Metabolic analysis of 242 Streptomyces strains using genome-scale metabolic models

Abstract

Streptomyces strains have been acknowledged as a potential source of novel natural compounds based on their capability of producing diverse secondary metabolites. As a result, genome sequencing and genome mining studies for Streptomyces have been actively conducted. However, to our knowledge, systematic analysis of their metabolism has not been conducted sufficiently despite the importance of metabolism in relation with the biosynthesis of secondary metabolites. Here, we analyzed so-called ‘pan-reactome’ of 242 Streptomyces strains by using their genome-scale metabolic models (GEMs). GEMs were reconstructed through our in-house automatic reconstruction system where a GEM for a specific strain was built from a publicly available template model based on sequence alignment analysis and biosynthetic gene cluster prediction. The resulting GEMs of Streptomyces strains were used to examine metabolic characteristics of the 242 Streptomyces strains with focus on growth capability under a large number of growth conditions, gene essentiality, and biosynthetic capabilities of secondary metabolite precursors. This genus-wide study will help better understand the metabolic potential of the Streptomyces strains, which will in turn facilitate metabolic engineering of Streptomyces for the enhanced production of important secondary metabolites.