Abstract :
Interactions of organisms with
their environment are complex and environmental regulation at different
levels of biological organization is often non-linear. Therefore, the
genotype to phenotype continuum requires study at multiple levels of
organization. While studies of transcriptome regulation are now common
for many species, quantitative studies of environmental effects on
proteomes are needed. Here we report the generation of a
data-independent acquisition (DIA) assay library that enables
simultaneous targeted proteomics of thousands of Oreochromis
niloticus kidney proteins using a label- and gel-free workflow that is
well suited for ecologically relevant field samples. We demonstrate the
usefulness of this DIA assay library by discerning environmental effects
on the kidney proteome of O. niloticus . Moreover, we demonstrate
that the DIA assay library approach generates data that are
complimentary rather than redundant to transcriptomics data. Transcript
and protein abundance differences in kidneys of tilapia acclimated to
freshwater and brackish water (25 g/kg) were correlated for 2114 unique
genes. A high degree of non-linearity in salinity-dependent regulation
of transcriptomes and proteomes was revealed suggesting that the
regulation of O. niloticus renal function by environmental
salinity relies heavily on post-transcriptional mechanisms. The
application of functional enrichment analyses using STRING and KEGG to
DIA assay datasets is demonstrated by identifying myo -inositol
metabolism, antioxidant and xenobiotic functions, and signaling
mechanisms as key elements controlled by salinity in tilapia kidneys.
The DIA assay library resource presented here can be adopted for other
tissues and other organisms to study proteome dynamics during changing
ecological contexts.
Keywords: Adaptation, Aquaculture, Quantitative
proteomics, Teleost