Ferric uptake regulation protein Fur1 (VPARA_18200, A0A0H2M8T9; synonym fur) in Variovorax paradoxus strain TBEA6 is a 139-amino-acid cytosolic homodimeric metalloregulator of the Fur family (NCBIfam NF006999, Pfam PF01475, InterPro IPR002481, PANTHER PTHR33202:SF2) encoded on genomic contig JZWI01000008 (EMBL KLN57112.1). Fur1 comprises an N-terminal winged-helix DNA-binding domain (Gene3D 1.10.10.10, InterPro IPR036388) and a C-terminal dimerization and metal-binding domain (InterPro IPR043135) housing two distinct metal-coordination sites per monomer: a structural Zn(2+) site coordinated by four conserved cysteines at Cys92, Cys95 (92-CTSC-95), Cys132, and Cys135 (132-CGDC-135; PIRSR PIRSR602481-1), and a regulatory Fe(2+) (or Mn(2+)) sensing site coordinated by His86, Asp88 (within 85-THHDH-89), Glu107, and His124 (PIRSR PIRSR602481-2). Under iron-replete conditions, Fe(2+)-loaded holo-Fur1 binds conserved Fur-box operator sequences in target promoters and acts as a transcriptional repressor of iron-acquisition and siderophore biosynthesis/import genes, whereas iron limitation demetallates the regulatory site and derepresses siderophore-mediated iron uptake.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function; holo-Fur1 binds conserved Fur-box operator sequences in cis-regulatory promoter regions of iron-regulated genes via its N-terminal winged-helix domain. Reason: Fur-family ferric uptake regulators (NCBIfam NF006999, PANTHER PTHR33202:SF2) bind specific 19-bp palindromic Fur-box operator sequences overlapping iron-regulated promoters when complexed with Fe(2+) (PMID:8522528; matching PSEAE/fur and PSEPK/fur). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR PANTHER; PTHR33202:SF2; FERRIC UPTAKE REGULATION PROTEIN; 1. PMID:8522528 The DNA binding activity of the PA-Fur protein was confirmed by gel mobility shift assays and DNase I footprints of the synthetic DNA fragment GATAAT GATAATCATTATC, representing a perfect "Fur box". |
| GO:0001216 DNA-binding transcription activator activity | IEA GO_REF:0000117 | MODIFY | Summary: Automated ARBA sign error; Fur acts predominantly as an Fe(2+)-dependent DNA-binding transcriptional repressor (GO:0001217) when bound to Fur-box operators. Reason: ARBA (ARBA00027660) annotated GO:0001216 (DNA-binding transcription activator activity), whereas bacterial Fur (NCBIfam NF006999, RuleBase RU364037, PANTHER PTHR33202:SF2) acts directly as an Fe(2+)-dependent transcriptional repressor of iron-uptake and siderophore genes (and indirectly activates iron-storage genes by repressing small regulatory RNAs; PMID:8522528). Refined laterally to GO:0001217 (DNA-binding transcription repressor activity), matching PSEAE/fur. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR NCBIfam; NF006999; fur; 1. PMID:8522528 Data indicating that the promoters of the pchR gene, encoding a transcriptional activator for pyochelin synthesis, and of the pvdS gene, encoding a positive regulator for pyoverdin production, are specifically recognized by Fur-Fe(II) are presented, suggesting that PA-Fur represses expression of pchR and pvdS during growth in an iron-replete environment. |
| GO:0003677 DNA binding | IEA GO_REF:0000104 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0000976 (transcription cis-regulatory region binding). Reason: GO:0003677 (DNA binding) is a broad ancestor term already entailed by GO:0000976 (transcription cis-regulatory region binding) accepted in this review. Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR InterPro; IPR036390; WH_DNA-bd_sf. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000120 | MODIFY | Summary: Correct but unsigned parent transcription factor term; refine to GO:0001217 (DNA-binding transcription repressor activity). Reason: GO:0003700 (DNA-binding transcription factor activity) is true of Fur1 but unsigned; refined to its specific child term GO:0001217 (DNA-binding transcription repressor activity), matching PSEAE/fur. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR PANTHER; PTHR33202:SF2; FERRIC UPTAKE REGULATION PROTEIN; 1. PMID:8522528 Data indicating that the promoters of the pchR gene, encoding a transcriptional activator for pyochelin synthesis, and of the pvdS gene, encoding a positive regulator for pyoverdin production, are specifically recognized by Fur-Fe(II) are presented, suggesting that PA-Fur represses expression of pchR and pvdS during growth in an iron-replete environment. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | TOO GENERAL | Summary: True but uninformative parent cellular component already entailed by the accepted specific child term GO:0005829 (cytosol). Reason: GO:0005737 (cytoplasm) is a general parent term already entailed by GO:0005829 (cytosol) accepted in this review. Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496, CC ECO:0000256|RuleBase:RU364037}. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: Core subcellular localization of the soluble 139-aa cytoplasmic Fur1 homodimer. Reason: Fur1 is a soluble 139-residue intracellular DNA-binding repressor (RuleBase RU364037) that senses cytosolic Fe(2+) and acts on chromosomal promoters in the cytosol (matching PSEAE/fur and PSEPK/fur). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496, CC ECO:0000256|RuleBase:RU364037}. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative unsigned parent process already entailed by the accepted specific child term GO:0045892 (negative regulation of DNA-templated transcription). Reason: GO:0006355 (regulation of DNA-templated transcription) is a general ancestor term already entailed by GO:0045892 (negative regulation of DNA-templated transcription) accepted in this review. Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR InterPro; IPR002481; FUR. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Supported non-core structural metal-binding activity; VPARA_18200 contains the conserved four-cysteine structural Zn(2+)-binding site (Cys92, Cys95, Cys132, Cys135; PIRSR PIRSR602481-1), while its regulatory iron-sensing activity is captured by NEW GO:0008198 (ferrous iron binding). Reason: Fur1 (VPARA_18200) retains all four conserved cysteines (Cys92 and Cys95 in 92-CTSC-95; Cys132 and Cys135 in 132-CGDC-135) of the canonical Fur structural Zn(2+) site (PIRSR PIRSR602481-1; PMID:12581348). Because Zn(2+) plays a structural role whereas Fe(2+) binding at the regulatory site (His86, Asp88, Glu107, His124) mediates iron sensing, GO:0008270 is retained as KEEP_AS_NON_CORE (matching PSEAE/fur). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt CC -!- COFACTOR: CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; CC Evidence={ECO:0000256|PIRSR:PIRSR602481-1}; CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|PIRSR:PIRSR602481-1}; PMID:12581348 Here, we present the first crystal structure of Fur from P. aeruginosa in complex with Zn2+ determined at a resolution of 1.8 A. Furthermore, X-ray absorption spectroscopic measurements and microPIXE analysis were performed in order to characterize the distinct zinc and iron binding sites in solution. |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: True for a DNA-binding repressor bound to Fur-box operator DNA, but a transient nucleoprotein complex that is non-core relative to GO:0000976. Reason: Matching PSEAE/fur, holo-Fur1 forms a protein-DNA complex when bound to Fur-box operators (PMID:8522528), which is true but adds little beyond the accepted operator-binding molecular function GO:0000976 and is kept as KEEP_AS_NON_CORE. Supporting Evidence: PMID:8522528 The DNA binding activity of the PA-Fur protein was confirmed by gel mobility shift assays and DNase I footprints of the synthetic DNA fragment GATAAT GATAATCATTATC, representing a perfect "Fur box". |
| GO:0045892 negative regulation of DNA-templated transcription | IEA GO_REF:0000118 | ACCEPT | Summary: Core biological process; Fe(2+)-bound holo-Fur1 represses transcription of target iron-acquisition genes under iron-replete conditions. Reason: Repression of iron-regulated promoters via Fur-box binding is the primary conserved biological process of bacterial Fur (NCBIfam NF006999, PANTHER PTHR33202:SF2; PMID:8522528). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR PANTHER; PTHR33202:SF2; FERRIC UPTAKE REGULATION PROTEIN; 1. PMID:8522528 Data indicating that the promoters of the pchR gene, encoding a transcriptional activator for pyochelin synthesis, and of the pvdS gene, encoding a positive regulator for pyoverdin production, are specifically recognized by Fur-Fe(II) are presented, suggesting that PA-Fur represses expression of pchR and pvdS during growth in an iron-replete environment. |
| GO:0045893 positive regulation of DNA-templated transcription | IEA GO_REF:0000108 | MODIFY | Summary: Propagated via inter-ontology link from the ARBA GO:0001216 row; refine laterally to GO:0045892 (negative regulation of DNA-templated transcription) to match Fur1's direct repressor role. Reason: GO:0045893 was inferred automatically (GO_REF:0000108) from the ARBA GO:0001216 row. Because Fur1 acts directly as an Fe(2+)-dependent transcriptional repressor (GO:0001217), this row is modified laterally to GO:0045892 (negative regulation of DNA-templated transcription), which is already accepted on this review. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:8522528 Data indicating that the promoters of the pchR gene, encoding a transcriptional activator for pyochelin synthesis, and of the pvdS gene, encoding a positive regulator for pyoverdin production, are specifically recognized by Fur-Fe(II) are presented, suggesting that PA-Fur represses expression of pchR and pvdS during growth in an iron-replete environment. |
| GO:1900376 regulation of secondary metabolite biosynthetic process | IEA GO_REF:0000118 | TOO GENERAL | Summary: True but uninformative parent process already entailed by the accepted specific child term GO:1900705 (negative regulation of siderophore biosynthetic process). Reason: GO:1900376 (regulation of secondary metabolite biosynthetic process) is an ancestor of GO:1900705 (negative regulation of siderophore biosynthetic process) already accepted in this review. Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR PANTHER; PTHR33202:SF2; FERRIC UPTAKE REGULATION PROTEIN; 1. |
| GO:1900705 negative regulation of siderophore biosynthetic process | IEA GO_REF:0000118 | ACCEPT | Summary: Core biological process; Variovorax paradoxus synthesizes vacidobactin and variobactin siderophores and Fur1 is the conserved iron-responsive repressor of siderophore biosynthesis under iron-replete conditions. Reason: Variovorax paradoxus is a siderophore-producing bacterium (synthesizing vacidobactin A/B and variobactin A/B; PMID:26412281), and Fur1 (NCBIfam NF006999, PANTHER PTHR33202:SF2) is the canonical iron-sensing repressor that downregulates siderophore biosynthesis when intracellular iron is sufficient (PMID:8522528; matching PSEAE/fur and PSEPK/fur). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt DR PANTHER; PTHR33202:SF2; FERRIC UPTAKE REGULATION PROTEIN; 1. PMID:8522528 Data indicating that the promoters of the pchR gene, encoding a transcriptional activator for pyochelin synthesis, and of the pvdS gene, encoding a positive regulator for pyoverdin production, are specifically recognized by Fur-Fe(II) are presented, suggesting that PA-Fur represses expression of pchR and pvdS during growth in an iron-replete environment. PMID:26412281 Isolation of these indicated metabolites provided the novel compounds vacidobactin A and B, which are methylmalonate-incorporating acidobactins and represent the first natural products isolated from Variovorax |
| GO:0008198 ferrous iron binding | IC file:VARPD/fur1/fur1-uniprot.txt | NEW | Summary: Core regulatory metal-sensing activity at the conserved His86-Asp88-Glu107-His124 Fe(2+)-binding site (PIRSR PIRSR602481-2). Reason: Inferred by curator (IC) from PIRSR PIRSR602481-2, which annotates Fe(2+) cofactor binding (1 Fe(2+) ion per subunit) coordinated by the conserved regulatory site residues His86, Asp88, Glu107, and His124 in VPARA_18200 (supported by spectroscopic and structural characterization of bacterial Fur; PMID:8522528, PMID:12581348; matching PSEAE/fur and PSEPK/fur). Supporting Evidence: file:VARPD/fur1/fur1-uniprot.txt CC -!- COFACTOR: CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000256|PIRSR:PIRSR602481-2}; CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; CC Evidence={ECO:0000256|PIRSR:PIRSR602481-2}; CC Note=Binds 1 Mn(2+) or Fe(2+) ion per subunit. CC {ECO:0000256|PIRSR:PIRSR602481-2}; file:VARPD/fur1/fur1-uniprot.txt FT BINDING 86 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000256|PIRSR:PIRSR602481-2" PMID:12581348 Furthermore, X-ray absorption spectroscopic measurements and microPIXE analysis were performed in order to characterize the distinct zinc and iron binding sites in solution. |
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Download this section (compressed HTML)Q: Does Variovorax paradoxus Fur1 (VPARA_18200) directly bind Fur-box operators upstream of the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) ferric-siderophore uptake operon and the vacidobactin/variobactin NRPS/PKS biosynthetic gene clusters under iron-replete conditions?
Suggested experts: Vasil ML, Cornelis P
Experiment: Purify recombinant Variovorax paradoxus Fur1 (A0A0H2M8T9) and perform Mn(2+)/Fe(2+)-dependent DNase I footprinting and ChIP-seq across the promoter regions of the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) operon and siderophore biosynthetic clusters.
Hypothesis: Holo-Fur1 binds Fur-box operators upstream of exbD5-exbB4-tonB-bfrD1 and siderophore biosynthetic operons in an Fe(2+)-dependent manner to repress their transcription under iron sufficiency.
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