Sunday, January 30, 2011

Why only hungry K.lactis have sex?

One of my professors at the Univeristy of Valencia used to tell us that a Yeast's life was "mainly driven by food and sex", referring to the relevance and impact in this single-cell organisms of the signalling pathways in response to starvation, presence of nutrients or pheromones. One particular species of yeast, the diary yeast Kluyveromyces lactis, seemed to have combined both stimuli into a single pathway, requiring both starvation and pheromone signals to mate. Although this was known for decades, the specific mechanism and how it had evolved remained a mystery.

In a recent paper by the group of Alexander Johnson (UCSF), the origin of such phenotype has been established, by comparing regulation of mating genes in K. lactis, Saccharomyces cerevisiae, and Candida albicans. The evolutionary mechanism involved is that of a transcriptional rewiring, in which the core mating genes have been put under the control of the gene responsible for signalling starvation (RME1), which in turn is now also controlled by the mating factors (a/alpha). This intercalation of a new step within the mating signalling pathway effectively results in both stimuli being necessary for mating.

How could this happen? the implied scenario involves the acquisition of regulation by mating factors for RME1, at least four core mating genes loosing their reponsive elements to the mating factors - rather than change of the binding site of the factor, which was found to be similar to that in the other yeasts-, and the same genes acquiring responsive elements to RME1. 9 transitions in total. The first one (RME1 under control of mating) also occurs in S. cerevisiae, so it seems to have pre-dated the re-programming of the core mating genes control, effectively paving the way for the final rewiring. To unveil the order of the  other 8 transitions, one would need to find intermediate states in other yeasts. Given the potential deleterious effects of a mating gene loosing pheromone control, and the low probability of loosing one binding factor while acquiring the other one in four genes, I envision an intermediary state where the genes where responding to both RME1/mating factors. Then, the lost in a single core mating gene of the direct response to mating factors would render the pheromone-responsive elements in the other core genes non-functional (three of this core genes encode proteins that should be combined into a heterotrimer to function), thus leaving the only functional route that passing through RME1. Accumulating mutations would have then simply removed the pheromone-response site.

An interesting story of how regulation can effectively be altered by evolution in small steps.  Another important connection is that of the fact that for many fungi, most particularly pathogens such as Candida glabrata, we lack direct observation of the mating cycle although they conserve intact the mating genes and for some we have indirect evidence that they mate. Perhaps it all comes down to very specific requirements for mating, achieved by intercalating layers of regulation of mating genes as that found in K. lactis.

Friday, January 28, 2011

Map of scientific collaborations

My brother pointed to me this map of scientific collaboration between researchers made by  Olivier H. Beauchesne. Inspired by a similar map drawn for facebook friends, O. Beauchesne used a bibliographical database to trace links between universities if their respective researchers were co-authoring articles.

The result is an amazing picture, that shows that, as for many other things, research is unevenly distributed around the world. With a clear North/South divide, research and economic centres overlap almost completely. As expected, North-america, Europe and Japan are the most densely connected areas. Emerging research countries such as India, China, and Brasil can also be recognized. Within Europe, South UK, Paris, the Netherlands, and Switzerland/Austria seem to form research hubs. Perhaps influenced by language and cultural ties, Spain and Portugal are relatively well connected to central and south-American countries.

Barcelona, where my lab is located, appears to be the most densely connected research pole in Spain.

Wednesday, January 19, 2011

A PLoS currents for the Tree of Life

 I recently discovered that PLoS Currents has opened a new track for the Tree of Life: PLoS Currents: Tree Of Life.

 PLoS currents is yet another form of publishing scientific results. A small group of editors and reviewers reviews every paper to check that it is t is " a legitimate work of science and does not contain any obvious methodological, ethical or legal violations." If that's the case papers are published immediately (and indexed in Pubmed). Another novelty is that all the publication procedure is based on a web-based tool called google-knol.

 So far there are only 4 articles (or "knols"?) and they all seem pertinent to the topic, one of them was very useful to me, since it described a compilation of benchmark datasets for phylogeny. 

 It looks worth to keep an eye.