Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition

Hirata, Akira; Okada, Keisuke; Yoshii, Kazuaki; Shiraishi, Hiroaki; Saijo, Shinya; Yonezawa, Kazuya; Shimizu, Nobutaka; Hori, Hiroyuki

doi:10.1093/nar/gkz856

Cited by 21 publications

(37 citation statements)

References 69 publications

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Section: Wdr6 At Position 34 (mentioning

confidence: 99%

“…During the submission of our work, the biochemical and structural studies of S. cerevisiae Trm7-Trm734 (PDB ID: 6JP6) have been published online (Hirata et al, 2019). The structural model shows that Trm7 is a class I-type Rossmann-fold MTase, and Trm734 comprises three WD40 repeat domains (Hirata et al, 2019). They showed that Trm7-Trm734 are able to catalyze both G37-and A37-tRNAs for Nm34 formation and that m 1 G37 is not an essential element for catalysis (Hirata et al, 2019).…”

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

“…The structural model shows that Trm7 is a class I-type Rossmann-fold MTase, and Trm734 comprises three WD40 repeat domains (Hirata et al, 2019). They showed that Trm7-Trm734 are able to catalyze both G37-and A37-tRNAs for Nm34 formation and that m 1 G37 is not an essential element for catalysis (Hirata et al, 2019). Conversely, the presence of m 1 G37 could accelerate Nm34 formation (Hirata et al, 2019).…”

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

“…They showed that Trm7-Trm734 are able to catalyze both G37-and A37-tRNAs for Nm34 formation and that m 1 G37 is not an essential element for catalysis (Hirata et al, 2019). Conversely, the presence of m 1 G37 could accelerate Nm34 formation (Hirata et al, 2019). Therefore, FTSJ1-WDR6 may have strict substrate discrimination mechanisms compared to Trm7-Trm734.…”

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

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Intellectual disability‐associated gene ftsj1 is responsible for 2′‐O‐methylation of specific tRNAs

Wang

et al. 2020

EMBO Reports

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tRNA modifications at the anti-codon loop are critical for accurate decoding. FTSJ1 was hypothesized to be a human tRNA 2 0-Omethyltransferase. tRNA Phe (GAA) from intellectual disability patients with mutations in ftsj1 lacks 2 0-O-methylation at C32 and G34 (Cm32 and Gm34). However, the catalytic activity, RNA substrates, and pathogenic mechanism of FTSJ1 remain unknown, owing, in part, to the difficulty in reconstituting enzymatic activity in vitro. Here, we identify an interacting protein of FTSJ1, WDR6. For the first time, we reconstitute the 2 0-O-methylation activity of the FTSJ1-WDR6 complex in vitro, which occurs at position 34 of specific tRNAs with m 1 G37 as a prerequisite. We find that modifications at positions 32, 34, and 37 are interdependent and occur in a hierarchical order in vivo. We also show that the translation efficiency of the UUU codon, but not the UUC codon decoded by tRNA Phe (GAA), is reduced in ftsj1 knockout cells. Bioinformatics analysis reveals that almost 40% of the high TTT-biased genes are related to brain/nervous functions. Our data potentially enhance our understanding of the relationship between FTSJ1 and nervous system development.

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Section: Wdr6 At Position 34 (mentioning

confidence: 99%

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

Section: Wdr6 At Position 34 (mentioning

confidence: 99%

See 2 more Smart Citations

Intellectual disability‐associated gene ftsj1 is responsible for 2′‐O‐methylation of specific tRNAs

Wang

et al. 2020

EMBO Reports

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“…Fig. 5 B illustrates a validation in solution of the heterodimeric complex between the tRNA methyltransferase Trm7 and its partner subunit Trm734 from Saccharomyces cerevisiae ( Hirata et al. 2019 ).…”

mentioning

confidence: 99%

Methods, development and applications of small-angle X-ray scattering to characterize biological macromolecules in solution

Vela

Svergun

2020

Current Research in Structural Biology

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Applications of small-angle X-ray scattering (SAXS) in structural biology are reviewed. A brief introduction of the SAXS basics is followed by the presentation of the structural features of biological macromolecules in solution that can be assessed by SAXS. The approaches are considered allowing one to obtain low resolution three-dimensional (3D) structural models and to describe assembly states and conformations. Metrics and descriptors required for the assessment of model quality are presented and recent biological applications of SAXS are shown.

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Transfer RNA Synthesis and Regulation

Hori¹,

Hirata²,

Ueda³

et al. 2021

Encyclopedia of Life Sciences

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Transfer ribonucleic acid (tRNA), which is primarily transcribed from tRNA genes by RNA polymerase, matures via several steps: processing, splicing, CCA addition and posttranscriptional modifications. Primary transcripts of tRNA genes contain extra 5′ and 3′ sequences, which are removed by a set of nucleases. In addition, some primary transcripts contain introns, which are spliced out by specific endonucleases or in self‐splicing reactions. The ligation of exons generally requires a tRNA ligase. In some species, the CCA sequences present at the 3′‐termini of all mature tRNAs are not encoded in the tRNA genes but are added posttranscriptionally by a CCA‐adding enzyme. All mature tRNA molecules contain modified nucleotides, generated by specific tRNA modification enzymes or guide RNA systems. Recent studies have revealed that tRNA‐derived fragments act on biological phenomena such as regulation of translation. Furthermore, numerous tRNA‐like small RNAs have been found by genome sequencing. Key Concepts tRNA is transcribed from tRNA genes by RNA polymerase and matures through processing, splicing, CCA addition and posttranscriptional modification. Synthesis of tRNA is regulated by promoter activity and specific factors, depending on the nutrient conditions of the cell. The relative amounts of tRNA are regulated by several factors: copy number of tRNA genes, transcriptional activity and degradation by various nucleases. Primary transcripts of tRNA genes contain extra 5′ and 3′ sequences, which are removed by a set of nucleases. In some cases, tRNA transcripts contain introns, which are spliced out by specific endonuclease or the group I intron reaction. The two resultant fragments are joined by RNA ligase or the self‐splicing reaction. CCA‐adding enzyme regulates the amount of active tRNA by introducing the CCA sequence at the C ‐terminus of tRNA. tRNA possesses a variety of modified nucleotides, which are introduced by specific tRNA modification enzymes. Several modifications of tRNA play important roles in the translation process: promotion, expansion, restriction, and/or alteration of codon–anticodon interactions; stabilisation of tRNA structure; recognition by translation factors and aminoacyl‐tRNA synthetases; etc. Several modified nucleotides in tRNA are involved in RNA quality control systems, regulation of tRNA transport, infection and immune responses. Fragments derived from tRNA are not degradation products of tRNA but function as regulator molecules for translation and gene expression. In living cells, tRNA‐like small RNAs, which are often aminoacylated, have been found and may possess several physiological functions.

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Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition

Cited by 21 publications

References 69 publications

Intellectual disability‐associated gene ftsj1 is responsible for 2′‐O‐methylation of specific tRNAs

Intellectual disability‐associated gene ftsj1 is responsible for 2′‐O‐methylation of specific tRNAs

Methods, development and applications of small-angle X-ray scattering to characterize biological macromolecules in solution

Transfer RNA Synthesis and Regulation

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