Genome-wide identification of the TRAF gene family in humpback grouper (Cromileptes altivelis) and analysis of their expression in response to Vibrio harveyi challenge

Xiaona Xu; Peng Wang; Huibang Sun; Dongxue Xia; Hai Huang; Quanqi Zhang; Jinxiang Liu

doi:10.1016/j.fsi.2024.109959

Genome-wide identification of the TRAF gene family in humpback grouper (Cromileptes altivelis) and analysis of their expression in response to Vibrio harveyi challenge

Fish Shellfish Immunol. 2024 Oct 10:109959. doi: 10.1016/j.fsi.2024.109959. Online ahead of print.

Authors

Xiaona Xu¹, Peng Wang², Huibang Sun³, Dongxue Xia⁴, Hai Huang⁵, Quanqi Zhang⁶, Jinxiang Liu⁷

Affiliations

¹ MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China. Electronic address: 15236838157@163.com.
² MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China. Electronic address: wp954119843@163.com.
³ MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China. Electronic address: shb@stu.ouc.edu.cn.
⁴ MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China. Electronic address: xiagaogao0124@163.com.
⁵ MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China. Electronic address: huanghai74@126.com.
⁶ MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China; Hainan Seed Industry Laboratory, Sanya, China. Electronic address: qzhang@ouc.edu.cn.
⁷ MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China; Hainan Seed Industry Laboratory, Sanya, China. Electronic address: liujinxiang@ouc.edu.cn.

PMID: 39395597
DOI: 10.1016/j.fsi.2024.109959

Abstract

TRAF (Tumor necrosis factor receptor-associated factor) proteins are key mediators of signal transduction in cell signaling and immune regulation within the toll-like receptor (TLR) and tumor necrosis factor (TNFR) superfamily. Despite the importance of TRAF genes in teleost innate immunity, study on their functions in C. altivelis is limited. This study utilized bioinformatics methods to identify and named eight TRAF genes (CaTRAF2a, CaTRAF2a-like, CaTRAF2b, CaTRAF3, CaTRAF4a, CaTRAF5, CaTRAF6 and CaTRAF7) in C. altivelis. Phylogenetic, syntenic and molecular evolution revealed that all CaTRAF members were evolutionarily conserved in teleost. Domain analysis indicated the presence of a conserved N-terminal RING finger domain in all CaTRAF proteins. Most CaTRAF proteins also featured a MATH domain at the C-terminal, with the exception of CaTRAF7 which contained seven repeat WD40 domains. In addition, qRT-PCR was used to detect the expression patterns of nine different tissues and eight different embryonic development stages of healthy fish, and it was found that there were spatial and tissue specificities among the members. HE staining revealed evident pathological lesions in the tissues post V. harveyi infection. Atrophy and significant bending of the gill lamellae were observed in the gills, while irregular cell shapes, increased fat vacuoles, and enlarged cell volume were noted in the liver. Intestinal tissues displayed thickening of the muscle layer, elongation of intestinal villi, and increased folds. Moreover, the expression of TRAF gene changed significantly after V. harveyi infection. These results would help to clarify the molecular role of CaTRAF gene in the regulation of immune and inflammatory responses in C. altivelis.

Keywords: Cromileptes altivelis; TRAF; V. harveyi infection; gene expression; innate immunity.