Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates

Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that extrinsicfactors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.

Automated summary

Engineering synthetic heterotrophy is crucial for efficient utilization of renewable and waste substrates. The utilization of hemicellulosic pentose in yeast remains challenging. By harmonizing cellular and engineering objectives, highest growth rates and yields can be achieved with minimal metabolic engineering effort. Upstream genes directing pentose flux into central carbon metabolism are identified as rate-limiting factors. Moreover, yeast metabolism shows high adaptability to non-native substrates, making extensive systems metabolic engineering unnecessary.