Abstract
ABSTRACTAnimals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies.This article has an associated First Person interview with the first author of the paper.
Highlights
Adipose is a complex organ that participates in energy storage, thermogenesis, immunity and regulation of metabolic homeostasis
We show that a larger number of unique proteins, including those involved in metabolism and protein translation, can be identified in samples lysed using QIA with the added benefit of RNA isolation, and that de novo peptide sequencing (PEAKS Studio) combined with database search increases sensitivity of protein identification compared with database search alone (SEQUEST in Proteome Discoverer)
We report the first elephant seal outer blubber layer proteome containing a number of metabolic enzymes and adipokines of interest to
Summary
Adipose is a complex organ that participates in energy storage, thermogenesis, immunity and regulation of metabolic homeostasis. While adipose tissue has been studied extensively in humans and laboratory animals due to the emergence of a global obesity epidemic, non-model organisms can provide fundamental information on metabolic adaptations in animals and potentially novel insights into mechanisms by which adipose function is dysregulated in disease (Grabek et al, 2015; Houser et al, 2013). Such insights can be rapidly obtained via non-targeted approaches. Most proteomics studies of marine mammals to date have used tissue matrices other than blubber (Neely et al, 2015a, b; Sobolesky et al, 2016)
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