Pathogen recognition receptors in channel catfish: I. Identification, phylogeny and expression of NOD-like receptors

Innate immune system plays a significant role in all multicellular organisms. The key feature of the system is its ability to recognize and respond to invading microorganisms. Vertebrates including teleost fish have evolved an array of pathogen recognition receptors (PRRs) for detecting and responding to various pathogen-associated molecular patterns (PAMPs), including Toll-like receptors (TLRs), nucleotide-binding domain, leucine-rich repeat containing receptors (NLRs), and the retinoic acid inducible gene I (RIG-I) like receptors (RLRs). In this study, we identified 22 NLRs including six members of the NLR-A subfamily (NODs), two members of the NLR-B subfamily, 11 members of the NLR-C subfamily, and three genes that do not belong to any of these three subfamilies: Apaf1, CIITA, and NACHT-P1. Phylogenetic analysis indicated that orthologs of the mammalian NOD1, NOD2, NOD3, NOD4, and NOD5 were all identified in catfish. In addition, an additional truncated NOD3-like gene was also identified in catfish. While the identities of subfamily A NLRs could be established, the identities of the NLR-B and NLR-C subfamilies were inconclusive at present. Expression of representative NLR genes was analyzed using RT-PCR and qRT-PCR. In healthy catfish tissues, all the tested NLR genes were found to be ubiquitously expressed in all 11 tested catfish tissues. Analysis of expression of these representative NLR genes after bacterial infection with Edwardsiella ictaluri revealed a significant up-regulation of all tested genes in the spleen and liver, but a significant down-regulation in the intestine and head kidney, suggesting their involvement in the immune responses of catfish against the intracellular bacterial pathogen in a tissue-specific manner. The up-regulation and down-regulation of the tested genes exhibited an amazing similarity of expression profiles after infection, suggesting the co-regulation of these genes.