GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models.

ARBA machine-learning IEA annotations for cis-regulatory region binding and protein-DNA complex; reviewed against UniProt and the sigma-54 literature for this gene.

GO_REF:0000120

Combined automated GO annotation using multiple IEA methods.

Combined IEA source for DNA-binding transcription activator activity; assessed as over-annotation because sigma-54 provides promoter specificity rather than acting as a classical activator.

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms.

InterPro2GO IEA source mapping the sigma-54 InterPro domains (IPR000394, IPR007046, IPR007634) to sigma factor activity, DNA binding, and transcription initiation; consistent with UniProt family assignment.

GO_REF:0000108

Gene Ontology annotation based on Ensembl/UniProtKB orthology or projection pipelines.

Orthology/projection IEA source for regulation of transcription initiation; consistent with the conserved role of sigma-54 in gating initiation.

PMID:23320542

Evidence for self-association of the alternative sigma factor sigma54.

PMID:19570137

Activation and repression of a sigmaN-dependent promoter naturally lacking upstream activation sequences.

file:PSEPK/rpoN/rpoN-uniprot.txt

UniProtKB reviewed entry for rpoN

file:PSEPK/rpoN/rpoN-deep-research-falcon.md

Falcon deep research report for rpoN (Pseudomonas putida KT2440, UniProt P0A171)

"RpoN (σ54, also called σN) is an **alternative sigma factor** that binds the bacterial RNA polymerase (RNAP) core enzyme to form an RNAP holoenzyme"
"σ54 recognizes promoters with conserved elements at **−24 and −12** relative to the transcription start site"
"transcription initiation requires **specialized enhancer-binding proteins (EBPs)** that contain **AAA+ ATPase domains** to **remodel σ54** using ATP hydrolysis"
"the σ54-RNAP holoenzyme can bind its promoter but is **blocked from forming a transcriptionally competent open complex** without help"
"Its primary function is to provide **promoter recognition specificity** to the RNAP holoenzyme at σ54 promoters"
"RpoN is **not an enzyme** and does **not catalyze a chemical reaction**"
"As a sigma factor, RpoN functions in the **cytoplasm** in association with RNAP and promoter DNA"
"an **N-terminal activator-interacting domain** and a **C-terminal DNA-binding domain**"
"a **single σ54** can interface with **many EBPs**, enabling regulation of diverse processes (motility, secretion, nutrient assimilation)"
"glnL/glnG (NtrB/NtrC system)** and chemotaxis/flagellar genes, consistent with σ54 involvement in broader nutrient-response networks"
"K1-T6SS expression is **repressed** by **RpoN (σ54)** and by **FleQ**"
"the authors interpret the RpoN effect as **likely indirect**"
"making RpoN a **global transcriptional hub** rather than an enzyme with a substrate"