NCU01245 encodes the Neurospora crassa ortholog of RPC4 (C53 in budding yeast, POLR3D in human), a noncatalytic subunit specific to nuclear RNA polymerase III. The 516-residue protein has a long, compositionally biased and largely disordered N-terminal region and a conserved C-terminal RPC4 domain (Pfam PF05132, residues 345-494). By orthology with yeast C53, it forms a peripheral TFIIF-like heterodimer with the C37/RPC5 subunit; this module helps open promoter DNA for initiation, slows elongation so that the enzyme recognises oligo(dT) terminators, and, together with C11, supports facilitated recycling of the polymerase onto the same gene. It thereby contributes to synthesis of tRNAs and other short polymerase III transcripts in the nucleus. It is not itself a catalytic polymerase subunit.
Summary: InterPro2GO mapping from the RPC4 domain. Yeast C53 photo-cross-links to the template DNA strand near the active centre, but only inside the assembled elongation complex; no autonomous DNA-binding activity is shown.
Reason: Retained as non-core rather than accepted. The only experimental basis for DNA contact by an RPC4 family member is photochemical cross-linking of a C53 segment to the transcribed strand in the yeast pol III elongation complex (PMID:19940126, abstract only), which shows proximity within the 17-subunit enzyme, not a DNA-binding activity of the subunit. Yeast RPC53 itself carries DNA binding only by the same InterPro2GO IEA, and the PAINT node PTN000334172 propagates complex membership and tRNA transcription but no DNA-binding term. No more specific DNA-binding term is supported, so the term is kept at this level but not treated as core; the subunit's role is structural/regulatory within pol III.
Protein-RNA and protein-DNA photochemical cross-linking analysis places a segment of C53 close to the RNA 3' end and transcribed DNA strand at the catalytic center of the pol III elongation complex.
Summary: Nuclear location follows from membership in RNA polymerase III, a nucleoplasmic enzyme; the UniProt subcellular-location line itself rests on an ARBA rule.
Reason: Accepted. The UniProt nucleus statement is an ARBA prediction and is not used as evidence. The location is instead inferred from the well-supported assignment of NCU01245 to the RPC4/C53 subunit of pol III (PANTHER PTHR13408:SF0, the subfamily containing yeast RPC53 and human POLR3D), the enzyme that transcribes nuclear tRNA and 5S rRNA genes. No Neurospora localization experiment exists.
Summary: Core: NCU01245 is the RPC4/C53 subunit of RNA polymerase III. PAINT IBA from PTN000334172 (eukaryote-wide node; yeast RPC53 and human POLR3D seeds).
Reason: Accepted as core. NCU01245 is in PANTHER subfamily PTHR13408:SF0 together with the experimentally characterised yeast RPC53 (P25441) and human POLR3D (P05423), and PAINT placed the complex-membership assertion at the eukaryote-level node PTN000334172 from which NCU01245 descends. Yeast C53 is a stoichiometric pol III subunit that co-purifies with C37 and C11 as a separable subassembly. The Neurospora protein retains the conserved C-terminal RPC4 domain (residues 345-494) that mediates the C53-C37 interaction. The IBA and InterPro IEA rows make the same claim and are treated consistently.
The interaction between HsRPC5 and HsRPC53, the human orthologue of C53, is also conserved, paralleling the association of yeast C37 and C53 subunits, and is mediated by the domains conserved within their yeast counterparts
file:NEUCR/NCU01245/NCU01245-uniprot.txt
DR PANTHER; PTHR13408:SF0; DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4; 1.
Summary: Core: NCU01245 is the RPC4/C53 subunit of RNA polymerase III. InterPro2GO mapping from IPR007811 (RPC4).
Reason: Accepted as core. NCU01245 is in PANTHER subfamily PTHR13408:SF0 together with the experimentally characterised yeast RPC53 (P25441) and human POLR3D (P05423), and PAINT placed the complex-membership assertion at the eukaryote-level node PTN000334172 from which NCU01245 descends. Yeast C53 is a stoichiometric pol III subunit that co-purifies with C37 and C11 as a separable subassembly. The Neurospora protein retains the conserved C-terminal RPC4 domain (residues 345-494) that mediates the C53-C37 interaction. The IBA and InterPro IEA rows make the same claim and are treated consistently.
The interaction between HsRPC5 and HsRPC53, the human orthologue of C53, is also conserved, paralleling the association of yeast C37 and C53 subunits, and is mediated by the domains conserved within their yeast counterparts
file:NEUCR/NCU01245/NCU01245-uniprot.txt
DR PANTHER; PTHR13408:SF0; DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4; 1.
Summary: Pol III subunits participate in all pol III transcription (tRNA, 5S rRNA, U6 snRNA and others); InterPro2GO mapping from IPR007811.
Reason: Accepted. As a subunit of the enzyme, RPC4 does part of the work of every pol III transcription cycle: the yeast C37-C53 module is needed for terminator recognition and, with C11, for reinitiation. The general term is appropriate here because pol III transcribes 5S rRNA, U6 snRNA and other RNAs besides tRNAs; the more specific GO:0042797 tRNA transcription is also carried (IBA). Initiation- and termination-specific child terms carried by yeast RPC53 (IDA) were not propagated by PAINT, and are not added here.
the presence of the C37-C53 complex required the simultaneous addition of C11 to Pol IIIdelta for the enzyme to reinitiate after the first round of transcription
GO:0042797 tRNA transcription by RNA polymerase III
IBA GO_REF:0000033
ACCEPT
Summary: PAINT IBA from PTN000334172, seeded by yeast RPC53 experimental annotations; tRNA genes are the main pol III targets.
Reason: Accepted as core. The IBD at PTN000334172 was placed by a PAINT curator from yeast RPC53 (IDA, IMP) and NCU01245 is inside that eukaryote-wide clade, in the same RPC4 subfamily (SF0). In reconstituted yeast pol III, C53-C37 is needed for terminator recognition and for facilitated reinitiation, so the subunit contributes directly to the transcription cycle rather than acting as an upstream regulator. No Neurospora-specific data exist.
We show that the C53/C37 subcomplex additionally plays a role in formation of the initiation-ready open promoter complex
Core Functions
Noncatalytic RPC4/C53 subunit of nuclear RNA polymerase III. With its partner C37/RPC5 it forms a TFIIF-like peripheral module that supports promoter opening, terminator recognition and facilitated reinitiation during transcription of tRNA and other pol III genes.
The interaction between HsRPC5 and HsRPC53, the human orthologue of C53, is also conserved, paralleling the association of yeast C37 and C53 subunits, and is mediated by the domains conserved within their yeast counterparts
Q: Should the initiation (GO:0006384) and termination (GO:0006386) terms that yeast RPC53 carries by IDA be propagated across the RPC4 subfamily, or does the PAINT curator's restriction to complex membership and tRNA transcription reflect uncertainty about how widely the C53-C37 termination mechanism is conserved?
Suggested Experiments
Experiment: Conditional depletion of NCU01245 in N. crassa combined with nascent-RNA or 3'-end mapping of tRNA genes to test whether loss of RPC4 causes terminator readthrough, as reported for C53-C37-deficient yeast pol III; and tagged-protein affinity purification to confirm association with the Neurospora C37 ortholog and pol III core.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
NCU01245 is the conserved RPC4/C53 subunit of nuclear RNA polymerase III. It associates with the C37 subunit and supports promoter opening, transcription termination and polymerase recycling during synthesis of tRNAs and other polymerase III RNAs. Its role is structural and regulatory within the enzyme complex.
Review rationale: The RPC4-specific domain identifies the C53 subunit of nuclear RNA polymerase III, and reconstitution of the characterized yeast polymerase shows that the C37-C53 module is needed for terminator recognition and reinitiation. The predicted term is correct and is already carried by NCU01245 in GOA (InterPro2GO IEA), where the gene review accepts it as appropriately general because polymerase III transcribes 5S rRNA, U6 snRNA and other RNAs besides tRNAs; the narrower tRNA transcription by RNA polymerase III (GO:0042797, IBA) is also present. The role is participation as a noncatalytic enzyme subunit.
Supporting Evidence:
PMID:16362040: "The specific requirement for the C37-C53 complex in terminator recognition was determined."
PMID:19940126: "Protein-RNA and protein-DNA photochemical cross-linking analysis places a segment of C53 close to the RNA 3' end and transcribed DNA strand at the catalytic center of the pol III elongation complex."