Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Burgess, A.; David, R.; Searle, I.
    Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae (2015), BMC Plant Biol., 15, 199.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.202 trm4a and trm4b, phylogenetic analysis Arabidopsis thaliana

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.1.1.202 nucleus
-
 Arabidopsis thaliana 5634
-
2.1.1.204 nucleus
-
 Arabidopsis thaliana 5634
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.202 additional information Arabidopsis thaliana identification of single-nucleotide resolution of cytosine 5-methylation sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview. The enzyme does not methylate cytosines at structural positions C47, C48, C49 and C72. Identification of modified cytosines in Arabidopsis thaliana nuclear transcribed tRNAs which are dependent on RMTases TRDMT1 and TRM4B. No cytosine 5-methylation sites are detected in Arabidopsis chloroplast or mitochondrial tRNAs, which is in contrast to animal mitochondrial tRNAs ?
-
 ?
2.1.1.202 additional information Brassica rapa identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview ?
-
 ?
2.1.1.202 additional information Triticum turgidum subsp. durum identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview ?
-
 ?
2.1.1.202 additional information Ginkgo biloba identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview ?
-
 ?
2.1.1.202 additional information Nannochloropsis oculata identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview ?
-
 ?
2.1.1.202 additional information Caulerpa taxifolia identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview ?
-
 ?
2.1.1.204 S-adenosyl-L-methionine + cytosine38 in tRNAAsp(GTC) Arabidopsis thaliana
-
 S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp(GTC)
-
 ?
2.1.1.204 S-adenosyl-L-methionine + cytosine38 in tRNAGly(GCC) Arabidopsis thaliana
-
 S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAGly(GCC)
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.202 Arabidopsis thaliana
-
 two putative TRM4/NSUN2 paralogues, TRM4A and TRM4B
-
2.1.1.202 Brassica rapa
-
-
-
2.1.1.202 Caulerpa taxifolia
-
-
-
2.1.1.202 Ginkgo biloba
-
-
-
2.1.1.202 Nannochloropsis oculata
-
-
-
2.1.1.202 Triticum turgidum subsp. durum
-
-
-
2.1.1.204 Arabidopsis thaliana
-
-
-

Source Tissue

EC Number Source Tissue Comment Organism Textmining
2.1.1.202 additional information tRNAHis m5C levels are unusually responsive to yeast growth conditions Nannochloropsis oculata
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.202 additional information identification of single-nucleotide resolution of cytosine 5-methylation sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview. The enzyme does not methylate cytosines at structural positions C47, C48, C49 and C72. Identification of modified cytosines in Arabidopsis thaliana nuclear transcribed tRNAs which are dependent on RMTases TRDMT1 and TRM4B. No cytosine 5-methylation sites are detected in Arabidopsis chloroplast or mitochondrial tRNAs, which is in contrast to animal mitochondrial tRNAs Arabidopsis thaliana ?
-
 ?
2.1.1.202 additional information identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview Brassica rapa ?
-
 ?
2.1.1.202 additional information identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview Triticum turgidum subsp. durum ?
-
 ?
2.1.1.202 additional information identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview Ginkgo biloba ?
-
 ?
2.1.1.202 additional information identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview Nannochloropsis oculata ?
-
 ?
2.1.1.202 additional information identification of single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview Caulerpa taxifolia ?
-
 ?
2.1.1.202 additional information motif I is essential for methyltransferase activity and is required for S-adenosyl-L-methionine binding and catalysis. Enzyme variant Trm4a is lacking motif I in contrast to enzyme variant Trm4b Arabidopsis thaliana ?
-
 ?
2.1.1.204 S-adenosyl-L-methionine + cytosine38 in tRNAAsp(GTC)
-
 Arabidopsis thaliana S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp(GTC)
-
 ?
2.1.1.204 S-adenosyl-L-methionine + cytosine38 in tRNAGly(GCC)
-
 Arabidopsis thaliana S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAGly(GCC)
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.1.1.202 TRM4
-
 Arabidopsis thaliana
2.1.1.202 TRM4
-
 Brassica rapa
2.1.1.202 TRM4
-
 Triticum turgidum subsp. durum
2.1.1.202 TRM4
-
 Ginkgo biloba
2.1.1.202 TRM4
-
 Nannochloropsis oculata
2.1.1.202 TRM4
-
 Caulerpa taxifolia
2.1.1.202 TRM4A
-
 Arabidopsis thaliana
2.1.1.202 TRM4B
-
 Arabidopsis thaliana
2.1.1.204 DNA methyltransferase 2
-
 Arabidopsis thaliana
2.1.1.204 Dnmt2
-
 Arabidopsis thaliana
2.1.1.204 transfer RNA aspartic acid methyltransferase 1
-
 Arabidopsis thaliana
2.1.1.204 TRDMT1
-
 Arabidopsis thaliana

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.202 S-adenosyl-L-methionine
-
 Arabidopsis thaliana
2.1.1.202 S-adenosyl-L-methionine
-
 Brassica rapa
2.1.1.202 S-adenosyl-L-methionine
-
 Triticum turgidum subsp. durum
2.1.1.202 S-adenosyl-L-methionine
-
 Ginkgo biloba
2.1.1.202 S-adenosyl-L-methionine
-
 Nannochloropsis oculata
2.1.1.202 S-adenosyl-L-methionine
-
 Caulerpa taxifolia
2.1.1.204 S-adenosyl-L-methionine
-
 Arabidopsis thaliana

General Information

EC Number General Information Comment Organism
2.1.1.202 evolution both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed Caulerpa taxifolia
2.1.1.202 evolution both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed, overview Brassica rapa
2.1.1.202 evolution both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed, overview Ginkgo biloba
2.1.1.202 evolution both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites were conserved across all species analysed Triticum turgidum subsp. durum
2.1.1.202 evolution both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites were conserved across all species analysed Nannochloropsis oculata
2.1.1.202 evolution Identification of m5C sites in nuclear, chloroplast and mitochondrial tRNAs. 39 cytosine 5-methylation sites are identified at 5 structural positions and are located in tRNA secondary structure at positions C38, C48, C49, C50 and C72, pattern of methylation in individual tRNA isodecoders, overview. Identification of single-nucleotide resolution of cytosine 5-methylation sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species. Both the nucleotide position and percent methylation of tRNAs and rRNAs cytosine 5-methylation sites are conserved across all species analysed, overview Arabidopsis thaliana
2.1.1.202 malfunction in trm4a defective mutants, the cytosine 5-methylation profile is the same as wild-type, showing that TRM4A is not required for methylation of any of the detected tRNAs. In contrast for trm4b-1 and trm4b-2 mutants, a total of 18 sites have no detectable methylation and 7 sites have reduced methylation when compared to wild-type, the sites are corresponding to structural positions C48, C49, and C50. trdmt1/trm4b double mutants are hypersensitive to the antibiotic hygromycin B Arabidopsis thaliana
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism Brassica rapa
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism Triticum turgidum subsp. durum
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism Ginkgo biloba
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism Nannochloropsis oculata
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism Caulerpa taxifolia
2.1.1.202 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine is an important modification that regulates RNA metabolism. Nuclear tRNA methylation requires two evolutionarily conserved methyltransferases, TRDMT1 and TRM4B Arabidopsis thaliana
2.1.1.204 evolution identification of single-nucleotide resolution of cytosine 5-methylation sites in non-coding ribosomal RNAs and transfer RNAs of all three subcellular transcriptomes across six diverse species, overview. Both the nucleotide position and percent methylation of tRNAs and rRNAs cytosine 5-methylation sites are conserved across all species analysed, overview Arabidopsis thaliana
2.1.1.204 malfunction trdmt1/trm4b double mutants are hypersensitive to the antibiotic hygromycin B. Non-methylated C38 in trdmt1-defective plants results in loss of HpyCH4IV restriction site Arabidopsis thaliana
2.1.1.204 physiological function post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine is an important modification that regulates RNA metabolism. Identification of cytosine 5-methylation sites in nuclear, chloroplast and mitochondrial tRNAs. Nuclear tRNA methylation requires two evolutionarily conserved methyltransferases, TRDMT1 and TRM4B, EC 2.1.1.202 Arabidopsis thaliana