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

Automatic assignment of GO terms using logical inference, based on on inter-ontology links

Logical-inference IEA source for regulation of transcription initiation, inferred from sigma factor activity; 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"

PMID:27777366

Effect of Crc and Hfq proteins on the transcription, processing, and stability of the Pseudomonas putida CrcZ sRNA

crcZ and crcY transcription depends on CbrB and RpoN in P. putida.

"The crcZ and crcY genes are transcribed from promoters PcrcZ and PcrcY, respectively, a process that relies on the CbrB transcriptional activator and the RpoN σ factor."

PMID:20080802

Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa.

RpoN and CbrA/CbrB are required for crcZ expression in P. aeruginosa.

"The sigma factor RpoN and the CbrA/CbrB two-component system, which is known to maintain a healthy carbon-nitrogen balance, were necessary for crcZ expression."