July 16, 2012
Most strains of Saccharomyces cerevisiae don’t stick together very well. And hardly any of them form biofilms. But it would be very useful to have a better understanding of why some strains like to stick together and others do not.
Stickiness helps in any process where you want the yeast to do something and then get rid of it. An obvious example is ethanol production either for energy or to make our beer and wine. After sticky yeast are done with their job of making the alcohol, they simply fall to the bottom of the fermentor or float on the surface in a biofilm (the “flor”). This makes the step of separating the yeast from the finished product that much easier.
Understanding more details of yeast stickiness would also be useful for studying harmful yeast. Adhesion to other cells and to substrates is an important factor in pathogenesis. It would be nice to investigate this phenomenon in the more tractable brewer’s yeast.
The Ibeas lab has decided to figure out why most strains of S. cerevisiae can’t flocculate by comparing one of the few that can (the “flor” strain used to make sherry) to a reference strain that can’t. They previously showed that a key gene in the process, FLO11 (also known as MUC1), is expressed at much higher levels in flor. They were also able to show that a large part of this increased expression comes from a 111 base pair deletion in the FLO11 promoter in this particular strain.
In a recent paper in GENETICS, Barrales and coworkers set out to investigate why the loss of these 111 base pairs leads to increased gene expression. They were able to conclude that the deletion does not significantly affect histone occupancy at the promoter. What they could see was that histone placement was affected and that PHO23 may play a significant role in this.
The researchers had previously shown that the histone deacetylase complex (HDAC) Rpd3L was important for maximal FLO11 activity. They next wanted to determine if this complex was the major player in explaining the increased activity of the 111 bp deletion FLO11 promoter (Δ111) over the wild type (WT) one. They did this by comparing the level of mRNA made by each promoter in strains lacking either the Pho23p or the Rpd3p subunits of the Rpd3L complex. They found that the Δ111 construct was much more severely compromised by the loss of PHO23 than was the WT one. (A bit confusingly, neither was much affected by the loss of RPD3.)
Given that PHO23 is part of a complex that affects chromatin, the next thing the researchers did was look at the histones in and around both FLO11 promoters. They found that PHO23 was involved in maintaining an open chromatin structure at the FLO11 promoter but that deleting the 111 base pairs didn’t affect this process significantly.
Where they started to see subtle differences was when they looked at histone placement as opposed to occupancy. Using micrococcal nuclease protection to map chromatin structure, they found a number of differences between the two promoters, centered on the deletion and the TATA box, and deleting PHO23 affected the two promoters in different ways.
It appears that FLO11 is upregulated in the flor strain because the deletion of 111 base pairs leads to an altered chromatin structure. The next steps will be to figure out what this means and then to use that knowledge to create stickier yeast. We’ll end up with a better understanding of transcriptional regulation and adhesion, and beer and wine makers may end up with even better self separating yeast.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
Categories: Research Spotlight