biostudies-literatureCarter MSNIGMS NIH HHS696-705https://www.ebi.ac.uk/biostudies/studies/S-EPMC6435334biostudies-literatureUnknown14(7)Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which arNature chemical biologyFunctional assignment of multiple catabolic pathways for D-apiose.PMC6435334P01 GM118303U54 GM093342Al-Obaidi NGhosh AGerlt JAVetting MWBonanno JBHuang HCarter MSAlmo SCBouvier JTZhang XZallot RGAndersen HMFrancisco BSfalseFunctional assignment of multiple catabolic pathways for D-apiose.Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which ar2018-01-01T00:00:00Z2018 Jul2026-05-03T12:19:13.867Z2019-06-06T21:03:04ZS-EPMC64353342986714210.1038/s41589-018-0067-7