Genome-wide identification and stress-responsive expression analysis of matrix metalloproteinases in large yellow croaker (Larimichthys crocea)

Matrix metalloproteinases (MMPs) are a class of zinc-dependent endopeptidases that play a key role in degrading extracellular matrix (ECM) components and are involved in a variety of immune and stress processes. Although the immune functions of MMPs in various species have been studied, the systematic identification of them in Larimichthys crocea and their expression regulation under environmental stress remains unclear. In this study, through genome-wide data mining, 16 LcMMPs ( LcMMP2 , 9 , 11 , 14–21 , 23–25 , 28 , 30 ) were identified in L. crocea . And a series of analysis was conducted on its evolutionary relationship, gene structure, molecular evolution, and expression patterns under Pseudomonas plecoglossicida infection and hypoxia stress. Phylogenetic analysis indicated that the MMPs were highly conserved in teleosts. Analysis of gene structure and conserved motifs further revealed the conservation of its sequence and structure. Expression profile analysis demonstrated that LcMMPs exhibited differential expression under different stresses, suggesting that they had functional differentiation in response to biological and abiotic stresses. It was worth noting that both LcMMP9 and LcMMP25 were significantly down-regulated in the spleen under two kinds of stress, suggesting that they might participate in core regulatory processes in the coordinated response to multiple environmental stresses. Protein-protein interaction network analysis further revealed the potential interaction relationships between LcMMPs and metalloproteinase inhibitors, ECM macromolecules, and immune-related proteins. This study provided an important foundation for in-depth analysis of the function of the MMP genes in the large yellow croaker during environmental adaptation and its molecular regulatory mechanism.