Origin of Lactose Fermentation in <i>Kluyveromyces lactis</i> by Interspecies Transfer of a Neofunctionalized Gene Cluster During Domestication

Abstract

Humans have used yeasts to make cheese and kefir for millennia, but the ability to ferment the milk sugar lactose is found in only a few yeast species, of which the foremost is Kluyveromyces lactis. Two genes, LAC12 (lactose permease) and LAC4 (lactase), are sufficient for lactose uptake and hydrolysis to glucose and galactose. Here, we show that these genes have a complex evolutionary history in the genus Kluyveromyces that is likely the result of human activity during domestication. We show that their ancestral role was in a combined lactose and cellobiose assimilation system, which used Lac12 to import both of these sugars into the cell, and then hydrolyzed lactose using Lac4, and cellobiose using a cellobiase, Cel2. A second cellobiose transporter Cel1 was also present ancestrally. In the K. lactis lineage, however, the ancestral LAC12 and LAC4 were lost and a separate upheaval in the sister species K. marxianus resulted in loss of CEL1 and quadruplication of LAC12. Among its four LAC12 genes, one became neofunctionalized as an efficient lactose transporter capable of supporting fermentation, specifically in dairy strains of K. marxianus where it formed a LAC4-LAC12-CEL2 gene cluster, while another remained a cellobiose transporter. Then, the ability to ferment lactose was acquired by K. lactis var. lactis by introgression of a 15 kb subtelomeric region containing LAC12 and LAC4 from a dairy strain of K. marxianus. The genomic history of the LAC genes shows that strong selective pressures were imposed on yeasts by early dairy farmers.