RpoN (sigma-54) is an alternative sigma factor that directs bacterial RNA polymerase to recognize -24/-12 type promoters. Unlike the housekeeping sigma-70, sigma-54 forms a transcriptionally inactive closed complex with RNAP that absolutely requires ATP hydrolysis by enhancer-binding proteins (EBPs) to transition to the open complex and initiate transcription. In D. vulgaris Hildenborough, sigma-54 regulates an extensive regulon of 36 regulons covering 201 protein-coding genes, including flagellar assembly, nitrogen fixation/assimilation, biofilm formation, the anaerobe-specific Orange Protein (ORP) complex, and various metabolic pathways. The protein contains three characteristic domains: an N-terminal activator-interaction domain (AID) that contacts EBPs, a central core-binding domain (CBD) that associates with RNAP core, and a C-terminal DNA-binding domain (DBD) for -24/-12 promoter recognition.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0016987
sigma factor activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Sigma factor activity is the core molecular function of rpoN. Sigma-54 acts as the promoter specificity subunit for -24/-12 class promoters in bacteria. The protein combines with the RNAP core to form a holoenzyme that recognizes specific promoter elements.
Reason: This is the primary molecular function of sigma-54. The deep research confirms that rpoN encodes the sigma-54 factor that directs RNAP to -24/-12 promoters. The D. vulgaris sigma-54 promoter consensus is tGGcacg (-24) and tTGCt (-12). This annotation directly reflects the core biochemical activity of the protein.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
sigma54 is a promoter specificity factor for -24/-12 class promoters that, unlike sigma70, forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription
|
|
GO:0001216
DNA-binding transcription activator activity
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This annotation is mechanistically incorrect for sigma-54. Unlike sigma-70, sigma-54 does NOT have intrinsic transcription activator activity. Instead, sigma-54 forms a CLOSED complex that actively blocks transcription initiation until EBPs provide the ATP-dependent remodeling signal. Sigma-54 is better characterized as a transcription specificity factor that gates promoter access.
Reason: The deep research clearly establishes that sigma-54 forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs to form the open complex. This is fundamentally different from transcription activators which directly enhance transcription. Sigma-54 actually INHIBITS transcription until EBPs activate it. The IEA annotation from InterPro domains IPR000394 and IPR007634 conflates promoter recognition with transcription activation, which are mechanistically distinct for sigma-54. GO:0016987 (sigma factor activity) correctly captures this function.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
sigma54 forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
Structural work shows sigma54 occludes DNA loading and must be reorganized by EBP contact with the sigma54 N-terminus
|
|
GO:0003677
DNA binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Sigma-54 has a C-terminal DNA-binding domain (DBD, Pfam PF04552) that recognizes -24/-12 promoter elements. However, this DNA binding occurs only in the context of the RNAP holoenzyme - sigma-54 does not bind DNA on its own.
Reason: The UniProt entry documents the RNA polymerase sigma factor 54 DNA-binding domain (residues 315-473). This is a legitimate function, although the GO term definition notes that sigma does not bind DNA on its own, but when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The deep research confirms sigma-54 recognizes specific -24/-12 promoter elements in D. vulgaris.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
D. vulgaris-specific sigma54 promoter consensus: derived -24/-12 elements are tGGcacg (-24) and tTGCt (-12). A refined set of 87 sigma54-dependent promoters was compiled
|
|
GO:0016779
nucleotidyltransferase activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: This annotation is INCORRECT. Sigma factors do not have nucleotidyltransferase activity. The catalytic activity of RNA polymerase (RNA synthesis) is performed by the core subunits (beta, beta-prime), not by the sigma factor. Sigma-54 is a promoter specificity subunit that determines WHERE transcription occurs, not an enzyme that catalyzes nucleotide transfer.
Reason: This is a clear over-annotation based on the UniProtKB keyword KW-0548 (Nucleotidyltransferase). The keyword mapping is inappropriate for sigma factors. The sigma subunit provides promoter recognition but does not participate in the catalytic RNA synthesis reaction. The GO term GO:0016987 definition explicitly states that sigma factors bind specifically to promoter elements and are released once elongation begins - they are not catalytic subunits. Sigma-54 lacks any nucleotidyltransferase domain.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-uniprot.txt
Belongs to the sigma-54 factor family
|
|
GO:0016740
transferase activity
|
IEA
GO_REF:0000043 |
REMOVE |
Summary: This annotation is INCORRECT for the same reason as nucleotidyltransferase activity. Sigma-54 has no catalytic transferase function. It is a regulatory subunit that provides promoter specificity, not an enzyme.
Reason: This is a parent term of nucleotidyltransferase activity and is equally inappropriate. Sigma factors are NOT enzymes. The UniProtKB keyword mapping (KW-0808, Transferase) is incorrect for sigma factors, which function as promoter specificity factors rather than catalytic subunits. No transferase domain is present in sigma-54 domain architecture.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-uniprot.txt
Belongs to the sigma-54 factor family
|
|
GO:0000428
DNA-directed RNA polymerase complex
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Sigma-54 is a subunit of the bacterial RNA polymerase holoenzyme complex. When associated with the core RNAP (alpha2-beta-beta-prime), it forms the sigma-54 holoenzyme that recognizes -24/-12 promoters.
Reason: This cellular component annotation is correct. Sigma-54 associates with the RNAP core via its central core-binding domain (CBD, Pfam PF04963) to form the holoenzyme. The deep research confirms sigma-54 operates in the bacterial nucleoid as part of the RNAP holoenzyme, acting at chromosomal promoters.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
sigma54 operates in the bacterial nucleoid as part of the RNAP holoenzyme, acting at chromosomal promoters
|
|
GO:0006352
DNA-templated transcription initiation
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Sigma-54 is directly involved in transcription initiation at -24/-12 promoters, although its mechanism is distinct from sigma-70 in that it requires EBP activation. Once activated, sigma-54 participates in the transition from closed to open complex.
Reason: This biological process annotation is appropriate. Sigma-54 is essential for transcription initiation at its cognate promoters. The requirement for EBP activation does not negate its role in initiation - it defines the specific mechanism. In D. vulgaris, 87 sigma-54-dependent promoters drive transcription initiation of 85 operons.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
The reconstructed D. vulgaris sigma54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs, associated with 87 sigma54-dependent promoters upstream of 85 operons
|
|
GO:0006355
regulation of DNA-templated transcription
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: Sigma-54 regulates transcription by determining which promoters are recognized by RNAP. In D. vulgaris, sigma-54 regulates 201 protein-coding genes across 36 regulons covering diverse functions including motility, nitrogen metabolism, and biofilm formation.
Reason: Sigma-54 is a key transcriptional regulator that controls expression of specific gene sets. The D. vulgaris sigma-54 regulon is well characterized and includes flagellar genes, nitrogen fixation, amino acid catabolism, and stress responses. This is a core function of sigma factors.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
The reconstructed D. vulgaris sigma54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
Enriched functions include flagellar assembly and cell-exterior structures
|
|
GO:0045893
positive regulation of DNA-templated transcription
|
IEA
GO_REF:0000108 |
MODIFY |
Summary: This annotation is problematic because sigma-54 does not positively regulate transcription in isolation - it forms a CLOSED complex that blocks transcription until activated by EBPs. The positive regulation comes from the EBPs, not from sigma-54 itself.
Reason: The logical inference from GO:0001216 (DNA-binding transcription activator activity) to GO:0045893 is based on the incorrect premise that sigma-54 has activator activity. Sigma-54 actually forms a closed complex that must be opened by EBPs. The more accurate annotation is GO:0006355 (regulation of DNA-templated transcription), which is already present. Sigma-54 enables transcription of specific genes when activated, but the positive regulation comes from the EBP signal, not sigma-54.
Proposed replacements:
regulation of DNA-templated transcription
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
sigma54 forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs
|
|
GO:2000142
regulation of DNA-templated transcription initiation
|
IEA
GO_REF:0000108 |
ACCEPT |
Summary: Sigma-54 does regulate transcription initiation by determining which promoters are recognized and by controlling the transition from closed to open complex (via EBP requirement). This is more specific than GO:0006355 but accurately reflects sigma-54 function.
Reason: This annotation correctly captures that sigma-54 regulates the initiation step of transcription. The sigma-54-dependent promoters require both sigma-54 for recognition and EBPs for activation, representing a regulatory checkpoint at initiation. The logical inference from GO:0016987 (sigma factor activity) to this term is valid.
Supporting Evidence:
file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
sigma54 is a promoter specificity factor for -24/-12 class promoters
|
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template_variables:
organism: DESVH
gene_id: Q72BK7
gene_symbol: rpoN
uniprot_accession: Q72BK7
protein_description: 'SubName: Full=RNA polymerase sigma-54 factor {ECO:0000313|EMBL:AAS96106.1};'
gene_info: Name=rpoN {ECO:0000313|EMBL:AAS96106.1}; OrderedLocusNames=DVU_1628 {ECO:0000313|EMBL:AAS96106.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Belongs to the sigma-54 factor family.
protein_domains: RNA_pol_sigma_54. (IPR000394); RNA_pol_sigma_54_core-bd. (IPR007046);
RNA_pol_sigma_54_DNA-bd. (IPR007634); RpoN_core-bd_sf. (IPR038709); Sigma54_AID
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BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'rpoN' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene rpoN (gene ID: Q72BK7, UniProt: Q72BK7) in DESVH.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'rpoN' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene rpoN (gene ID: Q72BK7, UniProt: Q72BK7) in DESVH.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Title: Functional annotation of rpoN (Q72BK7) from Nitratidesulfovibrio (Desulfovibrio) vulgaris Hildenborough: σ54-dependent transcription, regulons, and EBPs
Abstract
We verified the identity of rpoN (UniProt Q72BK7) from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) Hildenborough as encoding the σ54 (RpoN) alternative sigma factor, characterized by conserved activator interaction and DNA-binding domains typical of the σ54 family. We synthesize organism-specific evidence for σ54-dependent regulation, enhancer-binding proteins (EBPs), motif features, and processes regulated in D. vulgaris, and we integrate 2023–2024 developments relevant to sulfate-reducing bacteria (SRB). Where appropriate, cross-species mechanistic studies anchor definitions and mechanisms.
Identity verification and domains
• Gene symbol and organism: rpoN encodes σ54 (RpoN) in D. vulgaris Hildenborough (also known as Nitratidesulfovibrio vulgaris Hildenborough), a model SRB (Kazakov et al., 2015). (kazakov2015σ54dependentregulomein pages 1-3)
• Domain architecture: σ54 comprises an N-terminal activator-interaction domain (AID; PF00309), a central core-binding domain (CBD; PF04963), and a C-terminal DNA-binding domain (DBD; PF04552). These assignments and the σ54 promoter recognition properties are corroborated by comparative analyses of σ54 domains and promoters across bacteria. (carrerareyna2025analysisandcomparison pages 2-4, carrerareyna2025analysisandcomparison pages 28-30, carrerareyna2025analysisandcomparison pages 1-2)
Molecular function, mechanism, and localization
• Function: σ54 is a promoter specificity factor for −24/−12 class promoters that, unlike σ70, forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription. (kazakov2015σ54dependentregulomein pages 1-3, carrerareyna2025analysisandcomparison pages 1-2, bush2014interdomainrepressionin pages 67-68)
• Mechanism: EBPs bind upstream activating sequences (UASs), assemble (typically hexamers), and, upon signal-dependent activation, hydrolyze ATP to remodel σ54 within the closed complex. DNA looping, often aided by IHF/HU, brings EBPs to σ54-RNAP. Structural work shows σ54 occludes DNA loading and must be reorganized by EBP contact with the σ54 N-terminus. (bush2014interdomainrepressionin pages 67-68, kazakov2015σ54dependentregulomein pages 1-3)
• Localization: σ54 operates in the bacterial nucleoid as part of the RNAP holoenzyme, acting at chromosomal promoters; EBPs bind UASs typically ≥100 bp upstream and contact the σ54-RNAP via looping. (kazakov2015σ54dependentregulomein pages 1-3)
Promoter motif features
• D. vulgaris-specific σ54 promoter consensus: derived −24/−12 elements are tGGcacg (−24) and tTGCt (−12). A refined set of 87 σ54-dependent promoters was compiled by combining comparative genomics with 5′-RNA-seq and motif analysis. (kazakov2015σ54dependentregulomein pages 13-14)
σ54 regulome size and composition in D. vulgaris
• Counts: The reconstructed D. vulgaris σ54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs, associated with 87 σ54-dependent promoters upstream of 85 operons. Most regulons are small (1–4 operons), but some EBPs regulate larger sets (e.g., 6–12 operons). (kazakov2015σ54dependentregulomein pages 1-3, kazakov2015σ54dependentregulomein pages 5-7)
• Process categories: Enriched functions include flagellar assembly and cell-exterior structures (~37 operons), and metabolic/transport modules (~24 operons) such as ammonia assimilation, nitrogen fixation, amino acid/amide catabolism, carboxylic-acid metabolism; direct σ54 control was also inferred for pyruvate metabolism and a type III secretion system. (kazakov2015σ54dependentregulomein pages 5-7, kazakov2015σ54dependentregulomein pages 1-3)
Key σ54-dependent systems and EBPs in D. vulgaris
• Orange Protein (ORP) complex operons: Two divergent operons (orp1: DVU2107–DVU2109; orp2: DVU2103–DVU2105) are transcribed by σ54-RNAP and co-regulated by a cognate EBP, DVU2106. IHF is required for robust transcription, with two functional IHF sites identified between the promoters. DVU2106 contains PAS-like sensory domain features and retrocontrols its expression; ORP complex composition (DVU2103/2104/2105/2108/2109) was validated by pulldown. (Fiévet et al., 2011, J. Bacteriol.; Fiévet et al., 2014, PLoS ONE). (fievet2011theanaerobespecificorange pages 1-2, fievet2011theanaerobespecificorange pages 12-13, fievet2014ihfisrequired pages 1-2, fievet2014ihfisrequired pages 8-9)
• DVU2956 EBP (σ54-dependent): Controls a biofilm-to-planktonic switch; overexpression reduces biofilm formation by ~70%, deletion increases biofilm and raises H2S production by ~131%. Mechanistically influences the Hmc complex (DVU0531–DVU0536) and Fe-only hydrogenase (hydA/hydB; DVU1769/DVU1770). Also regulates DVU2960 and DVU2962 downstream. (Zhu et al., 2019, Environ. Microbiol.). (zhu2019σ54dependentregulator pages 1-2)
• Additional EBPs and targets: D. vulgaris encodes 37 σ54-associated EBPs; 25 harbor the canonical GAFTGA σ54-interaction motif, with variants in others. Examples include DVU0110 (linked to exopolysaccharide/biofilm and transport), DVUA0057 (exopolysaccharide/biofilm), DVUA0143 (nitrogenase operon), and DVU2894 (flagellar module; conserved inverted repeat yGTCA–N6–TGACr). Many EBP genes co-localize with σ54 promoters. (kazakov2015σ54dependentregulomein pages 3-4, kazakov2015σ54dependentregulomein pages 13-14, kazakov2015σ54dependentregulomein pages 4-5)
Current applications and real-world implementations (SRB context)
• Biofilm control and corrosion: DVU2956’s σ54-dependent regulation modulates biofilm and H2S outputs, pointing to genetic control points with potential to mitigate microbiologically influenced corrosion by SRB. (zhu2019σ54dependentregulator pages 1-2)
• Anaerobe-specific systems: ORP σ54/IHF-dependent operons exemplify anaerobe-specific regulation that may modulate cell division/morphology and redox-related protein complexes under strict anaerobiosis. (fievet2011theanaerobespecificorange pages 1-2, fievet2011theanaerobespecificorange pages 12-13)
2023–2024 updates relevant to SRB/deltaproteobacteria
• SRB biofilm studies (2024): RpoN (σ54) was explicitly monitored in Oleidesulfovibrio alaskensis G20 biofilms on copper and graphene-coated copper, framed as a key activator of stress, motility, and survival-associated genes; the study described σ54-dependent two-component signaling as central to adaptation under surface/biofilm contexts. (Gopalakrishnan et al., 2024, Microorganisms, Aug 2024). (gopalakrishnan2024impactofgraphene pages 5-8)
• Comparative cross-phyla perspective (2025, included for motif/domain currency): Large-scale analysis across 16 phyla confirmed σ54 promoter architecture, domain composition, and broad process coverage (nitrogen, motility, secretion, biofilms), providing updated reference PSSMs and an online database (aRpoNDB). (carrerareyna2025analysisandcomparison pages 2-4, carrerareyna2025analysisandcomparison pages 28-30, carrerareyna2025analysisandcomparison pages 1-2)
Expert consensus and mechanistic reviews
• EBPs as specialized σ54 activators: EBPs universally use a central AAA+ ATPase with the σ54-interacting GAFTGA loop; regulation is typically via phosphorylation (NtrC-like), ligand sensing (PAS/GAF/V4R), or partner proteins (e.g., PspA–PspF). (bush2014interdomainrepressionin pages 67-68)
• σ54 structural mechanism: σ54 stabilizes a closed RNAP–promoter complex; EBP ATPase action is required to reorganize σ54 and enable DNA melting and template loading. (kazakov2015σ54dependentregulomein pages 1-3)
Relevant statistics and specific examples
• Network size: 36 regulons; 201 protein-coding genes + 4 ncRNAs; 87 σ54 promoters upstream of 85 operons; 37 EBPs in D. vulgaris Hildenborough; 25 EBPs with exact GAFTGA motif. (kazakov2015σ54dependentregulomein pages 1-3, kazakov2015σ54dependentregulomein pages 5-7, kazakov2015σ54dependentregulomein pages 3-4)
• Functional distribution: ≈37 operons for flagella/cell exterior; ≈24 operons for metabolism/transport, including nitrogen fixation/assimilation and carboxylic-acid metabolism; additional modules in amino acid/amide catabolism and type III secretion. (kazakov2015σ54dependentregulomein pages 5-7)
• Promoter consensus: tGGcacg (−24), tTGCt (−12); UASs upstream, with IHF sites facilitating looping at ORP promoters. (kazakov2015σ54dependentregulomein pages 13-14, fievet2014ihfisrequired pages 1-2)
• EBP exemplars: DVU2106 (ORP; PAS-type; σ54/IHF dependent), DVU2956 (biofilm/planktonic/H2S; Hmc and hydrogenase), DVU0110 and DVUA0057 (EPS/biofilm), DVUA0143 (nitrogenase), DVU2894 (flagella). (fievet2011theanaerobespecificorange pages 1-2, fievet2011theanaerobespecificorange pages 12-13, zhu2019σ54dependentregulator pages 1-2, kazakov2015σ54dependentregulomein pages 3-4, kazakov2015σ54dependentregulomein pages 13-14, kazakov2015σ54dependentregulomein pages 4-5)
Conclusions and functional annotation for rpoN (Q72BK7)
• Primary function: rpoN encodes σ54, the alternative sigma factor that directs RNAP to −24/−12 promoters and absolutely requires EBP ATPase activity for transcription initiation; it broadly controls motility/flagella, extracellular structures, nitrogen and carbon metabolism, secretion, and stress-adaptive systems in D. vulgaris. (kazakov2015σ54dependentregulomein pages 1-3, kazakov2015σ54dependentregulomein pages 5-7)
• Localization: cytosolic, acting at chromosomal promoters within the nucleoid as part of the RNAP holoenzyme; function requires DNA looping and EBP contact. (kazakov2015σ54dependentregulomein pages 1-3)
• Pathways: σ54-dependent operons include ORP (DVU2103–2105; DVU2107–2109) with EBP DVU2106 and IHF; biofilm/H2S control via EBP DVU2956 targeting Hmc and Fe-only hydrogenase; broader regulons encompass nitrogen fixation/assimilation and motility. (fievet2011theanaerobespecificorange pages 1-2, fievet2011theanaerobespecificorange pages 12-13, fievet2014ihfisrequired pages 1-2, zhu2019σ54dependentregulator pages 1-2, kazakov2015σ54dependentregulomein pages 5-7)
• 2023–2024 perspective: SRB biofilm studies continued to track σ54 as a central stress/biofilm regulator in deltaproteobacteria, supporting its relevance to corrosion and surface-associated growth. (gopalakrishnan2024impactofgraphene pages 5-8)
Data availability, URLs, dates
• Kazakov et al., 2015, BMC Genomics, Nov 2015. DOI: 10.1186/s12864-015-2176-y; URL: https://doi.org/10.1186/s12864-015-2176-y. (kazakov2015σ54dependentregulomein pages 5-7, kazakov2015σ54dependentregulomein pages 3-4, kazakov2015σ54dependentregulomein pages 1-3, kazakov2015σ54dependentregulomein pages 13-14, kazakov2015σ54dependentregulomein pages 4-5)
• Fiévet et al., 2011, J. Bacteriol., Jul 2011; DOI: 10.1128/JB.00044-11; URL: https://doi.org/10.1128/JB.00044-11. (fievet2011theanaerobespecificorange pages 1-2, fievet2011theanaerobespecificorange pages 12-13)
• Fiévet et al., 2014, PLoS ONE, Jan 21, 2014; DOI: 10.1371/journal.pone.0086507; URL: https://doi.org/10.1371/journal.pone.0086507. (fievet2014ihfisrequired pages 1-2, fievet2014ihfisrequired pages 8-9)
• Zhu et al., 2019, Environmental Microbiology, May 2019; DOI: 10.1111/1462-2920.14679; URL: https://doi.org/10.1111/1462-2920.14679. (zhu2019σ54dependentregulator pages 1-2)
• Gopalakrishnan et al., 2024, Microorganisms, Aug 2024; DOI: 10.3390/microorganisms12091759; URL: https://doi.org/10.3390/microorganisms12091759. (gopalakrishnan2024impactofgraphene pages 5-8)
• Carrera-Reyna et al., 2025, PLOS ONE, Aug 2025; DOI: 10.1371/journal.pone.0327805; URL: https://doi.org/10.1371/journal.pone.0327805. (carrerareyna2025analysisandcomparison pages 2-4, carrerareyna2025analysisandcomparison pages 28-30, carrerareyna2025analysisandcomparison pages 1-2)
Limitations
Direct experimental characterization of Q72BK7 in D. vulgaris Hildenborough at the protein level is limited in the cited set; most functional assertions are based on the well-established σ54 mechanism and organism-level regulon mapping coupled with EBP functional studies. Additional 2023–2024 D. vulgaris-specific experiments on σ54 per se were not identified in this search, though SRB-level studies tracked RpoN expression in biofilm contexts.
Overall, rpoN (Q72BK7) encodes σ54, a central transcriptional regulator in D. vulgaris Hildenborough with an extensive sigmulon controlling motility, extracellular structures, nitrogen/carbon metabolism, secretion, and stress/biofilm-associated pathways, activated exclusively by specialized σ54 EBPs.
References
(kazakov2015σ54dependentregulomein pages 1-3): Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, and Pavel S. Novichkov. Σ54-dependent regulome in desulfovibrio vulgaris hildenborough. BMC Genomics, Nov 2015. URL: https://doi.org/10.1186/s12864-015-2176-y, doi:10.1186/s12864-015-2176-y. This article has 21 citations and is from a peer-reviewed journal.
(carrerareyna2025analysisandcomparison pages 2-4): Maricela Carrera-Reyna, Edna Cruz-Flores, and Enrique Merino. Analysis and comparison of the bacterial σ54 regulon: evidence of phylogenetic trends in gene regulation. PLOS One, Aug 2025. URL: https://doi.org/10.1371/journal.pone.0327805, doi:10.1371/journal.pone.0327805. This article has 1 citations and is from a peer-reviewed journal.
(carrerareyna2025analysisandcomparison pages 28-30): Maricela Carrera-Reyna, Edna Cruz-Flores, and Enrique Merino. Analysis and comparison of the bacterial σ54 regulon: evidence of phylogenetic trends in gene regulation. PLOS One, Aug 2025. URL: https://doi.org/10.1371/journal.pone.0327805, doi:10.1371/journal.pone.0327805. This article has 1 citations and is from a peer-reviewed journal.
(carrerareyna2025analysisandcomparison pages 1-2): Maricela Carrera-Reyna, Edna Cruz-Flores, and Enrique Merino. Analysis and comparison of the bacterial σ54 regulon: evidence of phylogenetic trends in gene regulation. PLOS One, Aug 2025. URL: https://doi.org/10.1371/journal.pone.0327805, doi:10.1371/journal.pone.0327805. This article has 1 citations and is from a peer-reviewed journal.
(bush2014interdomainrepressionin pages 67-68): M Bush. Interdomain repression in the enhancer binding protein norr. Unknown journal, 2014.
(kazakov2015σ54dependentregulomein pages 13-14): Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, and Pavel S. Novichkov. Σ54-dependent regulome in desulfovibrio vulgaris hildenborough. BMC Genomics, Nov 2015. URL: https://doi.org/10.1186/s12864-015-2176-y, doi:10.1186/s12864-015-2176-y. This article has 21 citations and is from a peer-reviewed journal.
(kazakov2015σ54dependentregulomein pages 5-7): Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, and Pavel S. Novichkov. Σ54-dependent regulome in desulfovibrio vulgaris hildenborough. BMC Genomics, Nov 2015. URL: https://doi.org/10.1186/s12864-015-2176-y, doi:10.1186/s12864-015-2176-y. This article has 21 citations and is from a peer-reviewed journal.
(fievet2011theanaerobespecificorange pages 1-2): Anouchka Fiévet, Laetitia My, Eric Cascales, Mireille Ansaldi, Sofia R. Pauleta, Isabel Moura, Zorah Dermoun, Christophe S. Bernard, Alain Dolla, and Corinne Aubert. The anaerobe-specific orange protein complex of desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ 54 and a cognate transcriptional regulator. Journal of Bacteriology, 193:3207-3219, Jul 2011. URL: https://doi.org/10.1128/jb.00044-11, doi:10.1128/jb.00044-11. This article has 27 citations and is from a peer-reviewed journal.
(fievet2011theanaerobespecificorange pages 12-13): Anouchka Fiévet, Laetitia My, Eric Cascales, Mireille Ansaldi, Sofia R. Pauleta, Isabel Moura, Zorah Dermoun, Christophe S. Bernard, Alain Dolla, and Corinne Aubert. The anaerobe-specific orange protein complex of desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ 54 and a cognate transcriptional regulator. Journal of Bacteriology, 193:3207-3219, Jul 2011. URL: https://doi.org/10.1128/jb.00044-11, doi:10.1128/jb.00044-11. This article has 27 citations and is from a peer-reviewed journal.
(fievet2014ihfisrequired pages 1-2): Anouchka Fiévet, Eric Cascales, Odile Valette, Alain Dolla, and Corinne Aubert. Ihf is required for the transcriptional regulation of the desulfovibrio vulgaris hildenborough orp operons. PLoS ONE, 9:e86507, Jan 2014. URL: https://doi.org/10.1371/journal.pone.0086507, doi:10.1371/journal.pone.0086507. This article has 11 citations and is from a peer-reviewed journal.
(fievet2014ihfisrequired pages 8-9): Anouchka Fiévet, Eric Cascales, Odile Valette, Alain Dolla, and Corinne Aubert. Ihf is required for the transcriptional regulation of the desulfovibrio vulgaris hildenborough orp operons. PLoS ONE, 9:e86507, Jan 2014. URL: https://doi.org/10.1371/journal.pone.0086507, doi:10.1371/journal.pone.0086507. This article has 11 citations and is from a peer-reviewed journal.
(zhu2019σ54dependentregulator pages 1-2): Lei Zhu, Ting Gong, Thammajun L. Wood, Ryota Yamasaki, and Thomas K. Wood. Σ54 -dependent regulator dvu2956 switches desulfovibrio vulgaris from biofilm formation to planktonic growth and regulates hydrogen sulfide production. Environmental microbiology, 21:3564-3576, May 2019. URL: https://doi.org/10.1111/1462-2920.14679, doi:10.1111/1462-2920.14679. This article has 27 citations and is from a domain leading peer-reviewed journal.
(kazakov2015σ54dependentregulomein pages 3-4): Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, and Pavel S. Novichkov. Σ54-dependent regulome in desulfovibrio vulgaris hildenborough. BMC Genomics, Nov 2015. URL: https://doi.org/10.1186/s12864-015-2176-y, doi:10.1186/s12864-015-2176-y. This article has 21 citations and is from a peer-reviewed journal.
(kazakov2015σ54dependentregulomein pages 4-5): Alexey E. Kazakov, Lara Rajeev, Amy Chen, Eric G. Luning, Inna Dubchak, Aindrila Mukhopadhyay, and Pavel S. Novichkov. Σ54-dependent regulome in desulfovibrio vulgaris hildenborough. BMC Genomics, Nov 2015. URL: https://doi.org/10.1186/s12864-015-2176-y, doi:10.1186/s12864-015-2176-y. This article has 21 citations and is from a peer-reviewed journal.
(gopalakrishnan2024impactofgraphene pages 5-8): Vinoj Gopalakrishnan, Priya Saxena, Payal Thakur, Alexey Lipatov, and Rajesh K. Sani. Impact of graphene layers on genetic expression and regulation within sulfate-reducing biofilms. Microorganisms, 12:1759, Aug 2024. URL: https://doi.org/10.3390/microorganisms12091759, doi:10.3390/microorganisms12091759. This article has 1 citations and is from a poor quality or predatory journal.
id: Q72BK7
gene_symbol: rpoN
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris Hildenborough
description: >-
RpoN (sigma-54) is an alternative sigma factor that directs bacterial RNA polymerase
to recognize -24/-12 type promoters. Unlike the housekeeping sigma-70, sigma-54 forms
a transcriptionally inactive closed complex with RNAP that absolutely requires ATP
hydrolysis by enhancer-binding proteins (EBPs) to transition to the open complex and
initiate transcription. In D. vulgaris Hildenborough, sigma-54 regulates an extensive
regulon of 36 regulons covering 201 protein-coding genes, including flagellar assembly,
nitrogen fixation/assimilation, biofilm formation, the anaerobe-specific Orange Protein
(ORP) complex, and various metabolic pathways. The protein contains three characteristic
domains: an N-terminal activator-interaction domain (AID) that contacts EBPs, a central
core-binding domain (CBD) that associates with RNAP core, and a C-terminal DNA-binding
domain (DBD) for -24/-12 promoter recognition.
existing_annotations:
- term:
id: GO:0016987
label: sigma factor activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Sigma factor activity is the core molecular function of rpoN. Sigma-54 acts as the
promoter specificity subunit for -24/-12 class promoters in bacteria. The protein
combines with the RNAP core to form a holoenzyme that recognizes specific promoter
elements.
action: ACCEPT
reason: >-
This is the primary molecular function of sigma-54. The deep research confirms that
rpoN encodes the sigma-54 factor that directs RNAP to -24/-12 promoters. The D. vulgaris
sigma-54 promoter consensus is tGGcacg (-24) and tTGCt (-12). This annotation directly
reflects the core biochemical activity of the protein.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 is a promoter specificity factor for -24/-12 class promoters that, unlike sigma70, forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription"
- term:
id: GO:0001216
label: DNA-binding transcription activator activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation is mechanistically incorrect for sigma-54. Unlike sigma-70, sigma-54
does NOT have intrinsic transcription activator activity. Instead, sigma-54 forms a
CLOSED complex that actively blocks transcription initiation until EBPs provide the
ATP-dependent remodeling signal. Sigma-54 is better characterized as a transcription
specificity factor that gates promoter access.
action: REMOVE
reason: >-
The deep research clearly establishes that sigma-54 forms a transcriptionally inactive
closed complex with RNAP and requires ATP-dependent remodeling by EBPs to form the open
complex. This is fundamentally different from transcription activators which directly
enhance transcription. Sigma-54 actually INHIBITS transcription until EBPs activate it.
The IEA annotation from InterPro domains IPR000394 and IPR007634 conflates promoter
recognition with transcription activation, which are mechanistically distinct for sigma-54.
GO:0016987 (sigma factor activity) correctly captures this function.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription"
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "Structural work shows sigma54 occludes DNA loading and must be reorganized by EBP contact with the sigma54 N-terminus"
- term:
id: GO:0003677
label: DNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Sigma-54 has a C-terminal DNA-binding domain (DBD, Pfam PF04552) that recognizes
-24/-12 promoter elements. However, this DNA binding occurs only in the context
of the RNAP holoenzyme - sigma-54 does not bind DNA on its own.
action: ACCEPT
reason: >-
The UniProt entry documents the RNA polymerase sigma factor 54 DNA-binding domain
(residues 315-473). This is a legitimate function, although the GO term definition
notes that sigma does not bind DNA on its own, but when combined with the core to form
the holoenzyme, the sigma factor binds specifically to promoter elements. The deep
research confirms sigma-54 recognizes specific -24/-12 promoter elements in D. vulgaris.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "D. vulgaris-specific sigma54 promoter consensus: derived -24/-12 elements are tGGcacg (-24) and tTGCt (-12). A refined set of 87 sigma54-dependent promoters was compiled"
- term:
id: GO:0016779
label: nucleotidyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This annotation is INCORRECT. Sigma factors do not have nucleotidyltransferase activity.
The catalytic activity of RNA polymerase (RNA synthesis) is performed by the core subunits
(beta, beta-prime), not by the sigma factor. Sigma-54 is a promoter specificity subunit
that determines WHERE transcription occurs, not an enzyme that catalyzes nucleotide transfer.
action: REMOVE
reason: >-
This is a clear over-annotation based on the UniProtKB keyword KW-0548 (Nucleotidyltransferase).
The keyword mapping is inappropriate for sigma factors. The sigma subunit provides promoter
recognition but does not participate in the catalytic RNA synthesis reaction. The GO term
GO:0016987 definition explicitly states that sigma factors bind specifically to promoter
elements and are released once elongation begins - they are not catalytic subunits.
Sigma-54 lacks any nucleotidyltransferase domain.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-uniprot.txt
supporting_text: "Belongs to the sigma-54 factor family"
- term:
id: GO:0016740
label: transferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This annotation is INCORRECT for the same reason as nucleotidyltransferase activity.
Sigma-54 has no catalytic transferase function. It is a regulatory subunit that provides
promoter specificity, not an enzyme.
action: REMOVE
reason: >-
This is a parent term of nucleotidyltransferase activity and is equally inappropriate.
Sigma factors are NOT enzymes. The UniProtKB keyword mapping (KW-0808, Transferase) is
incorrect for sigma factors, which function as promoter specificity factors rather than
catalytic subunits. No transferase domain is present in sigma-54 domain architecture.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-uniprot.txt
supporting_text: "Belongs to the sigma-54 factor family"
- term:
id: GO:0000428
label: DNA-directed RNA polymerase complex
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
Sigma-54 is a subunit of the bacterial RNA polymerase holoenzyme complex. When associated
with the core RNAP (alpha2-beta-beta-prime), it forms the sigma-54 holoenzyme that
recognizes -24/-12 promoters.
action: ACCEPT
reason: >-
This cellular component annotation is correct. Sigma-54 associates with the RNAP core
via its central core-binding domain (CBD, Pfam PF04963) to form the holoenzyme. The
deep research confirms sigma-54 operates in the bacterial nucleoid as part of the
RNAP holoenzyme, acting at chromosomal promoters.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 operates in the bacterial nucleoid as part of the RNAP holoenzyme, acting at chromosomal promoters"
- term:
id: GO:0006352
label: DNA-templated transcription initiation
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Sigma-54 is directly involved in transcription initiation at -24/-12 promoters,
although its mechanism is distinct from sigma-70 in that it requires EBP activation.
Once activated, sigma-54 participates in the transition from closed to open complex.
action: ACCEPT
reason: >-
This biological process annotation is appropriate. Sigma-54 is essential for
transcription initiation at its cognate promoters. The requirement for EBP activation
does not negate its role in initiation - it defines the specific mechanism. In D. vulgaris,
87 sigma-54-dependent promoters drive transcription initiation of 85 operons.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "requires ATP-dependent remodeling by EBPs (AAA+ ATPases) to form the open complex and initiate transcription"
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "The reconstructed D. vulgaris sigma54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs, associated with 87 sigma54-dependent promoters upstream of 85 operons"
- term:
id: GO:0006355
label: regulation of DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
Sigma-54 regulates transcription by determining which promoters are recognized by RNAP.
In D. vulgaris, sigma-54 regulates 201 protein-coding genes across 36 regulons covering
diverse functions including motility, nitrogen metabolism, and biofilm formation.
action: ACCEPT
reason: >-
Sigma-54 is a key transcriptional regulator that controls expression of specific gene
sets. The D. vulgaris sigma-54 regulon is well characterized and includes flagellar
genes, nitrogen fixation, amino acid catabolism, and stress responses. This is a core
function of sigma factors.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "The reconstructed D. vulgaris sigma54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs"
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "Enriched functions include flagellar assembly and cell-exterior structures"
- term:
id: GO:0045893
label: positive regulation of DNA-templated transcription
evidence_type: IEA
original_reference_id: GO_REF:0000108
review:
summary: >-
This annotation is problematic because sigma-54 does not positively regulate transcription
in isolation - it forms a CLOSED complex that blocks transcription until activated by EBPs.
The positive regulation comes from the EBPs, not from sigma-54 itself.
action: MODIFY
reason: >-
The logical inference from GO:0001216 (DNA-binding transcription activator activity) to
GO:0045893 is based on the incorrect premise that sigma-54 has activator activity. Sigma-54
actually forms a closed complex that must be opened by EBPs. The more accurate annotation
is GO:0006355 (regulation of DNA-templated transcription), which is already present.
Sigma-54 enables transcription of specific genes when activated, but the positive regulation
comes from the EBP signal, not sigma-54.
proposed_replacement_terms:
- id: GO:0006355
label: regulation of DNA-templated transcription
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 forms a transcriptionally inactive closed complex with RNAP and requires ATP-dependent remodeling by EBPs"
- term:
id: GO:2000142
label: regulation of DNA-templated transcription initiation
evidence_type: IEA
original_reference_id: GO_REF:0000108
review:
summary: >-
Sigma-54 does regulate transcription initiation by determining which promoters are
recognized and by controlling the transition from closed to open complex (via EBP
requirement). This is more specific than GO:0006355 but accurately reflects sigma-54
function.
action: ACCEPT
reason: >-
This annotation correctly captures that sigma-54 regulates the initiation step of
transcription. The sigma-54-dependent promoters require both sigma-54 for recognition
and EBPs for activation, representing a regulatory checkpoint at initiation. The
logical inference from GO:0016987 (sigma factor activity) to this term is valid.
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 is a promoter specificity factor for -24/-12 class promoters"
references:
- id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
title: "Deep research report on rpoN (Q72BK7) sigma-54 in Desulfovibrio vulgaris"
findings:
- statement: D. vulgaris sigma-54 regulome includes 36 regulons, 201 protein-coding genes, 87 promoters
supporting_text: "The reconstructed D. vulgaris sigma54 sigmulon includes 36 regulons covering 201 protein-coding genes and 4 non-coding RNAs, associated with 87 sigma54-dependent promoters upstream of 85 operons"
- statement: Sigma-54 promoter consensus is tGGcacg (-24) and tTGCt (-12)
supporting_text: "derived -24/-12 elements are tGGcacg (-24) and tTGCt (-12)"
- statement: D. vulgaris encodes 37 sigma-54-associated EBPs
supporting_text: "D. vulgaris encodes 37 sigma54-associated EBPs; 25 harbor the canonical GAFTGA sigma54-interaction motif"
- statement: Regulated processes include flagella, nitrogen metabolism, biofilm, type III secretion
supporting_text: "Enriched functions include flagellar assembly and cell-exterior structures"
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000108
title: Automatic assignment of GO terms using logical inference, based on inter-ontology links
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
core_functions:
- description: >-
The primary molecular function of rpoN is sigma factor activity, directing RNA polymerase
to -24/-12 type promoters. This is supported by domain architecture (AID, CBD, DBD domains),
sequence family membership (sigma-54 family), and functional characterization in D. vulgaris
showing 87 sigma-54-dependent promoters with consensus tGGcacg/-24 and tTGCt/-12.
molecular_function:
id: GO:0016987
label: sigma factor activity
directly_involved_in:
- id: GO:2000142
label: regulation of DNA-templated transcription initiation
- id: GO:0006352
label: DNA-templated transcription initiation
in_complex:
id: GO:0000428
label: DNA-directed RNA polymerase complex
supported_by:
- reference_id: file:DESVH/Q72BK7/Q72BK7-deep-research-falcon.md
supporting_text: "sigma54 is a promoter specificity factor for -24/-12 class promoters"