Identification, characterization, and expression analysis of clip-domain serine protease genes in the silkworm, Bombyx mori.

Clip-domain serine proteases (CLIPs), characterized by regulatory module clip domains, constitute an important serine protease family identified in insects and other arthropods. They participate in host immune response and embryonic development in a cascade-activated manner. Here, we present a genome-wide identification and expression analysis of CLIP genes in the silkworm, Bombyx mori. A total of 26 CLIP genes were identified in the silkworm genome. Bioinformatics analysis indicated that these CLIPs clustered into four subfamilies (CLIPA-D), and exhibit a close evolutionary relationship with CLIPs of Manduca sexta. Tissue expression profiling revealed that silkworm CLIP genes are mainly expressed in the integument, head, fat body, and hemocytes. Temporal expression profiles showed that 15 CLIP genes were predominantly expressed during the fifth-instar larval stage, early and later period of the pupal stage, and adult stage, whereas 10 CLIP genes were mainly expressed in the wandering stage and middle to later period of the pupal stage in the integument. Pathogens and 20-hydroxyecdysone (20E) induction analysis indicated that 14 CLIP genes were positively regulated by 20E, 9 were negatively regulated by 20E but positively regulated by pathogens, and 5 were positively regulated by both factors in the integument. Together, these results suggested that silkworm CLIP genes may play multiple functions in integument development, including melanization of new cuticle, molting and immune defense. Our data provide a comprehensive understanding of CLIP genes in the silkworm integument and lays a foundation for further functional studies of CLIP genes in the silkworm.