RfC38 (ortholog of human RFC3) is one of the four AAA+ small subunits of replication factor C, the ATP-dependent clamp loader that opens PCNA and places it on primer-template DNA so that polymerases delta and epsilon elongate processively. The same small subunits assemble with alternative large subunits into RFC-like complexes; in Drosophila RfC38 co-purifies with Elg1 in the Elg1 complex that unloads PCNA from chromatin after replication. RfC38 is a nuclear protein essential for viability.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic DNA binding (InterPro-based). Reason: RFC small subunits contact primer-template DNA within the clamp loader, so the subunit's own DNA binding is real; no more specific DNA-binding term is supported by the evidence. It is peripheral to the core complex activity, recorded as contributes_to GO:0003689 DNA clamp loader activity. |
| GO:0003689 DNA clamp loader activity | IBA GO_REF:0000033 | ACCEPT | Summary: Contributes to the DNA clamp (PCNA) loader activity of the RFC heteropentamer. Reason: As an activator-1 small subunit, this protein is one of the four AAA+ subunits shared by RFC and the RFC-like complexes; the clamp-loader activity is a property of the assembled complex, so contributes_to is the correct qualifier. PAINT IBA from the activator-1 small-subunit clade; WITH/FROM donors are the budding yeast RFC2-5 small subunits (SGD:S000000291, S000003829, S000005234, S000005454) and human RFC2-5 (UniProtKB:P35249, P35250, P40937, P40938). The fly protein sits squarely inside this clade. Supporting Evidence: PMID:8999859 It is a molecular matchmaker required for loading of proliferating cell nuclear antigen (PCNA) onto double-stranded DNA file:DROME/RfC38/RfC38-uniprot.txt is necessary for ATP-dependent loading of proliferating cell nuclear antigen (PCNA) onto primed DNA |
| GO:0003689 DNA clamp loader activity | ISS GO_REF:0000024 | ACCEPT | Summary: Contributes to the DNA clamp (PCNA) loader activity of the RFC heteropentamer (ISS). Reason: Transfer from characterized yeast/human RFC small subunits is sound for this highly conserved subunit; the activity belongs to the complex, hence contributes_to. Supporting Evidence: PMID:8999859 It is a molecular matchmaker required for loading of proliferating cell nuclear antigen (PCNA) onto double-stranded DNA file:DROME/RfC38/RfC38-uniprot.txt is necessary for ATP-dependent loading of proliferating cell nuclear antigen (PCNA) onto primed DNA |
| GO:0005515 protein binding | IPI PMID:20353594 Building and analyzing protein interactome networks by cross... | REMOVE | Summary: Protein binding from high-throughput interactome screens. Reason: The partners recorded in GOA WITH/FROM are other RFC small subunits, i.e. intra-complex contacts that are already captured by part_of GO:0005663 DNA replication factor C complex and GO:0031391 Elg1 RFC-like complex. Bare protein binding adds no functional information. |
| GO:0005515 protein binding | IPI PMID:38944040 Next-generation Drosophila protein interactome map and its f... | REMOVE | Summary: Protein binding from high-throughput interactome screens. Reason: The partners recorded in GOA WITH/FROM are other RFC small subunits, i.e. intra-complex contacts that are already captured by part_of GO:0005663 DNA replication factor C complex and GO:0031391 Elg1 RFC-like complex. Bare protein binding adds no functional information. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nucleus. Reason: RFC and the RFC-like complexes act on chromatin in the nucleus during S phase. The UniProt subcellular location is ARBA-only, so the support cited is fly biochemistry: Rfc38 peptides copurified with Br140 and Elg1 in the Flag affinity purifications of PMID:27198229, which that study ran on S2 cell nuclear extracts. This is copurification from a nuclear fraction, not imaging, but together with the conserved nuclear role of the RFC clamp loaders it supports the nucleus term. Supporting Evidence: PMID:27198229 the Enok complex was isolated using Flag affinity purification from S2 cell nuclear extracts PMID:27198229 MudPIT analysis of Br140 purification identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nucleus. Reason: RFC and the RFC-like complexes act on chromatin in the nucleus during S phase. The UniProt subcellular location is ARBA-only, so the support cited is fly biochemistry: Rfc38 peptides copurified with Br140 and Elg1 in the Flag affinity purifications of PMID:27198229, which that study ran on S2 cell nuclear extracts. This is copurification from a nuclear fraction, not imaging, but together with the conserved nuclear role of the RFC clamp loaders it supports the nucleus term. Supporting Evidence: PMID:27198229 the Enok complex was isolated using Flag affinity purification from S2 cell nuclear extracts PMID:27198229 MudPIT analysis of Br140 purification identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 |
| GO:0005634 nucleus | NAS PMID:24204884 The elongin complex antagonizes the chromatin factor Corto f... | ACCEPT | Summary: Nucleus. Reason: RFC and the RFC-like complexes act on chromatin in the nucleus during S phase. The UniProt subcellular location is ARBA-only, so the support cited is fly biochemistry: Rfc38 peptides copurified with Br140 and Elg1 in the Flag affinity purifications of PMID:27198229, which that study ran on S2 cell nuclear extracts. This is copurification from a nuclear fraction, not imaging, but together with the conserved nuclear role of the RFC clamp loaders it supports the nucleus term. Supporting Evidence: PMID:27198229 the Enok complex was isolated using Flag affinity purification from S2 cell nuclear extracts PMID:27198229 MudPIT analysis of Br140 purification identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 |
| GO:0005663 DNA replication factor C complex | IBA GO_REF:0000033 | ACCEPT | Summary: Subunit of the replication factor C (RFC) complex. Reason: The four activator-1 small subunits (RfC4, RfC38, RfC3, CG8142/Rfc37) combine with the large subunit Gnf1 to form the RFC heteropentamer. Supporting Evidence: PMID:8999859 Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and repair file:DROME/RfC38/RfC38-uniprot.txt is necessary for ATP-dependent loading of proliferating cell nuclear antigen (PCNA) onto primed DNA |
| GO:0005663 DNA replication factor C complex | ISS GO_REF:0000024 | ACCEPT | Summary: Subunit of the replication factor C (RFC) complex. Reason: The four activator-1 small subunits (RfC4, RfC38, RfC3, CG8142/Rfc37) combine with the large subunit Gnf1 to form the RFC heteropentamer. Supporting Evidence: PMID:8999859 Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and repair file:DROME/RfC38/RfC38-uniprot.txt is necessary for ATP-dependent loading of proliferating cell nuclear antigen (PCNA) onto primed DNA |
| GO:0005694 chromosome | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Chromosome (ARBA). Reason: RFC acts on chromatin at replication forks, so chromosome is correct; no fly evidence supports a more specific chromosomal location (e.g. replication fork), and the curated core location is nucleus. The falcon deep research reports that RfC38 is enriched on nascent DNA in S2-cell iPOND proteomics, consistent with chromatin association at replication forks. Supporting Evidence: file:DROME/RfC38/RfC38-deep-research-falcon.md in a network enriched on newly synthesized DNA |
| GO:0006260 DNA replication | IEA GO_REF:0000002 | MODIFY | Summary: DNA replication (general). Reason: Correct but less specific than the evidence supports; replaced by GO:0006261 DNA-templated DNA replication, which the gene already carries (IBA) and which is the core process. Proposed replacements: DNA-templated DNA replication Supporting Evidence: PMID:8999859 Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and repair |
| GO:0006261 DNA-templated DNA replication | IBA GO_REF:0000033 | ACCEPT | Summary: DNA-templated DNA replication. Reason: Core process for an RFC subunit: the clamp loader places PCNA on primer-template junctions to make polymerase delta and epsilon processive. PAINT IBA from the activator-1 small-subunit clade; WITH/FROM donors are the budding yeast RFC2-5 small subunits plus fission yeast and other RFC subunits (SGD:S000000291, S000003829, S000005234, S000005454) and human RFC2-5 (UniProtKB:P35249, P35250, P40937, P40938). The fly protein sits squarely inside this clade. Supporting Evidence: PMID:8999859 for PCNA-dependent DNA elongation by DNA polymerases delta and epsilon |
| GO:0006271 DNA strand elongation involved in DNA replication | IEA GO_REF:0000117 | ACCEPT | Summary: DNA strand elongation involved in DNA replication. Reason: RFC-loaded PCNA is required for processive strand elongation by polymerases delta and epsilon; this is the specific replication step the complex serves. For the NAS row, the cited paper (PMID:24204884) does not discuss RFC, but the claim is well supported by RFC biochemistry. Supporting Evidence: PMID:8999859 for PCNA-dependent DNA elongation by DNA polymerases delta and epsilon |
| GO:0006271 DNA strand elongation involved in DNA replication | NAS PMID:24204884 The elongin complex antagonizes the chromatin factor Corto f... | ACCEPT | Summary: DNA strand elongation involved in DNA replication. Reason: RFC-loaded PCNA is required for processive strand elongation by polymerases delta and epsilon; this is the specific replication step the complex serves. For the NAS row, the cited paper (PMID:24204884) does not discuss RFC, but the claim is well supported by RFC biochemistry. Supporting Evidence: PMID:8999859 for PCNA-dependent DNA elongation by DNA polymerases delta and epsilon |
| GO:0006272 leading strand elongation | ISS GO_REF:0000024 | ACCEPT | Summary: Leading strand elongation (ISS). Reason: RFC loads PCNA for polymerase epsilon on the leading strand (as well as for polymerase delta on the lagging strand); the ISS transfer from yeast/human RFC subunits is sound. Supporting Evidence: PMID:8999859 for PCNA-dependent DNA elongation by DNA polymerases delta and epsilon |
| GO:0006281 DNA repair | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: DNA repair. Reason: RFC loads PCNA for repair DNA synthesis (e.g. mismatch, nucleotide excision and base excision repair gap filling); a genuine but secondary use of the replication clamp loader. Supporting Evidence: PMID:8999859 Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and repair |
| GO:0006281 DNA repair | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: DNA repair. Reason: RFC loads PCNA for repair DNA synthesis (e.g. mismatch, nucleotide excision and base excision repair gap filling); a genuine but secondary use of the replication clamp loader. Supporting Evidence: PMID:8999859 Replication factor C (RF-C) is a heteropentameric protein essential for DNA replication and repair |
| GO:0007062 sister chromatid cohesion | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Sister chromatid cohesion (ISS). Reason: The small subunits are shared with the Ctf18-RFC alternative clamp loader, which promotes cohesion establishment in yeast and vertebrates; for the fly subunits this is inferred by similarity only and is not their core role. |
| GO:0008094 ATP-dependent activity, acting on DNA | IEA GO_REF:0000117 | MODIFY | Summary: ATP-dependent activity, acting on DNA (ARBA). Reason: Correct but a generic parent of GO:0003689 DNA clamp loader activity, which the evidence supports and which the gene already carries (as contributes_to, since the activity belongs to the RFC complex). Proposed replacements: DNA clamp loader activity |
| GO:0031391 Elg1 RFC-like complex | IDA PMID:27198229 The Enok acetyltransferase complex interacts with Elg1 and n... | ACCEPT | Summary: Subunit of the Elg1 RFC-like (PCNA unloader) complex. Reason: MudPIT of affinity-purified Flag-Elg1 and Flag-Br140 recovered Elg1 together with all four small subunits. For the IPI row, the cited PMID:24204884 does not mention RFC; the membership is nonetheless directly supported by PMID:27198229. Supporting Evidence: PMID:27198229 identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 |
| GO:0031391 Elg1 RFC-like complex | IPI PMID:24204884 The elongin complex antagonizes the chromatin factor Corto f... | ACCEPT | Summary: Subunit of the Elg1 RFC-like (PCNA unloader) complex. Reason: MudPIT of affinity-purified Flag-Elg1 and Flag-Br140 recovered Elg1 together with all four small subunits. For the IPI row, the cited PMID:24204884 does not mention RFC; the membership is nonetheless directly supported by PMID:27198229. Supporting Evidence: PMID:27198229 identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 |
| GO:0032991 protein-containing complex | IEA GO_REF:0000117 | MODIFY | Summary: Protein-containing complex (ARBA). Reason: Uninformative parent of the specific complexes GO:0005663 DNA replication factor C complex and GO:0031391 Elg1 RFC-like complex, both of which the gene already carries. Proposed replacements: DNA replication factor C complex |
| GO:0061860 DNA clamp unloader activity | IDA PMID:27198229 The Enok acetyltransferase complex interacts with Elg1 and n... | NEW | Summary: Contributes to the PCNA-unloading activity of the Elg1 RFC-like complex. Reason: RfC38 co-purifies with Elg1 and the other three small subunits as the Elg1 PCNA-unloader complex (part_of GO:0031391 by IDA), and depleting the large subunit elg1 raises chromatin-bound PCNA in S2 cells. The unloader activity belongs to the heteropentamer, so it is asserted with contributes_to, mirroring contributes_to GO:0003689 for RFC; elg1 itself carries GO:0061860 (IBA). Applied identically to RfC4, RfC38, RfC3 and CG8142. Supporting Evidence: PMID:27198229 identified peptides from all components of the Elg1 PCNA-unloader complex: Elg1, Rfc4, Rfc38, CG8142, and Rfc3 PMID:27198229 knocking down elg1 using dsRNAs did not affect total PCNA levels but resulted in increases in the levels of both chromatin-bound PCNA and monoubiquitinated PCNA |
Loading supporting content…
Download this section (compressed HTML)Q: Does the Drosophila Ctf18-RFC complex exist and use the same four small subunits, and do the fly small subunits therefore contribute to cohesion establishment as in yeast?
Q: Which of the four small-subunit ATP sites are required for PCNA unloading by the Drosophila Elg1 complex, as opposed to loading by RFC?
Experiment: Reconstitute Drosophila RFC and Elg1-RLC from recombinant subunits and measure PCNA loading and unloading on primed templates, testing Walker A/B mutants of each small subunit.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)