Developing microbial cell factories for natural product biosynthesis through codon harmonization and pathway balancing

To advance the biobased economy, sustainable and scalable bioprocesses are required. Microbial fermentation has proven to be a successful approach in the production of valuable natural products, biofuels, biodegradable polymers, or food and feed. Various microorganisms can be used to develop such biomanufacturing processes, like fungi synthesizing the antibiotic penicillin or baker’s yeast making bio-ethanol. While these organisms natively produce penicillin or ethanol, the development of novel fermentation processes often requires genetic engineering through the introduction of heterologous DNA. However, when doing so, it is important to match the codon usage in the heterologous host to that of the native producer, an approach called codon harmonization. This strategy enhances heterologous gene expression by optimizing translation efficiency and protein functionality. Additionally, when introducing heterologous DNA, it is essential to precisely control gene expression to reach an optimal metabolic flux towards the desired product. This is often achieved through fine-tuning the promoter-terminator combination of heterologous genes. Altogether, these approaches enhance the expression of foreign DNA in a heterologous host, providing it with new functionalities such as increasing its robustness to cope with the complex composition of (industrial) waste and side streams. Here, I present an in-depth analysis of various open-source codon harmonization tools and their performance towards mimicking the codon usage of native hosts in a heterologous host [1], as well as a Golden Gate (GG) assembly system for efficient pathway balancing in Streptomyces species. Integrating these strategies offers a powerful approach to develop microbial cell factories useful in natural product biosynthesis and beyond. [1] An exploratory in silico comparison of open-source codon harmonization tools. Willems, Hectors, Rombaut et al. (2023). Microbial Cell Factories 22(1):227.