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protein coding gene - trm402 (SPAC23C4.17) - tRNA (cytosine-5-)-methyltransferase

Gene summary

Standard name
trm402
Systematic ID
SPAC23C4.17
Product
tRNA (cytosine-5-)-methyltransferase
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
trm4, trm4b
UniProt ID
O13935
ORFeome ID
28/28B11
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1058352..1061166 forward strand

Annotation

Disease association

MONDO:0012613 - intellectual disability, autosomal recessive 5

References:

GO biological process

GO:0030488 - tRNA methylation

References:

GO:0002127 - tRNA wobble base cytosine methylation

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GO cellular component

GO:0005737 - cytoplasm

References:

GO:0005634 - nucleus

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GO molecular function

GO:0062152 - mRNA (cytidine-5-)-methyltransferase activity

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GO:0016428 - tRNA (cytidine-N5)-methyltransferase activity

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GO:0000049 - tRNA binding

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Modification

MOD:01148 - ubiquitinylated lysine

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Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

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PomGeneEx:0000012 - RNA level decreased

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PomGeneEx:0000029 - RNA level decreased during Core Environmental Stress Response

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Quantitative gene expression

PBO:0006310 - protein level

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PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0000151 - abnormal meiotic chromosome segregation

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Genotypes:

FYPO:0001766 - abnormal tRNA methylation

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Genotypes:

FYPO:0009077 - increased cell population growth on ethanol carbon source

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Genotypes:

FYPO:0009094 - increased cell population growth on lysine and proline nitrogen source

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Genotypes:

FYPO:0009098 - increased cell population growth on mannitol carbon source

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Genotypes:

FYPO:0001769 - increased tRNA-Asp C38 methylation

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Genotypes:

FYPO:0001020 - normal growth on calcium

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Genotypes:

FYPO:0001764 - normal tRNA-Asp C48, C49, C60, C61 and C62 methylation

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Genotypes:

FYPO:0001453 - resistance to ethanol

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Genotypes:

FYPO:0009087 - resistance to magnesium chloride and sodium dodecyl sulfate

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Genotypes:

FYPO:0000799 - sensitive to diamide

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Genotypes:

FYPO:0002060 - viable vegetative cell population

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Genotypes:

FYPO:0002177 - viable vegetative cell with normal cell morphology

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Genotypes:

Taxonomic conservation

PBO:0011067 - conserved in bacteria

PBO:0011065 - conserved in eukaryotes

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Warnings

PBO:0000070 - gene structure updated

References:

Protein features

IDNameInterPro nameDB name
PF01189Methyltr_RsmB-FMeTrfase_RsmB-F_NOP2_catPfam
PF25376Pre-PUA_NSUN2Pre-PUA_NSUN2Pfam
PF25378PUA_NSUN2PUA_NSUN2Pfam
cd02440AdoMet_MTasesCDD
PS01153NOL1_NOP2_SUNRsmB/NOL1/NOP2-like_CSPROSITE patterns
PS51686SAM_MT_RSMB_NOPMeTrfase_RsmB-F_NOP2_domPROSITE profiles
PR02008RCMTFAMILYRCMTPRINTS
PR02011RCMTNCL1RCMT_NCL1PRINTS
G3DSA:3.40.50.150:FF:000112CATH-FunFam
G3DSA:3.40.50.150SAM-dependent_MTases_sfCATH-Gene3D
SSF53335SAM-dependent_MTases_sfSUPERFAMILY
PTHR22808RCMTPANTHER

Orthologs

References / Literature

PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:30646830 - Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases Trm4a and Trm4b in fission yeast.
Müller M et al. RNA Biol 2019 Mar;16(3):249-256
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
PMID:12529438 - Global transcriptional responses of fission yeast to environmental stress.
Chen D et al. Mol Biol Cell 2003 Jan;14(1):214-29
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:26771498 - A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
Vo TV et al. Cell 2016 Jan 14;164(1-2):310-323
PMID:23074192 - Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling.
Becker M et al. Nucleic Acids Res 2012 Dec;40(22):11648-58
PMID:29259000 - Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen.
Blyth J et al. Genetics 2018 Feb;208(2):589-603
PMID:34706246 - Cross talk between the upstream exon-intron junction and Prp2 facilitates splicing of non-consensus introns.
Hümmer S et al. Cell Rep 2021 Oct 26;37(4):109893
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
GO_REF:0000033 - Annotation inferences using phylogenetic trees