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Antioxydant system genes in Euplotes sp

Name: 
Diana Ferro
Team: 
University of Münster, Germany
Host: 
University of Camerino, Italy
Date: 
Monday, November 9, 2015 to Friday, November 20, 2015
Report: 

In the period between the 9th and the 20th of current month I took part in a brief research experience in Prof. Miceli laboratory at the University of Camerino. During these two weeks I had the opportunity to extend my current research on the antioxidant system in eukaryotic cells to other organisms belonging to the alveolata phylum.

My current research activity focuses on the evolution of glutathione peroxidase genes (gpx). This class of genes codifies for enzymes that are included in the antioxidant system and contributes to protect the cellular redox homeostasis. GPX enzymes use glutathione as a substrate during the catalytic reaction that removes peroxide from the cytoplasm. The evolution of gpx reconstructed by Margis and co-workers in 2008 highlights the presence of difficulties to identify a common ancestor for gpx isoforms. The absence of a mutual ancestor for some gene clusters could represent the result of duplication events, gene losses, horizontal gene transfers and evolutionary convergences. In particular, in 2008 a phylogenetic comparison between GPX proteins belonging to know metazoan sequences showed a curious distribution of the protozoan GPX sequences across the phylogenetic tree. They form two distinct clusters: one cluster contains isoforms with high similarity to the isoform 7 and 8 of vertebrates, the other cluster is represented by isoforms similar to the isoform 4 from vertebrate’s and other invertebrate’s GPX proteins.

In our days, this unusual and unexpected “evolutionary pattern" can be easily investigated adding new information from in-silico computational biotechnology. During my research experience in Camerino I applied my knowledge in handling transcriptomic and genomic data to analyze Euplotes crassus, Euplotes focardii and Euplotes harpa sequence databases (Data Author: Miceli et all., 2015; Petroni et al., 2015)*. Using a comparative approach, I performed a screening of the RNAseq databases in order to identify transcripts that can codify for GPX proteins. The collected sequences will be merged with Tetrahymena sp and Paramecium sp sequences and then, the alveolata GPx collection will be used for a Bayesian Phylogenetic Analysis that will provide a more complete evolutionary history for these antioxidant system genes in ciliates. Moreover, where a reference genome was available, the promoter region was identified and, using a custom python pipeline, putative conserved regulatory regions were mapped. In particular, I searched for conserved regulatory elements, that have strong relation with detoxification from reactive oxygen species, like: antioxidant responsive elements (ARE), half- AREs, xenobiotic regulatory elements (XRE) and metal responsive elements (MRE). All the data obtained during the two research weeks will be included in a manuscript in preparation that will provide new insights about the function and evolution of gpx genes in ciliates.

 

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