When yeast or bacteria are genetically engineered to consume a novel feedstock, they may develop a case of metabolic indigestion. That is, these engineered organisms may end up with nutrient metabolic pathways that are poorly integrated with downstream pathways for nutrient assimilation and cell growth.
Unlike natural organisms, which incorporate catabolic genes into a group of genes called a regulon, engineered organisms may admit catabolic genes outside such regulons, in which case the genes may be expressed constitutively, continually, without regard for any regulatory contingencies. It a sense, natural organisms have a table d’hôte genomic menu, whereas that for engineered organisms is à la carte.
To ensure a better gastronomical experience for engineered yeast, scientists based at Tufts University adopted a table d’hôte approach. They took a set of regulatory genes, called a galactose (GAL) regulon, that normally processes galactose—a favorite on the yeast menu of nutrients—and replaced some of the genes with those that become activated by, and direct the breakdown of, an alternative nutrient, namely, xylose. All other genes in the GAL regulon were unchanged. In doing so, they preserved a more natural interaction between the genes that govern feeding and those that govern survival. The new synthetic regulon, dubbed XYL, enabled the yeast cells to grow more rapidly and to higher cell densities.
“Instead of building a metabolic framework from the ground up, we can reverse engineer existing regulons to enable an organism to thrive on a novel nutrient,” said Nikhil U. Nair, Ph.D., assistant professor of chemical and biological engineering at Tufts. “Adapting native regulons can be a significantly faster path toward the design of new synthetic organisms for industrial applications.”
Dr. Nair is the corresponding author of a new study (“A Semi-Synthetic Regulon Enables Rapid Growth of Yeast on Xylose”) that appeared March 26 in Nature Communications. This study describes how by partially and fully uncoupling GAL-responsive regulation and metabolism in Saccharomyces cerevisiae, the Tufts team demonstrated the significant growth benefits conferred by the GAL regulon.
“…by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy,” wrote the article’s authors. “This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth.”
In synthetic biology, organisms such as bacteria or yeast may be transformed into “mini-factories” when fed nutrients to produce a wide range of products, from pharmaceuticals to industrial chemicals and biofuels. However, a central challenge has been the efficient conversion of abundant feedstocks into the final product, particularly when the feedstock is not something the bacteria or yeast normally “eat.”
“Instead of building a metabolic framework from the ground up, we can reverse engineer existing regulons to enable an organism to thrive on a novel nutrient,” explained Dr. Nair. “Adapting native regulons can be a significantly faster path toward the design of new synthetic organisms for industrial applications.”
One such application is the production of ethanol as a biofuel. Concerns have been raised that diverting significant portions of crops, such as corn, to biofuel production could have a negative impact on availability and cost of the food supply. However, xylose is a sugar derived from the otherwise indigestible parts of plant material. The ability to ferment xylose can be a path to biofuel production that does not compete with the food supply.
As part of the study, Dr. Nair and his team took a closer look at what exactly accounted for the improved survival of the xylose-eating yeast organism. They found numerous genes activated in the XYL regulon–controlled yeast that upregulated pathways involved in growth, such as cell wall maintenance, cell division, mitochondrial biogenesis, and adenosine triphosphate production. Yeast strains that had constitutive (mostly unregulated) control of xylose metabolism triggered pathways related to cell stress, starvation, and DNA damage.
“Our study applied this approach to xylose, but it suggests a broader principle—adapting native regulons for the efficient assimilation of other non-native sugars and nutrients,” assersted Dr. Nair. “Nature has already done the work of tuning genes and metabolic pathways to the environment of the organism. Let's make use of that when introducing something new on the menu.”
