Cross-species Analysis Reveals Evolving and Conserved Features of the Nuclear Factor κB (NF-κB) Proteins

NF-kappa B is a key regulator of immune gene expression in metazoans. It is currently unclear what changes occurred in NF-kappa B during animal evolution and what features remained conserved. To address this question, we compared the biochemical and functional properties of NF-kappa B proteins derived from human and the starlet sea anemone (Nematostella vectensis) in 1) a high-throughput assay of in vitro preferences for DNA sequences, 2) ChIP analysis of in vivo recruitment to the promoters of target genes, 3) a LUMIER-assisted examination of interactions with cofactors, and 4) a transactivation assay. We observed a remarkable evolutionary conservation of the DNA binding preferences of the animal NF-kappa B orthologs. We also show that NF-kappa B dimerization properties, nuclear localization signals, and binding to cytosolic I kappa Bs are conserved. Surprisingly, the Bcl3-type nuclear I kappa B proteins functionally pair up only with NF-kappa B derived from their own species. The basis of the differential NF-kappa B recognition by I kappa B subfamilies is discussed.