RPB9_CAEEL
ID RPB9_CAEEL Reviewed; 167 AA.
AC Q965S0;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=DNA-directed RNA polymerase II subunit rpb-9 {ECO:0000305};
DE Short=RNA polymerase II subunit B9 {ECO:0000305};
DE AltName: Full=DNA-directed RNA polymerase II subunit 9 {ECO:0000305};
GN Name=rpb-9 {ECO:0000312|WormBase:Y97E10AR.5};
GN ORFNames=Y97E10AR.5 {ECO:0000312|WormBase:Y97E10AR.5};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1] {ECO:0000312|Proteomes:UP000001940}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2] {ECO:0000305}
RP FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II COMPLEX, TISSUE
RP SPECIFICITY, AND MUTAGENESIS OF 140-GLN--GLU-167.
RX PubMed=33533030; DOI=10.15252/embj.2020105565;
RA Berkyurek A.C., Furlan G., Lampersberger L., Beltran T., Weick E.M.,
RA Nischwitz E., Cunha Navarro I., Braukmann F., Akay A., Price J., Butter F.,
RA Sarkies P., Miska E.A.;
RT "The RNA polymerase II subunit RPB-9 recruits the integrator complex to
RT terminate Caenorhabditis elegans piRNA transcription.";
RL EMBO J. 0:0-0(2021).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates
CC (By similarity). Component of RNA polymerase II which synthesizes mRNA
CC precursors and many functional non-coding RNAs (Probable). Pol II is
CC the central component of the basal RNA polymerase II transcription
CC machinery (By similarity). It is composed of mobile elements that move
CC relative to each other (By similarity). RPB9 is part of the upper jaw
CC surrounding the central large cleft and thought to grab the incoming
CC DNA template (By similarity). Recruits ints-6, a component of the
CC Integrator complex to PIWI-interacting RNA (piRNA) genes, to mediate
CC Integrator complex-dependent cleavage of 3' ends of nascent transcripts
CC upon RNA Pol II backtracking to terminate transcription and generate
CC piRNA precursors (PubMed:33533030). Promotes the biogenesis of
CC secondary 22G-siRNAs (a class of 22 nucleotide siRNAs that possess a
CC triphosphorylated guanine residue at the 5'-end) (PubMed:33533030).
CC Involved in gene silencing mediated by a class of 21 nucleotide piRNAs
CC that possess a uracil residue at the 5'-end (also called 21U-RNAs) and
CC guide the Piwi protein prg-1 to its DNA targets for silencing
CC (PubMed:33533030). Plays a role in small RNA-directed transgenerational
CC epigenetic inheritance (also called RNAe) over several generations
CC (PubMed:33533030). Not required for the transgenerational inheritance
CC of exogenous small interfering RNAs (RNAi) (PubMed:33533030). May play
CC a role in the silencing of the DNA transposable elements from the DNA
CC transposon families, Chapaev-2 and CEMUDR1 (PubMed:33533030).
CC {ECO:0000250|UniProtKB:P36954, ECO:0000269|PubMed:33533030,
CC ECO:0000305|PubMed:33533030}.
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. {ECO:0000305|PubMed:33533030}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:P36954}.
CC -!- TISSUE SPECIFICITY: Expressed in the soma and in the germline.
CC {ECO:0000269|PubMed:33533030}.
CC -!- SIMILARITY: Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11
CC RNA polymerase family. {ECO:0000305}.
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DR EMBL; BX284605; CCD71182.1; -; Genomic_DNA.
DR RefSeq; NP_505062.1; NM_072661.4.
DR AlphaFoldDB; Q965S0; -.
DR SMR; Q965S0; -.
DR STRING; 6239.Y97E10AR.5; -.
DR EPD; Q965S0; -.
DR PaxDb; Q965S0; -.
DR PeptideAtlas; Q965S0; -.
DR EnsemblMetazoa; Y97E10AR.5.1; Y97E10AR.5.1; WBGene00022400.
DR GeneID; 179178; -.
DR KEGG; cel:CELE_Y97E10AR.5; -.
DR UCSC; Y97E10AR.5; c. elegans.
DR CTD; 179178; -.
DR WormBase; Y97E10AR.5; CE26319; WBGene00022400; rpb-9.
DR eggNOG; KOG2691; Eukaryota.
DR GeneTree; ENSGT00550000075063; -.
DR HOGENOM; CLU_093932_0_0_1; -.
DR InParanoid; Q965S0; -.
DR OMA; CRDCNNM; -.
DR OrthoDB; 1421187at2759; -.
DR PhylomeDB; Q965S0; -.
DR Reactome; R-CEL-112382; Formation of RNA Pol II elongation complex.
DR Reactome; R-CEL-113418; Formation of the Early Elongation Complex.
DR Reactome; R-CEL-5578749; Transcriptional regulation by small RNAs.
DR Reactome; R-CEL-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-CEL-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-CEL-6782135; Dual incision in TC-NER.
DR Reactome; R-CEL-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-CEL-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-CEL-6803529; FGFR2 alternative splicing.
DR Reactome; R-CEL-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-CEL-72086; mRNA Capping.
DR Reactome; R-CEL-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-CEL-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-CEL-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-CEL-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-CEL-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-CEL-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-CEL-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-CEL-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-CEL-9018519; Estrogen-dependent gene expression.
DR Proteomes; UP000001940; Chromosome V.
DR Bgee; WBGene00022400; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IBA:GO_Central.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0001193; P:maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006379; P:mRNA cleavage; IEA:InterPro.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
DR CDD; cd10508; Zn-ribbon_RPB9; 1.
DR InterPro; IPR019761; DNA-dir_RNA_pol-M_15_CS.
DR InterPro; IPR001529; DNA-dir_RNA_pol_M/15kDasu.
DR InterPro; IPR012164; Rpa12/Rpb9/Rpc10/TFS.
DR InterPro; IPR034012; Zn_ribbon_RPB9_C.
DR InterPro; IPR001222; Znf_TFIIS.
DR PANTHER; PTHR11239; PTHR11239; 1.
DR Pfam; PF02150; RNA_POL_M_15KD; 1.
DR Pfam; PF01096; TFIIS_C; 1.
DR SMART; SM00661; RPOL9; 1.
DR SMART; SM00440; ZnF_C2C2; 1.
DR PROSITE; PS01030; RNA_POL_M_15KD; 1.
DR PROSITE; PS51133; ZF_TFIIS_2; 1.
PE 1: Evidence at protein level;
KW DNA-directed RNA polymerase; Metal-binding; Nucleus; Reference proteome;
KW RNA-mediated gene silencing; Transcription; Zinc; Zinc-finger.
FT CHAIN 1..167
FT /note="DNA-directed RNA polymerase II subunit rpb-9"
FT /id="PRO_0000453574"
FT ZN_FING 59..84
FT /note="C4-type"
FT /evidence="ECO:0000255"
FT ZN_FING 124..166
FT /note="TFIIS-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT REGION 28..49
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 59
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 62
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 84
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 128
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 156
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 161
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT MUTAGEN 140..167
FT /note="Missing: In mj261; defective gene silencing mediated
FT by a class of 21 nucleotide PIWI-interacting RNAs (piRNAs)
FT that possess a uracil residue at the 5'-end (also called
FT 21U-RNAs). Reduces the levels of mature piRNAs. Disrupts
FT the inheritance of endogenous small RNA-induced gene
FT silencing. Does not disrupt the inheritance of exogenous
FT small RNA-induced gene silencing. Reduces binding of RNA
FT polymerase II to DNA transposable elements from the DNA
FT transposon families, Chapaev-2 and CEMUDR1. Disrupts the
FT accumulation of inst-6 at piRNA genes and as a results
FT decreases the number of 20 nucleotide long 3' nascent RNA
FT cleavage fragments, which is an indicator of reduced
FT Integrator complex activity."
FT /evidence="ECO:0000269|PubMed:33533030"
SQ SEQUENCE 167 AA; 19335 MW; EB06D2F04E10ED87 CRC64;
MYLQLKSKLE NVLSYFFRKM SQGYDNYDDM YDQNGASPAP SQNEKPGKSG PGFVGIKFCP
ECNNMLYPRE DKESRVLMYS CRNCEHREVA ANPCIYVNKL VHEIDELTQI VGDIIHDPTL
PKTEEHQCPV CGKSKAVFFQ AQTKKAEEEM RLYYVCASQD CQHRWTE
