Adaptive evolution in yeast reveals many genetic pathways to biofilm formation

Yeast biofilm formation contributes in both positive and negative ways to industrial processes. In brewing, yeast biofilms and clumps act as a desirable natural filtration system; in other industrial processes like biofuel production, biofilms can be highly disruptive and damaging to equipment. This dichotomy demonstrates the importance of understanding and manipulating the genetic determinants of biofilm-related traits to achieve industrially desirable outcomes on both ends of the spectrum. Experimental evolution in the laboratory provides a unique testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae can use to achieve biofilm phenotypes. The popular lab strain S288C is non-flocculant due to a nonsense mutation in the gene encoding transcription factor Flo8, which regulates flocculation. Despite this mutation, these strains frequently evolve the ability to clump and/or stick to surfaces during the course of experimental evolution in chemostat culture. These evolved strains therefore present an opportunity to examine bypass suppressors of Flo8 and alternative mechanisms for biofilm formation.

We have sequenced 24 such evolved clones. Interestingly, none of the strains reverted the point mutation in FLO8. As previously found, we recovered multiple loss of function mutations in ACE2, which cause mother-daughter separation defects. We also checked for repeat expansions in Flo8-regulated genes FLO1 and FLO11, known to be involved in true flocculation, and identified a clear expansion in one clone. Additional candidate mutations are currently being tested for novel associations with biofilm formation. This work applies adaptive evolution to better understand the genetic complexity of an industrially valuable phenotype.