A regulatory network analysis of phenotypic plasticity in yeast

Networks are everywhere. Trying to catch connecting flights as we shuttle from one airport to the next can make distances between cities seem even greater than they are. Discovering that you are sitting next to a friend of a friend on one of those flights (social contact networks) can make the world seem a much smaller place. Diverse networks, from airports to social interactions to genes and proteins, often have surprisingly similar structure. In all of these networks, some nodes are highly connected to many other nodes, while most tend to have just a few connections. Molecular biologists have found that the connectedness of genes and proteins is correlated with a range of phenomena, from how essential genes are, to the rates at which they have evolved, to the probability that they are lost over evolutionary time. In the yeast gene regulatory network, some genes are turned on and off by just one ’regulatory gene’ while others are influenced by ten or more regulatory genes. In a study of this network, to be published in the May 2005 issue of American Naturalist, Daniel E. L. Promislow (University of Georgia) now shows that network structure can be used to understand ecological relevant traits.

Promislow analyzes the yeast gene regulatory to understand how genes influence phenotypic plasticity. ’Phenotypic plasticity’ refers to the ability of genetically identical organisms to alter their phenotype in response to an environmental change. For example, genetically identical plants grown in sun versus shade will soon look very different from one another.

It turns out that some species are more plastic than others. Until now, we have not been able to determine what kinds of genes determine whether or not an organism displays phenotypic plasticity. A previous study measured variation in activity level for each of the roughly 6000 genes found in yeast across a range of stressful environments. Some genes varied enormously in their expression levels from one environment to the next, while others were relatively constant. That is, some genes were more plastic than others. Promislow has now discovered that the more regulators a gene has, the more plastic the gene. Furthermore, he shows that the plasticity of a gene depends on its function. From these simple patterns, we gain insight into the complex genetic architecture that determines how well an organism can respond to environmental change.