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protein coding gene - nuc1 (SPBC4C3.05c) - DNA-directed RNA polymerase I complex large subunit Nuc1

Gene summary

Standard name
nuc1
Systematic ID
SPBC4C3.05c
Product
DNA-directed RNA polymerase I complex large subunit Nuc1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
rpa1, rpa190
UniProt ID
P15398
ORFeome ID
34/34B06
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 3127833..3133199 forward strand

Annotation

PBO:0000445 - 2.7.7.6

Complementation

PBO:0012291 - functionally complements S. cerevisiae YOR341W

References:

Disease association

MONDO:0014651 - acrofacial dysostosis Cincinnati type

References:

MONDO:0958018 - leukodystrophy, hypomyelinating, 27

References:

GO biological process

GO:0042790 - nucleolar large rRNA transcription by RNA polymerase I

References:

GO:0006363 - termination of RNA polymerase I transcription

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GO:0006362 - transcription elongation by RNA polymerase I

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GO:0006361 - transcription initiation at RNA polymerase I promoter

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GO cellular component

GO:0005829 - cytosol

References:

GO:0005730 - nucleolus

References:

GO:0005736 - RNA polymerase I complex

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GO molecular function

GO:0003677 - DNA binding

References:

GO:0003899 - DNA-directed RNA polymerase activity

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Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:00047 - O-phospho-L-threonine

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MOD:00696 - phosphorylated residue

References:

MOD:01149 - sumoylated lysine

References:

MOD:01148 - ubiquitinylated lysine

References:

Multi-locus phenotype

FYPO:0005350 - abnormal chromatin organization resulting in peripheral chromatin distribution

References:

Genotypes:

FYPO:0001355 - decreased vegetative cell population growth

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0004506 - abnormal nucleolar chromatin organization resulting in peripheral chromatin distribution

References:

Genotypes:

FYPO:0003687 - abnormal protein localization to nucleolus

References:

Genotypes:

FYPO:0003688 - abolished protein localization to nucleolus

References:

Genotypes:

FYPO:0003694 - decreased mature 18S rRNA level

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Genotypes:

FYPO:0001324 - decreased protein level during vegetative growth

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Genotypes:

FYPO:0002391 - decreased protein localization to chromatin at rDNA

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Genotypes:

FYPO:0003119 - increased nuclear polyadenylated mRNA level during vegetative growth

References:

Genotypes:

FYPO:0001991 - inviable after spore germination, without cell division

References:

Genotypes:

FYPO:0002151 - inviable spore

References:

Genotypes:

FYPO:0001489 - inviable vegetative cell

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0001387 - loss of viability at high temperature

References:

Genotypes:

FYPO:0002053 - normal DNA topoisomerase II activity

References:

Genotypes:

FYPO:0002625 - normal protein localization to chromatin rDNA

References:

Genotypes:

FYPO:0002901 - normal protein localization to kinetochore during vegetative growth

References:

Genotypes:

FYPO:0001234 - slow vegetative cell population growth

References:

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)

Protein features

IDNameInterPro nameDB name
PF00623RNA_pol_Rpb1_2RNA_pol_asuPfam
PF04983RNA_pol_Rpb1_3RNA_pol_Rpb1_3Pfam
PF04997RNA_pol_Rpb1_1RNA_pol_Rpb1_1Pfam
PF04998RNA_pol_Rpb1_5RNA_pol_Rpb1_5Pfam
PF05000RNA_pol_Rpb1_4RNA_pol_Rpb1_4Pfam
cd01435RNAP_I_RPA1_NDNA-dir_RNA_pol1_lsu_NCDD
cd02735RNAP_I_Rpa1_CDNA-dir_RNA_pol1_lsu_CCDD
SM00663RPOLA_NRNA_pol_NSMART
G3DSA:1.10.150.390:FF:000005CATH-FunFam
G3DSA:1.10.274.100:FF:000006CATH-FunFam
G3DSA:1.10.357.120:FF:000002CATH-FunFam
G3DSA:2.40.40.20:FF:000019CATH-FunFam
G3DSA:3.30.1490.180:FF:000003CATH-FunFam
G3DSA:4.10.860.120:FF:000006CATH-FunFam
G3DSA:1.10.132.30Rpb1_funnel_sfCATH-Gene3D
G3DSA:1.10.150.390CATH-Gene3D
G3DSA:1.10.274.100RNA_pol_Rpb1_3_sfCATH-Gene3D
G3DSA:1.10.357.120CATH-Gene3D
G3DSA:2.40.40.20CATH-Gene3D
G3DSA:3.30.1490.180CATH-Gene3D
G3DSA:3.30.70.2850CATH-Gene3D
G3DSA:4.10.860.120RNA_pol_Rpb1_clamp_domainCATH-Gene3D
G3DSA:6.10.250.2940CATH-Gene3D
SSF64484SUPERFAMILY
PTHR19376DNA-dir_RpoC_beta_primePANTHER
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Negative-Polyelectrolytedisorder_predictionMobiDB-Negative-Polyelectrolyte
mobidb-lite-Polyampholytedisorder_predictionMobiDB-Polyampholyte

Orthologs

References / Literature

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:11254133 - Isolation and characterization of the fission yeast gene Sprpa12+ reveals that the conserved C-terminal zinc-finger region is dispensable for the function of its product.
Imazawa Y et al. Mol Gen Genet 2001 Feb;264(6):852-9
PMID:21712547 - Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast.
Koch A et al. Sci Signal 2011 Jun 28;4(179):rs6
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
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:33536435 - Conserved strategies of RNA polymerase I hibernation and activation.
Heiss FB et al. Nat Commun 2021 Feb 03;12(1):758
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:24818994 - The S. pombe translation initiation factor eIF4G is Sumoylated and associates with the SUMO protease Ulp2.
Jongjitwimol J et al. PLoS One 2014;9(5):e94182
PMID:32062975 - Phosphoproteomics Reveals Novel Targets and Phosphoprotein Networks in Cell Cycle Mediated by Dsk1 Kinase.
Wu M et al. J Proteome Res 2020 Apr 03;19(4):1776-1787
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:18362178 - Dissection of the essential steps for condensin accumulation at kinetochores and rDNAs during fission yeast mitosis.
Nakazawa N et al. J Cell Biol 2008 Mar 24;180(6):1115-31
PMID:19547744 - Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
Beltrao P et al. PLoS Biol 2009 Jun 16;7(6):e1000134
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: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:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:25963819 - Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly.
Lucena R et al. J Cell Biol 2015 May 11;209(3):387-402
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:27738016 - RNA interference is essential for cellular quiescence.
Roche B et al. Science 2016 Nov 11;354(6313)
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
PMID:27401558 - The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.
Lemay JF et al. Genes Dev 2016 Jul 01;30(13):1558-72
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
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:11560889 - Multiple interactions among the components of the recombinational DNA repair system in Schizosaccharomyces pombe.
Tsutsui Y et al. Genetics 2001 Sep;159(1):91-105
PMID:24210919 - Mtr4-like protein coordinates nuclear RNA processing for heterochromatin assembly and for telomere maintenance.
Lee NN et al. Cell 2013 Nov 21;155(5):1061-74
PMID:21340088 - Microarray-based target identification using drug hypersensitive fission yeast expressing ORFeome.
Arita Y et al. Mol Biosyst 2011 May;7(5):1463-72
PMID:30321377 - Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome.
Telekawa C et al. Nucleic Acids Res 2018 Nov 30;46(21):11169-11183
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
PMID:26412298 - A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.
Beckley JR et al. Mol Cell Proteomics 2015 Dec;14(12):3132-41
PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.
Lee J et al. Nat Commun 2017 Feb 20;8:14527
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:17538026 - The nucleolar Net1/Cfi1-related protein Dnt1 antagonizes the septation initiation network in fission yeast.
Jin QW et al. Mol Biol Cell 2007 Aug;18(8):2924-34
PMID:40132111 - A fission yeast CENP-B homologue Abp1 prevents RNAi-mediated heterochromatin formation at ribosomal DNA repeats.
Tsunemine S et al. Genetics 2025 Mar 25;
PMID:9738888 - Mapping of Rpb3 and Rpb5 contact sites on two large subunits, Rpb1 and Rpb2, of the RNA polymerase II from fission yeast.
Miyao T et al. Mol Gen Genet 1998 Jul;259(1):123-9
GO_REF:0000002 - Comments
PMID:2854522 - Cloning and sequence determination of the gene encoding the largest subunit of the fission yeast Schizosaccharomyces pombe RNA polymerase I.
Yamagishi M et al. Gene 1988 Dec 30;74(2):503-15
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:16453724 - Isolation and characterization of Schizosaccharomyces pombe cutmutants that block nuclear division but not cytokinesis.
Hirano T et al. EMBO J 1986 Nov;5(11):2973-9
GO_REF:0000117 - Electronic Gene Ontology annotations created by ARBA machine learning models
PMID:15161942 - The nucleolus is involved in mRNA export from the nucleus in fission yeast.
Ideue T et al. J Cell Sci 2004 Jun 15;117(Pt 14):2887-95
PMID:40406582 - The Schizosaccharomyces pombe nucleolar protein Nsk1 modulates rDNA silencing during interphase.
Chen JS et al. MicroPubl Biol 2025;2025
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:21095590 - DDK phosphorylates checkpoint clamp component Rad9 and promotes its release from damaged chromatin.
Furuya K et al. Mol Cell 2010 Nov 24;40(4):606-18
PMID:22730331 - Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 ubiquitin-selective segregase by small ubiquitin-like modifier protein (SUMO) and ubiquitin in SUMO-targeted ubiquitin ligase-mediated genome stability functions.
Nie M et al. J Biol Chem 2012 Aug 24;287(35):29610-9
PMID:37913773 - TOR inactivation triggers heterochromatin formation in rDNA during glucose starvation.
Hirai H et al. Cell Rep 2023 Nov 28;42(11):113320
PMID:27298342 - Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks.
Willis NA et al. Proc Natl Acad Sci U S A 2016 Jun 28;113(26):E3676-85
PMID:39705284 - Proteomic and phosphoproteomic analyses reveal that TORC1 is reactivated by pheromone signaling during sexual reproduction in fission yeast.
Bérard M et al. PLoS Biol 2024 Dec 20;22(12):e3002963
PMID:31064814 - Proximity-dependent biotinylation mediated by TurboID to identify protein-protein interaction networks in yeast.
Larochelle M et al. J Cell Sci 2019 May 31;132(11)
PMID:18257517 - Phosphoproteome analysis of fission yeast.
Wilson-Grady JT et al. J Proteome Res 2008 Mar;7(3):1088-97
PMID:2537310 - Essential roles of the RNA polymerase I largest subunit and DNA topoisomerases in the formation of fission yeast nucleolus.
Hirano T et al. J Cell Biol 1989 Feb;108(2):243-53
PMID:27984744 - Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.
Joh RI et al. Mol Cell 2016 Dec 15;64(6):1088-1101
PMID:24013502 - Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries.
Wang J et al. Genes Dev 2013 Sep 01;27(17):1886-902