Documenting the unique biology of gammarids by means of high-throughput proteogenomics

Abstract

International audienceNext-generation proteomics is able to offer in-depth insights into the physiology of organisms by identifying and quantifying thousands of proteins. However, this is only possible for model organisms for which the genome has been sequenced and carefully annotated, a requirement far from being a standard for amphipods. Here, we proposed a novel approach for quickly identifying novel proteins of the freshwater amphipod, Gammarus fossarum, an ecologically relevant species, by the alliance of genomic and proteomic, i.e. proteogenomics. For identifing protein-encoding genes, we characterized by deep RNA-seq the transcriptome of key physiological organs: the female and male reproductive system, the cephalon and the hepatopancreatic caecum. Then, we generated a six-reading frame translation protein database for interpreting protein data measured in parallel on the four tissues by high-throughput proteomics. A total of 1,033,282 MS/MS spectra was recorded and assigned with the RNA-seq derived database, resulting in 1,624 proteins identified. The function of these proteins was tentatively assigned by PSI-BLAST searches but functional annotation resulted quite scarce with the identification of numerous orphans. As demonstrated from the Daphnia pulex genome, lineage specific genes are more likely linked to the organism unique biology and have been shown to be amongst the most responsive to environmental challenges. Therefore, our dataset, the first identification of genes and proteins ever done at such large scale for the Gammarus genus, is of utmost importance for a comprehensive understanding of their key physiological functions and molecular mechanisms related to stress response. The perspectives of this work will address the use of this resource in ecotoxicology. We are currently focusing our attention on proteins involved in reproduction processes. Our study should result in interesting biomarkers for freshwater biomonitoring based on the G. fossarum sentinel