Genomic analysis of NF-kappa B signaling pathway reveals its complexity in Crassostrea gigas

• Published in: Fish & Shellfish Immunology
• Main Authors: Yu, Mingjia, Chen, Jianming, Bao, Yongbo, Li, Jun
• Format: Report
• Language: English
• Published: ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD 2018
• Subjects: Fisheries; Immunology; Marine & Freshwater Biology; Veterinary Sciences; Crassostra gigas; NF-kappa B; Genome; Evolution; CASEIN KINASE-II; PACIFIC OYSTER; TRANSCRIPTION FACTORS; ALPHA PROTEOLYSIS; IMMUNE-RESPONSE; DROSOPHILA; ACTIVATION; PROTEINS; GENES; PHOSPHORYLATION; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: http://ir.gig.ac.cn/handle/344008/43947; https://doi.org/10.1016/j.fsi.2017.11.034

NF-kappa B signaling pathway is an evolutionarily conserved pathway that plays highly important roles in several developmental, cellular and immune response processes. With the recent release of the draft Pacific oyster (Crassostra gigas) genome sequence, we have sought to identify the various components of the NF-kappa B signaling pathway in these mollusks and investigate their gene structure. We further constructed phylogenetic trees to establish the evolutionary relationship of the oyster proteins with their homologues in vertebrates and invertebrates using BLASTX and neighbor-joining method. We report the presence of two classic NF-kappa B/Rel homologues in the pacific oyster namely Cgp100 and CgRel, which possess characteristic RHD domain and a consensus nuclear localization signal, similar to mammalian homologues and an additional CgRel-like protein, unique to C. gigas. Further, in addition to two classical I kappa B homologues, CgI kappa B1 and CgI kappa B2, we have identified three atypical I kappa B family members namely CgI kappa 133, CgI kappa B4 and CgBCL3 which lack the I kappa B degradation motif and consist of only one exon that might have arisen by retrotransposition from CgI kappa Bl. Finally, we report the presence of three IKKs and one NEMO genes in oyster genome, named CgIKK1, CgIKK2, CgIKK3 and CgNEMO, respectively. While CgIKK1 and CgIKK3 domain structure is similar to their mammalian homologues, CgIKK2 was found to lack the HLH and NBD domains. Overall, the high conservation of the NF-kappa B/Rel, I kappa B and IKK family components in the pacific oyster and their structural similarity to the vertebrate and invertebrate homologues underline the functional importance of this pathway in regulation of critical cellular processes across species.