An Oxidative Pathway of Deoxyribose Catabolism

High-throughput​ ​genetics​ ​is​ ​a ​ ​powerful ​ ​approach ​ ​to ​ ​identify​ ​new​ ​genes​ ​involved ​ ​in ​ ​bacterial carbon ​ ​catabolism.​ ​Here,​ ​we ​ ​used ​ ​genome-wide ​ ​fitness​ ​assays​ ​to ​ ​identify​ ​a ​ ​novel ​ ​pathway​ ​for 2-deoxy-D-ribose ​ ​catabolism​ ​in ​ ​​Pseudomonas​ ​simiae​ ​​WCS417.​ ​The ​ ​genes​ ​that​ ​were ​ ​important for​ ​deoxyribose ​ ​utilization ​ ​but​ ​not​ ​in ​ ​other​ ​conditions​ ​included ​ ​two ​ ​putative ​ ​dehydrogenases,​ ​a lactonase,​ ​a ​ ​β-keto ​ ​acid ​ ​cleavage ​ ​enzyme,​ ​and ​ ​a ​ ​glycerate ​ ​kinase.​ ​We ​ ​propose ​ ​that deoxyribose ​ ​is​ ​oxidized ​ ​twice ​ ​to ​ ​2-deoxy-3-keto-D-ribonoate ​ ​(a ​ ​β-keto ​ ​acid)​ ​before ​ ​cleavage ​ ​to D-glycerate,​ ​which ​ ​is​ ​phosphorylated ​ ​and ​ ​enters​ ​lower​ ​glycolysis.​ ​We ​ ​purified ​ ​the ​ ​two dehydrogenases​ ​and ​ ​reconstituted ​ ​the ​ ​enzymatic​ ​pathway​ ​for​ ​the ​ ​conversion ​ ​of​ ​deoxyribose ​ ​to 2-deoxy-3-keto-D-ribonoate ​ ​​in​ ​vitro​.