Substrate tRNA Recognition Mechanism of Eubacterial tRNA (m1A58) Methyltransferase (TrmI)

Takuma, Hiroyuki; Ushio, Natsumi; Minoji, Masayuki; Kazayama, Ai; Shigi, Naoki; Hirata, Akira; Tomikawa, Chie; Ochi, Akira; Hori, Hiroyuki

doi:10.1074/jbc.m114.606038

Cited by 32 publications

(37 citation statements)

References 60 publications

(101 reference statements)

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“…For instance, TrmI from T. thermophilus preferentially methylates T. thermophilus tRNA Phe than S. cerevisiae tRNA Phe . It was also shown that the access of TrmI to A 58 requires disruption of the interaction between T and D loops, and indeed, disruption of T and D loop interactions accelerates the methylation [42]. In Fig.…”

Section: Recognition Of Trna Substratementioning

confidence: 75%

“…Y78 is a good candidate for the stabilization of the flipped-out adenine given its position in the catalytic pocket, the structure and the dramatic decrease of kcat of the TrmI Y78A mutant. D170 is a crucial residue, universally conserved, that makes hydrogen bonds with both the SAM co-factor and the adenine to be methylated [28,42]. We could not obtained co-crystal of the D170A mutant with either SAM or SAH whereas SAM was present in the catalytic pocket in the crystal structure of Y78A mutant and SAH in the wild-type protein structure.…”

Section: Structures Of Trmi Catalytic Mutants (D170a Y78a)mentioning

confidence: 84%

“…The N-terminal domain forms one groove of the tetramer and was proposed to be in contact with the variable loop or the D/anticodon stems of the tRNA [28,50]. A recent paper shows that an RNA containing the 3′-part of the acceptor stem, the T arm and the variable loop is a very good substrate of TrmI whereas one containing the D/T/anticodons arms and the variable loop was a poor substrate [42]. Therefore, the N-terminal domain most probably grasp the variable loop of substrate tRNAs and its mobility is probably essential in this interaction to keep the adenine in the catalytic pocket.…”

Section: Structures Of Trmi Catalytic Mutants (D170a Y78a)mentioning

confidence: 99%

“…It was recently shown that the activity of T. thermophilus TrmI is dependent on precise sequence determinants of its tRNA substrate [42] and that the sequence of tRNA will impact the m 1 A 58 activity of TrmI. For instance, TrmI from T. thermophilus preferentially methylates T. thermophilus tRNA Phe than S. cerevisiae tRNA Phe .…”

Section: Recognition Of Trna Substratementioning

confidence: 99%

“…We then discuss tRNA recognition and m 1 A catalytic mechanism by TrmIs in the lens of these structures and of newly published data describing tRNA determinants for TrmI recognition [42].…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI

Dégut

Ponchon

Folly-Klan

et al. 2016

Biophysical Chemistry

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Section: Recognition Of Trna Substratementioning

confidence: 75%

Section: Structures Of Trmi Catalytic Mutants (D170a Y78a)mentioning

confidence: 84%

Section: Structures Of Trmi Catalytic Mutants (D170a Y78a)mentioning

confidence: 99%

Section: Recognition Of Trna Substratementioning

confidence: 99%

“…We then discuss tRNA recognition and m 1 A catalytic mechanism by TrmIs in the lens of these structures and of newly published data describing tRNA determinants for TrmI recognition [42].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI

Dégut

Ponchon

Folly-Klan

et al. 2016

Biophysical Chemistry

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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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To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

Barraud

Tisné

2019

IUBMB Life

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Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3′‐CCA amino‐acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126–1140, 2019

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Substrate tRNA Recognition Mechanism of Eubacterial tRNA (m1A58) Methyltransferase (TrmI)

Cited by 32 publications

References 60 publications

The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI

The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI

Transfer RNA Synthesis and Regulation

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

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