Approaches for completing metabolic networks through metabolite damage and repair discovery

Abstract

Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated “metabolite repair enzymes.” Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.

Graphical abstract

Highlights

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  Underground metabolism can generate useful, useless, or toxic metabolites.

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  Damaged metabolites can be produced non-enzymatically or owing to enzyme promiscuity.

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  Metabolite repair enzymes eliminate damaged metabolites or pre-empt their formation.

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  Tools to discover underground pathways could be used to reveal hidden repair systems.

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  Metabolite repair is crucial to account for in disease and metabolic engineering.