Pseudomonad lanthanide-switch PQQ alcohol oxidation

A reusable pseudomonad module coupling PedS2/PedR2 two-component signaling to metal-conditioned periplasmic alcohol oxidation. In the absence of usable lanthanides, phosphorylated PedR2 favors expression of the calcium-dependent PQQ alcohol dehydrogenase PedE. Lanthanide availability shifts the system toward the lanthanide-dependent paralog PedH. Both enzymes oxidize diverse alcohols in the periplasm and pass electrons to cytochrome c. PQQ biosynthesis, downstream aldehyde metabolism, and lanthanide uptake are adjacent systems and are outside this module. The enzymes carry the cytochrome-c alcohol dehydrogenase assignment, but their specific physiological cytochrome c partner in KT2440 remains inferred.

Scope is deliberately pseudomonad (CONCRETE, NCBITaxon:286) rather than generalized to all lanthanide switches. A calcium/lanthanide switch between PQQ dehydrogenases also operates in methylotrophs such as Methylorubrum extorquens (MxaFI versus XoxF methanol dehydrogenases), but that system is an analogous rather than homologous circuit: its enzymes are methanol dehydrogenases of a different PANTHER subfamily (PTHR32303:SF4, cytochrome cL-linked), and its control runs through other regulators (MxbD/MxbM, MxcQ/MxcE) with XoxF itself required for the switch. Merging the two would assert a shared PedS2/PedR2 regulatory architecture that has not been shown outside Pseudomonas. The methylotroph switch is better modeled as a sibling module, and the M. extorquens lanthanide-dependent ethanol dehydrogenase ExaF, although in the same SF20 subfamily as PedE and PedH, is not added as a member because its regulation is not PedS2/PedR2-mediated. P. putida KT2440 proteins are exemplars of the Ped system, not species-specific required members. PANTHER groundings were adopted from the maintainer grounding pass and checked against interpro/panther/panther.obo and the UniProt PANTHER cross-references: PedS2 is PTHR24421 (SF10), PedR2 is PTHR43214 (SF43), and PedE and PedH are both PTHR32303:SF20. Each family id grounds only the generic activity (sensor kinase, response regulator, cytochrome c-linked alcohol dehydrogenase), as recorded in the FamilyReviews; the lanthanide responsiveness of PedS2, the pedE/pedH targets of PedR2, and the metal dependence that separates the PedE and PedH variants are member-level properties supported by PMID:28655819 and PMID:30158283. Because SF20 does not separate the two metal variants, each variant keeps only its own paralog as representative member. The PedS2/PedR2 bundle is a simple two-component instance of MODULE:two_component_relay without the Hpt tier; it declares `conforms_to` that template WITH_DEVIATIONS for the collapsed Hpt step, as the template prescribes and as the Kdp and Ntr modules do. PedH-dependent feedback on pedE/pedH transcription is retained as a knowledge gap rather than assigning PedH a transcription-regulatory molecular function.