Phosphate regulon transcriptional regulatory protein PhoB1 (VPARA_10430, A0A0H2M7F4) in Variovorax paradoxus strain TBEA6 is a 230-amino-acid cytosolic OmpR/PhoB-family two-component response regulator (InterPro IPR011879, NCBIfam TIGR02154, PANTHER PTHR48111:SF40) encoded on genomic contig JZWI01000005 (EMBL KLN58031.1) between its cognate sensor histidine kinase phoR1 (VPARA_10420) and phoU (VPARA_10440) within the phoR1-phoB1-phoU-pstB-pstA-pstC-pstS-ppx cluster (VPARA_10420-VPARA_10490). PhoB1 comprises an N-terminal CheY-like receiver domain (PROSITE PS50110, Pfam PF00072, CDD cd17618, residues 5-121) containing the invariant aspartyl-phosphate acceptor Asp54 (50-LILLDWMLPGQSG-62) and a C-terminal winged-helix DNA-binding effector domain (PROSITE PS51755, Pfam PF00486, CDD cd00383, residues 130-226). Under inorganic phosphate limitation, phosphorylation of Asp54 by PhoR1 induces PhoB1 homodimerization and binding to Pho-box cis-regulatory sequences upstream of Pho regulon promoters to activate transcription of high-affinity phosphate acquisition and starvation response genes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000156 phosphorelay response regulator activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function; the N-terminal CheY-like receiver domain (PROSITE PS50110, residues 5-121) accepts a phosphoryl group at Asp54 from the cognate sensor histidine kinase PhoR1. Reason: PhoB1 possesses a canonical N-terminal response regulator receiver domain (PROSITE PS50110, CDD cd17618, InterPro IPR011879, NCBIfam TIGR02154) with the conserved phosphoacceptor Asp54 (MOD_RES 54, 4-aspartylphosphate) phosphorylated by PhoR1 under phosphate limitation (PMID:24563032). Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt FT DOMAIN 5..121 FT /note="Response regulatory" FT /evidence="ECO:0000259|PROSITE:PS50110" file:VARPD/phoB1/phoB1-uniprot.txt FT MOD_RES 54 FT /note="4-aspartylphosphate" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00169" PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: Core biological process of the PhoR1-PhoB1 two-component phosphorelay signaling pair. Reason: PhoB1 is the response regulator partner of the PhoR1 sensor histidine kinase (VPARA_10420) in the two-component phosphorelay pathway that transduces extracellular phosphate limitation into transcriptional activation (PMID:24563032). Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. PMID:24563032 The hub of the signaling pathway consists of the two-component signaling proteins PhoB and PhoR ( 6 ). |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function; phosphorylated PhoB1 dimers bind Pho-box cis-regulatory sequences upstream of Pho regulon promoters via the C-terminal OmpR/PhoB-type winged-helix domain (PROSITE PS51755, residues 130-226). Reason: PhoB1 contains a C-terminal OmpR/PhoB-type winged-helix DNA-binding domain (PROSITE PS51755, Pfam PF00486, residues 130-226) that binds direct-repeat Pho-box operator sites in target promoters upon Asp54 phosphorylation (PMID:24563032). Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt FT DOMAIN 130..226 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000259|PROSITE:PS51755" FT DNA_BIND 130..226 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | 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 that adds no specificity beyond GO:0000976 (transcription cis-regulatory region binding) already accepted in this review. Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt FT DNA_BIND 130..226 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" |
| 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/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: Core subcellular localization of the soluble 230-aa cytoplasmic PhoB1 response regulator. Reason: PhoB1 lacks transmembrane segments or signal peptides and functions in the bacterial cytosol, where it receives a phosphoryl group from the cytoplasmic kinase domain of PhoR1 and binds chromosomal promoters. Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | MODIFY | Summary: Correct but unsigned parent process; refine to GO:0045893 (positive regulation of DNA-templated transcription). Reason: Phosphorylated PhoB1 acts as a positive transcriptional activator that recruits RNA polymerase to Pho-box promoters under phosphate limitation (PMID:24563032); refine unsigned GO:0006355 to its specific descendant GO:0045893 (positive regulation of DNA-templated transcription). Proposed replacements: positive regulation of DNA-templated transcription Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
| GO:0006817 phosphate ion transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO over-annotation of a transcription factor with the transport process of its target operon; replace with GO:0016036 (cellular response to phosphate starvation). Reason: PhoB1 is a cytosolic DNA-binding response regulator that transcriptionally activates the pstSCAB phosphate transporter operon during phosphate starvation rather than physically transporting phosphate ions itself; replace GO:0006817 with GO:0016036 (cellular response to phosphate starvation). Proposed replacements: cellular response to phosphate starvation Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. PMID:24563032 Robust growth in many bacteria is dependent upon proper regulation of the adaptive response to phosphate (P i ) limitation. This response enables cells to acquire P i with high affinity and utilize alternate phosphorous sources. |
| GO:0032993 protein-DNA complex | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: True for phosphorylated PhoB1 dimers bound to Pho-box operator DNA, retained as non-core alongside GO:0000976. Reason: Phosphorylated PhoB1 forms a nucleoprotein complex on Pho-box promoter DNA to recruit RNA polymerase (PMID:24563032), which is true but non-core relative to its molecular functions GO:0000976 and GO:0001216. Supporting Evidence: PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
| GO:0001216 DNA-binding transcription activator activity | IC file:VARPD/phoB1/phoB1-uniprot.txt | NEW | Summary: Core molecular function; phosphorylated PhoB1 binds Pho-box promoters and directly activates transcription of the Pho regulon. Reason: Inferred by curator (IC) from PhoB family classification (NCBIfam TIGR02154, PANTHER PTHR48111:SF40) and OmpR/PhoB-type DNA-binding domain (PROSITE PS51755) in file:VARPD/phoB1/phoB1-uniprot.txt and experimental characterization of bacterial PhoB (PMID:24563032). Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt FT DNA_BIND 130..226 FT /note="OmpR/PhoB-type" FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01091" PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
| GO:0016036 cellular response to phosphate starvation | IC file:VARPD/phoB1/phoB1-uniprot.txt | NEW | Summary: Core biological process; PhoB1 is the master transcriptional effector of the cellular response to inorganic phosphate starvation. Reason: Inferred by curator (IC) from PhoB family classification in file:VARPD/phoB1/phoB1-uniprot.txt, operon co-localization with phoR1 and pstSCAB-phoU (VPARA_10420-VPARA_10480), and PMID:24563032. Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. PMID:24563032 PhoU, along with the high-affinity, P i -specific ATP-binding cassette transporter PstSCAB and the two-component proteins PhoR and PhoB, is absolutely required for P i signaling in Escherichia coli . |
| GO:0045893 positive regulation of DNA-templated transcription | IC file:VARPD/phoB1/phoB1-uniprot.txt | NEW | Summary: Core biological process; phosphorylated PhoB1 positively regulates transcription of Pho regulon genes during phosphate limitation. Reason: Inferred by curator (IC) from PhoB family classification in file:VARPD/phoB1/phoB1-uniprot.txt and PMID:24563032. Supporting Evidence: file:VARPD/phoB1/phoB1-uniprot.txt DR NCBIfam; TIGR02154; PhoB; 1. DR PANTHER; PTHR48111:SF40; PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB; 1. PMID:24563032 PhoB is a typical winged-helix response regulator that upon aspartyl phosphorylation forms a dimer, which binds to DNA sequences upstream of Pho regulon genes to recruit RNA polymerase and initiate transcription ( 7 β 10 ). |
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Download this section (compressed HTML)Q: Beyond the canonical pstSCAB-phoU-phoB1-phoR1-ppx gene cluster (VPARA_10420-VPARA_10490), does phosphorylated PhoB1 in Variovorax paradoxus TBEA6 directly activate phosphonate utilization, alkaline phosphatase, or organosulfur/siderophore cross-regulation operons under rhizosphere phosphate limitation?
Suggested experts: McCleary WR, Wanner BL
Experiment: Perform ChIP-seq of FLAG-tagged PhoB1 (VPARA_10430) and RNA-seq comparing wild-type and ΞphoB1 Variovorax paradoxus TBEA6 under phosphate-replete (2 mM Pi) versus phosphate-starved (50 uM Pi) conditions.
Hypothesis: Phosphorylated PhoB1 binds conserved Pho-box direct repeats upstream of the pstS-pstC-pstA-pstB-phoU-phoB1-phoR1 cluster and accessory phosphorus scavenging operons to activate their transcription during Pi starvation.
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