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Organismal physiology, morphology, and behavior are based on the function of structural proteins and enzymes. Proteins represent the central regulatory plane in the genome to phenome continuum. The protein complement of cells and tissues (the proteome) is highly dynamic and mirrors environmental and developmental influences on organismal phenotypes. Therefore, dynamic proteomes are excellent bioindicators of environmental exposure. Comprehensive blueprints of environmental exposures are reflected in specific proteome states and capturing those states is achieved by quantitative proteomics. We have developed quantitative proteomics workflows to characterize environmental influences on proteome states and proteome dynamics of euryhaline and euryhthermal fish populations in coastal areas. These workflows utilize tissue- and cell-specific assay libraries for data-independent acquisition (DIA) or Sequentially Windowed Acquisition of all THeoretically possible MSMS spectra (SWATH) mass spectrometry. Qunatitative proteome datasets generated with these workflows are highly accurate and they consistently cover precisely defined sets of proteomes. This consistent coverage renders systematic and long-term network and topological data analysis (TDA) approaches feasible. These workflows and approaches are explained and their application to coastal fish biology is discussed using selected datasets as examples. The data presented illustrate that habitat differences such as salinity and temperature changes are readily captured in state changes of tissue-specific proteomes. The overall topology of proteome states is indicative of particular tissues, species, and environmental contexts and is therefore suitable for deducing functional and phenotypic consequences of environmental changes on coastal organisms.
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This content will become publicly available on February 9, 2026
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates
ABSTRACT Fluctuating salinity is symptomatic of climate change challenging aquatic species. The melting of polar ice, rising sea levels, coastal surface and groundwater salinization, and increased evaporation in arid habitats alter salinity worldwide. Moreover, the frequency and intensity of extreme weather events such as rainstorms and floods increase, causing rapid shifts in brackish and coastal habitat salinity. Such salinity alterations disrupt homeostasis and ultimately diminish the fitness, of aquatic organisms by interfering with metabolism, reproduction, immunity, and other critical aspects of physiology. Proteins are central to these physiological mechanisms. They represent the molecular building blocks of phenotypes that govern organismal responses to environmental challenges. Environmental cues regulate proteins in a concerted fashion, necessitating holistic analyses of proteomes for comprehending salinity stress responses. Proteomics approaches reveal molecular causes of population declines and enable holistic bioindication geared toward timely interventions to prevent local extinctions. Proteomics analyses of salinity effects on aquatic organisms have been performed since the mid‐1990s, propelled by the invention of two‐dimensional protein gels, soft ionization techniques for mass spectrometry (MS), and nano‐liquid chromatography in the 1970s and 1980s. This review summarizes the current knowledge on salinity regulation of proteomes from aquatic organisms, including key methodological advances over the past decades.
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- Award ID(s):
- 2209383
- PAR ID:
- 10608690
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- PROTEOMICS
- ISSN:
- 1615-9853
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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