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Literature summary for 2.1.1.202 extracted from
- 5-Methylcytosine RNA methylation in Arabidopsis thaliana (2017), Mol. Plant, 10, 1387-1399 .
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | generation of Arabidopsis thaliana T-DNA insertion mutants of potential mRNA m5C methyltransferases (RCMTs), and of single mutants of TRM4B, trm4b-3 and trm4b-4, the latter exhibit defects in root development. The fulllength transcript of TRM4B and its 3' fragment downstream of the T-DNA insertion sites are greatly decreased in trm4b-3 and undetectable in trm4b-4, implying that trm4b-3 and trm4b-4 could be reduction-of function and loss-of-function mutants, respectively | Arabidopsis thaliana |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| nucleolus | - |
Arabidopsis thaliana | 5730 | - |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| S-adenosyl-L-methionine + cytosine in tRNA precursor | Arabidopsis thaliana | - |
S-adenosyl-L-homocysteine + 5-methylcytosine in tRNA precursor | - |
? |  |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | - |
- |
- |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| cauline leaf | - |
Arabidopsis thaliana | - |
| flower | - |
Arabidopsis thaliana | - |
| flower bud | - |
Arabidopsis thaliana | - |
| additional information | transcriptome-wide profiling of m5C RNA in Arabidopsis thaliana is made by applying m5C RNA immunoprecipitation followed by a deepsequencing approach (m5C-RIP-seq). LC-MS/MS and dot blot analyses reveal a dynamic pattern of m5C mRNA modification in various tissues and at different developmental stages. m5C-RIP-seq analysis identified 6045m5C peaks in 4465 expressed genes in young seedlings. m5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. Spatial change in m5C levels in different tissues | Arabidopsis thaliana | - |
| root | - |
Arabidopsis thaliana | - |
| rosette leaf | - |
Arabidopsis thaliana | - |
| seedling | slightly increasing trend of m5C modification in mRNA from 3- to 15-day-old whole seedlings undergoing vegetative, floral transitional, and reproductive stages | Arabidopsis thaliana | - |
| silique | - |
Arabidopsis thaliana | - |
| stem | - |
Arabidopsis thaliana | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| S-adenosyl-L-methionine + cytosine in tRNA precursor | - |
Arabidopsis thaliana | S-adenosyl-L-homocysteine + 5-methylcytosine in tRNA precursor | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| M5C RNA methyltransferase | - |
Arabidopsis thaliana |
| RNA (cytosine-5)-methyltransferase | - |
Arabidopsis thaliana |
| TRM4B | - |
Arabidopsis thaliana |
| tRNA-specific methyltransferase 4B | - |
Arabidopsis thaliana |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| S-adenosyl-L-methionine | - |
Arabidopsis thaliana | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | mutations in TRM4B display defects in root development and decreased m5C peaks. TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m5C levels | Arabidopsis thaliana |
| physiological function | TRM4B encodes a potential mRNA m5C methyltransferase (RCMT). 5-methylcytosine (m5C) is a DNA modification predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. tRNA-specific methyltransferase 4B (TRM4B) serves as a potential mRNA m5C methyltransferase. Transcriptome-wide profiling of m5C RNA in Arabidopsis thaliana is made by applying m5C RNA immunoprecipitation followed by a deepsequencing approach (m5C-RIP-seq). LC-MS/MS and dot blot analyses reveal a dynamic pattern of m5C mRNA modification in various tissues and at different developmental stages. m5C-RIP-seq analysis identified 6045m5C peaks in 4465 expressed genes in young seedlings. m5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. An RNA (cytosine-5)-methyltransferase, tRNA-specific methyltransferase 4B (TRM4B), exhibits m5C RNA methyltransferase activity positively correlated with transcript levels of genes in root development. m5C in mRNA is an epitranscriptome marker in Arabidopsis thaliana, and the regulation of this modification is an integral part of gene regulatory networks underlying plant development | Arabidopsis thaliana |
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