We’ve done it with plants and animals. Most of the time, it’s involved some aspect of their morphology, such as the introduction or exaggeration of some physical trait for our benefit through artificial selection. But with fungi, domestication is different.
“If you think of the classic case of domestication in plants and animals, they involved a lot of changes in morphology,” said Antonis Rokas, assistant professor of biological sciences at Vanderbilt University. “But, in fungi, what we’re seeing for the first time, is that almost entirely all the changes are changes in metabolism. So, there’s change in the physiology much more in microbes than in development.”
In the paper, Rokas and his team propose that a thousand years ago, A. oryzae was once a toxigenic microbe that more closely resembled A. flavus than today’s strains do. But that was before sake brewers began working with the fungus, turning A. oryzae into a cell factory to produce the enzymes and metabolites that are necessary to breakdown rice starch into sugar, which is then converted into alcohol by yeast. Through this artificial selection process, the genes involved in sugar production were upregulated, while the genes involved in the production of toxins were down-regulated.
“We think that part of the reason is that when you make sake, you actually have together both A. oryzae and Saccharomyces cerevisiae, the yeast that makes the alcohol. So, this coexistence has selected for A. oryzae to act friendly to the yeast,” said Rokas.
To perform the comparative genetic analysis, Rokas and his team collected genomic data that described the variation between both A. oryzae as well as its wild relative. They then collected gene expression data for some strains of both species when grown on rice. Finally, as part of their three-layer analysis, the lab collected proteomic data that showed the abundance of particular proteins during growth on rice again from each of the fungi.
“The main challenge was distilling down and trying to find the biology amidst these really huge data sets. We were dealing with gigabytes of data, but we’re lucky enough to have a super computer so the majority of the analysis was done there,” said Rokas.
To gain a better understanding about the process of microbial domestication, Rokas plans to study several other domesticated microbes. “In the way that we have a sort of consensus on the process of domestication of several different plants and animals, it would be nice to get the same kind of consensus or picture of how the domestication process works in microbes,” said Rokas.