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.

Integrated Metabolomics and Transcriptomic Analysis of Hepatopancreas in Different Living Status Macrobrachium nipponense in Response to Hypoxia

“…It was clearly observed that the expression of Mn-ENO significantly increased with the decrease of oxygen concentration ( Figure 6 , p < 0.05), indicating that ENO plays an important role in promoting the anaerobic metabolism in M. nipponense after hypoxia. The rising trend of Mn-ENO in M. nipponense is the same as it is in Ruditapes philippinarum (Adams et Reeve, 1850) [ 27 ]. However, different from R. philippinarum , the expression of Mn-ENO in the hypoxia group was always lower than that in the control group ( Figure 7 , p < 0.05).…”

“…As the research has developed in this field, Mn-LDH and Mn-ENO , which are directly related to lactate, have become more prominent in the field of vision. Mn-LDH reduces pyruvate to lactic acid under hypoxia, preventing the inhibition of glycolysis and ATP synthesis due to the buildup of pyruvate [ 27 ]. It was clearly observed that Mn-LDH decreased with the gradual deterioration of survival status under hypoxia ( Figure 5 ).…”

Transcriptome Analysis of Crassostrea sikamea (♀) × Crassostrea gigas (♂) Hybrids Under Hypoxia in Occluded Water

“…The Notch family has four transmembrane receptors (Notch1-Notch4) and five ligands (Kadesch, 2004). In the previous studies, fibropellin-1, related to the Notch protein, drastically increased when post chronic hypoxia in the clam Ruditapes philippinarum (Nie et al, 2020) and the NOTCHs were upregulated in Hermodice carunculata under hypoxia (Grimes et al, 2021). Notch signaling was originally identified as a pleiotropic mediator of cell fate in invertebrates, which has recently emerged as an important regulator of immune cells (Radtke et al, 2013;Vanderbeck and Maillard, 2021).…”

RNA-Sequencing Analysis of the Spleen and Gill of Takifugu rubripes in Response to Vibrio harveyi Infection

“…Sequencing technology is widely applied in aquaculture (21)(22)(23)(24). RNA-sequencing technology can effectively reveal genes that are engaged in immune responses and expressed in response to the presence of toxicants or infection (25)(26)(27).…”