fliA encodes the flagellar alternative sigma factor Sigma-28 in Pseudomonas putida KT2440. It confers promoter specificity on RNA polymerase for flagella-related genes, so its core biological role is sigma factor activity and transcription initiation rather than RNA polymerase catalytic activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: DNA binding is not entirely wrong for a sigma factor-containing holoenzyme, but it is too generic as a standalone description of FliA. The precise molecular function is sigma factor activity. Reason: GO:0016987 captures promoter-specific sigma-factor function better than generic DNA binding. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt RNA polymerase sigma factor FliA file:PSEPK/fliA/fliA-goa.tsv GO:0003677 DNA binding file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440, FliAβs **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **Ο28-type promoters** to activate late flagellar/chemotaxis transcription. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: FliA is a transcription regulatory factor, but the generic DNA-binding transcription factor term is less precise than sigma factor activity for a bacterial RNA polymerase sigma subunit. Reason: Replace the broad transcription-factor term with the specific sigma factor molecular function. Proposed replacements: sigma factor activity Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt RNA polymerase sigma factor FliA file:PSEPK/fliA/fliA-uniprot.txt Belongs to the sigma-70 factor family. FliA subfamily. file:PSEPK/fliA/fliA-deep-research-falcon.md **FliA is an alternative sigma factor** that binds core RNA polymerase (RNAP) to alter promoter recognition specificity. In *P. putida* KT2440, this is explicitly described as FliA βconferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),β consistent with sigma-factor biology. |
| GO:0003899 DNA-directed RNA polymerase activity | IEA GO_REF:0000002 | REMOVE | Summary: This annotation should be removed. FliA is a sigma factor that helps RNA polymerase initiate at flagellar promoters; it is not the catalytic RNA polymerase enzyme. Reason: RNA polymerase catalytic activity belongs to the core polymerase complex, whereas FliA provides promoter specificity. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt Sigma factors are initiation factors that promote the file:PSEPK/fliA/fliA-goa.tsv GO:0003899 DNA-directed RNA polymerase activity file:PSEPK/fliA/fliA-deep-research-falcon.md **FliA is an alternative sigma factor** that binds core RNA polymerase (RNAP) to alter promoter recognition specificity. In *P. putida* KT2440, this is explicitly described as FliA βconferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),β consistent with sigma-factor biology. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: This location annotation is appropriate for a bacterial sigma factor that associates with cytoplasmic RNA polymerase. Reason: UniProt places FliA in the cytoplasm. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm file:PSEPK/fliA/fliA-goa.tsv GO:0005737 cytoplasm file:PSEPK/fliA/fliA-deep-research-falcon.md FliA is not a secreted or membrane-embedded protein; it functions by **associating with cytosolic RNAP** and acting at **chromosomal promoters**. KT2440 literature describes FliA as conferring promoter specificity to core RNAP, implying its functional localization is the cytosol/nucleoid region where RNAP-DNA transcription occurs. |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000120 | ACCEPT | Summary: This is a core process annotation. Sigma factors act at transcription initiation by directing RNA polymerase to specific promoters. Reason: FliA controls initiation at flagella-related promoters. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt Sigma factors are initiation factors that promote the file:PSEPK/fliA/fliA-goa.tsv GO:0006352 DNA-templated transcription initiation file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440, FliAβs **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **Ο28-type promoters** to activate late flagellar/chemotaxis transcription. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | MODIFY | Summary: This broad transcription-regulation term is directionally correct but less informative than the initiation-specific process term already present. Reason: GO:2000142 is already present and ACCEPTED in this review; this MODIFY means the broad parent term should be dropped in favor of the existing initiation-specific term. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt controls the expression of flagella-related genes file:PSEPK/fliA/fliA-goa.tsv GO:0006355 regulation of DNA-templated transcription file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440, FliAβs **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **Ο28-type promoters** to activate late flagellar/chemotaxis transcription. |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000104 | MODIFY | Summary: Regulation of gene expression is too broad for FliA. The direct process is regulation of transcription initiation through sigma-factor promoter recognition. Reason: GO:2000142 is already present and ACCEPTED in this review; this MODIFY removes a redundant high-level gene-expression parent in favor of the existing initiation-specific term. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt controls the expression of flagella-related genes file:PSEPK/fliA/fliA-goa.tsv GO:0010468 regulation of gene expression file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440, FliAβs **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **Ο28-type promoters** to activate late flagellar/chemotaxis transcription. |
| GO:0016987 sigma factor activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the correct core molecular function for FliA. The protein is explicitly annotated as an RNA polymerase sigma factor and a sigma-70 family FliA subfamily member. Reason: Sigma factor activity captures FliA promoter-specificity function. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt RecName: Full=RNA polymerase sigma factor FliA file:PSEPK/fliA/fliA-uniprot.txt Belongs to the sigma-70 factor family. FliA subfamily. file:PSEPK/fliA/fliA-goa.tsv GO:0016987 sigma factor activity file:PSEPK/fliA/fliA-deep-research-falcon.md **FliA is an alternative sigma factor** that binds core RNA polymerase (RNAP) to alter promoter recognition specificity. In *P. putida* KT2440, this is explicitly described as FliA βconferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),β consistent with sigma-factor biology. |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: This is the best specific regulatory process term in the current annotation set. FliA regulates transcription at initiation by directing RNA polymerase to flagellar promoters. Reason: The logical inference from sigma factor activity to regulation of transcription initiation is biologically appropriate. Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt Sigma factors are initiation factors that promote the file:PSEPK/fliA/fliA-goa.tsv GO:2000142 regulation of DNA-templated transcription initiation file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440, FliAβs **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **Ο28-type promoters** to activate late flagellar/chemotaxis transcription. |
| GO:0044780 bacterial-type flagellum assembly | IEA | NEW | Summary: As the Class III (late-tier) flagellar sigma factor, FliA directs transcription of the genes that build the flagellar filament, a stator complex, and the chemotaxis apparatus, so it is functionally involved in completing bacterial-type flagellum assembly. This process is absent from the current IEA-only annotation set but is well supported by KT2440 primary literature summarized in the falcon deep research. Reason: KT2440 primary literature places FliA at the late tier of the flagellar cascade, where its transcriptional output completes filament, stator, and chemotaxis biogenesis; this flagellum-assembly process role complements the molecular sigma factor function and is not captured by the existing transcription-centric terms. Supporting Evidence: file:PSEPK/fliA/fliA-deep-research-falcon.md **Class III:** **FliA-dependent** transcription enables synthesis of the **filament**, at least one **stator** complex, and completion of the **chemotaxis apparatus**. file:PSEPK/fliA/fliA-deep-research-falcon.md In KT2440 the late output of FliA activity is explicitly described: **filament synthesis**, activation of at least one **stator complex**, and completion of the **chemotaxis apparatus**. |
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Download this section (compressed HTML)Q: Which KT2440 flagellar promoters are directly FliA-dependent rather than indirectly affected by the broader flagellar hierarchy?
Experiment: Compare RNA-seq and promoter-reporter activity in wild-type, fliA deletion, and complemented strains during flagellar gene induction.
Hypothesis: FliA directly activates a defined late flagellar promoter set in KT2440.
Type: transcriptomics and promoter reporter analysis
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Download this section (compressed HTML)The YAML description field was revised to keep it as a standalone biological summary. Project-specific curation framing moved here instead.
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