Biosynthesis of the high-value natural products bottromycin and pamamycin from lignin-, plastic- and seaweed-based monomers using engineered Streptomyces lividans
Background. Transforming waste and non-food materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry, optimizing the use of resources while reducing environmental footprints. Yet, despite these advancements, the production of high-value natural products often continues to rely on first-generation substrates, underscoring the intricate processes and specific requirements of their biosynthesis. This is also true for Streptomyces lividans, a renowned host organism celebrated for its capacity to produce and uncover a wide array of natural products, attributed to its genetic versatility and potent secondary metabolism. Given this context, it becomes imperative to assess and optimize this microorganism for the synthesis of natural products specifically from waste and non-food substrates.  Results. We metabolically engineered S. lividans TK24 to heterologously produce the ribosomally synthesized and post-translationally modified peptide, bottromycin, as well as the polyketide, pamamycin. The modified strains successfully produced these compounds using waste and non-food model substrates like protocatechuate (derived from lignin), 4-hydroxybenzoate (sourced from plastic waste), and mannitol (from seaweed). Comprehensive transcriptomic and metabolomic analyses offered insights into how these substrates influenced the cellular metabolism of S. lividans. When evaluating production efficiency, S. lividans showcased remarkable tolerance, especially in a fed-batch process using a mineral medium containing the toxic aromatic 4-hydroxybenzoate, leading to enhanced and highly selective bottromycin production. Additionally, it generated a unique spectrum of pamamycins when cultured in mannitol-rich seaweed extract without the need for added nutrients. Conclusion. Our study showcases the successful production of high-value natural products using varied waste and non-food raw materials, thereby circumventing the reliance on costly, food-competing resources. S. lividans exhibited remarkable adaptability and resilience across these diverse substrates. When cultured on aromatic compounds, it displayed a distinct array of intracellular CoA esters, presenting promising avenues for polyketide production. Future research could focus on enhancing S. lividans' substrate utilization pathways to more efficiently process the intricate mixtures commonly found in waste and non-food sources. Overall design: Whole transcriptomes of a bottromycin production strain derived from cells grown on three different substrates (manitol, 4-hydroxybenzoate, and 3,4-dihydroxybenzoate) using 3 biological replicates each.