Discovering a new catabolic pathway of D-ribonate in Mycobacterium smegmatis

Abstract

In vivo growth study indicates that Mycobacterium smegmatis could utilize D-ribonate as sole carbon source under an unknown pathway. To clarify this pathway, we start with the statistical analysis of genome neighborhood networks(GNNs) of erythrulose kinase which has been approved to participate in several sugars' degradation. In M. smegmatis, two novel dehydrogenases (3HCDH & ADH_short) and one unknown isomerase (AP_endonuc) are targeted and characterized, for the catabolism of D-ribonate in this organism, this acid sugar is firstly oxidized into 2-keto-D-ribonate by a dehydrogenase, and then sequentially isomerized to 3-keto D-ribonate by an AP_endonuc isomerase; afterward, through decarboxylation, this 3-keto sugar acid is degraded into D-erythrulose which enters a known pathway through erythrulose kinase. Additionally, several other acid sugars (L-ribonate, D/L-lyxonate, L-threonate and D-erythronate) have been proved to be catalyzed by same enzymes and proceed with a similar catabolic pathway.

Keywords: 2, 3-keto tautomerase; Acid sugar metabolism; D-ribonate catabolism; Mycobacterium smegmatis.