FliA is the alternative sigma factor that directs RNA polymerase to late flagellar promoters in Pseudomonas putida KT2440. It controls filament production and other late motility functions. FliA also promotes transcription of the phosphodiesterase gene bifA, providing feedback between flagellar gene expression, c-di-GMP levels and swimming. Its activity is expected to be restrained by the anti-sigma factor FlgM until the flagellar export checkpoint is reached.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: FliA supplies promoter specificity as the sigma subunit of RNA polymerase. Reason: DNA recognition is true in the RNA-polymerase holoenzyme. Refine the generic DNA-binding term to the supported sigma-factor activity; lack of autonomous DNA binding is not evidence against promoter recognition. Proposed replacements: sigma factor activity Supporting Evidence: file:PSEPK/fliA/fliA-uniprot.txt Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. |
| 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-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-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-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-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-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 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: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-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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