Transcriptome analysis reveals differential immune related genes expression in Ruditapes philippinarum under hypoxia stress: Potential HIF and NF-κB crosstalk in immune responses in clam

Abstract

Background: Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Benthic communities are the most sensitive parts of the coastal ecosystem to eutrophication and resulting hypoxia. As a filter-feeding organism living in the seafloor sediment, Ruditapes philippinarum represents an excellent "sentinel" species to assess the quality of marine environment. In order to gain insight into the molecular response and acclimatization mechanisms to hypoxia stress in marine invertebrates, we examined hypoxia-induced changes in immune-related gene expression and gene pathways involved in hypoxia regulation of R. philippinarum. Results: We investigated the response of the Manila clam R. philippinarum to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and time course qPCR analysis. A total of 75 genes were captured significantly differentially expressed, and were categorized into antioxidant/oxidative stress response, chaperones/heat shock proteins, immune alteration, and cell proliferation/apoptosis. Fourteen hypoxia responsive genes were validated significantly up/down regulated at different time 0, 2, 5, and 8 d in gills of R. philippinarum in hypoxia challenged group. Functional enrichment analysis revealed the HIF signaling pathway and NF-κB signaling pathway play pivotal roles in hypoxia tolerance and resistance in R. philippinarum. Conclusion: The HIF signaling pathway and NF-κB signaling pathway play a critical role in hypoxia tolerance and resistance in Manila clam. The immune and defense related genes and pathways obtained here gain a fundamental understanding of the hypoxia stress in marine bivalves and provide important insights into the physiological acclimation, immune response and defense activity under hypoxia challenge. The reduced metabolism is a consequence of counterbalancing investments in immune defense against other physiological processes.

Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)

“…We saw an increase in expression of Fibropellin-1 in the bearded fireworm after the second hypoxic timepoint in the intermittent hypoxia trial (over 18 h after initial hypoxic exposure) which corresponds well with the clam’s drastic increase in this gene after 2 days of chronic hypoxia. However, it is important to note that a significant decrease in expression of Fibropellin-1 was seen after 5 and 8 days in the clam 81 . During our chronic hypoxia exposure experiment, we were only able to sample after 7 days, so we may have missed this spike in expression, but our intermittent experiment allows us to see a similar response.…”

“…Fibropellin-1, related to Notch protein-binding, was recently shown to have drastically increased in expression post chronic hypoxia in the clam Ruditapes philippinarum 81 . In the current study, we see a similar expression pattern in the intermittent but not chronic hypoxia trial.…”

Evidence of multiple genome duplication events inMytilusevolution

“…The TolB-like protein, involved in a tol-dependent translocation system (Carr et al, 2000). The RING finger protein 170, which mediates the ubiquitination and degradation of inositol 1,4,5-trisphosphate receptors, and it is involved in immune response functions (Song et al, 2019) and finally, Fibropellin, a cell adhesion protein (Nie et al, 2020). Only a limited number of gene clusters appear to be under positive selection amongst those commonly used in immunity, stress response and shell formation comparative studies (in green), and the majority of the genes clusters showed negative selection with the exception of four, which resulted to be all involved in immune response pathways (Gerdol and Venier, 2015).…”