Dear Dr Zeke,
Thank you for your interest in our article. From your comments we have to conclude that you have misunderstood or misinterpreted our work. In our answer we try to clarify some of your comments.
1. The evolution of protein kinases was not the topic of our paper. In the introduction we made the comparison between the protein kinases and protein phosphatases to demonstrate the significant differences between the evolution of the two enzyme families. It is well known from the literature that the kinases evolved from a common ancestor, they have a wide distribution and a well conserved catalytic domain. On the other hand, the phosphatase catalytic subunits are less numerous but more diverse. Separate phosphatase families utilise distinct catalytic mechanisms and are clearly different from each other according to their structures and origins. These solid facts support the assumption that kinases appeared before phosphatases. It is more likely that the kinases phosphorylated their substrates and produced phosphoproteins before the phosphatases had a chance to remove the phosphates, than the concerted evolution of the two enzyme families suggested in your comment. In the absence of phosphoproteins what could have been the function of the phosphatases? Our scenario is in agreement with the most important rule of evolution, natural selection, telling that only the advantageous mutations can persist. In the case of the PPP phosphatase family the precursor enzyme adenosine tetraphosphatase underwent several rounds of mutations until it become suitable to accommodate phospho-Ser or phospho-Thr residues into its catalytic cleft. How can you imagine these complex structural changes happening in the absence of the relevant phosphoprotein substrates? Only after the evolution of the first phosphatase can we speak about concerted evolution, but we cannot deny that there was a distinct time laps between the evolution of the kinases and the phosphatases.
2. We have never stated that molecular evolution happened only in a single enzyme family. To the contrary we are aware of the fact that many different genes could have changed at the same time in a given organism. However based on this argument you cannot question the value of analysing the changes in a given enzyme family. If you believe that only global changes are important you overlook the significance of fine details. Remember, global genome changes originate from the union of individual gene mutations.
3. You ask why we concentrate on the more dynamic members of the PPP family instead of the core enzymes. There are two reasons for that: (i) we have a long tradition in the investigation of the novel phosphatases and we were very much interested in finding out why the classical and molecular genetics approaches failed so many times in the search for the functional significance of these enzymes. (ii) The classical core enzymes have already been characterised in more details. We focused our paper on the uncharted areas and doing so we highlighted new discoveries in this field that deserved more attention and a full fetched documentation.
4. You state that our analysis has been restricted, but forget about the obvious obstacles that prevented the broadening our approach. In our paper we investigated all of the fully sequenced insect genomes that were published at the time of writing. In addition we have to stress that the Drosophila specific novel members of the PPP enzyme family are not present in any other organism including animals, plants and fungi. The extension of our work in the direction of additional species would have been meaningless.
5. What about flies and bees? It is a complete misunderstanding to say that we questioned the close genetic relationships between the two species. The take-home message of our paper is the opposite again. We know very well that these insects are close relatives, and most of their gene families are similar to each other. Here we point out, that contrary to general expectations the members of the PPP family took a different evolutionary path in the Drosophiliadae. Thus, we presented a case telling that the predictive value of general genome comparisons is limited. It is a wrong approach to assume that all of the enzyme families are similar in similar organisms.
6. You also ask if our conclusions are valid for other phosphatase families of the fruit flies. From the introduction (paragraph 1) it is clear that contrary to the kinases the phosphatase families are distinct even in the same organisms. Consequently, we are not in the position to tell anything about them. The lesion we learnt is clear-cut, do not jump into predictions based on assumptions and uncertain analogies, but analyse all of the members of a gene family carefully one by one, since Nature is much more colourful than you would have ever imagined.