protein coding gene - ytm1 (SPAC890.04c) - ribosome biogenesis WD repeat WDR12/Ytm1 protein

Gene summary

Standard name: ytm1
Systematic ID: SPAC890.04c
Product: ribosome biogenesis WD repeat WDR12/Ytm1 protein
Organism: Schizosaccharomyces pombe (fission yeast)
UniProt ID: Q9URY0
ORFeome ID: 35/35B12
Characterisation status: biological role published
Feature type: mRNA gene
Genomic location: chromosome I: 5007016..5008878 reverse strand

Annotation

GO biological process

GO:1902626 - assembly of large subunit precursor of preribosome

References:

PMID:36423630

GO cellular component

GO:0000785 - chromatin

References:

PMID:22146723

GO:0005730 - nucleolus

References:

PMID:27667686

GO:0005634 - nucleus

References:

PMID:16823372

GO:0070545 - PeBoW complex

References:

GO_REF:0000033

GO:0030684 - preribosome

References:

PMID:36423630

GO:0030687 - preribosome, large subunit precursor

References:

GO_REF:0000033

GO:0000785 - chromatin

References:

PMID:36423630

Modification

MOD:00046 - O-phospho-L-serine

References:

PMID:25720772

MOD:00047 - O-phospho-L-threonine

References:

PMID:18257517

MOD:01149 - sumoylated lysine

References:

PMID:26537787

MOD:01148 - ubiquitinylated lysine

References:

PMID:37970674

Protein features

PBO:0111751 - WD repeat protein

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

PMID:23101633

Single locus phenotype

FYPO:0000311 - inviable after spore germination with normal, unseptated germ tube morphology

References:

PMID:23697806

Genotypes:

ytm1delta

FYPO:0002151 - inviable spore

References:

PMID:23697806

Genotypes:

ytm1delta

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

ytm1delta

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

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
PF00400	WD40	WD40_rpt	Pfam
PF08154	NLE	NLE	Pfam
PS00678	WD_REPEATS_1	WD40_repeat_CS	PROSITE patterns
PS50082	WD_REPEATS_2	WD40_rpt	PROSITE profiles
PS50294	WD_REPEATS_REGION		PROSITE profiles
SM00320	WD40	WD40_rpt	SMART
PR00320	GPROTEINBRPT	WD40_PAC1	PRINTS
G3DSA:2.130.10.10		WD40/YVTN_repeat-like_dom_sf	CATH-Gene3D
SSF50978		WD40_repeat_dom_sf	SUPERFAMILY
PTHR19855			PANTHER
MF_03029	WDR12	WDR12/Ytm1	HAMAP

Orthologs

WDR12 (HGNC:14098) Homo sapiens
ytm1 (SJAG_02759) Schizosaccharomyces japonicus
YTM1 (YOR272W) Saccharomyces cerevisiae

References / Literature

GO_REF:0000033 - Annotation inferences using phylogenetic trees
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:38051102 - Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis.: Tai YT et al. Mol Cell Biol 2023 Dec 05;:1-18
PMID:27667686 - Potent, Reversible, and Specific Chemical Inhibitors of Eukaryotic Ribosome Biogenesis.: Kawashima SA et al. Cell 2016 Oct 06;167(2):512-524.e14
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: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: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:18257517 - Phosphoproteome analysis of fission yeast.: Wilson-Grady JT et al. J Proteome Res 2008 Mar;7(3):1088-97
PMID:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.: Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
PMID:21436456 - Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA.: Zhang K et al. Science 2011 Mar 25;331(6024):1624-7
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:36423630 - Chromatin localization of nucleophosmin organizes ribosome biogenesis.: Ugolini I et al. Mol Cell 2022 Dec 01;82(23):4443-4457.e9
PMID:21511999 - Comparative functional genomics of the fission yeasts.: Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.: Egan ED et al. RNA 2014 Jun;20(6):867-81
PMID:22146723 - Systematic localization study on novel proteins encoded by meiotically up-regulated ORFs in fission yeast.: Ikebe C et al. Biosci Biotechnol Biochem 2011;75(12):2364-70
PMID:26537787 - Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.: Køhler JB et al. Nat Commun 2015 Nov 05;6:8827
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:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.: Strachan J et al. J Cell Sci 2023 Dec 01;136(23)