Genome-wide identification, evolutionary and expression analyses of the NF-κB family, the IκB inhibitors, IKK-associated genes in grass carp (Ctenopharyngodon idella), and their responses to bacterial and viral infections

Abstract

The nuclear factor kappa B (NF-κB) signaling pathway plays an indispensable role in defending against bacterial infections. However, the complete repertoire of its core components-NF-κB transcription factors, IκB inhibitors, the canonical IKK complex, and IKK-related kinases-remains unclear in most teleosts. In this study, we conducted a genome-wide analysis of grass carp (Ctenopharyngodon idella) and systematically identified five NF-κB family members (RelA and NF-κB1 as core canonical effectors; RelB and NF-κB2 as non-canonical effectors; plus c-Rel), seven inhibitor of NF-κB (IκB) members (including the classical inhibitor IκBα with two subtypes: IκBαa and IκBαb, as well as IκBβ, IκBNS, IκBζ, IκBε, and Bcl-3), three components of the canonical IKK complex (IKKα, IKKβ, and IKKγ/NEMO), and two IKK-related kinases (TBK1 and IKKε). These genes are distributed across 13 chromosomes. Synteny analysis revealed that the chromosomal arrangement of these three gene complexes is highly conserved in cyprinids. Both sequence and phylogenetic analyses demonstrated that the members within each complex are highly conserved. Transcriptomic data revealed that members of the NF-κB, IκB, canonical IKK complex, and IKK-related kinase are widely expressed in various tissues, with NF-κB2, IκBαa, IκBαb, and TBK1 exhibiting relatively high basal expression levels across tissues and actively responding to bacterial and viral challenges. qRT-PCR analysis further confirmed that the expression of most members changed significantly in the spleen and head kidney of grass carp following infection with grass carp reovirus (GCRV-II) or Aeromonas hydrophila. In conclusion, this comprehensive and systematic analyses on NF-κB, IκB, the canonical IKK complex, and IKK-related kinases establishes a crucial molecular foundation for subsequent functional research on the NF-κB and interferon-associated signaling pathways in teleost.

Keywords: Aeromonas hydrophila; GCRV-II; Grass carp (Ctenopharyngodon idella); IKK; IκB; NF-κB; mRNA expression.