Biography

I studied Biotechnology (undergraduate) and Bioinformatics (master) at the University of Bologna. I came to the Bionformatics and Genomics group in January 2008, initially just for the final project of my Bioinformatics master, then for a PhD until 2013, and finally for a short postdoc in 2015. In between, I visited the lab of Vadim Gladyshev at Harvard Medical School in Boston, USA, and the lab of John Atkins at University College Cork, Ireland.

Resumé

I investigate the evolution of selenoproteins, proteins containing a selenocysteine residue (Sec, the 21st amino acid). Sec is inserted co-translationally, as standard amino acids, 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. A set of factors is required to express selenoproteins, both to produce Sec and to insert it in response to SECIS (Sec machinery). Selenocysteine has an specific elongation factor, and a specific tRNA.

Selenoproteins are usually missed or wrongly annotated, since standard prediction program avoid the UGA codon within the coding sequence. So, it is necessary to develop specific tools for selenoproteins predictions.

Selenoprofiles [1] (http://big.crg.cat/services/selenoprofiles) is a profile based pipeline able to annotate known selenoprotein families, also useful for gene prediction of any protein.
SECISearch3 [2] is instead a program for the prediction of eukaryotic SECIS elements. The program is combined with blastx in Seblastian [2], which predicts known or novel selenoproteins in nucleotide sequences. It searches for homology in candidates to proteins in a reference database (ncbi nr), focusing on UGA/Sec or UGA/Cys alignments. SECISearch3 and Seblastian are available in a webserver at http://seblastian.crg.es.

Marco Mariotti

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Joined: 2009-10-07

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