rpoN (PP_0952; synonym ntrA) encodes sigma-54 (Ο54/ΟN), an alternative RNA polymerase sigma factor. It binds the bacterial RNA polymerase core enzyme to form a holoenzyme that recognizes the distinct -24/-12 class of promoters (conserved GGN10GC element) rather than the Ο70-type -35/-10 promoters. The Ο54-RNAP holoenzyme binds its promoter but is held in a transcriptionally inert closed complex until an enhancer-binding protein (bEBP, e.g. NtrC, XylR, FleQ) uses AAA+ ATPase activity to remodel Ο54 and trigger ATP-dependent open-complex formation. Because a single Ο54 interfaces with many signal-responsive bEBPs, RpoN acts as a global transcriptional hub controlling nitrogen assimilation, flagellar/chemotaxis genes, secretion systems, and aromatic/xyl catabolic operons in P. putida KT2440.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000117 | ACCEPT | Summary: RpoN/sigma-54 recognizes sigma-54 promoter elements (the -24/-12 motif) as part of the RNA polymerase holoenzyme. Reason: Retain cis-regulatory region binding in the sigma-factor context; sigma-54 directly recognizes the conserved -24/-12 promoter motif. Supporting Evidence: PMID:19570137 sigma(N) recognition motif file:PSEPK/rpoN/rpoN-deep-research-falcon.md Ο54 recognizes promoters with conserved elements at **β24 and β12** relative to the transcription start site |
| GO:0001216 DNA-binding transcription activator activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: DNA-binding transcription activator activity is not the best model for a sigma factor. RpoN provides promoter-recognition specificity to the holoenzyme; transcriptional activation of sigma-54 promoters is driven by separate AAA+ enhancer-binding proteins, not by RpoN acting as a classical DNA-binding activator. Reason: RpoN specifies RNA polymerase promoter recognition and initiation rather than acting as a conventional transcription activator; the principal activation step is ATP-dependent remodelling of sigma-54 by enhancer-binding proteins. Retain sigma factor activity (GO:0016987) as the precise MF. Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md Its primary function is to provide **promoter recognition specificity** to the RNAP holoenzyme at Ο54 promoters file:PSEPK/rpoN/rpoN-deep-research-falcon.md transcription initiation requires **specialized enhancer-binding proteins (EBPs)** that contain **AAA+ ATPase domains** to **remodel Ο54** using ATP hydrolysis |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Generic DNA binding is true (RpoN has a C-terminal DNA-binding domain and HTH/RPON box) but is less informative than sigma factor activity and promoter binding. Reason: Retain the more specific GO:0016987 (sigma factor activity) and GO:0000976 (cis-regulatory region binding) instead of generic DNA binding. Supporting Evidence: PMID:19570137 preformed E-sigma(N)-PatzR closed complex file:PSEPK/rpoN/rpoN-deep-research-falcon.md an **N-terminal activator-interacting domain** and a **C-terminal DNA-binding domain** |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000002 | ACCEPT | Summary: RpoN functions in DNA-templated transcription initiation by directing the holoenzyme to sigma-54 promoters and supporting open-complex formation after activator remodelling. Reason: Retain the transcription initiation process annotation; this is a core part of sigma-factor function. Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md the Ο54-RNAP holoenzyme can bind its promoter but is **blocked from forming a transcriptionally competent open complex** without help |
| GO:0016987 sigma factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: Sigma factor activity is the core molecular function of RpoN. As the sigma-54 (ΟN) subunit it confers -24/-12 promoter specificity on the RNA polymerase core enzyme. Reason: Retain as the precise molecular-function annotation for this gene. Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md RpoN (Ο54, also called ΟN) is an **alternative sigma factor** that binds the bacterial RNA polymerase (RNAP) core enzyme to form an RNAP holoenzyme file:PSEPK/rpoN/rpoN-uniprot.txt Sigma factors are initiation factors |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Protein-DNA complex is supported for promoter-bound E-sigma54 complexes but is not the core function. Reason: Retain as non-core complex context; the functionally salient state is the E-sigma54 closed complex at the promoter. Supporting Evidence: PMID:19570137 preformed E-sigma(N)-PatzR closed complex |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: RpoN regulates transcription initiation by directing sigma-54-dependent promoter recognition and gating initiation through enhancer-binding-protein-controlled open-complex formation. Reason: Retain this process annotation; sigma-54 systems are tightly gated at the initiation step by signal-responsive bEBPs. Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md a **single Ο54** can interface with **many EBPs**, enabling regulation of diverse processes (motility, secretion, nutrient assimilation) |
| GO:0042802 identical protein binding | IPI PMID:23320542 Evidence for self-association of the alternative sigma facto... | KEEP AS NON CORE | Summary: Self-association of sigma-54 is experimentally supported (region I and region III inter-monomer contacts) but is ancillary to sigma factor activity. Reason: Retain as a non-core interaction feature; self-association may represent an auto-antagonistic regulatory state rather than the holoenzyme function. Supporting Evidence: PMID:23320542 interacts stably with itself |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:19570137 Activation and repression of a sigmaN-dependent promoter nat... | ACCEPT | Summary: RpoN/sigma-54 recognizes sigma-54 promoter elements (the -24/-12 / sigma(N) recognition motif) as part of RNA polymerase holoenzyme. Reason: Retain cis-regulatory region binding in the sigma-factor context, experimentally supported at the PatzR sigma(N) promoter. Supporting Evidence: PMID:19570137 sigma(N) recognition motif |
| GO:0001216 DNA-binding transcription activator activity | IPI PMID:19570137 Activation and repression of a sigmaN-dependent promoter nat... | MARK AS OVER ANNOTATED | Summary: DNA-binding transcription activator activity is not the best model for a sigma factor; activation of sigma-54 promoters depends on separate AAA+ enhancer-binding proteins. Reason: RpoN specifies RNA polymerase promoter recognition and initiation rather than acting as a conventional transcription activator; retain sigma factor activity (GO:0016987). Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md Its primary function is to provide **promoter recognition specificity** to the RNAP holoenzyme at Ο54 promoters |
| GO:0032993 protein-DNA complex | IPI PMID:19570137 Activation and repression of a sigmaN-dependent promoter nat... | KEEP AS NON CORE | Summary: Protein-DNA complex is supported for promoter-bound E-sigma54 complexes but is not the core function. Reason: Retain as non-core complex context; reflects the E-sigma54 promoter-bound closed complex. Supporting Evidence: PMID:19570137 preformed E-sigma(N)-PatzR closed complex |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:19570137 Activation and repression of a sigmaN-dependent promoter nat... | ACCEPT | Summary: RpoN positively regulates transcription at sigma-54-dependent promoters (e.g. PatzR activated by NtrC) once the closed complex is remodelled to an open complex. Reason: Retain as process context for sigma-54-dependent transcription; experimentally supported for the NtrC-activated PatzR sigma(N) promoter. Supporting Evidence: PMID:19570137 activated by NtrC and repressed by AtzR |
| GO:0001000 bacterial-type RNA polymerase core enzyme binding | ISS file:PSEPK/rpoN/rpoN-deep-research-falcon.md | NEW | Summary: RpoN/sigma-54 binds the bacterial RNA polymerase core enzyme to form the holoenzyme that recognizes -24/-12 promoters. This defining interaction with core RNAP is not currently captured in the GOA record. Reason: The sigma factor's core mechanism is to associate with the bacterial RNA polymerase core enzyme; this more precise MF is well supported by the sigma-54 literature but is missing from existing GOA annotations. Assigned by conserved sigma-54-family mechanism (ISS); no KT2440-specific structural experiment is cited. Supporting Evidence: file:PSEPK/rpoN/rpoN-deep-research-falcon.md RpoN (Ο54, also called ΟN) is an **alternative sigma factor** that binds the bacterial RNA polymerase (RNAP) core enzyme to form an RNAP holoenzyme |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Which KT2440 promoters are directly dependent on RpoN under nutrient-limited and aromatic-compound growth conditions?
Suggested experts: Bacterial transcription and sigma-54 regulon experts
Q: Is the RpoN-dependent repression of the K1-T6SS gene cluster mediated by an RpoN-activated repressor, and which enhancer-binding protein (e.g. FleQ) couples to RpoN at this locus?
Suggested experts: Pseudomonas T6SS and sigma-54 regulation experts
Experiment: Combine RpoN ChIP-seq with transcriptomics in wild type and rpoN deletion/depletion strains across nitrogen limitation and aromatic-substrate growth to distinguish direct promoter targets from secondary (indirect) effects.
Type: ChIP-seq and condition-specific RNA-seq
Experiment: Test direct sigma-54 binding at candidate -24/-12 motifs (including the K1-T6SS promoter region) by in vitro EMSA/footprinting with purified E-sigma54 holoenzyme to confirm whether RpoN-dependent regulation is direct or indirect.
Type: In vitro EMSA and DNase I footprinting with purified holoenzyme
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)