Molecular Cloning of clpX Gene from Vibrio alginolyticus HY9901 and Its Bioinformatics Analysis

According to the clpX gene sequence of Vibrio alginolyticus HY9901, a pair of specific primers were designed, and the full length was cloned by PCR and subjected to bioinformatics analysis. The results showed that the clpX gene was 1281 bp in length and encoded 426 amino acids. Its molecular structure formula was C3842H6405N1281O1598S260, with a theoretical protein molecular weight of approximately 1 044 473.4 kDa and a theoretical pI value of 5.04. The clpX gene was predominantly situated within the cytoplasm, exhibiting unstable and hydrophilic protein characteristics. It possessed a signal peptide cleavage site, lacked a transmembrane region, and was not associated with any KEGG metabolic pathway. Additionally, it possessed 2 glycine phosphorylation sites, a CAMP-dependent protein kinase phosphorylation site, a C-terminal amidation modification site, 6 protein kinase C phosphorylation sites, 7 microbody C-terminal target signal sites, and an ATP/GTP site. The clpX phylogenetic tree was constructed using the MEGA 5.0 software via the neighbor-joining method. The results demonstrated that the clpX of V. alginolyticus exhibited up to 100% affinity with the clpX of Vibrio spp. The single subunit 3D structure model of the ClpX protein was obtained using the SWISS-MODEL program. A structural and functional analysis of the protein revealed the presence of three distinct ClpX structural and functional domains. In the prediction of secondary structure, the proportions of α-helix, random coil, β-sheet and extended strand were 40.38%, 37.09%, 5.40% and 17.14%, respectively. The analysis of the ClpX protein through the STRING database revealed that the proteins interacting with the ClpX protein were Tig, Atpd, Hflb, Msrb-2, Rpod, Clpp, Clpa, Lon-1, Hfq, and ANP63951.1. A computational analysis of the ClpX protein identified a number of post-translational modification sites, including phosphorylation, acetylation, ubiquitination, glycosylation, methylation, S-palmitoylation, and lactylation. The significance of this study is to analyze the function of the clpX gene and establish a robust foundation for subsequent investigations into the mechanism of the clpX gene in Vibrio alginolyticus.