Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex

Abstract

Although the microcrustacean Daphnia is becoming an organism of choice for proteomic studies, protein expression across its life cycle have not been fully characterized. Proteomes of adult females, juveniles, asexually produced embryos, and the ephippia‐resting stages containing sexually produced diapausing freezing‐ and desiccation‐resistant embryos are analyzed. Overall, proteins with known molecular functions are more likely to be detected than proteins with no detectable orthology. Similarly, proteins with stronger gene model support in two independent genome assemblies can be detected, than those without such support. This suggests that the proteomics pipeline can be applied to verify hypothesized proteins, even given questionable reference gene models. In particular, upregulation of vitellogenins and downregulation of actins and myosins in embryos of both types, relative to juveniles and adults, and overrepresentation of cell‐cycle related proteins in the developing embryos, relative to diapausing embryos and adults, are observed. Upregulation of small heat‐shock proteins and peroxidases, as well as overrepresentation of stress‐response proteins in the ephippium relative to the asexually produced non‐diapausing embryos, is found. The ephippium also shows upregulation of three trehalose‐synthesis proteins and downregulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.

Improving the proteome coverage of Daphnia magna ‐ implications for future ecotoxicoproteomics studies

“…Our experimental approach may therefore be useful to investigate the effects of aquatic micro-and nanoplastic pollution on daphnids [29][30][31][32], since Daphnia, as filterfeeder, is particularly exposed to particulate contaminants. Compared to other proteomic studies on D. pulex [9,33,34] as well as studies on D. magna from our lab [29,[35][36][37], our dataset and spectral library, containing data from 58186 unique D. magna peptides and 6027 proteins, represents one of the largest libraries and may be the base for future studies addressing the proteomes of daphnids.…”