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Integrated transcriptome and Ribosome Profiling analyses elucidate the liver response of rainbow trout (Oncorhynchus mykiss) to heat stress [Ribo-seq]

ABSTRACT: Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.

ORGANISM(S): Oncorhynchus mykiss

PROVIDER: GSE263547 | GEO | 2024/04/16

REPOSITORIES: GEO

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Project description:With the continuous intensification of global warming, extreme climate fluctuations and high-density farming, heat stress severely restrict the survival and yield of the world economic cold-water rainbow trout (Oncorhynchus mykiss). With the development of nanotechnology, Nano-selenium (Nano-Se) has become an ideal and ecological Se nutrient source additive and free radical scavenger with its outstanding advantages of high biological activity and low toxicity. Herein, fish were fed to two levels Nano-Se at 18°C for 9 days: CG18 (0 mg/kg) and Se18 (5 mg/kg). Afterward, the temperature of each group was raised to 24°C and exposed for 8 h (CG24, Se24). DIA/SWATH technique was used to analyze the proteome changes in rainbow trout liver under heat stress (CG18-CG24) and used this process as a control, focusing on comparison the proteome changes in heat stress after the addition of Nano-Se (Se18-Se24). Results showed that 223 and 269 differentially abundant proteins in CG18-CG24 and Se18-Se24, respectively, mainly including apoptosis, heat shock protein (HSPs), selenoprotein and lipid-related proteins. Compared with the CG18-CG24 group, the Se18-Se24 group increased the up-regulated abundance of HSPs (Hsp70, Hsp90a.1, Hspa8, Hsp30, DNAJA4 and DNAJB1); partially restored the down-regulated abundance of selenoprotein (MsrB2); significantly down-regulated the abundance of lipid-related protein (CYP51, EBP, DHCR7, DHCR24 and APOB) and decreased the abundance of pro-apoptotic protein (Caspase8 and Bad). PPI results indicated that Nano-Se may inhibit apoptosis through up-regulating Hsp70, Hsp90a.1, Hspa8 and DNAJb1, and Hsp70/Hspa8 and MsrB2 may synergistically exert antioxidant defense effects under heat stress. Overall, our results demonstrated that Nano-Se takes protective roles in rainbow trout against heat stress by strengthening protein repair, recovering antioxidant enzyme activity, alleviating lipid metabolism and improving apoptosis. The present study provided novel insights into Nano-Se- mediated tolerance of rainbow trout against heat stress at the proteomic level.

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Integrated transcriptome and Ribosome Profiling analyses elucidate the liver response of rainbow trout (Oncorhynchus mykiss) to heat stress [Ribo-seq]

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