Getting more complex and gaining.... nothing

 The origin of complexity is a highly debated issue in biology. For instance, many functions in the cell are carried out by intricate macro-molecular complexes formed of a multitude of subunits. When tracing the evolution of such complexes, as we did with mitochondrial Complex I, one often finds that the number of subunits have increased through time. However, the addition of subunits not always seems to correlate with the acquisition of novel functions, which would provide a selective advantage for the increase in complexity.  Can we think of a mechanism promoting a trend for increasing complexity in the absence of a selective advantage provided by a novel function?.

 A recent paper by Finnigan and colleagues show a plausible mechanism and present evidence that this may have been responsible for the acquisition of a novel subunit in fungal vacuolar ATPases (depicted below).

 This molecular machines that pump protons across membranes have a membrane ring (in green in the figure) formed by 6 units. In vertebrates two different subunits (originated from the duplication of an ancestral gene) form the 6-units ring in a 1:5, stoichiometry. In fungi a more recent duplication brought about one more subunit type so that the ring is formed by the products of three different genes in a 1:1:4 organization. Using ancestral sequence resurrection (I love that name!), a technique that consists of reconstructing most likely ancestral sequences and then synthesizing them in the lab, they show that a single mutation acquired early in each paralogue, was sufficient for making the two of them indispensable. Thus, such model could explain a trend to increase complexity in multi-paralogue complexes (those comprised by some subunits derived from duplicated genes) without a requirement for an initial selective advantage.  

 In a way, I see this model as a special type of sub-functionalization. That is, the two new paralogues would in sum make the same function that was performed by the ancestral gene. In the absence of more examples we do not know how widespread is this mechanism, but the fact that it does require few likely events and that it actually constitutes a "ratchet" (as noted by W Ford Doolittle), that is once you gain that complexity you don't go back, one would expect to have occurred in several of many multi-paralogue complexes, at least in some lineages. 

 Perhaps this could explain an intersting finding we did some years ago when looking at the evolution of the mitochondrial electron transport chain in fungi (mostly formed by multi-protein complexes): the amount of duplications in members of this complexes was of the same level as other proteins. This is in contrast to the gene-dosage effect hypothesis that states that complexes would tend to duplicate only when the stochiometry is conserved (that is in when the whole complex duplicates, e.g in whole genome duplications). 

 Finally, another remark that I always do when seeing ancestral sequence resurrection working is that the fact that ancestral reconstructions display the expected biochemical activities (e.g by complementing extant sequences) is an indication that the models of evolution we use are not that wrong after all.

 

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.