Strategy for searching potential partner genes of Drosophila melanogaster Sws gene

Abstract

Aim. The Drosophila swiss cheese (sws) gene is a mammalian ortholog of neuropathy target esterase (NTE or PNPLA6). This protein is involved in the functioning of the nervous system and causes some kinds of polyneuropathy with the mechanism unknown. Genes-interactors of the sws gene should be found to investigate the cellular mechanism of SWS/NTE-dependent neuropathy formation and to find out what signaling pathways SWS is involved in. Methods. The search was done in the Drosophila database – Flybase, in the NCBI (Gene) database to search for orthologs, and the String web resource was used in the case of potential protein interactions. Results. Only four experimentally identified genes-interactors were listed in the Flybase. Based on the expression changes data of 28 genes at PNPLA6 silencing, a theoretical search for the corresponding orthologs in Drosophila was done. The in silico assay predicted 10 proteins that are probably functioning within one metabolic pathway. Conclusions. The methods applied gave us a wide list of genes that can interact with sws at different levels: from the expression pattern to the phenotype. Therefore, 25 potentially partner genes were selected to verify the genetic interaction of these genes in vivo.
 Keywords: gene swiss cheese, neuropathy target esterase, neurodegeneration, in silico analysis, genes interaction, Drosophila melanogaster.