fleQ

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000976 transcription cis-regulatory region binding	IMP PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	TOO GENERAL	Summary: CollecTF rows for binding at transcription cis-regulatory regions. Correct; the more specific GO:0000987 (is_a GO:0000976) is accepted on the IDA and IBA rows. Reason: Entailed by GO:0000987, accepted elsewhere in this review. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0000976 transcription cis-regulatory region binding	IMP PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	TOO GENERAL	Summary: CollecTF rows for binding at transcription cis-regulatory regions. Correct; the more specific GO:0000987 (is_a GO:0000976) is accepted on the IDA and IBA rows. Reason: Entailed by GO:0000987, accepted elsewhere in this review. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0000976 transcription cis-regulatory region binding	IPI PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	TOO GENERAL	Summary: CollecTF rows for binding at transcription cis-regulatory regions. Correct; the more specific GO:0000987 (is_a GO:0000976) is accepted on the IDA and IBA rows. Reason: Entailed by GO:0000987, accepted elsewhere in this review. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0000976 transcription cis-regulatory region binding	IPI PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	TOO GENERAL	Summary: CollecTF rows for binding at transcription cis-regulatory regions. Correct; the more specific GO:0000987 (is_a GO:0000976) is accepted on the IDA and IBA rows. Reason: Entailed by GO:0000987, accepted elsewhere in this review. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0000987 cis-regulatory region sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: IBA from PTN000787214 (cis-regulatory region sequence-specific DNA binding), seeded by FleQ (PseudoCAP IDA) and by E. coli GlrR, FhlA and NorR (EcoCyc IDA). The node term suits the clade. Reason: FleQ binds specific sites at flagellar and pel promoters. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:22581773 FleQ binds to two sites called box 1 and 2.
GO:0000987 cis-regulatory region sequence-specific DNA binding	IDA PMID:18485075 Identification of FleQ from Pseudomonas aeruginosa as a c-di...	ACCEPT	Summary: PseudoCAP IDA and one of the four seeds of the PTN000787214 IBD. Gel-shift assays show purified FleQ binding pel promoter DNA, and the binding is inhibited by c-di-GMP. Reason: Sound seed: direct in vitro binding of purified FleQ to a promoter region it regulates. Supporting Evidence: PMID:18485075 FleQ binds to pel promoter DNA and that this binding is inhibited by c-di-GMP.
GO:0001216 DNA-binding transcription activator activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA from the PTN000787214 IBD, seeded by FleQ itself (PseudoCAP and CollecTF), X. campestris FleQ, P. aeruginosa CbrB, V. cholerae FlrA (VC_2135) and VC_0665, and Geobacter GnfM (CollecTF IMP/IPI). FleQ in its own WITH/FROM is expected. The term suits a clade of sigma-54 enhancer-binding proteins. Reason: FleQ activates class II flagellar promoters and the pelA promoter (box 1) by binding cis-regulatory DNA. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0001216 DNA-binding transcription activator activity	IMP PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	ACCEPT	Summary: Direct evidence that FleQ is a DNA-binding transcriptional activator: binding to defined enhancer sites at flagellar promoters and at pelA box 1, with mutation of the sites abolishing activation in vivo. Reason: Core activity, supported by binding and promoter-mutant fusion data. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:12218010 Mutagenesis of the FleQ binding site in the flhA promoter confirmed its functionality in vivo. PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0001216 DNA-binding transcription activator activity	IMP PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	ACCEPT	Summary: PseudoCAP IMP and one of the six seeds of the PTN000787214 IBD (DNA-binding transcription activator activity). The full text shows by footprinting that FleQ binds box 1 and box 2 of the pelA promoter, and box-mutant pelA-lacZ fusions in fleQ and fleN backgrounds show that FleQ activates expression from box 1 in response to c-di-GMP. Reason: Sound seed. Binding to the site plus loss of activation when the site or fleQ is mutated is direct evidence for DNA-binding activator activity. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP. PMID:22581773 FleQ binds to two sites called box 1 and 2.
GO:0001216 DNA-binding transcription activator activity	IPI PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	ACCEPT	Summary: Direct evidence that FleQ is a DNA-binding transcriptional activator: binding to defined enhancer sites at flagellar promoters and at pelA box 1, with mutation of the sites abolishing activation in vivo. Reason: Core activity, supported by binding and promoter-mutant fusion data. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:12218010 Mutagenesis of the FleQ binding site in the flhA promoter confirmed its functionality in vivo. PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0001216 DNA-binding transcription activator activity	IPI PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	ACCEPT	Summary: Direct evidence that FleQ is a DNA-binding transcriptional activator: binding to defined enhancer sites at flagellar promoters and at pelA box 1, with mutation of the sites abolishing activation in vivo. Reason: Core activity, supported by binding and promoter-mutant fusion data. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:12218010 Mutagenesis of the FleQ binding site in the flhA promoter confirmed its functionality in vivo. PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0001217 DNA-binding transcription repressor activity	IMP PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	ACCEPT	Summary: FleQ represses pelA transcription from box 2 in the absence of c-di-GMP; DNA binding at the site and box-mutant fusions support repressor activity. Reason: Second core activity of FleQ at the pel promoter. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP. PMID:18485075 FleQ binds to pel promoter DNA and that this binding is inhibited by c-di-GMP.
GO:0001217 DNA-binding transcription repressor activity	IPI PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	ACCEPT	Summary: FleQ represses pelA transcription from box 2 in the absence of c-di-GMP; DNA binding at the site and box-mutant fusions support repressor activity. Reason: Second core activity of FleQ at the pel promoter. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP. PMID:18485075 FleQ binds to pel promoter DNA and that this binding is inhibited by c-di-GMP.
GO:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO from the sigma-54 interaction domain. FleQ has ATPase activity and a perfectly conserved Walker A motif, and c-di-GMP competes with ATP at that site. Reason: ATP binding and hydrolysis by the AAA+ domain are part of the enhancer-binding protein mechanism, and the c-di-GMP data place ATP at the Walker A site. Supporting Evidence: PMID:24167275 a relatively low concentration of c-di-GMP competitively inhibited FleQ ATPase activity PMID:24167275 a FleQ Walker A motif mutant failed to bind c-di-GMP
GO:0006351 DNA-templated transcription	IDA PMID:9287015 A transcriptional activator, FleQ, regulates mucin adhesion ...	MODIFY	Summary: PseudoCAP IDA to DNA-templated transcription itself. The paper (abstract) shows FleQ- and RpoN-dependent fleSR promoter activity, which is regulation of transcription by an activator, not the transcription process carried out by RNA polymerase. Reason: By GO practice transcription factors are annotated to regulation of transcription. The evidence supports GO:0045893 positive regulation of DNA-templated transcription, which the gene already carries. Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: PMID:9287015 Promoter fusion experiments showed that the fleSR operon was regulated by RpoN and FleQ.
GO:0006355 regulation of DNA-templated transcription	IDA PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	TOO GENERAL	Summary: Regulation of transcription. Correct; positive (GO:0045893) and negative (GO:0045892) regulation are both accepted in this review. Reason: Entailed by GO:0045893 and GO:0045892 (both is_a GO:0006355), accepted elsewhere. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	TOO GENERAL	Summary: Regulation of transcription. Correct; positive (GO:0045893) and negative (GO:0045892) regulation are both accepted in this review. Reason: Entailed by GO:0045893 and GO:0045892 (both is_a GO:0006355), accepted elsewhere. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:0010811 positive regulation of cell-substrate adhesion	IMP PMID:9287015 A transcriptional activator, FleQ, regulates mucin adhesion ...	KEEP AS NON CORE	Summary: fleQ insertion mutant loses mucin adhesion and motility, restored by complementation. Mucin adhesion of P. aeruginosa depends on flagellar components, so this is a downstream consequence of FleQ's control of flagellar genes. Reason: Real but indirect phenotype of the flagellar regulator. Supporting Evidence: PMID:9287015 A chromosomal insertional mutation in the fleQ gene abolished mucin adhesion and motility of P. aeruginosa PAK and PAK-NP.
GO:0032993 protein-DNA complex	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: IBA from PTN000787214, seeded by the same CollecTF and PseudoCAP set as the activator activity. The node term holds for DNA-bound enhancer-binding proteins. Reason: Consistent with the experimental rows; non-core restatement of DNA binding. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0032993 protein-DNA complex	IMP PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	KEEP AS NON CORE	Summary: FleQ bound at its promoter sites forms a protein-DNA complex (gel shift, footprinting). Reason: True but it restates the DNA-binding activity rather than adding a location of function. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0032993 protein-DNA complex	IMP PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	KEEP AS NON CORE	Summary: FleQ bound at its promoter sites forms a protein-DNA complex (gel shift, footprinting). Reason: True but it restates the DNA-binding activity rather than adding a location of function. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0032993 protein-DNA complex	IPI PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	KEEP AS NON CORE	Summary: FleQ bound at its promoter sites forms a protein-DNA complex (gel shift, footprinting). Reason: True but it restates the DNA-binding activity rather than adding a location of function. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0032993 protein-DNA complex	IPI PMID:22581773 The FleQ protein from Pseudomonas aeruginosa functions as bo...	KEEP AS NON CORE	Summary: FleQ bound at its promoter sites forms a protein-DNA complex (gel shift, footprinting). Reason: True but it restates the DNA-binding activity rather than adding a location of function. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0035438 cyclic-di-GMP binding	IDA PMID:18485075 Identification of FleQ from Pseudomonas aeruginosa as a c-di...	ACCEPT	Summary: FleQ binds radiolabelled c-di-GMP in vitro, and a Walker A mutant fails to bind it; c-di-GMP competitively inhibits FleQ ATPase. Reason: Direct binding data; c-di-GMP binding is how FleQ senses the second messenger. Supporting Evidence: PMID:18485075 FleQ binds radiolabelled c-di-GMP in vitro. PMID:24167275 a FleQ Walker A motif mutant failed to bind c-di-GMP
GO:0035438 cyclic-di-GMP binding	IPI PMID:24167275 Cyclic diguanosine monophosphate represses bacterial flagell...	ACCEPT	Summary: FleQ binds radiolabelled c-di-GMP in vitro, and a Walker A mutant fails to bind it; c-di-GMP competitively inhibits FleQ ATPase. Reason: Direct binding data; c-di-GMP binding is how FleQ senses the second messenger. Supporting Evidence: PMID:18485075 FleQ binds radiolabelled c-di-GMP in vitro. PMID:24167275 a FleQ Walker A motif mutant failed to bind c-di-GMP
GO:0043565 sequence-specific DNA binding	IEA GO_REF:0000002	TOO GENERAL	Summary: InterPro2GO from the Fis-type HTH. Correct; GO:0000987 (is_a GO:0043565) is accepted. Reason: Entailed by GO:0000987. Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding.
GO:0045892 negative regulation of DNA-templated transcription	IEA GO_REF:0000108	ACCEPT	Summary: Inter-ontology inference from the repressor activity row. FleQ represses pelA transcription without c-di-GMP. Reason: Follows from the accepted repressor activity. Supporting Evidence: PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP. PMID:18485075 FleQ binds to pel promoter DNA and that this binding is inhibited by c-di-GMP.
GO:0045893 positive regulation of DNA-templated transcription	IBA GO_REF:0000033	ACCEPT	Summary: IBA from PTN000787214 (positive regulation of DNA-templated transcription), seeded by ten experimental annotations (EcoCyc GlrR, PspF, RtcR, PrpR, AtoC; CollecTF; PseudoCAP AlgB). FleQ activates flagellar and pel transcription. Reason: Consistent with the activator activity; the node assessment is in the notes. Supporting Evidence: PMID:14617143 Class II genes including fleSR, encoding a two-component regulatory system require FleQ and RpoN (sigma54) for their transcriptional activation. PMID:22581773 FleQ acts as a repressor in the absence of c-di-GMP and as an activator in the presence of c-di-GMP.
GO:1901202 negative regulation of extracellular matrix assembly	IMP PMID:18485075 Identification of FleQ from Pseudomonas aeruginosa as a c-di...	KEEP AS NON CORE	Summary: FleQ represses pel exopolysaccharide transcription in vivo, relieved by c-di-GMP. The effect on matrix assembly is through transcription of the pel genes. Reason: Indirect, transcriptional effect on EPS matrix production; the core activity is captured by the repressor and DNA-binding terms. Supporting Evidence: PMID:18485075 FleQ binds to pel promoter DNA and that this binding is inhibited by c-di-GMP.
GO:1902021 regulation of bacterial-type flagellum-dependent cell motility	IMP PMID:14617143 A four-tiered transcriptional regulatory circuit controls fl...	ACCEPT	Summary: fleQ mutants are non-motile and FleQ heads the flagellar transcription hierarchy. Reason: FleQ is the master regulator of flagellar genes; regulation of flagellum-dependent motility is its main biological role. Supporting Evidence: PMID:9287015 A chromosomal insertional mutation in the fleQ gene abolished mucin adhesion and motility of P. aeruginosa PAK and PAK-NP. PMID:14617143 Class II genes including fleSR, encoding a two-component regulatory system require FleQ and RpoN (sigma54) for their transcriptional activation.
GO:1902021 regulation of bacterial-type flagellum-dependent cell motility	IMP PMID:9287015 A transcriptional activator, FleQ, regulates mucin adhesion ...	ACCEPT	Summary: fleQ mutants are non-motile and FleQ heads the flagellar transcription hierarchy. Reason: FleQ is the master regulator of flagellar genes; regulation of flagellum-dependent motility is its main biological role. Supporting Evidence: PMID:9287015 A chromosomal insertional mutation in the fleQ gene abolished mucin adhesion and motility of P. aeruginosa PAK and PAK-NP. PMID:14617143 Class II genes including fleSR, encoding a two-component regulatory system require FleQ and RpoN (sigma54) for their transcriptional activation.
GO:2000155 positive regulation of cilium-dependent cell motility	IMP PMID:12218010 FleQ, the major flagellar gene regulator in Pseudomonas aeru...	MODIFY	Summary: PseudoCAP IMP to positive regulation of cilium-dependent cell motility. GO:2000155 has an only_in_taxon Eukaryota constraint (checked in QuickGO, 2026-11-05): cilia are eukaryotic organelles. The paper concerns FleQ activation of bacterial flagellar gene promoters. Reason: Wrong organelle term for a bacterium. The evidence (FleQ binding to and activating flhA, fliE, fliL and fleSR promoters, with the flhA site needed in vivo) supports GO:1902210 positive regulation of bacterial-type flagellum assembly. Proposed replacements: positive regulation of bacterial-type flagellum assembly Supporting Evidence: PMID:12218010 Direct interaction of FleQ with flhA , fliE , fliL , and fleSR promoters was demonstrated by gel shift assay, along with experiments to conclusively determine the specificity of its binding. PMID:12218010 Mutagenesis of the FleQ binding site in the flhA promoter confirmed its functionality in vivo.

Gene Description

Existing Annotations Review

Core Functions

Sigma-54-dependent enhancer-binding transcriptional activator of the class II flagellar genes, binding enhancer sites at their promoters.

c-di-GMP-responsive repressor/activator of the pel exopolysaccharide operon: represses pelA from box 2 without c-di-GMP and activates from box 1 when c-di-GMP is bound.

Binds c-di-GMP at its Walker A ATP site, which inhibits its ATPase and modulates its transcriptional output.

References

Suggested Questions for Experts

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Notes

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