Genomic Analysis of the Proteasome Subunit Gene Family and Their Response to High Density and Saline-Alkali Stresses in Grass Carp

Abstract

The proteasome is a highly conserved polycatalytic enzyme that is required for cellular processes and is widely present in the nucleus and cytoplasm of archaea, as well as all eukaryotes. A total of 22 members of the proteasome subunit (CiPS) gene family were identified and characterized by scanning the grass carp (Ctenopharyngodon idella) genome. These genes were classified into two subfamilies, CiPSA and CiPSB, based on phylogenetic analysis, which was consistent with the results from other species. We examined the response of this gene family to high density and saline-alkali stresses in aquaculture using publicly available transcriptome data resources. In grass carp, CiPS member transcripts were detected in all tested tissues, with the highest expression level in the head kidney and the lowest in the liver. According to transcriptome-based expression analysis, CiPS genes play a role in response to environmental stresses in grass carp, mainly in the form of negative regulation. Interestingly, a cluster of members belonging to the CiPSB subfamily on a 15 kb region on chromosome segment CI01000319, including CiPSB8, 9, 9b, and 10, showed marked responses to high density and saline-alkali stress. It appears that CiPS genes confer stress tolerance through the regulation of common genes, as well as specific genes. In summary, our genome-wide characterization, evolutionary, and transcriptomic analysis of CiPS genes in grass carp provides valuable information for characterizing the molecular functions of these genes and utilizing them to improve stress tolerance in aquaculture.

Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress

“…The expression levels of proteasome subunit-encoding genes were increased in the muscles of rats with long-term high-intensity exercise and C. idellus infected with saprolegniasis, resulting in enhanced activity of 26S proteasome [ 83 , 84 ]. Genes encoding proteasome subunits in C. idellus head kidney tissue responded to high-density and saline-alkali stress mainly in negative regulation [ 85 ], similar to the results found in this study. The above results indicate that under acute heat stress, the significant downregulation of proteasome-related genes in T. ovatus may lead to lower levels of proteasome subunits, leading to the reduction or loss of 26S proteasome activity.…”

Proteomic Blueprint of Atlantic Cod (Gadus morhua) Otoliths Revealing Environmental Stress Insights through Label-Free Quantitative Shotgun Proteomics

“…Lysosomes (12.5%), genes associated with lysosomal function, suggest involvement in degrading and recycling cellular waste, cellular signalling, and energy metabolism [92,93]. Proteasome (12.5%) indicates a notable representation of genes involved in the proteasome pathway, which is critical for the cell cycle, cell survival, and cellular homeostasis [94]. Pentose phosphate pathway (12.5%), a significant number of genes are involved in this pathway, which is crucial for nucleotide synthesis and the generation of NADPH for reductive biosynthesis [95].…”