Bacterial sulfoquinovose catabolism (sulfoglycolysis and sulfo-SMO)

A reusable bacterial module for breakdown of sulfoquinovose (SQ; 6-deoxy-6-sulfo-D-glucose), the polar head group of the plant and cyanobacterial sulfolipid sulfoquinovosyl diacylglycerol. An optional glycoside hydrolase first releases free SQ from sulfoquinovosyl glycerides. SQ is then consumed by one of several alternative, biochemically characterized routes. Three C-C bond cleavage (sulfoglycolytic) routes split the C6 sulfosugar into a non-sulfonated C3 unit used for growth and the C3 organosulfonate 3-sulfolactaldehyde (SLA), which is then reduced to 2,3-dihydroxypropane-1-sulfonate (DHPS) or oxidized to 3-sulfolactate (SL) for excretion: the sulfo-EMP route (SQ isomerase, sulfofructose kinase, sulfofructose-1-phosphate aldolase), the sulfo-ED route (SQ dehydrogenase, sulfogluconolactonase, sulfogluconate dehydratase, KDSG aldolase), and the sulfo-SFT route (SQ isomerase and sulfofructose transaldolase). In the oxidative sulfo-SMO route a two-component flavin-dependent SQ monooxygenase cleaves the C-S bond, releasing sulfite and 6-dehydroglucose, which is reduced to glucose so that all six carbons are used. Uptake, regulation, and downstream mineralization of DHPS, SL or sulfite by other enzymes or community members are outside the module boundary.

Boundary decision. The routes share one input (SQ, released by an optional sulfoquinovosidase) and one ecological role (use of the sulfosugar as carbon and energy source), but no route-defining enzyme is shared across all of them; SQ isomerase is shared only by sulfo-EMP and sulfo-SFT, and SLA dehydrogenase only by sulfo-ED and sulfo-SFT. They are therefore modeled as alternative implementations in a single route variant_set (selection ONE_OR_MORE, because some bacteria carry more than one route) rather than as four standalone modules, with each variant carrying its own ordered parts and connections. The terminal SLA reduction or oxidation is modeled inside each route with the enzyme documented for that route's exemplar organism; the same SLA-redox alternatives recur across routes (for example, Arthrobacter sulfo-EMP clusters use an SLA dehydrogenase instead of YihU, and anaerobic sulfo-SFT clusters use an SLA reductase instead of SftD/SlaB), as summarized in PMID:41676062 and PMID:32919372. Not modeled: the sulfo-ASDO route (Fe(II)/2-oxoglutarate-dependent SQ dioxygenase SqoD) and the sulfo-TK route (SF transketolase SqwGH), which have fewer characterized reference proteins in UniProtKB; the EMP2-specific kinase and aldolase SqiK and SqiA of the sulfo-EMP2 variant (its isomerase SqvD is shared with sulfo-SFT and is modeled there); the SQ mutarotases YihR/SqvB (EC 5.1.3.43, RHEA:59228), because no UniProtKB entry carries that activity (E. coli YihR, P32139, is still named "Uncharacterized protein YihR") and GO has no term mapped to RHEA:59228, so the alpha-to-beta anomer step is recorded on the top-level connection instead; SQ and sulfoquinovosyl glyceride uptake systems (YihO, SmoEFGH); the transcriptional repressor CsqR; and downstream desulfonation of DHPS, SL, isethionate or 3-sulfopropionate (HpsGH, SuyAB, IseG, HpfG and related enzymes), which is a distinct community-level module. Reaction chaining across the non-CoA sulfosugar intermediates was checked manually against the cited Rhea equations. Ontology gaps noted for GO editors: GO has specific molecular-function terms only for the sulfo-EMP reactions (GO:0061593, GO:0061594, GO:0061595, GO:0061596) and for sulfoquinovosidase (GO:1990929); the sulfo-ED (EC 1.1.1.390, 3.1.1.99, 4.2.1.162, 4.1.2.58), sulfo-SFT (EC 2.2.1.14), SQ monooxygenase (EC 1.14.14.181) and 6-dehydroglucose reductase (EC 1.1.1.432) reactions have Rhea entries but no rhea2go/ec2go mapping, so their annotons use the nearest existing parent GO term with the exact Rhea reaction as evidence. GO:0061722 sulphoglycolysis (is_a GO:1902777) is defined as "The chemical reactions and pathways resulting in the breakdown of 6-sulfoquinovose(1-) resulting in the formation of glycerone phosphate (DHAP) and pyruvate." (OLS, checked 2026-10-10). That covers the DHAP-forming sulfo-EMP route and the pyruvate-forming sulfo-ED route, but not the F6P-forming sulfo-SFT route or the sulfite-releasing sulfo-SMO route; the root concept therefore uses the broader parent GO:1902777. Adjacency. The SmoC/SmoA step is an SQ-specific instance of the two-component reduced-flavin desulfonation motif modeled abstractly in modules/bacterial_alkanesulfonate_uptake_desulfonation.yaml (ssued_desulfonation): SmoA fills the reductase tier (GO:0052874 FMN reductase, NADH) and SmoC the oxygenase tier (GO:0008726), differing from the SsuE/SsuD abstract motif only in the SQ-specific substrate and the NADH versus NADPH reductase cofactor. A formal conforms_to is not declared because this module collapses the two-component system into one reaction node rather than the template's two parts, but that module covers promiscuous SsuD/SsuE alkanesulfonate desulfonation, so there is no overlap in members. Downstream desulfonation of DHPS, SL and sulfite is left to community-level modules as stated above. Family grounding. Every member protein's PANTHER family has a family review under interpro/panther/ (PTHR46959, PTHR15108, PTHR10584, PTHR39340, PTHR22981, PTHR43639, PTHR10907, PTHR43183, PTHR30502, PTHR43353, PTHR36120, PTHR10683, PTHR42991, PTHR42847, PTHR30466, PTHR43364). Where a verified subfamily holds all representative members the annoton names it (PTHR46959:SF2, PTHR10584:SF157, PTHR39340:SF1, PTHR43639:SF1, PTHR43183:SF2, PTHR43353:SF5, PTHR36120:SF1, PTHR10683:SF40, PTHR42991:SF1, PTHR42847:SF4, PTHR30466:SF11, PTHR43364:SF1); the YihS, YihU, lactonase and KDSG aldolase steps keep the family id (PTHR15108, PTHR22981, PTHR10907, PTHR30502) as a membership record. Four family descriptors raise a FAMILY_FUNCTION_UNREVIEWED notice because their family reviews deliberately leave the step's activity UNRESOLVED at family or subfamily level: YihS (PTHR15108 has no subfamily for the enterobacterial YihS clade), YihT (PTHR39340:SF1 also holds Firmicutes LacD tagatose-1,6-bisphosphate aldolases), YihU (PTHR22981:SF7 also holds the 3-hydroxyisobutyrate dehydrogenases) and SmoA (PTHR30466:SF11 members differ in flavin and reductant preference). The verified ids are kept because they record membership; the activity itself rests on the representative members' gene reviews and, for YihS and YihV, on the PAINT nodes PTN001431668 and PTN000061922 cited on those annotons. PAINT nodes considered and not cited: PTN000541321 (PTHR22981 root) and PTN002462421 (PTHR43639 root) assert only generic oxidoreductase parents of the annotons' functions; PTN008681047 (PTHR43353) propagates succinate-semialdehyde dehydrogenase activity, which is only an in vitro activity of the SLA dehydrogenase PpSQ1_00395 and is judged NEEDS_PRUNING in the PTHR43353 family review; PTN002217485 (PTHR39340) and PTN000768559 (PTHR42847) are judged too deep in their family reviews. Representative members were not extended to Escherichia coli YgfF, human ALDH5A1 or Pseudomonas putida KT2440 SsuD, which do not perform the reactions of the steps concerned. Module-level deep research was not generated (the provider client could not run in the curation environment); the module rests on the cited primary literature and on the member gene reviews.