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 BCCT-family BetT transporter imports choline, the FAD-dependent, membrane-associated choline dehydrogenase BetA oxidizes choline to betaine aldehyde using a respiratory electron acceptor, and the soluble NAD-dependent betaine-aldehyde dehydrogenase BetB oxidizes the aldehyde to glycine betaine. The route was defined genetically and biochemically in Escherichia coli K-12. It is conserved in Pseudomonas, where P. putida KT2440 requires betBA for glycine-betaine synthesis from choline, and in other proteobacteria and Gram-positive bacteria that carry betA and betB.

The module begins with extracellular choline and ends with intracellular glycine betaine. Direct glycine-betaine uptake, downstream demethylation and catabolism, BetI and ArcA regulation, and alternative choline transporters (for example ABC-type CbcXWV) are outside the boundary. The two oxidation steps are performed by enzymes from unrelated families (GMC oxidoreductase BetA and aldehyde dehydrogenase BetB), so each step has its own family selector. Both selectors use the NCBIfam equivalog families TIGR01810 (betA; integrated in InterPro IPR011533) and TIGR01804 (BADH; IPR011264), which all four representatives carry, rather than PANTHER subfamilies. PTHR11552:SF147 also contains ecdysone oxidase, fatty-acid photodecarboxylase and other non-choline enzymes, and PTHR11699:SF228 joins BetB with vertebrate ALDH9A1 while P. putida BetB carries only a family-level PANTHER assignment. BetA was once described as bifunctional because crude E. coli membranes oxidized both choline and betaine aldehyde at similar rates (PMID:3512525). Purified E. coli BetA does not oxidize betaine aldehyde (PMID:39510372). Acinetobacter baumannii BetA does oxidize it in vitro (PMID:34431198). That paper does not name the acceptor; our inference is that it is not NAD+, because BetA is a GMC flavoprotein with an FAD site and no NAD-binding site. The NAD-dependent step is therefore assigned to BetB only, and the HAMAP-propagated GO:0008802 annotations on BetA are removed in the E. coli and P. putida gene reviews. Choline uptake uses an ORTHOLOG_OF selector anchored on E. coli BetT. P. putida KT2440 BetT-I (Q88CW9), the BCCT paralog next to betIBA, is a candidate member, not a grounded one, until its substrate is measured.