Bacterial trehalose synthesis from alpha-glucans and maltose

A reusable bacterial module covering two alternative routes that form trehalose from alpha-glucosides. In the coupled TreY-TreZ route, TreY rearranges the reducing-end linkage of an alpha-1,4-glucan to form maltooligosyltrehalose and TreZ hydrolytically releases trehalose. In the standalone TreS route, one enzyme reversibly interconverts maltose and trehalose; two sequence-distinct TreS groups carry this reaction, the classical GH13 TreS subfamily first described in Pimelobacter and a Pseudomonas-type TreS group. Trehalose synthesis from nucleotide sugars, trehalose degradation, upstream alpha-glucan or maltose supply, and TreS acting with maltokinase to feed GlgE-dependent alpha-glucan synthesis are outside the boundary.

The TreY-TreZ route and the standalone TreS route are alternative module implementations, not a three-step chain. The narrower reusable TreY-TreZ route is also represented in modules/trey_trez_trehalose_biosynthesis.yaml, and this variant uses the same subfamilies, PAINT node and exemplars; this broader module adds the alternative standalone TreS architecture. The module is species-neutral: each step is selected by family, and exemplars were chosen for experimental evidence (Arthrobacter sp. Q36 and M. tuberculosis TreY/TreZ, Pimelobacter sp. R48 and P. stutzeri CJ38 TreS), with P. putida KT2440 kept as one homology- or assay-supported exemplar per step. TreS is split into two family groups because they are sequence-distinct: classical TreS sits in PANTHER PTHR10357:SF219 with the TIGR02456 TreS N-terminal signature, whereas the Pseudomonas-type TreS (TIGR02455, InterPro IPR012665) is placed in PTHR10357 only at family level, so it is selected by its InterPro family. SF219 also contains TreS enzymes that work in another pathway context: mycobacterial TreS and the P. putida TreSB-maltokinase fusion (Q88FN0) are SF219 members but are not chosen as exemplars here, because in mycobacteria TreS runs mainly toward maltose and pairs with maltokinase to feed GlgE, which is modelled in modules/tres_mak_glge_branched_alpha_glucan_biosynthesis.yaml. Selecting SF219 for the standalone route therefore asserts catalytic capacity for the reaction, not that every SF219 member makes trehalose in vivo. All TreS reactions are reversible; the standalone route records demonstrated maltose-to-trehalose catalytic capacity, not established in vivo flux, and for KT2440 PP_2918/Q88IT1 the physiological direction remains unresolved. Five OpenScientist jobs (three genes, generic module, and module + ppu00500 + PSEPK) finished without producing reports; no provider output was reconstructed or inferred.