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Science Lesson: Basic biology

How yeast genomes change

Genomes are dynamic. Every time a living cell divides, a small number of mutations (i.e. changes to the DNA) occur randomly in the genome. When those mutations improve an organism’s chances of survival, they can be selectively perpetuated through successive generations. This continual and imperceptibly minute process powers the evolution and creation of all species, and ordinarily progresses at a glacial pace, with timescales in the thousands, if not millions, of years.

Changes to the genomes of organisms that give rise to the human diet (i.e. cereal crops like barley and food microbes like yeast), however, have been accelerated by human activity stretching back to the start of civilization. Even without the knowledge of genes and DNA, or even cells, humans have relied on selection of favorable variants. Yeast, for example, have changed quickly and substantially as they have evolved to occupy man-made environments such as in a bakery or beer fermentation. Even while humans had no understanding of genes and DNA, through the process of selection, brewers have shaped industrial strains to contain vast differences in their genomes. For example, consider how the genomes of brewer’s yeasts are more efficient at consuming maltose, and wine yeasts are more efficient at consuming fructose, the primary sugars in barley and grapes, respectively. In each of these cases, large multi-genic changes have given rise to favored variants.

The rate of change for yeast accelerated even further in modern industrial times when strains were deliberately shaped by the tastes and preferences of bakers, brewers, and their customers. Thanks to a number of recent genome sequencing efforts, we have learned just how much yeast genomes have changed over the last several hundred years. In a number of excellent studies, we have learned that industrial brewer’s yeast genomes have been domesticated by humans over the course of brewing history, much in the same way that wild cabbage was bred into broccoli, kale, and cauliflower, or how wolves were bred into various types of dogs.

When a mutation arises that makes the yeast better suited to its environment (i.e. faster maltose consumption, more resilient to the harsh conditions inside a fermentor), or creates a quality that brewers and beer drinkers prefer, these mutations may be consolidated into the genome by human intervention. To illustrate, let’s start with the example of isoamyl ester, the banana-flavored compound we introduced in What is a gene.

Consider a hypothetical scenario: Long ago, brewers everywhere used an “ancestral” brewer’s yeast strain that produced low levels of isoamyl ester during fermentation. Then one day, a random mutation occurred at a single brewery that resulted in a strain that produces more isoamyl ester. During the process of serial repitching—the practice of transferring an inoculum of yeast between successive batches of beer—some batches turned out with more banana flavor. Due to its popularity, brewers selectively repitched from the beer batches with the strongest banana flavor until the mutant strain was shared around the local brewing community, displacing the original yeast strain.

What’s the lesson here? Although DNA was first discovered less than 100 years ago (in 1928), humans have been intentionally shaping the genome of the organisms that ferment our foods and beverages for thousands of years, even if they didn’t understand the underlying mechanism. In the past several decades, new technologies have enabled groups—including Berkeley Yeast—to rewire yeast metabolism to precisely control the level of compounds that yeast already makes, or to program yeast to create virtually any chemical compound found in the natural world. While this is a profound advancement, it is but the latest innovation in the continuous evolution of an ancient practice.

Figure 1 - How random mutations lead to yeast with preferred qualities
Figure 1. How random mutations lead to yeast with preferred qualities.