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Literature summary for 2.1.1.202 extracted from
- Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae (2015), BMC Plant Biol., 15, 199.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| trm4a and trm4b, phylogenetic analysis | Arabidopsis thaliana |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| nucleus | - |
Arabidopsis thaliana | 5634 | - |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | ? | - |
? |  |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | - |
two putative TRM4/NSUN2 paralogues, TRM4A and TRM4B | - |
| Brassica rapa | - |
- |
- |
| Caulerpa taxifolia | - |
- |
- |
| Ginkgo biloba | - |
- |
- |
| Nannochloropsis oculata | - |
- |
- |
| Triticum turgidum subsp. durum | - |
- |
- |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| additional information | tRNAHis m5C levels are unusually responsive to yeast growth conditions | Nannochloropsis oculata | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
| 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 | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| TRM4 | - |
Arabidopsis thaliana |
| TRM4 | - |
Brassica rapa |
| TRM4 | - |
Triticum turgidum subsp. durum |
| TRM4 | - |
Ginkgo biloba |
| TRM4 | - |
Nannochloropsis oculata |
| TRM4 | - |
Caulerpa taxifolia |
| TRM4A | - |
Arabidopsis thaliana |
| TRM4B | - |
Arabidopsis thaliana |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| S-adenosyl-L-methionine | - |
Arabidopsis thaliana | |
| S-adenosyl-L-methionine | - |
Brassica rapa | |
| S-adenosyl-L-methionine | - |
Triticum turgidum subsp. durum | |
| S-adenosyl-L-methionine | - |
Ginkgo biloba | |
| S-adenosyl-L-methionine | - |
Nannochloropsis oculata | |
| S-adenosyl-L-methionine | - |
Caulerpa taxifolia | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed | Caulerpa taxifolia |
| evolution | both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed, overview | Brassica rapa |
| evolution | both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites are conserved across all species analysed, overview | Ginkgo biloba |
| evolution | both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites were conserved across all species analysed | Triticum turgidum subsp. durum |
| evolution | both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites were conserved across all species analysed | Nannochloropsis oculata |
| 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 |
| 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 |
| physiological function | post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism | Brassica rapa |
| 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 |
| physiological function | post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism | Ginkgo biloba |
| physiological function | post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism | Nannochloropsis oculata |
| physiological function | post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism | Caulerpa taxifolia |
| 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 |
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