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.

MODULE:pseudomonad_lanthanide_switch_pqq_alcohol_oxidationDRAFTCONCRETEBiological Processmodules/pseudomonad_lanthanide_switch_pqq_alcohol_oxidation.yaml
phosphorelay signal transduction systemGO:0000160 alcohol metabolic processGO:0006066
PMID:28655819
Functional role of lanthanides in enzymatic activity and transcriptional regulation of pyrroloquinoline quinone-dependent alcohol dehydrogenases in Pseudomonas putida KT2440
Establishes the overlapping alcohol substrate ranges and contrasting calcium versus lanthanide requirements of PedE and PedH.
PMID:30158283
The PedS2/PedR2 two-component system is crucial for the rare earth element switch in Pseudomonas putida KT2440
Establishes PedS2/PedR2 as the central phosphorelay controlling inverse pedE and pedH expression in response to lanthanide availability.
GO:0000160
phosphorelay signal transduction system
Defines the sensor-kinase and response-regulator relationship.
GO:0052934
alcohol dehydrogenase (cytochrome c) activity
Defines the shared catalytic activity of PedE and PedH.

The module is species-neutral but intentionally limited to the experimentally supported pseudomonad Ped system. Pseudomonas putida KT2440 proteins are exemplars, not species-specific required members. No PANTHER or PTN selector is asserted for PedS2 or PedR2 because their current broad family assignments do not establish this regulatory specificity. PedH-dependent feedback on pedE/pedH transcription is retained as a knowledge gap rather than assigning PedH a transcription-regulatory molecular function.

6Nodes
3Parts
1Variant Sets
2Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

53.8% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✓ present

  • pseudomonad_lanthanide_switch_pqq_alcohol_oxidation-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 4 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
exaE Q88JH7 ✓ ✓ ✓
pede Q88JH5 ✓ ✓ ✓
pedH Q88JH0 ✓ ✓ ✓
PP_2671 Q88JH8 ✓ ✓ ✓

Details

Context
PseudomonasNCBITaxon:286
Pseudomonad lanthanide-switch PQQ alcohol oxidationBiological Processpseudomonad_lanthanide_switch_pqq_alcohol_oxidation
phosphorelay signal transduction systemGO:0000160 alcohol metabolic processGO:0006066
Context
PseudomonasNCBITaxon:286

Connections

PedS2-dependent phosphorylation activates PedR2 output in the lanthanide-free state.
Phosphorylated PedR2 promotes the calcium-dependent PedE branch.
PedR2 contributes to repression of the PedH branch without lanthanides.
Part 1: lanthanide-responsive PedS2 sensor signaling
PedS2 sensor-kinase signalingSignaling Pathwaypeds2_sensor_signaling

Annotons

PedS2 phosphorelay sensor kinase
peds2_sensor_kinase
Participant: Family: pseudomonad PedS2 sensor-kinase family
Family:
pseudomonad PedS2 sensor-kinase family
Representative Members: PedS2 (Pseudomonas putida KT2440)UniProtKB:Q88JH8

Function

phosphorelay sensor kinase activityGO:0000155

Processes

phosphorelay signal transduction systemGO:0000160

Locations

membraneGO:0016020

Controls PedR2 phosphorylation according to the lanthanide-responsive physiological input; the direct molecular ligand remains unresolved.

Part 2: PedR2 transcriptional switch output
PedR2-dependent transcriptional controlBiological Processpedr2_transcriptional_output

Annotons

PedR2 phosphorelay response regulator
pedr2_response_regulator
Participant: Family: pseudomonad PedR2 response-regulator family
Family:
pseudomonad PedR2 response-regulator family
Representative Members: PedR2/ExaE (Pseudomonas putida KT2440)UniProtKB:Q88JH7

Function

phosphorelay response regulator activityGO:0000156

Processes

regulation of DNA-templated transcriptionGO:0006355

Phosphorylated PedR2 activates pedE expression and contributes to pedH repression when usable lanthanides are absent.

Part 3: metal-conditioned periplasmic PQQ alcohol oxidation
Alternative PedE/PedH alcohol oxidationReactionpqq_alcohol_oxidation
Variant set: Ped alcohol-dehydrogenase metal variants by catalytic metal availability (One Or More)
Calcium-dependent PedE alcohol oxidationReactionpede_calcium_oxidation

Annotons

Calcium-dependent PQQ alcohol dehydrogenase PedE
pede_alcohol_dehydrogenase
Participant: Family: calcium-dependent PedE-type PQQ alcohol dehydrogenase family
Family:
calcium-dependent PedE-type PQQ alcohol dehydrogenase family
Representative Members: PedE (Pseudomonas putida KT2440)UniProtKB:Q88JH5

Function

alcohol dehydrogenase (cytochrome c) activityGO:0052934
Substrates: alcohol oxidized cytochrome c
Products: aldehyde or ketone reduced cytochrome c

Processes

alcohol metabolic processGO:0006066

Locations

periplasmic spaceGO:0042597

Performs PQQ-dependent alcohol oxidation when calcium is available and the lanthanide switch favors pedE expression.

Lanthanide-dependent PedH alcohol oxidationReactionpedh_lanthanide_oxidation

Annotons

Lanthanide-dependent PQQ alcohol dehydrogenase PedH
pedh_alcohol_dehydrogenase
Participant: Family: lanthanide-dependent PedH-type PQQ alcohol dehydrogenase family
Family:
lanthanide-dependent PedH-type PQQ alcohol dehydrogenase family
Representative Members: PedH (Pseudomonas putida KT2440)UniProtKB:Q88JH0

Function

alcohol dehydrogenase (cytochrome c) activityGO:0052934
Substrates: alcohol oxidized cytochrome c
Products: aldehyde or ketone reduced cytochrome c

Processes

alcohol metabolic processGO:0006066

Locations

periplasmic spaceGO:0042597

Performs PQQ-dependent alcohol oxidation when usable lanthanides are available and the switch favors pedH.