The Evolution of Sedolisins in Eukaryotes, Bacteria and Archaea

MATÍAS IRAZOQUI; FACUNDO ORTS; ARJEN TEN HAVE

Rosario

Congreso; IV Congreso Argentino de Bioinformática y Biología Computacional; 2013

Asociación Argentina de Bioinformática y Biología Computacional

BackgroundProteases are enzymes that catalyze the hydrolysis of peptides. They are classified into different classes on the basis of their catalytic mechanism and further into about 50 clans and numerous families on the basis of similarity. Subtilisins and Sedolisins are homologous serine proteases. Where the basic subtilisins have the catalytic triad of His-Asp-Ser, the sedolisins family have the triad Glu-Asp-Ser and are most active at pH 3, unique among serine proteases. Although the sedolisin activity was first described in 2001, sedolisin homologues have been identified in all three superkingdoms. In addition, a novel subfamily was recently suggested to have evolved in bacteria (Siezen et al., 2007). It has been shown that the fungus Aspergillus fumigatus secretes at least three sedolisins with tripeptidyl-carboxyl peptidase activity and one with endoprotease activity. Initial studies on Botrytis cinerea have shown it encodes for seven sedolisins, three more as compared with other phytopathogens, which might be related to that the fact that it acidifies its medium and has been shown to depend on other acid hydrolases. Interestingly it has relatively few subtilisins. All facts together make sedolisins an interesting subject for molecular evolutionary studies in general and structure-function prediction analysis in particular. Here we present the first data on our analysis of real sedolisns.Materials and methods Sequence mining(Fig 1A) was performed using iterative HMMer profiling with profiles made on three MSAs. A first MSA consisting a eukaryotic sedolisins was obtained from MEROPs, the peptidase database. Then, a secondMSA, was made of bacterial sequences obtained from Siezen et al., 2007. HMMer profiling was performed against 450 complete proteomes, including Archaea, Bacteria and Eukaryotes. MSAs for the standard sedolisins were made with T-coffee, MAFFT, ProbCons and Promals3D and the best MSA was manually improved and subsequently trimmed with BMGE prior to phylogeny by PhyML. ResultsApproximately 800 sedolisins were identified in the iterative HMMer profiling search. 60% of the sequences belong to Bacteria (78 species), 30 % to Eukaryota (96 species) and 10 % to Archaea (23 species). Hence, sedolisins do form a superfamily. Phylogeny (Fig. 1B) shows that three to four sedolisin subfamilies are present in all three superkingdoms The topology suggests that sedolisins have evolved towards a superfamily after the bifurcation of eukaryotes and prokaryotes. Based on the obtained MSA and phylogeny we will perform structure function analysis initially be directed at the identification of the endo- and tripeptidyl activities and the possibility of convergent evolution.