methyltransferases are found in bacteria (TrmH, TrmD, and TrmJ); all methylate many more different substrates than TrmL [50]. Presumably, these enzymes acquired nucleic acid-binding domains as N- and C-terminal extensions that support recognition of multiple substrates, whereas the minimal SPOUT enzyme TrmL binds fewer substrates, making these extensions unnecessary.…”

Section: The Diversity Of Rna Methylations Methyltransferases and Tmentioning

confidence: 99%

The Evolution of Substrate Specificity by tRNA Modification Enzymes

2017

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All types of nucleic acids in cells undergo naturally occurring chemical modifications, including DNA, rRNA, mRNA, snRNA, and most prominently tRNA. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified [1]. In tRNA, the function of modifications varies; some modulate global and/or local RNA structure, and others directly impact decoding and may be essential for viability. Whichever the case, the overall importance of modifications is highlighted by both their evolutionary conservation and the fact that organisms use a substantial portion of their genomes to encode modification enzymes, far exceeding what is needed for the de novo synthesis of the canonical nucleotides themselves [2]. Although some modifications occur at exactly the same nucleotide position in tRNAs from the three domains of life, many can be found at various positions in a particular tRNA and their location may vary between and within different tRNAs. With this wild array of chemical diversity and substrate specificities, one of the big challenges in the tRNA modification field has been to better understand at a molecular level the modes of substrate recognition by the different modification enzymes; in this realm RNA binding rests at the heart of the problem. This chapter will focus on several examples of modification enzymes where their mode of RNA binding is well understood; from these, we will try to draw general conclusions and highlight growing themes that may be applicable to the RNA modification field at large.

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“…Some of the site-specific enzymes act on essentially all tRNAs containing an appropriate target residue, like TrmA from Escherichia coli , which methylates uridine at position 54 in practically all tRNAs that have this residue [9]. Other enzymes act only on a subset of available substrates that conform to their requirements of sequence, structure and/or presence of other modifications – examples include TrmL [10] and TruA [11] from E. coli .…”

Section: Introductionmentioning

confidence: 99%

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Machnicka

Dunin-Horkawicz

Crécy‐Lagard

et al. 2016

Methods

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tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as web server at http://genesilico.pl/trnamodpred/.

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Identification of determinants for tRNA substrate recognition byEscherichia coliC/U34 2′-O-methyltransferase

Abstract: (2015) Identification of determinants for tRNA substrate recognition by Escherichiacoli C/ U34 2′-O-methyltransferase, RNA Biology, 12:8, 900-911,

Cited by 33 publications

References 53 publications

Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

The Evolution of Substrate Specificity by tRNA Modification Enzymes

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

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