Population-specific renal proteomes of marine and freshwater three-spined sticklebacks

Quantitative proteomics was used to reveal biochemical differences in kidneys of marine and freshwater three-spined sticklebacks. More than 1500 unambiguous proteins were identified, 106 of which are robustly co-translationally modified. Amino-terminal acetylation sites for 94 and proline hydroxylation sites for 12 proteins, including 4 protein disulfide isomerases having the consensus motif APWCGHCK, were determined. More than 1500 proteins were quantified by LC-MS/MS yielding 120 proteins with consistent population-specific abundance differences. Twenty-five of these were selected for validation by data-independent acquisition (DIA) and spectral library based MS2 quantitation. A dense biochemical network was revealed, which promotes the synthesis of the organic osmolytes betaine, sorbitol, trimethylamine oxid (TMAO), and urea. It contains 33 of 49 proteins that are elevated in marine compared to freshwater sticklebacks, including the most highly elevated proteins (dimethylaniline monooxygenase, alanine-glyoxylate aminotransferase, glycine N-methyltransferase). Freshwater stickleback kidneys contain elevated levels of proteolytic, cytoskeletal, extracellular matrix, and calcium signaling proteins. Proteins that are most elevated in freshwater sticklebacks are ES1 protein homolog, apoptosis-associated speck-like protein containing a CARD and caspase 1. Protein-abundance network analysis demonstrates significantly higher levels of synchronized abundance control in marine sticklebacks. The significance of these findings for biochemical diversification of renal function in marine and FW sticklebacks is discussed.