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Bioinformatics on three letters

The peroxisome targeting signal PTS1 is not just three letters! PTS1 is much more than SKL. Mathematically speaking, SKL (Ser-Lys-Leu) is neither necessary not sufficient as a PTS1. The 'not necessary' part is clear: There are other PTS1 amino acid triplets represented by the code. But SKL is also not sufficient in the sense that when this consensus triplet is combined with unfavourable upstream amino acids, delivery to the peroxisome does not work. How do we find and analyse new PTS1 signals under these conditions? Thomas Lingner (now CSO of Genevention) has programmed a powerful maschine learning algorithm that we in this study applied to the yeast Saccharomyces cerevisiae. And, we found two new peroxisomal proteins that we named Pxp1 and Pxp2. These two peroxisomal proteins expand the PTS definition in yeast by two amino acids in position -3 that did not appear in other PTS1 proteins. Molecular medicine MSc student Christopher did a great job in the 'wet' part of this project.

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