protein coding gene - trm7 (SPAC4F10.03c) - tRNA (cytidine(32)-2'-O)-methyltransferase/tRNA (guanosine(34)-2'-O)-methyltransferase Trm7

Gene summary

Standard name: trm7
Systematic ID: SPAC4F10.03c
Product: tRNA (cytidine(32)-2'-O)-methyltransferase/tRNA (guanosine(34)-2'-O)-methyltransferase Trm7
Organism: Schizosaccharomyces pombe (fission yeast)
UniProt ID: O36015
ORFeome ID: 16/16F04
Characterisation status: biological role published
Feature type: mRNA gene
Genomic location: chromosome I: 4834655..4835973 reverse strand

Annotation

Disease association

MONDO:0010660 - intellectual disability, X-linked 9

References:

PB_REF:0000006

MONDO:0019181 - non-syndromic X-linked intellectual disability

References:

PMID:26310293

GO biological process

GO:0002181 - cytoplasmic translation

References:

GO_REF:0000033

GO:0030488 - tRNA methylation

References:

PMID:25404562

GO:0002130 - wobble position ribose methylation

References:

GO_REF:0000033

GO cellular component

GO:0005737 - cytoplasm

References:

GO_REF:0000033

GO molecular function

GO:0106339 - tRNA (cytidine(32)-2'-O-ribose)-methyltransferase activity

References:

PMID:25404562

GO:0106340 - tRNA (guanosine(34)-2'-O-ribose)-methyltransferase activity

References:

PMID:25404562

Modification

MOD:01148 - ubiquitinylated lysine

References:

PMID:37970674

Multi-locus phenotype

FYPO:0001890 - increased RNA level

References:

PMID:29596413

Genotypes:

FYPO:0000840 - normal RNA level

References:

PMID:29596413

Genotypes:

frs1-I406L(aa) trm7delta

FYPO:0002060 - viable vegetative cell population

References:

PMID:25404562

Genotypes:

SPATRNAPHE.01+(wild type)[Overexpression] trm7+(wild type)[Overexpression]

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

PMID:23101633

Single locus phenotype

FYPO:0007021 - abolished tRNA cytosine 2'-O-methylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0007022 - abolished tRNA guanosine 2'-O-methylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

References:

PMID:32101745

Genotypes:

trm7::Tn-seq

FYPO:0007024 - decreased tRNA guanosine 7-methylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0007025 - decreased tRNA guanosine N2-methylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0007026 - decreased tRNA wybutosine biosynthesis

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0001890 - increased RNA level

References:

PMID:29596413

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0007023 - increased tRNA guanosine 1-methylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0000951 - inviable small vegetative cell

References:

PMID:23697806

Genotypes:

trm7delta

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

trm7delta

FYPO:0006249 - normal tRNA aminoacylation

References:

PMID:29596413

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0007017 - normal tRNA pseudouridylation

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0001357 - normal vegetative cell population growth

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

FYPO:0001234 - slow vegetative cell population growth

References:

PMID:25404562

Genotypes:

trm7+(wild type)[Knockdown]

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)

Protein features

ID	Name	InterPro name	DB name
PF01728	FtsJ	RNA_MeTrfase_FtsJ_dom	PFAM
cd02440	AdoMet_MTases		CDD
G3DSA:3.40.50.150:FF:000176			FUNFAM
SSF53335	S-adenosyl-L-methionine-dependent methyltransferases	SAM-dependent_MTases_sf	SUPERFAMILY
G3DSA:3.40.50.150	Vaccinia Virus protein VP39	SAM-dependent_MTases_sf	GENE3D
PTHR10920	RIBOSOMAL RNA METHYLTRANSFERASE	RNA_methyltr_RlmE	PANTHER
MF_01547	RNA_methyltr_E	rRNA-MeTfrase_E	HAMAP
MF_03162	RNA_methyltr_E_TRM7	RNA_methyltr_E_TRM7	HAMAP

Orthologs

FTSJ1 (HGNC:13254) Homo sapiens
trm7 (SJAG_01269) Schizosaccharomyces japonicus
TRM7 (YBR061C) Saccharomyces cerevisiae

References / Literature

GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:21511999 - Comparative functional genomics of the fission yeasts.: Rhind N et al. Science 2011 May 20;332(6032):930-6
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:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.: Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:32101745 - Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.: Lee SY et al. Cell Rep 2020 Feb 25;30(8):2686-2698.e8
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
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:25404562 - Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes.: Guy MP et al. RNA 2015 Jan;21(1):61-74
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:26310293 - Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1.: Guy MP et al. Hum Mutat 2015 Dec;36(12):1176-87
PMID:29596413 - Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway.: Han L et al. PLoS Genet 2018 Mar;14(3):e1007288
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