RNA polymerase sigma factor SigA (RpoD) is the primary/housekeeping sigma-70 factor in Nitratidesulfovibrio vulgaris (formerly Desulfovibrio vulgaris) Hildenborough. Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. RpoD is the principal sigma factor during exponential growth, directing RNA polymerase to housekeeping gene promoters. The protein contains conserved sigma-70 domains: region 2 (recognizes -10 promoter element and promotes DNA melting), region 4 (contains helix-turn-helix motif that recognizes -35 promoter element), region 1.2 (contributes to promoter escape), and region 1.1 (modulates promoter complex formation). RpoD interacts transiently with the RNA polymerase catalytic core to form the holoenzyme and functions in the cytoplasm during transcription initiation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: This annotation is appropriate but represents an indirect consequence of sigma factor function rather than the core activity. Sigma factors directly participate in transcription initiation rather than regulating it. The term describes modulation of the frequency/rate of transcription initiation, whereas sigma factors are essential components of the transcription initiation machinery itself. Reason: While RpoD does influence transcription initiation rates by directing RNAP to promoters, this is a downstream effect of its primary sigma factor activity (GO:0016987). The core function is sigma factor activity enabling promoter recognition and transcription initiation, not regulation of that process. This annotation captures a true aspect of sigma factor biology but at a less precise level than the more specific terms. Supporting Evidence: file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Primary sigma factor (RpoD/SigA): The sigma-70-type primary sigma factor enables bacterial RNA polymerase (RNAP) to initiate transcription at housekeeping promoters under normal growth conditions. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: This annotation is correct but very general. RpoD binds DNA specifically at promoter sequences through its sigma-70 domains. Region 2 recognizes the -10 element and region 4 recognizes the -35 element via a helix-turn-helix motif (residues 550-569 in Q72B50). However, sigma factors do not bind DNA independently - they only recognize promoter DNA when complexed with RNAP core as part of the holoenzyme. Reason: DNA binding is a fundamental activity of sigma factors, although it occurs in the context of the holoenzyme complex. The UniProt entry documents a DNA_BIND region (H-T-H motif at residues 550-569) which directly supports this annotation. This is appropriately general for an IEA annotation. Supporting Evidence: UniProt:Q72B50 DNA_BIND 550..569 /note="H-T-H motif" /evidence="ECO:0000256|HAMAP-Rule:MF_00963" file:DESVH/Q72B50/Q72B50-deep-research-falcon.md region 2 recognizes the -10 element and promotes DNA melting; region 4 contains a helix-turn-helix that recognizes the -35 element |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: This annotation is INCORRECT for sigma factors. The GO term definition states that DNA-binding transcription factors modulate transcription via "selective and non-covalent binding to a specific double-stranded genomic DNA sequence within a cis-regulatory region." While sigma factors do recognize promoter elements, they do not function as transcription factors that independently bind DNA to regulate transcription. Sigma factors are integral components of the transcription machinery, not regulatory factors. Reason: Sigma factors have a distinct molecular function (GO:0016987 sigma factor activity) that is fundamentally different from transcription factor activity. Sigma factors do not bind DNA independently - they only bind promoter DNA when part of the RNAP holoenzyme. The GO guidelines explicitly note that sigma factors should be annotated to sigma factor activity, not transcription factor activity. This InterPro-derived annotation is an over-generalization. Proposed replacements: sigma factor activity Supporting Evidence: GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases... Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Encodes the primary sigma factor (SigA/RpoD) that binds RNAP core to form the holoenzyme and directs transcription initiation at housekeeping promoters |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: This cellular component annotation is correct. RpoD functions in the bacterial cytoplasm as part of the RNAP holoenzyme, binding core RNAP to engage promoter DNA during transcription initiation. This is consistent with UniProt subcellular location annotation and structural studies. Reason: Cytoplasmic localization is well-established for bacterial sigma factors. The UniProt entry explicitly states "SUBCELLULAR LOCATION: Cytoplasm" based on HAMAP rule MF_00963. The deep research confirms "Cellular localization: Cytoplasmic; functions within the RNAP holoenzyme engaging cytoplasmic DNA during transcription initiation." Supporting Evidence: UniProt:Q72B50 SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00963} file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Cellular localization: Cytoplasmic; functions within the RNAP holoenzyme engaging cytoplasmic DNA during transcription initiation |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000120 | ACCEPT | Summary: This is an excellent and appropriate biological process annotation for sigma factors. The primary function of RpoD is to enable transcription initiation by directing RNAP to promoters. The GO term describes "The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript." Reason: This is a core biological process annotation that accurately captures the essential role of sigma factors in transcription. RpoD directly participates in transcription initiation by forming the holoenzyme with RNAP core and recognizing promoter elements, which is precisely what this term describes. UniProt function annotation states sigma factors "promote the attachment of RNA polymerase to specific initiation sites." Supporting Evidence: UniProt:Q72B50 FUNCTION: Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Primary sigma factor (RpoD/SigA): The sigma-70-type primary sigma factor enables bacterial RNA polymerase (RNAP) to initiate transcription at housekeeping promoters under normal growth conditions. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: This annotation is redundant and less specific than GO:0006352 (DNA-templated transcription initiation). While sigma factors do influence transcription, they are more precisely involved in the initiation process itself rather than regulation of transcription broadly. This term is an ancestor of more specific transcription-related terms. Reason: This is a broader parent term that is technically true but not the most informative annotation for sigma factors. The more specific GO:0006352 (DNA-templated transcription initiation) better captures the precise role of sigma factors. This annotation is acceptable for completeness but represents an over-generalization of sigma factor function. Supporting Evidence: file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Central to transcription initiation of core cellular processes (housekeeping gene expression); thereby indirectly influences growth, metabolism, and stress-responsive regulons by setting basal transcriptional regimes |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: This is a very high-level annotation that is technically correct but not very informative. All sigma factors influence gene expression by directing RNAP to specific promoters, but this term is too general to be useful for understanding sigma factor function. Reason: While sigma factors do affect gene expression by determining which promoters are recognized by RNAP, this annotation is at too high a level of abstraction to be informative. More specific terms (GO:0006352, GO:0016987) better capture the actual molecular role of sigma factors. This annotation adds little value beyond the more specific terms. Supporting Evidence: file:DESVH/Q72B50/Q72B50-deep-research-falcon.md directs transcription initiation at housekeeping promoters during normal growth |
| GO:0016987 sigma factor activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the most precise and appropriate molecular function annotation for RpoD. Sigma factor activity is defined as the promoter specificity subunit of bacterial RNA polymerases that, when combined with the core enzyme to form the holoenzyme, binds specifically to promoter elements. This exactly describes the function of RpoD. Reason: This annotation is the core molecular function of RpoD. The GO term definition states "Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases... Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements." This precisely matches the known function of RpoD as the primary sigma factor. Supporting Evidence: UniProt:Q72B50 FUNCTION: Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth. UniProt:Q72B50 SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily. file:DESVH/Q72B50/Q72B50-deep-research-falcon.md Encodes the primary sigma factor (SigA/RpoD) that binds RNAP core to form the holoenzyme and directs transcription initiation at housekeeping promoters during normal growth |
| GO:0005515 protein binding | IPI PMID:26873250 Bacterial Interactomes: Interacting Protein Partners Share S... | MODIFY | Summary: This annotation is based on high-throughput AP-MS (affinity purification-mass spectrometry) data from the Butland et al. D. vulgaris interactome study. The UniProt entry shows RpoD interacts with DVU_1368 (Q72CB5) with 2 experiments in IntAct. However, "protein binding" is an uninformative term that should be replaced with a more specific binding term if possible. Reason: While the protein-protein interaction is experimentally supported, "protein binding" (GO:0005515) is explicitly discouraged in GO annotation guidelines as uninformative. For sigma factors, the known protein interactions are with RNAP core subunits (RpoA, RpoB, RpoC). The UniProt entry notes "Interacts transiently with the RNA polymerase catalytic core" and shows a motif for "Interaction with polymerase core subunit RpoC" at residues 380-383. A more appropriate term would be RNA polymerase binding or a related term. Proposed replacements: bacterial-type RNA polymerase core enzyme binding Supporting Evidence: UniProt:Q72B50 SUBUNIT: Interacts transiently with the RNA polymerase catalytic core. UniProt:Q72B50 MOTIF 380..383 /note="Interaction with polymerase core subunit RpoC" /evidence="ECO:0000256|HAMAP-Rule:MF_00963" PMID:26873250 Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs)... We have identified 459 high confidence PPIs from D. vulgaris |
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Download this section (compressed HTML)Q: What are the specific promoter sequence motifs recognized by RpoD in N. vulgaris?
Q: Are there alternative sigma factors in N. vulgaris that compete with RpoD under stress conditions?
Q: What is the identity and function of DVU_1368 (Q72CB5) that interacts with RpoD?
Experiment: ChIP-seq analysis to map RpoD binding sites genome-wide and identify the RpoD regulon
Hypothesis: RpoD binds to canonical -10/-35 promoter elements in N. vulgaris housekeeping genes
Type: ChIP-seq
Experiment: In vitro transcription assays with purified components to confirm promoter recognition specificity
Hypothesis: Purified RpoD enables RNAP to initiate transcription at predicted housekeeping promoters
Type: In vitro transcription assay
Experiment: Protein interaction studies to characterize the RpoD-RNAP core interaction interface
Hypothesis: RpoD interacts with RNAP core via the conserved sigma-70 region 2 and region 4 domains
Type: Co-immunoprecipitation or crosslinking mass spectrometry
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