Developing specific molecular biomarkers for thermal stress in salmonids

Abstract

BackgroundPacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue.ResultsCandidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon (O. nerka) and Chinook salmon (O. tshawytscha) (cool, 13–14 °C and warm temperatures 18–19 °C) over 5–7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies.ConclusionsThe results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5108-9) contains supplementary material, which is available to authorized users.

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish

“…Proteins identified as part of the cellular stress response included up regulation of HSPs, a common indicator of stress related to abiotic and biotic factors in fish and other organisms (Basu et al, 2002;Huth & Place, 2016). We also identified several cytochrome proteins involved in oxidative and metabolic processes, and associated with thermal stress responses in salmon (Akbarzadeh et al, 2018). SEPRH, FKBP, and RAS related proteins have also been previously identified as significantly expressed in marine fish under stress (Chen et al, 2018;Evans & Somero, 2009;.…”

Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen

“…Our results showed that five of the 10 upregulated genes at 18, including two paralogs of SERPINH and two paralogs of hsp90a and hsp70, were heat shock proteins. These genes are known to be the most frequent heat shock proteins (HSPs) in response to higher temperature across salmonids and other species studied (Akbarzadeh et al, 2018a). The importance of molecular chaperoning of macromolecules during higher temperature has been well established.…”

“…In particular, the heat shock response (HSR), defined as the ability of the HSPs to re-fold thermally damaged proteins and prevent their cytotoxic aggregation, is a well-described phenomenon across taxa (Logan and Buckley, 2015). The upregulation of many paralogs relating to HSP genes including SERPIN, HSP70, and HSP90a were also observed in adult Sockeye salmon in response to chronic elevated temperature (Akbarzadeh et al, 2018a;Jeffries et al, 2012;Jeffries et al, 2014b). Our literature review revealed that the above HSP genes are upregulated in more than 16 different fish species belonging to different taxa, including salmonids in response to high temperature (Akbarzadeh et al, 2018a).…”

“…As a non-lethal tool that uses gill tissue for measuring gene expression, we have already developed 93 candidate salinity (n = 37, Houde et al, 2018), temperature (n = 33, Akbarzadeh et al, 2018a), and dissolved oxygen (n = 23, Table S1) biomarkers for all Pacific salmon species. The candidate salinity biomarkers were originally developed and examined for broadly measuring the degree of smoltification (Houde et al, 2018).…”

“…In the present study, we specifically examine if the regulation of some of these genes may be directly influenced by salinity. The candidate temperature biomarkers were previously examined as a single stressor (Akbarzadeh et al, 2018a). In the present study, we specifically examine these biomarkers under multi-stressor conditions.…”