Two-component system OmpR/PhoB-family response regulator CzcR (VPARA_44930; 225 aa) in Variovorax paradoxus TBEA6, encoded in an operon with the sensor histidine kinase cusS (VPARA_44940) immediately downstream of czcA3-czcB-czcC-czcI (VPARA_44890-VPARA_44920) in the VPARA_44890-VPARA_44980 heavy-metal resistance island. Contains an N-terminal phosphorelay receiver domain (residues 2-115; Asp-51 phosphorylation site) and a C-terminal OmpR/PhoB-type winged-helix DNA-binding domain (residues 123-221) that regulates transcription of the czcCBA heavy-metal efflux operon in response to periplasmic Zn2+, Cd2+, and Co2+ sensed by CusS (CzcS).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000156 phosphorelay response regulator activity | IEA GO_REF:0000118 | ACCEPT | Summary: CzcR contains a canonical N-terminal CheY-like response regulatory receiver domain (residues 2-115; PROSITE:PS50110) with a conserved phosphoacceptor aspartate (Asp-51). Reason: Directly supported by the response regulator receiver domain (PROSITE:PS50110, residues 2-115) and conserved Asp-51 phosphorylation site, as well as homology to Cupriavidus metallidurans CH34 CzcR (PMID:10198000). Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt FT DOMAIN 2..115 FT /note="Response regulatory" FT /evidence="ECO:0000259|PROSITE:PS50110" file:VARPD/czcR/czcR-uniprot.txt FT MOD_RES 51 FT /note="4-aspartylphosphate" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00169" |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: CzcR functions as the response regulator partner of the cognate sensor histidine kinase CusS (VPARA_44940) in a heavy-metal-responsive two-component phosphorelay system. Reason: Well-supported by receiver domain architecture (InterPro:IPR001789), genomic co-localization with cusS (VPARA_44940), and characterization of the CzcRS two-component system (PMID:10198000). Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt DR NCBIfam; TIGR01387; cztR_silR_copR; 1. PMID:10198000 The CzcR putative response regulator was purified and shown to bind in the 5' region of czcN. |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000120 | ACCEPT | Summary: CzcR contains a C-terminal OmpR/PhoB-type winged-helix DNA-binding domain (residues 123-221; PROSITE:PS51755) that binds operator sequences upstream of target heavy-metal resistance promoters. Reason: Directly supported by the OmpR/PhoB-type winged-helix DNA-binding domain (PROSITE:PS51755, InterPro:IPR001867, InterPro:IPR039420) and experimental DNA binding of CzcR to the 5' region of the czc operon (PMID:10198000). Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt FT DNA_BIND 123..221 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | TOO GENERAL | Summary: Parent term of GO:0000976 (transcription cis-regulatory region binding), which is already accepted on this gene. Reason: True but uninformative because the more specific descendant term GO:0000976 (transcription cis-regulatory region binding) is already asserted and accepted in this review. Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt FT DNA_BIND 123..221 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: CzcR is a soluble cytoplasmic response regulator without signal peptides or transmembrane helices. Reason: Consistent with its cytoplasmic localization where it is phosphorylated by the cytoplasmic kinase domain of CusS (VPARA_44940) and binds chromosomal target promoters. Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt FT DOMAIN 2..115 FT /note="Response regulatory" FT /evidence="ECO:0000259|PROSITE:PS50110" |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | ACCEPT | Summary: CzcR regulates transcription of the czc heavy-metal resistance operon upon phosphorylation by CzcS/CusS. Reason: Experimental characterization of the Cupriavidus/Variovorax CzcRS two-component system (PMID:10198000) and the OmpR/PhoB-type winged-helix DNA-binding domain (PROSITE:PS51755, InterPro:IPR001867, NCBIfam:TIGR01387) establish that CzcR binds the 5' regulatory region of the czc locus and regulates czcCBA mRNA synthesis in response to Zn2+, Co2+, and Cd2+. Supporting Evidence: PMID:10198000 Experiments on (i) growth of these strains in liquid culture containing 5 mM Zn2+, (ii) induction of the beta-galactosidase in the reporter strains by zinc, cobalt, and cadmium, and (iii) cDNA analysis of czcCBA mRNA synthesis under inducing and noninducing conditions showed that the CzcRS two-component regulatory system is involved in Czc regulation. file:VARPD/czcR/czcR-uniprot.txt FT DNA_BIND 123..221 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Phosphorylated OmpR/PhoB-family response regulators form head-to-tail dimers bound to direct-repeat operator DNA. Reason: Transient association with target operator DNA as a protein-DNA complex is true of OmpR/PhoB-family response regulators, while the primary cellular localization of CzcR is the cytosol (GO:0005829). Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt FT DNA_BIND 123..221 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:10198000 Transcriptional organization of the czc heavy-metal homeosta... | NEW | Summary: CzcR is a DNA-binding transcription factor that regulates expression of the czcCBA heavy-metal efflux operon in response to Zn2+, Cd2+, and Co2+. Reason: CzcR possesses an OmpR/PhoB-type winged-helix DNA-binding domain (residues 123-221; PROSITE:PS51755) and is classified in NCBIfam:TIGR01387 (cztR_silR_copR); in Cupriavidus metallidurans CH34, CzcR binds the 5' regulatory region of the czc operon and regulates czcCBA mRNA synthesis as part of the CzcRS two-component system (PMID:10198000). Supporting Evidence: PMID:10198000 The CzcR putative response regulator was purified and shown to bind in the 5' region of czcN. PMID:10198000 Experiments on (i) growth of these strains in liquid culture containing 5 mM Zn2+, (ii) induction of the beta-galactosidase in the reporter strains by zinc, cobalt, and cadmium, and (iii) cDNA analysis of czcCBA mRNA synthesis under inducing and noninducing conditions showed that the CzcRS two-component regulatory system is involved in Czc regulation. file:VARPD/czcR/czcR-uniprot.txt DR NCBIfam; TIGR01387; cztR_silR_copR; 1. |
| GO:0010043 response to zinc ion | ISS PMID:10198000 Transcriptional organization of the czc heavy-metal homeosta... | NEW | Summary: CzcR mediates the transcriptional response to elevated periplasmic Zn2+, Cd2+, and Co2+ concentrations as part of the CzcR-CusS two-component system in the VPARA_44890-VPARA_44940 czc island. Reason: CzcR (VPARA_44930) is encoded in the conserved czcA3-czcB-czcC-czcI-czcR-cusS (VPARA_44890-VPARA_44940) operon cluster and belongs to the CzcR/CztR/CopR heavy-metal response regulator subfamily (NCBIfam:TIGR01387), which regulates heavy-metal efflux in response to Zn2+, Co2+, and Cd2+ (PMID:10198000). Supporting Evidence: file:VARPD/czcR/czcR-uniprot.txt DR NCBIfam; TIGR01387; cztR_silR_copR; 1. PMID:10198000 Experiments on (i) growth of these strains in liquid culture containing 5 mM Zn2+, (ii) induction of the beta-galactosidase in the reporter strains by zinc, cobalt, and cadmium, and (iii) cDNA analysis of czcCBA mRNA synthesis under inducing and noninducing conditions showed that the CzcRS two-component regulatory system is involved in Czc regulation. |
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Download this section (compressed HTML)Q: Does phosphorylated CzcR (VPARA_44930) bind only the czcA3 promoter region, or does it also co-regulate the adjacent cadA2 (VPARA_44980) P-type ATPase or outer-membrane porin expression in Variovorax paradoxus TBEA6?
Q: Does phosphorylated CzcR (VPARA_44930) act strictly as a direct transcriptional activator (GO:0001216 / GO:0045893) of the czcA3-czcB-czcC operon upon metal-induced phosphorylation by CusS (VPARA_44940), as suggested by reporter and mRNA induction in Cupriavidus metallidurans CH34 (van der Lelie et al. 1997; Grosse et al. 1999, PMID:10198000)?
Experiment: Perform electrophoretic mobility shift assays (EMSA) and ChIP-seq with purified acetyl-phosphate-phosphorylated CzcR (VPARA_44930) across the VPARA_44890-VPARA_44980 heavy-metal resistance island in Variovorax paradoxus TBEA6.
Hypothesis: Phospho-CzcR binds conserved direct-repeat OmpR-box motifs upstream of czcA3 (VPARA_44890) and czcI/czcR (VPARA_44920/VPARA_44930) to drive Zn2+/Cd2+/Co2+-inducible transcription.
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