fliA

UniProt ID: Q88EW1
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

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.

Existing Annotations Review

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, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” 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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” 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, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-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.
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, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-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.
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, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” 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, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-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**.

Core Functions

FliA is the Sigma-28 flagellar sigma factor that gives RNA polymerase promoter specificity for flagella-related genes and thereby controls transcription initiation.

Molecular Function:
sigma factor activity
Directly Involved In:
DNA-templated transcription initiation regulation of DNA-templated transcription initiation
Cellular Locations:
cytoplasm
Supporting Evidence:
  • file:PSEPK/fliA/fliA-uniprot.txt
    RecName: Full=RNA polymerase sigma factor FliA
  • file:PSEPK/fliA/fliA-uniprot.txt
    Sigma factors are initiation factors that promote the
  • file:PSEPK/fliA/fliA-uniprot.txt
    controls the expression of flagella-related genes
  • file:PSEPK/fliA/fliA-deep-research-falcon.md
    In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.

As the Class III (late-tier) sigma factor in the KT2440 flagellar transcriptional cascade, FliA directs transcription of genes required for flagellar filament synthesis, stator assembly, and chemotaxis, thereby positively driving bacterial-type flagellum biogenesis. Its activity is gated post-translationally by the anti-sigma factor FlgM, which is exported via the flagellar type III secretion system upon hook-basal body completion.

Molecular Function:
sigma factor activity
Directly Involved In:
bacterial-type flagellum assembly
Cellular Locations:
cytoplasm
Supporting Evidence:
  • 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**.
  • file:PSEPK/fliA/fliA-deep-research-falcon.md
    FliA is regulated by the **anti-sigma factor FlgM**, which sequesters FliA until flagellar assembly reaches a checkpoint. In *P. putida*, the “final tier” is triggered when FliA is **released from inactivation by FlgM**, after **FlgM secretion via the flagellar type III secretion system (FT3SS)** upon hook completion.

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000104
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
GO_REF:0000108
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
file:PSEPK/fliA/fliA-uniprot.txt
UniProtKB entry for fliA (RNA polymerase sigma factor FliA)
  • UniProt identifies fliA as RNA polymerase sigma factor FliA and supplies function, pathway, family, location, or GO cross-reference evidence used in this review.
file:PSEPK/fliA/fliA-goa.tsv
QuickGO GOA annotations for fliA
  • The fetched GOA table contains the automated annotations reviewed for fliA.
file:PSEPK/fliA/fliA-deep-research-falcon.md
Falcon (Edison Scientific) deep research report for fliA (P. putida KT2440)
  • The *Pseudomonas putida* KT2440 gene **fliA** encodes **FliA (σ28; sigma-28 / sigma-F)**, an alternative RNA polymerase sigma factor that directs transcription of **late (flagellar/chemotaxis) genes** in the flagellar regulatory cascade.
  • **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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology.
  • In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
  • **Class III:** **FliA-dependent** transcription enables synthesis of the **filament**, at least one **stator** complex, and completion of the **chemotaxis apparatus**.
  • 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**.
  • FliA is regulated by the **anti-sigma factor FlgM**, which sequesters FliA until flagellar assembly reaches a checkpoint. In *P. putida*, the “final tier” is triggered when FliA is **released from inactivation by FlgM**, after **FlgM secretion via the flagellar type III secretion system (FT3SS)** upon hook completion.
  • 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.
  • Leal-Morales et al. (2022) report systematic promoter motif discovery in the KT2440 flagellar cluster, with **21 putative flagellar promoters** and explicit identification of **FliA-dependent promoter motifs** upstream of **fliK2**, **fliC**, and **cheV**, and additional matches upstream of **fliS** and **flgM**.
  • A KT2440 targeted mechanistic study demonstrated that **bifA** (encoding a c-di-GMP phosphodiesterase) is **partly controlled by FliA**:

Suggested Questions for Experts

Q: Which KT2440 flagellar promoters are directly FliA-dependent rather than indirectly affected by the broader flagellar hierarchy?

Suggested Experiments

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

Deep Research

Falcon

(fliA-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 22 citations 2 artifacts 2026-06-01T09:26:38.580137
Edison artifact artifact-00 (text/markdown)
## Context ID: pqac-00000015 The document provides a summary of the flagellar transcriptional hierarchy and promoter motif alignments for *Pseudomonas putida*. (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: fliA (UniProt Q88EW1) in Pseudomonas putida KT2440 (PSEPK)

Executive summary

The Pseudomonas putida KT2440 gene fliA encodes FliA (σ28; sigma-28 / sigma-F), an alternative RNA polymerase sigma factor that directs transcription of late (flagellar/chemotaxis) genes in the flagellar regulatory cascade. In KT2440, FliA is positioned downstream of the master regulator FleQ and σ54 (RpoN) and is activated post-translationally by release from the anti-sigma factor FlgM after hook–basal body completion. Evidence in KT2440 further supports a role for FliA in coupling motility to the second messenger c-di-GMP through partial control of bifA, a c-di-GMP phosphodiesterase important for swimming behavior. (leal‐morales2022transcriptionalorganizationand pages 1-1, leal‐morales2022transcriptionalorganizationand pages 14-14, xiao2017expressionofthe pages 5-7)

1) Key concepts and definitions (current understanding)

1.1 What is FliA?

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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology. (xiao2017expressionofthe pages 4-5, xiao2017expressionofthe pages 5-7)

1.2 Flagellar transcriptional hierarchy in P. putida KT2440

A detailed KT2440 model describes a three-tier transcriptional cascade:
- Class I: fleQ is at the top of the hierarchy. (leal‐morales2022transcriptionalorganizationand pages 1-1)
- Class II: FleQ- and σ54-dependent genes encode most basal body/structural components and regulatory elements including fliA. (leal‐morales2022transcriptionalorganizationand pages 1-1, leal‐morales2022transcriptionalorganizationand media 34a91b68)
- Class III: FliA-dependent transcription enables synthesis of the filament, at least one stator complex, and completion of the chemotaxis apparatus. (leal‐morales2022transcriptionalorganizationand pages 1-1, leal‐morales2022transcriptionalorganizationand media 34a91b68)

Quantitatively, the KT2440 flagellar cluster is reported to contain 59 genes, organized into 11 operons with 22 primary/internal promoters, highlighting extensive transcriptional complexity that FliA participates in at the late tier. (leal‐morales2022transcriptionalorganizationand pages 1-1)

1.3 Anti-sigma factor control (FlgM–FliA module)

FliA is regulated by the anti-sigma factor FlgM, which sequesters FliA until flagellar assembly reaches a checkpoint. In P. putida, the “final tier” is triggered when FliA is released from inactivation by FlgM, after FlgM secretion via the flagellar type III secretion system (FT3SS) upon hook completion. (leal‐morales2022transcriptionalorganizationand pages 14-14)

A 2024 expert review in Pseudomonas further frames this as a conserved mechanism in which hook–basal body completion enables FlgM export and thus FliA activation. (oladosu2024fliptheswitch pages 3-4)

2) Recent developments and latest research (2023–2024 prioritized)

2.1 2024 synthesis of FliA/FlgM logic and target gene examples (authoritative review)

A 2024 review (focused on P. aeruginosa but widely used as a mechanistic reference for pseudomonads) summarizes:
- FliA (RpoF, σ28) drives Class IV flagellar gene expression once released from FlgM. (oladosu2024fliptheswitch pages 3-4)
- It lists representative FliA-dependent genes such as fliC, motAB, and multiple chemotaxis genes (e.g., cheAB, cheW, cheVR, cheYZ) and flgMN. (oladosu2024fliptheswitch pages 3-4)

Although these named targets are from P. aeruginosa, they align with P. putida KT2440’s late-tier role for FliA in completing filament/chemotaxis/stator function and provide an expert-curated framework for interpreting the conserved FliA module. (leal‐morales2022transcriptionalorganizationand pages 1-1, oladosu2024fliptheswitch pages 3-4)

2.2 2023 review: FliA’s integration with broader regulatory networks (cross-species, authoritative)

A 2023 review of P. aeruginosa transcriptional regulators states that σFliA (σ28) controls flagellar biosynthesis genes and is essential for motility, with its activity modulated by FlgM and additional partner-switching layers that interface with global signaling (Rsm-related pathways). (sanchezjimenez2023transcriptionalregulatorscontrolling pages 18-19)

The same review reports transcriptomic evidence in P. aeruginosa that a fliA mutant shows downregulation of multiple secretion-system genes (T2SS/T3SS/T6SS components), suggesting that in some pseudomonads FliA can be a broader node connecting motility and virulence-associated functions. This should be treated as cross-species context rather than KT2440-specific annotation. (sanchezjimenez2023transcriptionalregulatorscontrolling pages 19-21)

3) Functional annotation of P. putida KT2440 fliA: molecular function, processes, and pathways

3.1 Primary molecular function

In KT2440, FliA’s primary molecular function is to function as an RNAP sigma factor that recognizes σ28-type promoters to activate late flagellar/chemotaxis transcription. (leal‐morales2022transcriptionalorganizationand pages 1-1, xiao2017expressionofthe pages 4-5)

3.2 Biological process context: flagellar assembly and chemotaxis

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. (leal‐morales2022transcriptionalorganizationand pages 1-1)

The regulatory logic is consistent with a checkpoint model: completion of the hook triggers secretion of FlgM, which removes inhibition and enables robust transcription of late genes. (leal‐morales2022transcriptionalorganizationand pages 14-14)

3.3 Promoter motifs and direct promoter evidence in KT2440

Leal-Morales et al. (2022) report systematic promoter motif discovery in the KT2440 flagellar cluster, with 21 putative flagellar promoters and explicit identification of FliA-dependent promoter motifs upstream of fliK2, fliC, and cheV, and additional matches upstream of fliS and flgM. (leal‐morales2022transcriptionalorganizationand pages 6-6)

Promoter-motif alignments and the overall transcriptional cascade schematic are shown in the paper’s figures (promoter motif alignments and tiered cascade). (leal‐morales2022transcriptionalorganizationand media ffe1d522, leal‐morales2022transcriptionalorganizationand media 34a91b68)

A KT2440 targeted mechanistic study demonstrated that bifA (encoding a c-di-GMP phosphodiesterase) is partly controlled by FliA:
- fliA deletion caused an approximately twofold decrease in bifA transcription/promoter activity and produced a nonmotile phenotype that could be complemented by fliA expression. (xiao2017expressionofthe pages 4-5, xiao2017expressionofthe pages 1-2)
- 5′-RACE identified two transcription start sites for bifA (at 103 nt and 40 nt upstream of the start codon), with upstream σ70 and σ28 promoter elements, indicating dual control (basal σ70 and enhancing σ28/FliA). (xiao2017expressionofthe pages 5-7)
- Promoter mutagenesis in the σ28 region reduced activity in wild type but not in a fliA mutant, supporting FliA dependence for that promoter component. (xiao2017expressionofthe pages 5-7)

This establishes an experimentally supported mechanistic bridge between the flagellar sigma factor and second-messenger regulation relevant to motility transitions (swimming vs sessility). (xiao2017expressionofthe pages 5-7, xiao2017expressionofthe pages 8-9)

4) Cellular localization and site of action

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. (xiao2017expressionofthe pages 4-5, xiao2017expressionofthe pages 5-7)

Its activity is conditioned by flagellar assembly state via FlgM sequestration and export, a mechanism that ensures late genes are transcribed primarily after assembly has progressed. (leal‐morales2022transcriptionalorganizationand pages 14-14, xiao2017expressionofthe pages 1-2)

5) Relevant statistics and quantitative data (recent/primary)

5.1 Flagellar gene system architecture (KT2440)

  • 59 genes in the flagellar cluster (KT2440). (leal‐morales2022transcriptionalorganizationand pages 1-1)
  • 11 flagellar operons and 22 primary/internal promoters characterized. (leal‐morales2022transcriptionalorganizationand pages 1-1)
  • 21 putative flagellar promoters reported by motif analysis, with assignments to σ54, σ70, and FliA/σ28 classes. (leal‐morales2022transcriptionalorganizationand pages 6-6)

5.2 FliA-dependent promoter evidence and c-di-GMP measurements (KT2440)

  • ~2× decrease in bifA transcription/promoter activity in a ΔfliA mutant. (xiao2017expressionofthe pages 5-7, xiao2017expressionofthe pages 4-5)
  • Two bifA TSS at −103 and −40 nt upstream of start codon, consistent with dual σ70/σ28 promoter architecture. (xiao2017expressionofthe pages 5-7)
  • ~5× increase in bifA promoter activity in an E. coli reporter upon FliA expression (heterologous validation of sigma-dependent activation). (xiao2017expressionofthe pages 5-7)
  • Intracellular c-di-GMP measurements reported: 23.33 pmol/mg protein in WT vs 20.13 pmol/mg in the fliA mutant in the cited assay conditions. (xiao2017expressionofthe pages 5-7)

5.3 Upstream regulator quantitative context (FleQ ChIP-seq)

While not FliA itself, upstream master regulation shapes when fliA is expressed: FleQ ChIP-seq in KT2440 identified 103 putative FleQ binding sites, supporting FleQ as a broad regulator upstream of σ54-dependent class II genes that include fliA. (blancoromero2018genomewideanalysisof pages 1-2)

6) Current applications and real-world implementations

Direct industrial applications of P. putida KT2440 commonly leverage its metabolism and robustness; however, motility control is practically important in environmental and engineered contexts because it affects surface colonization, biofilm formation, and dispersal. In the KT2440 system, FliA is a key transcriptional node controlling late motility outputs and also modulates bifA/c-di-GMP, meaning that perturbing fliA (deletion or overexpression) can be used experimentally to:
- Disable or enhance swimming motility (ΔfliA nonmotile; FliA overexpression enhances swimming in a BifA-dependent manner). (xiao2017expressionofthe pages 4-5, xiao2017expressionofthe pages 8-9)
- Tune expression from σ28 promoters (e.g., engineered reporters or synthetic control elements based on σ28 motifs identified in the flagellar cluster). (leal‐morales2022transcriptionalorganizationand pages 6-6, leal‐morales2022transcriptionalorganizationand media ffe1d522)

These applications are most mature as research and synthetic biology strategies (motility/biofilm tuning and promoter engineering) rather than direct deployed products.

7) Expert analysis and interpretation

  1. Checkpointed transcription ensures cost-effective assembly. The FlgM-mediated sequestration mechanism ties FliA activity to structural completion of the hook–basal body, preventing premature expression of filament/late genes. This is described explicitly for P. putida and synthesized in recent expert reviews for pseudomonads. (leal‐morales2022transcriptionalorganizationand pages 14-14, oladosu2024fliptheswitch pages 3-4)

  2. FliA is a regulatory hub with feedback architecture. In P. putida, FliA promotes expression of flgM (negative feedback) and can drive transcription of upstream regulators (e.g., fleQ and fleSR as part of a larger operon), forming feed-forward/feedback loops that can stabilize a motility program once initiated. (leal‐morales2022transcriptionalorganizationand pages 14-14)

  3. Beyond canonical flagellar genes, FliA can couple motility and second-messenger signaling. In KT2440, FliA partly controls bifA, linking σ28 control to c-di-GMP turnover and swimming behavior. (xiao2017expressionofthe pages 5-7, xiao2017expressionofthe pages 8-9)

Evidence summary table

The following table compiles the most relevant KT2440-specific evidence and recent reviews used to support functional annotation and quantitative claims.

Source Year/date URL / DOI Evidence type Main findings Scope / notes
Leal-Morales et al., Environmental Microbiology Dec 2022 https://doi.org/10.1111/1462-2920.15857 Genetic regulation mapping, promoter architecture, operon analysis In P. putida KT2440, the flagellar cluster contains 59 genes, organized into 11 operons with 22 primary/internal promoters; the system follows a three-tier cascade in which FleQ is Class I, FleQ+σ54 control Class II genes including fliA, and FliA (σ28) activates Class III genes needed for filament synthesis, one stator, and chemotaxis completion (leal‐morales2022transcriptionalorganizationand pages 1-1). Promoter analysis identified 21 putative flagellar promoters overall, including FliA-dependent motifs upstream of fliK2, fliC, cheV, fliS, flgM; σ54-type motifs were found upstream of several earlier flagellar operons (leal‐morales2022transcriptionalorganizationand pages 6-6). The paper also describes FliA as central to feed-forward/feedback control: FliA activates late genes and promotes flgM expression, while hook completion enables FlgM export and FliA release (leal‐morales2022transcriptionalorganizationand pages 14-14, leal‐morales2022transcriptionalorganizationand media 34a91b68). KT2440-specific primary study; strongest source for operon counts, promoter classes, and regulatory hierarchy.
Xiao et al., MicrobiologyOpen Sep 2017 https://doi.org/10.1002/mbo3.402 Genetics, promoter-lacZ assays, 5′-RACE, qRT-PCR, c-di-GMP biochemistry Demonstrated that FliA partly controls bifA expression in P. putida KT2440: fliA deletion lowered bifA transcription about twofold and caused a nonmotile phenotype that was complemented by plasmid-borne fliA (xiao2017expressionofthe pages 4-5, xiao2017expressionofthe pages 1-2). 5′-RACE identified two bifA TSSs at 103 nt and 40 nt upstream of the start codon, with upstream σ70 and σ28 promoter elements; mutation of the σ28 promoter reduced activity, and FliA overexpression in an E. coli reporter increased activity about fivefold (xiao2017expressionofthe pages 5-7). Reported intracellular c-di-GMP values were 23.33 pmol/mg protein in WT vs 20.13 pmol/mg in the fliA mutant; FliA overexpression promoted swimming in a BifA-dependent manner (xiao2017expressionofthe pages 5-7, xiao2017expressionofthe pages 8-9). KT2440-specific primary study; strongest source for direct quantitative phenotypes, dual-promoter architecture at bifA, and c-di-GMP linkage.
Blanco-Romero et al., Scientific Reports Sep 2018 https://doi.org/10.1038/s41598-018-31371-z ChIP-seq, regulon mapping (FleQ) Defined upstream hierarchy around FliA by showing that FleQ is the master regulator of pseudomonad flagellar transcription and identified 103 putative FleQ binding sites in P. putida KT2440. FleQ works with σ54/RpoN to activate multiple early flagellar operons, including loci that feed into the layer containing fliA (blancoromero2018genomewideanalysisof pages 1-2). KT2440-specific primary study, but focuses on FleQ, not direct FliA targets; useful for upstream regulatory context.
Oladosu et al., Journal of Bacteriology Mar 2024 https://doi.org/10.1128/jb.00365-23 Expert review Summarizes authoritative current understanding in pseudomonads: FliA is constitutively expressed but post-translationally sequestered by FlgM; after hook-basal body completion, FlgM export frees FliA, enabling late/class IV transcription such as fliC, fleL, cheAB, motAB, cheW, cheVR, flgMN, cheYZ. The review also highlights integration of the FliA/FlgM module with broader signaling and c-di-GMP-linked lifestyle regulation (oladosu2024fliptheswitch pages 3-4). Cross-species Pseudomonas review centered on P. aeruginosa; used for conserved mechanistic interpretation, not KT2440-specific claims.
Lo et al., PLoS ONE May 2016 https://doi.org/10.1371/journal.pone.0155397 Transcriptomics, reporter assays, phenotype analysis Provides cross-species evidence that FliA regulates more than canonical flagellar genes: in P. aeruginosa, FliA affected expression of phosphodiesterase genes such as PA4367/bifA, linking FliA to c-di-GMP metabolism, swarming, and pigment production. The study also notes that excess FliA can trigger feedback through flgM, supporting careful dosage control of σ28 activity (lo2016regulationofmotility pages 11-14, lo2016regulationofmotility pages 14-15). Cross-species primary study; not KT2440-specific, but supports broader interpretation of FliA as a motility–c-di-GMP network node.

Table: This table compiles the key KT2440-specific and comparative Pseudomonas evidence for FliA (sigma-28), including regulatory hierarchy, promoter architecture, quantitative measurements, and broader expert interpretation. It is useful for separating direct evidence in P. putida KT2440 from conserved mechanisms inferred from related pseudomonads.

Limitations of this report (important)

  • Although the user provided UniProt/InterPro/HAMAP identifiers, this tool environment did not provide direct access to those databases for citable retrieval; therefore, database assertions are not independently cited beyond the user’s provided identity context. Functional annotation was grounded in KT2440 primary literature and authoritative reviews instead. (leal‐morales2022transcriptionalorganizationand pages 1-1, xiao2017expressionofthe pages 4-5)
  • 2023–2024 KT2440-specific primary studies directly centered on fliA were limited in the retrieved corpus; thus, 2023–2024 sources are primarily authoritative reviews and are explicitly labeled as cross-species where applicable. (oladosu2024fliptheswitch pages 3-4, sanchezjimenez2023transcriptionalregulatorscontrolling pages 19-21)

References

  1. (leal‐morales2022transcriptionalorganizationand pages 1-1): Antonio Leal‐Morales, Marta Pulido‐Sánchez, Aroa López‐Sánchez, and Fernando Govantes. Transcriptional organization and regulation of the pseudomonas putida flagellar system. Environmental Microbiology, 24:137-157, Dec 2022. URL: https://doi.org/10.1111/1462-2920.15857, doi:10.1111/1462-2920.15857. This article has 31 citations and is from a domain leading peer-reviewed journal.

  2. (leal‐morales2022transcriptionalorganizationand pages 14-14): Antonio Leal‐Morales, Marta Pulido‐Sánchez, Aroa López‐Sánchez, and Fernando Govantes. Transcriptional organization and regulation of the pseudomonas putida flagellar system. Environmental Microbiology, 24:137-157, Dec 2022. URL: https://doi.org/10.1111/1462-2920.15857, doi:10.1111/1462-2920.15857. This article has 31 citations and is from a domain leading peer-reviewed journal.

  3. (xiao2017expressionofthe pages 5-7): Yujie Xiao, Huizhong Liu, Hailing Nie, Shan Xie, Xuesong Luo, Wenli Chen, and Qiaoyun Huang. Expression of the phosphodiesterase bifa facilitating swimming motility is partly controlled by flia in pseudomonas putida kt2440. MicrobiologyOpen, 6:e00402, Sep 2017. URL: https://doi.org/10.1002/mbo3.402, doi:10.1002/mbo3.402. This article has 16 citations and is from a peer-reviewed journal.

  4. (xiao2017expressionofthe pages 4-5): Yujie Xiao, Huizhong Liu, Hailing Nie, Shan Xie, Xuesong Luo, Wenli Chen, and Qiaoyun Huang. Expression of the phosphodiesterase bifa facilitating swimming motility is partly controlled by flia in pseudomonas putida kt2440. MicrobiologyOpen, 6:e00402, Sep 2017. URL: https://doi.org/10.1002/mbo3.402, doi:10.1002/mbo3.402. This article has 16 citations and is from a peer-reviewed journal.

  5. (leal‐morales2022transcriptionalorganizationand media 34a91b68): Antonio Leal‐Morales, Marta Pulido‐Sánchez, Aroa López‐Sánchez, and Fernando Govantes. Transcriptional organization and regulation of the pseudomonas putida flagellar system. Environmental Microbiology, 24:137-157, Dec 2022. URL: https://doi.org/10.1111/1462-2920.15857, doi:10.1111/1462-2920.15857. This article has 31 citations and is from a domain leading peer-reviewed journal.

  6. (oladosu2024fliptheswitch pages 3-4): Victoria I. Oladosu, Soyoung Park, and Karin Sauer. Flip the switch: the role of fleq in modulating the transition between the free-living and sessile mode of growth in pseudomonas aeruginosa. Journal of Bacteriology, Mar 2024. URL: https://doi.org/10.1128/jb.00365-23, doi:10.1128/jb.00365-23. This article has 27 citations and is from a peer-reviewed journal.

  7. (sanchezjimenez2023transcriptionalregulatorscontrolling pages 18-19): Ana Sánchez-Jiménez, María A. Llamas, and Francisco Javier Marcos-Torres. Transcriptional regulators controlling virulence in pseudomonas aeruginosa. International Journal of Molecular Sciences, 24:11895, Jul 2023. URL: https://doi.org/10.3390/ijms241511895, doi:10.3390/ijms241511895. This article has 64 citations.

  8. (sanchezjimenez2023transcriptionalregulatorscontrolling pages 19-21): Ana Sánchez-Jiménez, María A. Llamas, and Francisco Javier Marcos-Torres. Transcriptional regulators controlling virulence in pseudomonas aeruginosa. International Journal of Molecular Sciences, 24:11895, Jul 2023. URL: https://doi.org/10.3390/ijms241511895, doi:10.3390/ijms241511895. This article has 64 citations.

  9. (leal‐morales2022transcriptionalorganizationand pages 6-6): Antonio Leal‐Morales, Marta Pulido‐Sánchez, Aroa López‐Sánchez, and Fernando Govantes. Transcriptional organization and regulation of the pseudomonas putida flagellar system. Environmental Microbiology, 24:137-157, Dec 2022. URL: https://doi.org/10.1111/1462-2920.15857, doi:10.1111/1462-2920.15857. This article has 31 citations and is from a domain leading peer-reviewed journal.

  10. (leal‐morales2022transcriptionalorganizationand media ffe1d522): Antonio Leal‐Morales, Marta Pulido‐Sánchez, Aroa López‐Sánchez, and Fernando Govantes. Transcriptional organization and regulation of the pseudomonas putida flagellar system. Environmental Microbiology, 24:137-157, Dec 2022. URL: https://doi.org/10.1111/1462-2920.15857, doi:10.1111/1462-2920.15857. This article has 31 citations and is from a domain leading peer-reviewed journal.

  11. (xiao2017expressionofthe pages 1-2): Yujie Xiao, Huizhong Liu, Hailing Nie, Shan Xie, Xuesong Luo, Wenli Chen, and Qiaoyun Huang. Expression of the phosphodiesterase bifa facilitating swimming motility is partly controlled by flia in pseudomonas putida kt2440. MicrobiologyOpen, 6:e00402, Sep 2017. URL: https://doi.org/10.1002/mbo3.402, doi:10.1002/mbo3.402. This article has 16 citations and is from a peer-reviewed journal.

  12. (xiao2017expressionofthe pages 8-9): Yujie Xiao, Huizhong Liu, Hailing Nie, Shan Xie, Xuesong Luo, Wenli Chen, and Qiaoyun Huang. Expression of the phosphodiesterase bifa facilitating swimming motility is partly controlled by flia in pseudomonas putida kt2440. MicrobiologyOpen, 6:e00402, Sep 2017. URL: https://doi.org/10.1002/mbo3.402, doi:10.1002/mbo3.402. This article has 16 citations and is from a peer-reviewed journal.

  13. (blancoromero2018genomewideanalysisof pages 1-2): Esther Blanco-Romero, Miguel Redondo-Nieto, Francisco Martínez-Granero, Daniel Garrido-Sanz, Maria Isabel Ramos-González, Marta Martín, and Rafael Rivilla. Genome-wide analysis of the fleq direct regulon in pseudomonas fluorescens f113 and pseudomonas putida kt2440. Scientific Reports, Sep 2018. URL: https://doi.org/10.1038/s41598-018-31371-z, doi:10.1038/s41598-018-31371-z. This article has 64 citations and is from a peer-reviewed journal.

  14. (lo2016regulationofmotility pages 11-14): Yi-Ling Lo, Lunda Shen, Chih-Hsuan Chang, Manish Bhuwan, Cheng-Hsun Chiu, and Hwan-You Chang. Regulation of motility and phenazine pigment production by flia is cyclic-di-gmp dependent in pseudomonas aeruginosa pao1. PLoS ONE, 11:e0155397, May 2016. URL: https://doi.org/10.1371/journal.pone.0155397, doi:10.1371/journal.pone.0155397. This article has 46 citations and is from a peer-reviewed journal.

  15. (lo2016regulationofmotility pages 14-15): Yi-Ling Lo, Lunda Shen, Chih-Hsuan Chang, Manish Bhuwan, Cheng-Hsun Chiu, and Hwan-You Chang. Regulation of motility and phenazine pigment production by flia is cyclic-di-gmp dependent in pseudomonas aeruginosa pao1. PLoS ONE, 11:e0155397, May 2016. URL: https://doi.org/10.1371/journal.pone.0155397, doi:10.1371/journal.pone.0155397. This article has 46 citations and is from a peer-reviewed journal.

Artifacts

Citations

  1. oladosu2024fliptheswitch pages 3-4
  2. sanchezjimenez2023transcriptionalregulatorscontrolling pages 18-19
  3. sanchezjimenez2023transcriptionalregulatorscontrolling pages 19-21
  4. xiao2017expressionofthe pages 5-7
  5. blancoromero2018genomewideanalysisof pages 1-2
  6. xiao2017expressionofthe pages 4-5
  7. xiao2017expressionofthe pages 1-2
  8. xiao2017expressionofthe pages 8-9
  9. lo2016regulationofmotility pages 11-14
  10. lo2016regulationofmotility pages 14-15
  11. ing
  12. https://doi.org/10.1111/1462-2920.15857
  13. https://doi.org/10.1002/mbo3.402
  14. https://doi.org/10.1038/s41598-018-31371-z
  15. https://doi.org/10.1128/jb.00365-23
  16. https://doi.org/10.1371/journal.pone.0155397
  17. https://doi.org/10.1111/1462-2920.15857,
  18. https://doi.org/10.1002/mbo3.402,
  19. https://doi.org/10.1128/jb.00365-23,
  20. https://doi.org/10.3390/ijms241511895,
  21. https://doi.org/10.1038/s41598-018-31371-z,
  22. https://doi.org/10.1371/journal.pone.0155397,

📚 Additional Documentation

Notes

(fliA-notes.md)

fliA review notes

Description cleanup note

The YAML description field was revised to keep it as a standalone biological summary. Project-specific curation framing moved here instead.

  • Moved out of the YAML description: curation should emphasize sigma factor activity and transcription initiation rather than RNA polymerase catalytic activity.

📄 View Raw YAML

 
id: Q88EW1
gene_symbol: fliA
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
  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.
existing_annotations:
- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0016987 captures promoter-specific sigma-factor function better than generic DNA binding.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: RNA polymerase sigma factor FliA
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0003677\tDNA binding"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- term:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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.
    action: MODIFY
    reason: Replace the broad transcription-factor term with the specific sigma factor molecular function.
    proposed_replacement_terms:
    - id: GO:0016987
      label: sigma factor activity
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: RNA polymerase sigma factor FliA
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: Belongs to the sigma-70 factor family. FliA subfamily.
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        **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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology.
- term:
    id: GO:0003899
    label: DNA-directed RNA polymerase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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.
    action: REMOVE
    reason: RNA polymerase catalytic activity belongs to the core polymerase complex, whereas FliA provides promoter specificity.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: Sigma factors are initiation factors that promote the
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0003899\tDNA-directed RNA polymerase activity"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        **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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This location annotation is appropriate for a bacterial sigma factor that associates with cytoplasmic RNA polymerase.
    action: ACCEPT
    reason: UniProt places FliA in the cytoplasm.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0005737\tcytoplasm"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        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.
- term:
    id: GO:0006352
    label: DNA-templated transcription initiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This is a core process annotation. Sigma factors act at transcription initiation by directing RNA polymerase to specific promoters.
    action: ACCEPT
    reason: FliA controls initiation at flagella-related promoters.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: Sigma factors are initiation factors that promote the
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0006352\tDNA-templated transcription initiation"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- term:
    id: GO:0006355
    label: regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This broad transcription-regulation term is directionally correct but less informative than the initiation-specific process term already present.
    action: MODIFY
    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_replacement_terms:
    - id: GO:2000142
      label: regulation of DNA-templated transcription initiation
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: controls the expression of flagella-related genes
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0006355\tregulation of DNA-templated transcription"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- term:
    id: GO:0010468
    label: regulation of gene expression
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: Regulation of gene expression is too broad for FliA. The direct process is regulation of transcription initiation through sigma-factor promoter recognition.
    action: MODIFY
    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_replacement_terms:
    - id: GO:2000142
      label: regulation of DNA-templated transcription initiation
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: controls the expression of flagella-related genes
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0010468\tregulation of gene expression"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- term:
    id: GO:0016987
    label: sigma factor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: ACCEPT
    reason: Sigma factor activity captures FliA promoter-specificity function.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: 'RecName: Full=RNA polymerase sigma factor FliA'
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: Belongs to the sigma-70 factor family. FliA subfamily.
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:0016987\tsigma factor activity"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        **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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology.
- term:
    id: GO:2000142
    label: regulation of DNA-templated transcription initiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    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.
    action: ACCEPT
    reason: The logical inference from sigma factor activity to regulation of transcription initiation is biologically appropriate.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
      supporting_text: Sigma factors are initiation factors that promote the
    - reference_id: file:PSEPK/fliA/fliA-goa.tsv
      supporting_text: "GO:2000142\tregulation of DNA-templated transcription initiation"
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- term:
    id: GO:0044780
    label: bacterial-type flagellum assembly
  evidence_type: IEA
  review:
    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.
    action: NEW
    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.
    supported_by:
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        **Class III:** **FliA-dependent** transcription enables synthesis of the **filament**, at least one **stator** complex, and completion of the **chemotaxis apparatus**.
    - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
      supporting_text: |-
        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**.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:PSEPK/fliA/fliA-uniprot.txt
  title: UniProtKB entry for fliA (RNA polymerase sigma factor FliA)
  findings:
  - statement: UniProt identifies fliA as RNA polymerase sigma factor FliA and supplies function, pathway, family, location, or GO cross-reference evidence used in this review.
- id: file:PSEPK/fliA/fliA-goa.tsv
  title: QuickGO GOA annotations for fliA
  findings:
  - statement: The fetched GOA table contains the automated annotations reviewed for fliA.
- id: file:PSEPK/fliA/fliA-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report for fliA (P. putida KT2440)
  findings:
  - statement: |-
      The *Pseudomonas putida* KT2440 gene **fliA** encodes **FliA (σ28; sigma-28 / sigma-F)**, an alternative RNA polymerase sigma factor that directs transcription of **late (flagellar/chemotaxis) genes** in the flagellar regulatory cascade.
  - statement: |-
      **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 “conferr[ing] promoter-recognition specificity to core RNA polymerase (RNAP),” consistent with sigma-factor biology.
  - statement: |-
      In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
  - statement: |-
      **Class III:** **FliA-dependent** transcription enables synthesis of the **filament**, at least one **stator** complex, and completion of the **chemotaxis apparatus**.
  - statement: |-
      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**.
  - statement: |-
      FliA is regulated by the **anti-sigma factor FlgM**, which sequesters FliA until flagellar assembly reaches a checkpoint. In *P. putida*, the “final tier” is triggered when FliA is **released from inactivation by FlgM**, after **FlgM secretion via the flagellar type III secretion system (FT3SS)** upon hook completion.
  - statement: |-
      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.
  - statement: |-
      Leal-Morales et al. (2022) report systematic promoter motif discovery in the KT2440 flagellar cluster, with **21 putative flagellar promoters** and explicit identification of **FliA-dependent promoter motifs** upstream of **fliK2**, **fliC**, and **cheV**, and additional matches upstream of **fliS** and **flgM**.
  - statement: |-
      A KT2440 targeted mechanistic study demonstrated that **bifA** (encoding a c-di-GMP phosphodiesterase) is **partly controlled by FliA**:
core_functions:
- description: FliA is the Sigma-28 flagellar sigma factor that gives RNA polymerase promoter specificity for flagella-related genes and thereby controls transcription initiation.
  molecular_function:
    id: GO:0016987
    label: sigma factor activity
  directly_involved_in:
  - id: GO:0006352
    label: DNA-templated transcription initiation
  - id: GO:2000142
    label: regulation of DNA-templated transcription initiation
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
    supporting_text: 'RecName: Full=RNA polymerase sigma factor FliA'
  - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
    supporting_text: Sigma factors are initiation factors that promote the
  - reference_id: file:PSEPK/fliA/fliA-uniprot.txt
    supporting_text: controls the expression of flagella-related genes
  - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
    supporting_text: |-
      In KT2440, FliA’s **primary molecular function** is to function as an **RNAP sigma factor** that recognizes **σ28-type promoters** to activate late flagellar/chemotaxis transcription.
- description: As the Class III (late-tier) sigma factor in the KT2440 flagellar transcriptional cascade, FliA directs transcription of genes required for flagellar filament synthesis, stator assembly, and chemotaxis, thereby positively driving bacterial-type flagellum biogenesis. Its activity is gated post-translationally by the anti-sigma factor FlgM, which is exported via the flagellar type III secretion system upon hook-basal body completion.
  molecular_function:
    id: GO:0016987
    label: sigma factor activity
  directly_involved_in:
  - id: GO:0044780
    label: bacterial-type flagellum assembly
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
    supporting_text: |-
      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**.
  - reference_id: file:PSEPK/fliA/fliA-deep-research-falcon.md
    supporting_text: |-
      FliA is regulated by the **anti-sigma factor FlgM**, which sequesters FliA until flagellar assembly reaches a checkpoint. In *P. putida*, the “final tier” is triggered when FliA is **released from inactivation by FlgM**, after **FlgM secretion via the flagellar type III secretion system (FT3SS)** upon hook completion.
proposed_new_terms: []
suggested_questions:
- question: Which KT2440 flagellar promoters are directly FliA-dependent rather than indirectly affected by the broader flagellar hierarchy?
suggested_experiments:
- hypothesis: FliA directly activates a defined late flagellar promoter set in KT2440.
  description: Compare RNA-seq and promoter-reporter activity in wild-type, fliA deletion, and complemented strains during flagellar gene induction.
  experiment_type: transcriptomics and promoter reporter analysis