RpoC is the beta' subunit of bacterial DNA-directed RNA polymerase (RNAP) in Nitratidesulfovibrio vulgaris Hildenborough (formerly Desulfovibrio vulgaris). This essential enzyme subunit forms the catalytic core of the RNAP holoenzyme (alpha2-beta-beta'-omega) and contains the active site for phosphodiester bond formation during transcription. The beta' subunit houses the bridge helix (BH), trigger loop (TL), and clamp/switch regions that govern DNA loading, open-complex formation, nucleotide addition, and pausing/termination dynamics. RpoC binds 1 Mg2+ ion at the active site (essential for catalysis) and 2 Zn2+ ions that play structural roles. In D. vulgaris, RpoC (DVU_2929) has been experimentally validated through proteomics and protein-protein interaction studies showing its association with other RNAP subunits including RpoB.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: The beta' subunit of RNAP contains the catalytic active site with conserved aspartate residues (D466, D468, D470 in Q727C6) that coordinate Mg2+ ions essential for phosphodiester bond formation during transcription. This is a well-established core function of the RpoC subunit based on UniProt annotation and extensive structural studies of bacterial RNAP (file:DESVH/Q727C6/Q727C6-deep-research-falcon.md). Reason: Magnesium binding is essential for RNAP catalytic activity. The UniProt entry clearly documents Mg2+ binding at residues 466, 468, and 470 based on HAMAP rule MF_01322. The deep research confirms the active-site metals via FEL and structural work (file:DESVH/Q727C6/Q727C6-deep-research-falcon.md). Supporting Evidence: UniProt:Q727C6 Binds 1 Mg(2+) ion per subunit |
| GO:0000428 DNA-directed RNA polymerase complex | IEA GO_REF:0000043 | ACCEPT | Summary: RpoC is a core component of the bacterial RNAP complex (alpha2-beta-beta'-omega). DvH proteomics and PPI studies confirm that DVU_2929 (RpoC) co-purifies with other RNAP subunits including RpoB (PMID:26873250, PMID:27099342). Reason: The beta' subunit is an integral component of the bacterial RNAP core enzyme. UniProt records experimental interaction evidence (IntAct) showing RpoC interacts with RpoB (Q727C7) with 4 experiments documented. This cellular component annotation accurately captures where RpoC functions. Supporting Evidence: UniProt:Q727C6 The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit file:DESVH/Q727C6/Q727C6-deep-research-falcon.md DVU_2929 encodes RpoC (RNAP beta') in DvH, supported by direct locus mapping, proteomic detection, and PPI evidence |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: RpoC contributes to DNA binding as part of the RNAP complex. The beta' subunit contains the clamp domain that contacts template DNA and helps maintain the transcription bubble. However, the beta' subunit alone is not the primary DNA-binding component - sigma factors provide promoter specificity. Reason: While the beta' subunit does contact DNA as part of the RNAP complex (through clamp/switch regions that help hold the DNA template), this annotation is appropriate at a general level. The domain-based inference (InterPro domains IPR000722, IPR006592, etc.) correctly identifies this function. The clamp dynamics of beta' are essential for DNA loading and bubble maintenance (file:DESVH/Q727C6/Q727C6-deep-research-falcon.md). Supporting Evidence: file:DESVH/Q727C6/Q727C6-deep-research-falcon.md Recent (2023-2024) structural work refines initiation models centered on beta' clamp dynamics and sigma loading |
| GO:0003899 DNA-directed RNA polymerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the primary molecular function of the RNAP complex, and RpoC contains the catalytic site (EC 2.7.7.6). The beta' subunit houses the bridge helix and trigger loop motifs essential for the nucleotide addition cycle. Reason: This annotation captures the core enzymatic function. While the complete RNAP complex is required for activity, the beta' subunit provides the active site residues for phosphodiester bond formation. The UniProt entry assigns EC 2.7.7.6 to this protein based on HAMAP annotation, and the deep research confirms the trigger loop functions in all three phases of the transcription cycle (file:DESVH/Q727C6/Q727C6-deep-research-falcon.md). Supporting Evidence: UniProt:Q727C6 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates file:DESVH/Q727C6/Q727C6-deep-research-falcon.md RpoC provides essential catalytic and structural functions - via BH, TL, and clamp/switch elements - in initiation, elongation, and termination |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000120 | ACCEPT | Summary: RpoC participates in all phases of transcription: initiation (promoter DNA loading, bubble formation via clamp dynamics), elongation (nucleotide addition cycle via trigger loop/bridge helix), and termination. Reason: This biological process annotation correctly captures the role of RpoC in transcription. The beta' subunit is essential for this process, and DVU_2929 has been quantified in DvH proteomes supporting its expression and function in the cell (file:DESVH/Q727C6/Q727C6-deep-research-falcon.md). Supporting Evidence: file:DESVH/Q727C6/Q727C6-deep-research-falcon.md Trigger loop functions in all three phases of the transcription cycle |
| GO:0008270 zinc ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: The beta' subunit contains two zinc-binding sites with conserved cysteine residues. In Q727C6, Zn2+ site 1 uses C75, C77, C90, C93, and Zn2+ site 2 uses residues at positions 809, 883, 890, 893. These zinc ions play structural roles in maintaining protein fold. Reason: Zinc binding is well documented for the RpoC subunit. The UniProt entry annotates 8 zinc-binding residues forming two distinct sites based on HAMAP rule MF_01322. This structural metal binding is conserved across bacterial RNAP beta' subunits. Supporting Evidence: UniProt:Q727C6 Binds 2 Zn(2+) ions per subunit |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: This is a parent term of the more specific nucleotidyltransferase activity and DNA-directed RNA polymerase activity. While correct, it is too general. Reason: This term is subsumed by the more specific GO:0003899 (DNA-directed RNA polymerase activity) and GO:0016779 (nucleotidyltransferase activity) annotations already present. Retaining this adds no additional information and represents redundant annotation at a less informative level. |
| GO:0016779 nucleotidyltransferase activity | IEA GO_REF:0000043 | ACCEPT | Summary: This is a parent term of DNA-directed RNA polymerase activity. The annotation is correct but less specific than GO:0003899. Reason: While GO:0003899 is more specific, this intermediate-level term from the UniProt keyword mapping is technically correct. The RNAP does transfer nucleotidyl groups (from NTPs to the growing RNA chain). This annotation is acceptable as a broader classification. |
| GO:0034062 5'-3' RNA polymerase activity | IEA GO_REF:0000116 | ACCEPT | Summary: This annotation from Rhea mapping correctly captures the directionality of RNA synthesis. RNAP synthesizes RNA in the 5' to 3' direction, adding nucleotides to the 3'-OH of the growing chain. Reason: This annotation based on the Rhea reaction mapping (RHEA:21248) is accurate and provides useful mechanistic information about the directionality of transcription. The reaction catalyzed is: RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate. Supporting Evidence: UniProt:Q727C6 Reaction=RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: General metal ion binding term that encompasses both Mg2+ and Zn2+ binding by RpoC. This is a parent term of the more specific metal binding annotations. Reason: This annotation is technically correct but is subsumed by the more specific GO:0000287 (magnesium ion binding) and GO:0008270 (zinc ion binding) annotations. The general term adds no additional information. |
| GO:0005515 protein binding | IPI PMID:26873250 Bacterial Interactomes: Interacting Protein Partners Share S... | MODIFY | Summary: This IPI annotation is based on AP-MS protein-protein interaction data from a systematic D. vulgaris interactome study. RpoC was shown to interact with RpoB (Q727C7), which is biologically expected as these are adjacent subunits in the RNAP complex (PMID:26873250). Reason: While the protein binding annotation captures a true interaction, "protein binding" (GO:0005515) is uninformative. The specific interaction is with RpoB within the RNAP complex. A more informative annotation would be to GO:0000428 (DNA-directed RNA polymerase complex) as a cellular component annotation, which already exists. The molecular function annotation should reflect the specific binding context. Proposed replacements: RNAP core enzyme binding Supporting Evidence: PMID:26873250 We have identified 459 high confidence PPIs from D. vulgaris |
| GO:0005515 protein binding | IPI PMID:27099342 Quantitative Tagless Copurification: A Method to Validate an... | MODIFY | Summary: This IPI annotation is from a quantitative tagless copurification study confirming RpoC-RpoB interaction through orthogonal chromatography steps. The interaction with Q727C7 (RpoB) was validated by copurification (PMID:27099342). Reason: Same rationale as the previous protein binding annotation. The evidence supports physical interaction between RpoC and RpoB within the RNAP complex, but "protein binding" is too general. The tagless copurification method provides independent validation of the RNAP subunit interactions. Proposed replacements: RNAP core enzyme binding Supporting Evidence: PMID:27099342 Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs |
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Download this section (compressed HTML)Q: Are there organism-specific features of the N. vulgaris RpoC that differ from E. coli or other model bacteria, particularly in regions targeted by antibiotics?
Q: Does N. vulgaris RpoC have any trigger loop insertions (like Si3 in cyanobacteria) that might affect its regulatory properties?
Experiment: Structural characterization of purified N. vulgaris RNAP by cryo-EM to determine if there are species-specific structural features. Most RNAP structural knowledge comes from E. coli, Thermus, and mycobacteria. Deltaproteobacteria like N. vulgaris may have unique features.
Experiment: Test susceptibility of N. vulgaris to fidaxomicin and myxopyronin-class RNAP inhibitors that target the clamp/switch region. These antibiotics target conserved beta'/sigma interfaces but species-specific sensitivities exist.
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