Genome-wide Characterization of Heat Shock Proteins in Channel Catfish (Ictalurus punctatus) and Determination of Their Involvement in Diseases

Abstract

Heat shock proteins (HSPs) consist of a large group of chaperones whose expression is induced by a number of stresses such as exposures to high temperature, hypoxia and infection. In this study, I identified a total of 93 HSPs in channel catfish (Ictalurus punctatus), with 13 members of small Hsp family, 57 members of Hsp40 family, 16 members of Hsp70/110 family, one member of Hsp60 family, one member of Hsp10 family and 5 members of Hsp90 family, through in silico analysis using RNA-Seq and genome databases. Phylogenetic and syntenic analyses were conducted with all the families of HSPs, which provided strong evidence in supporting the orthologies of these HSPs. Besides, two tandem repeat members of Hsp70/110s, hsp70.2 and hsp70.3 were not found located within the MHC-complex, which is a group of molecules that are essential in the antigen presenting process, suggesting different process of presenting the antigens or epitopes. Meta-analyses of bacterial challenged RNA-Seq datasets were conducted to analyze expression profile of catfish HSPs following bacterial infection of Flavobacterium columnarae (F. columbare) and Edwarsiella ictaluri (E. ictaluri). HSPs expression was analyzed through the early phase of immune response. As a result, a majority of catfish HSPs were found significantly expressed in gill and intestine after bacterial infections during the early immune response phase. A total of thirty Hsp40 genes were regulated under disease situations involving two tissues after two bacterial infections. Five Hsp90 genes, one Hsp60 gene, one Hsp10 gene and nine sHsp genes were significantly up/down-regulated after two bacterial infections. Twelve Hsp70/110s genes were significantly up/down-regulated after two bacterial infections. Different responses by the Hsp70/110s expression after the infection of F. columnarae and E. ictaluri revealed the different pathogenesis mechanism of the two bacteria. As an agonist ligand of TLR4, an import Pattern recognition receptor of innate immunity, Hsp70s showed a time pattern through the two bacterial infections in two tissues. Also a pathogen-specific response in host Hsp90 had been revealed. Hsp90s showed the most significant involvement at the 24 hours after challenging with F. columnarae. Both pathogen-specific and tissue-specific pattern were found in small Hsp family after both two bacterial infections. Additional meta-analysis were conducted on the comparisons of differences in gene expression profiles between resistant and susceptible fish at 0 h, and 1 h, 2 h, and 8 h after F. columnare challenge. A total of 18 catfish HSPs genes showed significant expression at basal level prior to F. columnare challenge, which is our great interest as these signatures could potentially serve as QTL or biomarkers for selection.