Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel 13C‐metabolite fingerprinting

For rapid analysis of microbial metabolisms,13C‐fingerprinting employs a set of tracers to generate unique labeling patterns in key amino acids that can highlight active pathways. In contrast to rigorous 13C‐metabolic flux analysis (13C‐MFA), this method aims to provide metabolic insights without expensive flux measurements. Using13C‐fingerprinting, we investigated the metabolic pathways in Rhodococcus opacus PD630, a promising biocatalyst for the conversion of lignocellulosic feedstocks into value‐added chemicals. Specifically, seven metabolic insights were gathered as follows: (1) glucose metabolism mainly via the Entner–Doudoroff (ED) pathway; (2) lack of glucose catabolite repression during phenol co‐utilization; (3) simultaneous operation of gluconeogenesis and the ED pathway for the co‐metabolism of glucose and phenol; (4) an active glyoxylate shunt in acetate‐fed culture; (5) high flux through anaplerotic pathways (e.g., malic enzyme and phosphoenolpyruvate carboxylase); (6) presence of alternative glycine synthesis pathway via glycine dehydrogenase; and (7) utilization of preferred exogenous amino acids (e.g., phenylalanine). Additionally, a13C‐fingerprinting kit was developed for studying the central metabolism of non‐model microbial species. This low‐cost kit can be used to characterize microbial metabolisms and facilitate the design‐build‐test‐learn cycle during the development of microbial cell factories. Biotechnol. Bioeng. 2016;113: 91–100. © 2015 Wiley Periodicals, Inc.

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