(605g) Invited Talk: Engineering Omnivorous Baker’s Yeast

The exploration of non-model yeasts for biomanufacturing applications is partly driven by the difficulty in engineering Saccharomyces cerevisiae for utilization of non-native but abundant substrates. Despite decades of effort, there has been no systematic analysis to identify the root cause behind the recalcitrance of this yeast for synthetic heterotrophy and how to overcome it for any non-native substrate. Through a combination of directed evolution, flux balancing, synthetic biology, systems biology, and network analysis, we find that the major limitation to substrate utilization is, extrinsic – genes that control the flux of the substrate into central carbon metabolism – and not any downstream (intrinsic) yeast-specific factor. We show that this holds true for structurally diverse substrates, which is a remarkable finding since the current assumption amongst researchers is that the limitations are largely intrinsic, and that each substrate needs a unique engineering strategy. Thus, our work turns the current long-standing paradigm on its head. We also show that by perturbing intrinsic factors, cells become less robust and are more sensitive to growth inhibitors commonly found in biomass hydrolysates. We conclude that much of the engineering approach insofar in the literature results in unnecessary and that strains end up being over-engineered with poor growth rates and/or robustness. Our described minimalistic, holistic engineering approach is more rapid, easier to optimize, and results in strains that maximize growth and robustness phenotypes.

Associated works: Endalur & Nair 2018 Nat Commun, Trivedi et al. 2022 bioRxiv, Sullivan et al. 2022 bioRxiv.