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 “extrinsic” factors—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. [Display omitted] •Native regulon can be repurposed for efficient utilization of non-native pentoses•Synthetic heterotrophy requires optimization of the “extrinsic”/heterologous genes•Perturbation of “intrinsic”/native genes is counterproductive or unnecessary Using semi-synthetic regulon, Trivedi et al. obtained high growth rates and biomass yields with minimal metabolic engineering effort on xylose and arabinose. They found that the bottleneck in achieving maximum possible growth rate was due to unoptimized “extrinsic” (heterologous genes) factors rather than “intrinsic” factors (e.g., native metabolic, regulatory genes).