Broad Genome Analysis Shows Yeasts Evolving by Subtraction

by Chris Barncard (University of Wisconsin--Madison) An unprecedented comparison of hundreds of species of yeasts has helped geneticists brew up an expansive picture of their evolution over the last hundreds of millions of years, including an analysis of the way they evolved individual appetites for particular food sources that may be a boon to biofuels research.

A team of researchers led by labs at the University of Wisconsin–Madison and Vanderbilt University sequenced and compared the genomes of 332 species of budding yeasts, all members of a subphylum of yeasts that multiply by producing daughter cells from buds on their surface. More than 200 of the yeast types had their genomes catalogued for the first time for the study, which was published today (Nov. 8, 2018) by the journal Cell.

That common ancestor is an ancient yeast whose progeny began about 400 million years ago to differentiate into the study’s hundreds of yeast species. That includes a fork about 5 million years ago that gave the world Saccharomyces cerevisiae, the yeast that brewers, bakers and wine-makers rely on to put alcohol in their bottles and rise in their bread.

Describing yeast metabolism and the related genes is important for bioenergy production, which relies on yeast and other microbes to turn plant cells into useful, renewable fuels or compounds that can be further refined into fuels.

“Plant biomass is very complex and breaks down into many different kinds of sugars and other molecules,” says (Chris Todd) Hittinger, whose lab is affiliated with the UW–Madison-based, Department of Energy-funded Great Lakes Bioenergy Research Center. “Ultimately what you want is a microbe that’s going to be able to eat as many of them as possible and turn them into something useful.”

Modern yeasts may have become pickier eaters, but the new analysis of their genomes can help biofuels researchers pinpoint helpful skills among a daunting number of candidate yeasts.

“If they want a yeast that’s good at fermenting a sugar like xylose, they don’t have to think, ‘Oh, no, there’s more than 1,000 kinds of yeasts. Where do I start?’” says Jacek Kominek, a Hittinger lab geneticist and (with Opulente) one of the lead authors of the Cell study. “This project gives them a foundation, another way to decide where the most interesting ones are.”

Better still, the new study’s data can help scientists delve further into the workings of those interesting yeasts to pick apart the genetic differences between a yeast that happily munches on a particular plant molecule and one that struggles with the same compound.

Some of them can pack away more than half their weight as oily lipids that are potential biodiesel precursors.

Collaborators on the study include researchers from the U.S. Department of Agriculture, South China Agricultural University, New York University, Purdue University, RIKEN BioResource Research Center and Center for Life Science Technologies in Japan, University of Ljubljana in Slovenia, Universidad Nacional del Comahue in Argentina, Universidade Federal de Minas Gerais in Brazil, and Westerdijk Fungal Biodiversity Institute. READ MORE