The main subject of my PhD thesis are selenoproteins. Selenoproteins are proteins which includes selenocysteine (the 21st aminoacid) in their aminoacid chain. This aminoacid is inserted cotranslationally, as standard aminoacids, but unlike them it lack a codon of its own in the genetic code. It is inserted in correspondence to a UGA codon (normally a stop) recoded by the presence of a stem-loop structure in the 3'UTR of selenoprotein transcripts - the SECIS element - read by a set of factors that we call the selenocysteine insertion machinery. Selenocysteine has an specific elongation factor, and a specific tRNA.

My PhD consists of several projects all related to the genomics of selenoproteins, arisen from needs, ideas and collaborations during these years. Anyway, I divide my PhD conceptually in two sections.

One is a methodological section. Selenoproteins are usually misannotated, since no standard prediction program will put a UGA codon within the coding sequence. So, it is necessary to develop specific tools for selenoproteins predictions. I am working on several methods for selenoprotein prediction in genomes. The most mature (it is already published) is Selenoprofiles, a profile based pipeline (see http://big.crg.cat/services/selenoprofiles).

The second section concerns the most biologically interesting aspects of selenoproteins, related to the evolutionary dynamics of selenoproteins and of the selenocysteine trait itself. In fact, although selenoproteins are found in all domains of life, we observe their absence in a number of minor and major lineages (fungi, higher plants, some insects). All selenocysteine machinery is usually absent in such species, too. How does the capability of producing and inserting an aminoacid got lost in these species? This is one of the questions that I'd like to answer.
We investigate the selenoprotein extinctions particularly in insects, where we observed many such events.
The selenoprotein extinctions feed the main question in the selenoprotein field, that is to say, what are the fundamental differences between selenocysteine and cysteine? why organisms take so much trouble in producing and inserting Sec, when we find homologues proteins with Cys? What is the nature of the selective pressure to keep Sec, so strong in vertebrates and so weak in insects, where selenocysteines are being lost or converted to cysteines?
We think that to understand the answer to these question, we must first describe the history of selenoproteins and of the selenocysteine trait in general across eukaryotes, and then across the whole tree of life.
To do this, we investigated the phylogenesis of a particular selenoprotein family, which is also necessary to produce selenocysteine: the SelenoPhosphate Synthetase.