Evolution of transcriptional regulatory networks in yeast populations

...or, all you ever wanted to know about wine yeast, but were afraid to ask
Duccio Cavalieri
Plenary Talk, Afternoon Session, 1 September (11th MGED Meeting, 1-4 September, 2008)

Volatile organics in: Grapes = 466 , Wine = 644, Difference= 178. The most ancient evidence from 3150 BC, in Egypt. However, the ecology of yeast has been mainly unknown. The probability of S.cerevisiae on a pristine grape is .0005, while per damaged grap is 25%, which means 10^4 - 10^5 (probably from clonal expansion). Proportion of damaged grapes is 1/1000. When there are many organisms (above 4%), cerevisiae is the only survivor. 88% of the S288c gene pool derives from EM93 isolated from rotten figs in Mercedes, California in 1938. Most regulatory genetic variation is due to a high rate of cis acting alleles and a small number of trans acting alleles.

Exploring the genome-environment interaction, and looking at mendelian segregation of expression profiles. One strain's colony, after 4 days' growth, produces an interesting and cohesive shape ('filigree'). Compared the parent to the first segregants. They found that 2 alleles were controlling the expression of 378 genes, or 6% of the genome. They tried to clone these genes from the recessive mutation, but failed after screening 300 false positives. Then, a few years later, tried to get the genes responsible for the phenotype via pathway analysis via a Fisher exact text followed by pathway correction. If you compare with the wt, there isn't a single significant pathway that segregates except the cell cycle stuff. Then he applied Bagel Analysis to extract absolute values and probabilities using bayesian statistics - discovered significance for amino acid transporters. They then did the same experiment, but with rich amino-acid medium, and with a minimal aa medium. The filigree strain has a mutation in SSY1, which causes a truncation. This means you lack the sensing part of the protein on the outside of the membrane, which means that the strain is blind to the amino acids in the media. This makes the yeast produce its own amino acids.

Only a small number of genes were differentially expressed based on the filigree phenotype. Ammonia mediates signalling between these cells. MEP1, MEP2, and MEP3, and PHD1 three were overexpressed in the strain. M28 is homozygous for a mutation causing non-disjunction of cells after cell division affecting AMN1 and GPA1. The daughter cell doesn't divide immediately after division, which creates 3d structures.

Means that the potential for differences in the various wine strains is quite high. The estimate of the relatedness between By4743 and Em93 (parent strain) is 90% similar. Most of the variation is not evenly distributed. Mutations in the aa, nitrogen sensing, and hap genes are highly pleiotropic. HDAC and SIR-SAS gene expression control provides the cell with a mechanism of epigenetic buffering of variation.

These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. :)