DIA assay libraries enable analyses of mRNA:protein
coregulation by ecological contexts
Determining the relationship between mRNA and protein abundance was an
important aim of this analysis, which shapes further analytical
approaches. This study found very low correlation between mRNA and
proteins in kidneys of fish acclimated from FW to BW. The proteins
identified as significant using the DIA assay library approach would not
have been identified from transcriptomics studies since none of the
corresponding mRNAs were significantly regulated. Therefore, functional
analyses based on proteome dynamics during salinity stress provide
additional rather than merely redundant information when compared with
mRNAseq analyses (see below). In theory, lack of coregulation between
the mRNA and protein levels of biological organization during salinity
acclimation can be attributed to both biological and technical causes.
From a technical standpoint, the dynamic range of protein quantity in a
tissue sample is several orders of magnitude greater than that for mRNA
(Buccitelli & Selbach, 2020). Because the protein dynamic range is so
much greater, differences in protein levels can be identified more
accurately. Biologically, because protein’s action and stability can be
modulated by post-translational modification (PTM), cells may not need
to alter mRNA levels in order to respond to a stressor (Jovanovic et
al., 2015), which has indeed been suggested for salinity stress
responses of euryhaline fish (Evans & Somero, 2009). Additionally,
proteins typically have a significantly longer half-life than mRNA and
are less prone to rapid changes, which reduces the overall variability
between replicates for proteins (Schwanhäusser et al., 2011).