PT - JOURNAL ARTICLE AU - Snorre Sulheim AU - TjaĊĦa Kumelj AU - Dino van Dissel AU - Ali Salehzadeh-Yazdi AU - Chao Du AU - Gilles P. van Wezel AU - Kay Nieselt AU - Eivind Almaas AU - Alexander Wentzel AU - Eduard J Kerkhoven TI - Genome-scale Model Constrained by Proteomics Reveals Metabolic Changes in <em>Streptomyces coelicolor</em> M1152 Compared to M145 AID - 10.1101/796722 DP - 2020 Jan 01 TA - bioRxiv PG - 796722 4099 - http://biorxiv.org/content/early/2020/02/25/796722.short 4100 - http://biorxiv.org/content/early/2020/02/25/796722.full AB - Many biosynthetic gene clusters (BGCs) in the genomes of environmental microorganisms require heterologous expression in order to realize their genetic potential, including cryptic and metagenomic BGCs. Streptomyces coelicolor M1152 is a widely used host strain for the heterologous expression of BGCs, as it has been genetically engineered for this purpose via the deletion of four of its native biosynthetic gene clusters (BGCs) and the introduction of a point mutation in the rpoB gene that encodes the beta subunit of RNA polymerase. This latter mutation was shown to have a strong positive impact on antibiotic biosynthesis via processes that remain poorly understood. Therefore, a systemic understanding of the consequences on cellular metabolism of the genomic changes of M1152 could greatly contribute to this understanding. Here we carried out a comparative analysis of M1152 and its ancestor strain M145, connecting observed phenotypic differences to changes in transcript and protein abundance. Measured protein abundance was used to constrain an amended genome-scale model (GEM) and to predict metabolic fluxes. This approach connects observed differences in growth rate and glucose consumption to changes in central carbon metabolism, accompanied by differential expression of important regulons. Our results suggest that precursor availability is not limiting the biosynthesis of secondary metabolites. This implies that alternative strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.Importance This study provides the first systems description of S. coelicolor M1152, an engineered host widely used for the heterologous expression of BGCs directing the synthesis of natural products. By combining time-series proteomics and transcriptomics, batch fermentation data and genome-scale modelling, we can connect observed phenotypes to known genetic modifications and find extensive metabolic rewiring in the M1152 strain compared to the wild-type stain M145. Our study indicates that the deletion of secondary metabolite biosynthetic pathways thought to enhance precursor availability, only has a minor impact on the ability of the modified strain to produced heterologous molecules. In contrast, the rpoB mutation is likely responsible for the most dramatic changes in regulatory features and precursor availability. The amended genome-scale model, reconstructed in an open-science framework, allowed us to contextualize the transcriptional changes. This framework facilitates further development by the research community in an organized manner, including version control, continuous integration and quality control and tracking of individual contributions.