Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A significant challenge is re-engineering a partially reductive PKS module to produce a saturated β-carbon through a reductive loop (RL) exchange. In this work, we sought to establish that chemo­informatics, a field traditionally used in drug discovery, offers a viable strategy for RL exchanges. We first introduced a set of donor RLs of diverse genetic origin and chemical substrates  into the first extension module of the lipomycin PKS (LipPKS1). Product titers of these engineered unimodular PKSs correlated with chemical structure similarity between the substrate of the donor RLs and recipient LipPKS1, reaching a titer of 165 mg/L of short-chain fatty acids produced by the host Streptomyces albus J1074. Expanding this method to larger intermediates that require bimodular communication, we introduced RLs of divergent chemo­similarity into LipPKS2 and determined triketide lactone production. Collectively, we observed a statistically significant correlation between atom pair chemo­similarity and production, establishing a new chemo­informatic method that may aid in the engineering of PKSs to produce desired, unnatural products.

To reduce the effects of greenhouse gas emissions on climate change, scientific efforts have sought to develop biofuels and bio‐based commodity chemicals as petrochemical replacements primarily for their environmental benefits. As the biological design space is far greater than chemical synthesis, there has been a drive to leverage this ability to create and replace fine and specialty chemicals. While polyketide synthases have traditionally been studied for their biosynthesis of pharmaceutical chemicals, the unique advantages of engineering polyketide synthases for the production of biofuels, commodity chemicals, and both pharmaceutical and nonpharmaceutical fine and specialty chemicals are discussed. With our increased understanding of polyketide biosynthetic logic, new computational tools for prospective polyketide synthesis pathways for the creation of existing and novel biochemicals are also outlined. © 2018 American Institute of Chemical Engineers AIChE J, 64: 4201–4207, 2018

Modular type I polyketide synthases (PKSs) are multifunctional proteins that are comprised of individual domains organized into modules. These modules act together to assemble complex polyketides from acyl-CoA substrates in a linear fashion. This assembly-line enzymology makes engineered PKSs a potential retro-biosynthetic platform to produce fuels, commodity chemicals, speciality chemicals, and pharmaceuticals in various host microorganisms, including bacteria and fungi. However, the realization of this potential is restricted by practical difficulties in strain engineering, protein overexpression, and titer/yield optimization. These challenges are becoming more possible to overcome due to technical advances in PKS design, engineered heterologous hosts, DNA synthesis and assembly, PKS heterologous expression, and analytical methodology. In this review, we highlight these technical advances in PKS engineering and provide practical considerations thereof.