Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production

Abstract

Summary Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor . Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.

Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters

“…To investigate how much the errors in the constructed metabolic pathways affect model predictions, we introduced both the literature-based and the BiGMeC pathway reconstructions into the consensus GEM of S. coelicolor (Sco-GEM) [ 16 ] and compared the maximal production rate of the final compound (Fig. 2 b).…”

“…We introduced each of the 943 reconstructed pathways into Sco-GEM [ 16 ], and predicted single-reaction knockout strategies improving the production of the final pathway product. Surprisingly, only 17 different reactions were suggested as a knockout target in one or more of the 943 in silico heterologous expression experiments (Fig.…”

“…However, the cloning and transfer of BGCs can be time-consuming and difficult depending on the genetic tools available for the native and the heterologous host strains, as well as the size of the BGC in question [ 15 ]. Additionally, it is not clear which host strain or which genetic modifications will maximize the yield of the secondary metabolite synthesized through the metabolic pathway catalyzed by the enzymes, or enzyme complexes, encoded by the heterologously expressed BGC [ 16 , 17 ].…”

Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing

“…As previously described, the development of high-throughput techniques has allowed to measure and quantify a high number of cellular molecular constituents from the different biological levels (genome, RNAs, proteins, metabolites, etc.). The analysis of omics data is giving lights about the interrelated or individual relationship of biological levels (genes, proteins, regulators, and metabolites) and the production of specialized metabolites [ 137 , 138 , 139 , 140 ]. However, the integration of multiple omics datasets for analyzing the interplay between biological levels is still a challenging task [ 141 , 142 , 143 , 144 , 145 , 146 ].…”

“…Application and use of genome-scale metabolic modeling of Streptomyces bacteria is currently an active field of study [ 138 , 145 , 162 , 163 , 164 ], including the modeling of S. clavuligerus metabolism ( Figure 4 ) [ 19 , 43 , 122 , 165 , 166 ].…”