Research

How often were housekeeping genes transferred between divergent organisms? It appears that these events were infrequent enough to extract the organismal evolution from the simultaneous analyses of different molecular markers. The transfer of housekeeping genes can be used to correlate the evolution in different parts of the tree of life.

What were the properties of the early eukaryotes? How did the different parts of the eukaryotic cell originate? Using V-ATPase A-subunits as molecular markers, we try to identify early branching eukaryotic lineages. This V-ATPase subunit appears more appropriate than other proteins and RNAs, because it contains many sites that are slow to undergo substitutions, and because the outgroup (archaeal ATPase catalytic subunits) is connected to the ingroup by a comparatively short branch. Some frequently encountered artifacts (e.g. microsporidia as a deep branching lineage) are not encountered when analyzing V-ATPase catalytic subunits.

How do enzymes with new properties (regulation of expression, enzyme properties) arise?
How is selection pressure maintained on nearly identical gene copies?
We currently study two small gene families in Arabidopsis: cell wall bound acid invertases and vacuolar ATPase B-subunits. In the former we have identified two very divergent isoforms. One of these is only expressed in flowers and siliques, the other in all other tissues tested. Surprisingly, the tissue specificity is not conserved between different species. The V-ATPase B-subunit encoding genes are much more similar to each other, each is present in differently processed transcripts, and so far, we have not detected significant differences in tissue specificity.

Different sites in proteins experience substitution events with different probability. This process, called 'among site rate variation', and 'substitution bias' greatly influence the velocity with which sequences accumulate observable differences. Accurate correction for multiple substitutions is necessary to precisely reconstruct the evolutionary history of proteins, and to date the early evolution with respect to time.

Do changes in the quaternary structure of ATPases correlate to changes in physiologic function? (proton pumping ATPase versus ATPsynthase?)
Did early eukaryotes use their V-ATPase for ATPsynthesis?
Was the eukaryotic ancestor an acidophile?
Is the subunit stoichiometry related to the ATP/proton ratio?

Inteins are intervening sequences that are transcribed and translated into protein. Only at the level of the protein do they selfsplice themselves out of the host protein. Inteins are found in pro- and eukaryotes. Usually they are located in the most conserved (and most important) part of the host protein. Do inteins confer any benefit to the organism? How do they spread between organisms?