Bacterial choline uptake and glycine betaine biosynthesis

A reusable bacterial module for choline uptake followed by its two-step oxidation to the compatible solute glycine betaine. A BetT-family transporter imports choline, FAD-dependent BetA oxidizes choline to betaine aldehyde, and NAD-dependent BetB oxidizes the aldehyde to glycine betaine.

MODULE:bacterial_choline_to_glycine_betaine_biosynthesisDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_choline_to_glycine_betaine_biosynthesis.yaml
glycine betaine biosynthetic process from cholineGO:0031456
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_choline_to_glycine_betaine_biosynthesis__upa00529-deep-research-openscientist.md
OpenScientist review of the module, UPA00529, and PSEPK
The resolved species-aware review marks all three steps covered, recovers BetT-I, BetA, and BetB despite their omission from the UniPathway bucket, and keeps BetI outside the catalytic module.
GO:0031456
glycine betaine biosynthetic process
GO:0031456 grounds the module. The route-specific term GO:0019285 (glycine betaine biosynthetic process from choline) was obsoleted in GO release 2026-07-26 with replaced_by GO:0031456; the consecutive oxidation of choline to glycine betaine is carried by the module structure rather than by the term.
PMID:1956285
DNA sequence and analysis of the bet genes encoding the osmoregulatory choline-glycine betaine pathway of Escherichia coli
Direct E. coli evidence establishes BetT as a proton-motive-force-driven, high-affinity choline transport system.
betT encoding a proton-motive-force-driven, high-affinity transport system for choline
PMID:26913973
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
The KT2440 genome reconstruction provides pathway and locus context, but its cached abstract does not expose a checkable BetT-I substrate assignment.
PMID:17116241
Uncoupling of choline-O-sulphate utilization from osmoprotection in Pseudomonas putida
Direct KT2440 genetic and biochemical evidence shows that betBA is required for conversion of choline to glycine betaine and separates this route from BetC-dependent choline-O-sulphate utilization.
file:PSEPK/betT-I/betT-I-ai-review.yaml
PSEPK betT-I gene review
Q88CW9 is curated as a BCCT-family transporter adjacent to betIBA; choline uptake remains a candidate substrate rather than a verified gene-level annotation.
file:PSEPK/betA/betA-ai-review.yaml
PSEPK betA gene review
Q88CW6 is curated as the FAD-dependent choline dehydrogenase that produces betaine aldehyde.
file:PSEPK/betB/betB-ai-review.yaml
PSEPK betB gene review
Q88CW7 is curated as the dedicated NAD-dependent betaine-aldehyde dehydrogenase.

The module begins with extracellular choline and ends with intracellular glycine betaine. Direct glycine-betaine uptake, downstream demethylation and catabolism, osmotic-stress regulation, and alternative choline transporter paralogs are outside the boundary. Some BetA-family proteins are described as bifunctional choline/betaine-aldehyde oxidoreductases. Bifunctionality is experimentally established for E. coli BetA P17444 despite the co-occurring BetB P17445, and the species-aware report also cites a Halomonas example. These establish an architecture-level possibility, not a direct assay of KT2440 BetA; organism-specific biochemical evidence should therefore be required before adding the BetB reaction to a Q88CW6 annoton.

4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

60.0% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_choline_to_glycine_betaine_biosynthesis deep-research report alongside the module YAML.

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 (2/5 grounded genes reviewed)

1 complete review(s) · 1 with deep research · 3 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
betA Q88CW6 ✓ 6/7 ✓
betB Q88CW7 ✓ ✓ ✗
Escherichia coli BetT choline transporter ortholog P0ABC9 ✗ — —
BetA (Escherichia coli K-12) P17444 ✗ — —
BetB (Escherichia coli K-12) P17445 ✗ — —

Details

Context
bacteriaNCBITaxon:2
Bacterial choline uptake and glycine betaine biosynthesisMetabolic Pathwaybacterial_choline_to_glycine_betaine_biosynthesis
glycine betaine biosynthetic process from cholineGO:0031456
Context
bacteriaNCBITaxon:2

Connections

BetT supplies intracellular choline to BetA.
BetA supplies betaine aldehyde to BetB.
Part 1: choline uptake
BetT-dependent choline uptakeTransport Stepbett_choline_uptake

Annotons

BetT choline transporter activity
bett_activity
Participant: Ortholog Of: Escherichia coli BetT choline transporter ortholog
Ortholog Of:
Escherichia coli BetT choline transporter orthologUniProtKB:P0ABC9 Choline-specific orthologs of characterized E. coli BetT; broad BCCT/PTHR30047:SF7 members with other substrates are excluded. PSEPK Q88CW9 remains a locus-associated candidate and is not used to define this selector.

Function

choline transmembrane transporter activityGO:0015220
Substrates: extracellular choline
Products: intracellular choline

Processes

choline transportGO:0015871

Locations

plasma membraneGO:0005886

Supplies intracellular choline to BetA.

Part 2: choline oxidation
BetA-dependent betaine aldehyde formationReactionbeta_betaine_aldehyde_formation

Annotons

BetA choline dehydrogenase activity
beta_activity
Participant: Family: FAD-dependent BetA family
Family:
FAD-dependent BetA familyInterPro:IPR011533
Representative Members: BetA (Pseudomonas putida KT2440)UniProtKB:Q88CW6 BetA (Escherichia coli K-12)UniProtKB:P17444

Function

choline dehydrogenase activityGO:0008812
Substrates: choline electron acceptor
Products: betaine aldehyde reduced electron acceptor

Processes

glycine betaine biosynthetic process from cholineGO:0031456

Locations

membraneGO:0016020

Produces the aldehyde substrate for BetB.

Part 3: glycine betaine formation
BetB-dependent glycine betaine formationReactionbetb_glycine_betaine_formation

Annotons

BetB betaine-aldehyde dehydrogenase activity
betb_activity
Participant: Family: BetB aldehyde dehydrogenase family
Family:
BetB aldehyde dehydrogenase familyInterPro:IPR011264
Representative Members: BetB (Pseudomonas putida KT2440)UniProtKB:Q88CW7 BetB (Escherichia coli K-12)UniProtKB:P17445

Function

betaine-aldehyde dehydrogenase (NAD+) activityGO:0008802
Substrates: betaine aldehyde NAD+ water
Products: glycine betaine NADH proton

Processes

glycine betaine biosynthetic process from cholineGO:0031456

Completes synthesis of the compatible solute glycine betaine.