Functional annotation pipeline for the analisys of microarray data with regards to subcellular protein localization

Abstract

Subcellular protein localization prediction is a bioinformatics approach (faster and cheaper than experimental procedure) to determine the targeting location of proteins into the cell organelles. Therefore, many programs exist to address this issue, but TPpred is the most up-to-date option regarding mitochondria targeting prediction. On the other hand, the development of a Drosophila melanogaster transgenic model to study mitochondria-related diseases in humans has brought up many questions. Some mitochondria mechanisms are still not explored. The translation pathways present in mitochondria have similarities to the ones present in the cytosol. But they are older, essential in the origins of live and also in the eukaryote cell development from prokaryotes. A new paralog of the seryl tRNA synthetize enzyme that catalyses aminoacylation of tRNASer was found in insects. The SLIMP protein, which is not a Seryl tRNA synthetases(SRS) anymore, is now known to interact with SRS2 and LON protease, a fact that can lead to a modulation in both mitochondrial translation and replication, respectively. A microarray of the knock-down of SLIMP expression in S2 D.melanogaster cells was performed and their analyzed row data gives rise to the current pipeline reported. The functional annotation pipeline developed is a new analysis procedure to describe differences in transcriptome considering mitochondria targeting status in a microarray-wide approach. Proportions tests is performed, which in our data did not report a significative increase or depletion of mitochondria targeted transcript products under the SLIMP knockdown condition. Moreover, the GO enrichment analysis suggested an imbalance in serine metabolism that extends to the selenocysteine biosynthetic pathway. CG1427 protein is behind this enrichment result, taking into account its up-regulation status from microarray and its mitochondria status from the Ttpred prediction. However, since this and other proteins (5%) are theoretical (one analysis step deals with genes having proteins targeted to mitochondria as well as outside of it, due to differences in their sequence from alternative splicing process), experimental evidence should support this results.