BaeSR Two-Component Signal Transduction System

PathBank:SMP0002123

This record covers the two-event BaeSR signal-transduction boundary in PathBank SMP0002123/PathWhiz PW002111: ATP-dependent BaeS autophosphorylation, followed by BaeR phosphorylation/activation. All six formal native reaction sides are represented. The second source equation omits the phosphorylated BaeS donor and dephosphorylated BaeS product; two additional graph edges explicitly identify those states as a literature-supported phosphotransfer interpretation, not native equation slots or separately measured stoichiometry. No phosphatase return reaction, direct ligand-binding step or extra regulon pathway is invented. The native pathway is assigned to species-level Escherichia coli (taxon 562), while the selected PWML complexes 4106, 4107, 12056 and 12057 and its BaeR protein 20851 have K-12 species 25 (taxon 83333). PWML BaeS 7583 retains generic E. coli species 3. Current P30847 and P69228 are K-12 reference chains. These identities do not relabel every historical mutant or expression host as MG1655, or demonstrate the pathway in every E. coli strain. Additional organisms in the global PWML biological-state dictionaries are preserved as source context and not added to the selected route. Four distinct native state assertions are preserved using separately qualified protein endpoints, without declaring a physiological assembly solely because PWML calls its drawing a ProteinComplex. PWML 4106 is the nominal unmodified BaeS state with one chain; 4107 is labelled BaeS-Phis250, with one chain and modification 6 linking protein 7583 to compound 1104. Unmodified BaeR 12056 and activated BaeR 12057 each contain protein 20851 with a nil component coefficient; 12057 also lists phosphate 1104 in a cofactor slot with a nil coefficient. Those nil values remain unspecified. The source supplies neither a physiological oligomer number nor proof of a noncovalent phosphate cofactor. BioPAX flattens PWML 4106 to Protein 7583, and both BaeR states 12056/12057 to the same Protein 20851_Cytoplasm. It represents 4107 as BaeS plus phosphate with component coefficients 1 and reciprocal intramolecular BindingFeatures, and also attaches the same modification feature to the base BaeS reactant. These encoding artifacts are retained in evidence and the full native ledger rather than interpreted as an already phosphorylated input, a free-phosphate assembly, or absence of a distinct activated BaeR state. Native state IDs are carried in qualifiers and evidence; chains use their verified UniProt identities. The native ATP and ADP structures are neutral stereochemical forms matching current CHEBI:15422 and CHEBI:16761, including their complete InChIKeys. This does not specify assay protonation. Native phosphate 1104 is more problematic: the archived BioPAX draws a phosphate trianion (O4P), whereas current BioPAX/PWML draws neutral phosphoric acid (H3O4P), yet retains CHEBI:18367 and PubChem 1061 cross-references to the trianion. Current CHEBI:26078 matches the neutral drawing. The retained native Phosphate participant records the conflicting source marker and remains isolated: no free-acid/free-Pi consumption, noncovalent-cofactor edge or chemical equivalence to a protein-bound phosphoryl group is asserted. Nagasawa et al. (1993) cloned the complete baeS and baeR coding sequences into pSU11S and pSU11R under lac control in pUC19 and expressed them in the DZ225 envZ-deletion derivative. BaeS was enriched in membranes washed with 4 M urea; BaeR was enriched in a cytosolic fraction by 45%-saturation ammonium sulfate precipitation. Figure 8A/C shows ATP-dependent BaeS radiolabeling and a BaeR-mobility band after combining those fractions, with vector controls. These are enriched fractions, not a purified BaeS/BaeR pair. The truncated original pSN25 construct belongs to BasS, not BaeS. The separate weak OmpR cross-phosphorylation experiment does not add OmpR to this core route. The 1993 phosphorylation mixture used 0.05 mM gamma-32P ATP and 50 mM KCl; the Results specify 5 mM CaCl2 and the Methods refer to TEDG buffer and prior procedures. This is an assay condition, not proof of a unique physiological calcium cofactor, an independently measured ATP affinity, or a complete cellular flux. Cognate phosphotransfer was inferred from the fraction experiment and is supported by reviewed BaeS/BaeR phosphorylation annotation. The 1993 study did not establish a natural sensed ligand and explicitly deferred deletion-mutant physiology. The historical BaeS sequence discrepancy is resolved without claiming sequence equivalence: D14054.1/BAA03140.1 encodes 466 residues, with historical residues 414–420 VPATVPA replacing current P30847 residues 414–421 GSRNRASG. The complete sequences agree before and after that interval, and UniProt explicitly records the conflict. D14054.1 BaeR translation BAA03141.1 is 240 residues and agrees with current P69228, although this reference comparison does not independently resequence an assayed plasmid. The 1993 paper prints BaeS coding endpoints 274–1671 and BaeR 1671–2390; the retained sequence record includes stop codons at 274–1674 and 1671–2393, respectively. Historical assay qualifications remain attached to catalytic edges. H250 in BaeS and D61 in BaeR are conserved candidate phosphoacceptors in the 1993 sequence comparison; current UniProt modified-residue annotations use PROSITE/ECO:0000255. The pathway therefore separates demonstrated phosphorylation from predicted residue assignment. The native BaeS-Phis250 name is preserved with that qualification. Current UniProt cites PMID 15522865 for BaeS autophosphorylation and BaeR phosphorylation; publisher whole-text attempts during this curation returned 403, and no full 2005 Methods or exact purified construct is claimed read. Those statements are attributed to the reviewed annotation rather than presented as freshly inspected 2005 experiments. BaeS membrane localization and BaeR cytoplasmic localization are consistent with the 1993 fractionation and the native states. The graph uses the verified current cellular-component terms for the reported compartments; current UniProt assigns BaeS to the cell inner membrane with experimental annotation and BaeR to cytoplasm with curator-inference evidence. The global PWML inner-membrane vocabulary and its source cross-reference are retained separately. Activity-dependent exclusivity and transport across the membrane are not inferred from localization. Specifically, native GO:0070258 is the active inner membrane pellicle complex term for an apicomplexan structure, not a bacterial inner membrane. GO:0005886 includes bacterial inner membrane as a narrow synonym; this curated location is not an exact mapping of the erroneous native GO assertion. Downstream context is bounded to the inspected 2002 and 2011 studies. Baranova and Nikaido demonstrate BaeR binding to the mdtA/yegM promoter and conditional expression/resistance in specific constructs and a hypersusceptible delta-acrAB host. The original pTrcBaeR replaces eight C-terminal residues with 17 vector residues; an intact pBAD control and a distinct C-terminal Val-Asp-His6 purification preparation are separate. Overexpression acts without BaeS, and the promoter-binding preparation was thought largely unphosphorylated; these results do not make phosphorylation universally obligatory for DNA binding. MdtD was not required for the reported resistance phenotype. Native ZraPSR/yicO/ygcL text and other regulon annotations are not automatically promoted to direct core edges. The 2011 reporter and mutant experiments show condition-dependent responses to flavonoids, tungstate, zinc and high indole concentrations. The complete image Table 2 differentiates inducing and noninducing flavonoid structures; the tested doses, reporters and strain backgrounds remain specific. Induction and the proposed MdtABC-efflux explanation do not demonstrate direct binding of those compounds to BaeS. The study did not find a BaeSR requirement for indole-mediated biofilm reduction under its conditions. These environmental and phenotype observations provide context, not extra chemical reactions or universal physiological triggers. Evidence comprises the complete 1993 primary PDF, complete 2002 and 2011 article texts and all ten associated image bodies, the whole current and archived native exports, whole reviewed protein records, and exact current chemical, taxon and historical-sequence originals. The malformed PWML drawing-only option prefix remains in the original; only a reversible separately bound reading copy has an artificial namespace. Source qualifications are retained in the record and ledgers.

Pathway type

two component phosphotransfer signaling

Organism scope

• Escherichia coli NCBITaxon:562
• Escherichia coli K-12 NCBITaxon:83333

Read the source YAML

Components and activities

Mechanistic edges

References

• PathBank:SMP0002123 BaeSR Two-Component Signal Transduction System: current complete BioPAX (source version: Whole current issuing BioPAX acquired 2026-10-12, 57 top-level objects, two reactions. Protein-state flattening, reused modification feature and source chemical conflict retained.)
• PathBank:PW002111 PathWhiz PW002111 complete PWML for PathBank SMP0002123 (source version: Whole current PWML acquired 2026-10-12. Raw undeclared drawing option prefix preserved. XPath reading uses only a separately bound reversible namespace insertion; derivative is not issuer authority.)
• UniProtKB:P30847 Signal transduction histidine-protein kinase BaeS (source version: Whole reviewed UniProt JSON; entry 194, sequence 2, annotation updated 2026-09-02. Reference identity, source evidence codes and construct distinctions retained.)
• UniProtKB:P69228 Transcriptional regulatory protein BaeR (source version: Whole reviewed UniProt JSON; entry 149, sequence 1, annotation updated 2026-09-02. Reference identity, source evidence codes and construct distinctions retained.)
• CHEBI:15422 ATP (source version: Complete released ChEBI issuing JSON acquired 2026-10-12; structure, charge, stereochemistry and secondary IDs inspected. Free species is not a protein-bound phosphoryl group.)
• CHEBI:16761 ADP (source version: Complete released ChEBI issuing JSON acquired 2026-10-12; structure, charge, stereochemistry and secondary IDs inspected. Free species is not a protein-bound phosphoryl group.)
• CHEBI:18367 phosphate(3−) (source version: Complete released ChEBI issuing JSON acquired 2026-10-12; structure, charge, stereochemistry and secondary IDs inspected. Free species is not a protein-bound phosphoryl group.)
• CHEBI:26078 phosphoric acid (source version: Complete released ChEBI issuing JSON acquired 2026-10-12; structure, charge, stereochemistry and secondary IDs inspected. Free species is not a protein-bound phosphoryl group.)
• PubChem:1061 Phosphate: whole PubChem compound record (source version: Whole CID1061 record acquired 2026-10-12; charge−3 and complete InChI distinguish the native current neutral-acid drawing.)
• NCBITaxon:562 Escherichia coli (source version: Complete two-taxon NCBI XML acquired 2026-10-12; exact selected TaxId subject distinguished from lineage entries.)
• NCBITaxon:83333 Escherichia coli K-12 (source version: Complete two-taxon NCBI XML acquired 2026-10-12; exact selected TaxId subject distinguished from lineage entries.)
• NCBIProtein:BAA03140.1 Historical BaeS BAA03140.1,466 residues (source version: Whole versioned protein record and D14054.1 coding provenance. Not identical to current 467-residue P30847.)
• NCBIProtein:BAA03141.1 Historical BaeR translation BAA03141.1 within complete D14054.1 (source version: Whole 2495-base D14054.1 record, including both complete CDSs. Reference digest binds this complete nucleotide original containing BAA03141.1, not a fabricated protein-only original.)
• PMID:8282725 Novel members of the two-component signal transduction genes in Escherichia coli (source version: Complete official 1993 PDF, all 8 pages freshly read during this author/preflight session; Figures 6–8 personally inspected. Full-length expression in enriched fractions, not a purified BaeS/BaeR pair.)
• PMID:12107134 The baeSR two-component regulatory system activates transcription of the yegMNOB (mdtABCD) transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate (source version: Complete 2002 PMC article text, tables, captions, bibliography read; all 5 original figure bodies acquired and personally inspected during authoring. Altered, His-tagged and intact BaeR preparations distinguished.)
• PMID:21515766 Characterization of the induction and cellular role of the BaeSR two-component envelope stress response of Escherichia coli (source version: Complete 2011 PMC article text, tables, captions, bibliography read; all 4 figure bodies and image Table 2 acquired and personally inspected. Induction is not proof of direct sensor ligand binding.)
• GO:0005886 plasma membrane (source version: Whole QuickGO three-term issuing response acquired 2026-10-12; exact selected active subject identified independently of the native erroneous GO:0070258 inner membrane pellicle complex cross-reference.)
• GO:0005737 cytoplasm (source version: Whole QuickGO three-term issuing response acquired 2026-10-12; exact selected active subject identified independently of the native erroneous GO:0070258 inner membrane pellicle complex cross-reference.)