The shuffle project

Most of my work in the last few years was computational, either looking at the evolution of protein-protein interactions or at the prediction of domain-peptide interactions. The nice thing of working on a lab were a lot of people were doing wet lab experiments was that I had the oportunity to, once in a while, grab some pipettes and participate in some of the work that was going on. One project that worked out well was published today (not open access sorry). My contribution to this project was small but it was a lot of fun and I am very interested in the topic that we worked on. We called it the shuffle project in lab.

The main objective of this work was to study how the addition of gene regulatory interactions impacts on a cell's fitness. We introduced different combinations of existing E.coli promoters and transcription/sigma factors either as plasmids or integrated in the genome. In effect, each construct mimics a duplication of one of the E.coli's sigma factors or transcription factors with a change in its promoter. We then tested the impact on fitness by measuring growth curves under different conditions or performing competition assays.

There were a couple of interesting findings but the two the I found most interesting were:
- The vast majority of the constructs had no measurable impact on growth even by testing different experimental conditions.
- A few constructs could out-compete the control in competition assays (stationary phase survival or passaging experiments in rich medium).

Both of these suggest that the gene regulatory network of E. coli is very tolerant to the addition of novel regulatory interactions. This is important because it tells us that regulatory networks are free to explore new interactions given that there is a limited impact on fitness. From this we could also argue that if there are many equivalent (nearly neutral) ways of regulating gene expression we can't expect to see individual gene regulatory interactions conserved across different species. There are a several recent studies, particularly in eukaryotic species, showing that there is in fact a fast divergence of transcription factor binding sites (see recent review by Brian B. Tuch and colleagues) and many other examples that show that although the selectable phenotype is found to be conserved the underlying interactions or regulations have diverged in different species. (see Tsong et al. and Lars Juhl Jensen et al.)

There are a couple of questions that come from these and other related works. What is the fractions of cellular interactions that are simple biologically irrelevant ? Is it possible to predict to what degree purifying selection restricts changes at different levels of cellular organization ? What is the extent of change in protein-protein interactions ?

Having previously worked on the evolution of protein-protein interactions this is the direction that most interests me. This is why I am currently looking at the evolution of phospho-regulation and signaling in eukaryotic species.