| Facing the emerged diseases in the scallop aquaculture, studies towards a better understanding of defence mechanisms in scallop could help us to constitute an approach to overcome the disease problem by optimizing the culture conditions, develop and enrich the marine invertebrate immunology, compare the innate and adaptive immunity, and provide evidence to confirm the origin of vertebrate immunity. Based on EST sequencing rapid amplification cDNA end (RACE) methods, the full length cDNA of lipopolysaccharide and β-1,3-glucan binding protein (LGBP) gene was cloned from Zhikong scallop (Chlamys farreri). With homologous cloning and RACE methods, the full length cDNA of short peptidoglycan recognition protein (PGRP-S1) was got from Zhikong scallop, confirmed by Virtual Northern Blotting. These sequences were analyzed by bioinformatics. Using RT-PCR, these two pattern recognition receptor (PRR) gene mRNA expression levels were primarily studied in hemolymph, gill, mantle, adductor muscle, gonad and hepatopancreas. LGBP mRNA expression levels were tested by RT-PCR under stimulation by gram negative bacteria and fungi. PGRP mRNA expression levels were measured by RT-PCR under stimulation by gram positive bacteria and gram negative bacteria. The full length cDNA of Zhikong scallop LGBP gene consists of 1850 nucleotides (nt). The 5'-untranslated region (UTR) is 127 nt, including three "stop codons". Open reading frame (ORF) is of 1323 nt. The 3'-UTR is 400 nt, including a canonical polyadenylation signal sequence (AATAAA) and poly A tail. LGBP nucleotide sequence conserves poorly with other known genes by BLASTN. Free energy of the mRNA second structure is -309.0kkcal/mol. The ORF of Zhikong scallop LGBP gene encodes a protein composed 440 amino acids (aa). The molecular weight (MW) is 47.16 kDa. The isoelectric point (PI) is 5.095. It has a transmembrane zone (146-180), and its flanking sequences lie out of membrane. It also has a glycosyl hydrolase family 16 (glycohydro16) domain (276-437) containing a virtual disulfide bond and binding sites for chloride and cadmic. Glycohydro16 domain has several beta-sheets, but no alpha-helix. The LGBP contains a potential N-glycosylation site (294-296), a potential polysaccharide binding motif (313-330), a glucan binding motif (341-350). Its C terminus is tryptophan rich (6.66%, 320-440). The second structure of LGBP has 10 % helix, 17 % sheet, 21 % turn and 53 % coil. Analyzed by BLASTP, the deduced amino acid sequence of Zhikong scallop LGBP gene shares high similarity with the blue shrimp (Penaeus stylirostris) LGBP (E=5e-72). Its amino acid sequence highly conserved with other PGRPs. The genetic distance among Zhikong scallop LGBP, Daphnia magna gram negative bacteria binding protein (GNBP), Daphnia rosea GNBP, Dapnia plulex GNBP, Suberites domuncula β-1,3-glucan binding protein (BGBP), Eisenia foetida LGBP is close. The proteins associated with Zhikong scallop LGBP have been reported in bacteria, fungi, poriferan, annelid, arthropod, echinodermata etc. In mollusk, this is the first LGBP homologous gene submitted in GenBank. The full length cDNA of Zhikong scallop PGRP-S1 gene consists of 1073 nt, The 5'-UTR is 59 nt, containing two "stop codons". Next is an ORF of 759 nt. Following is 3'-UTR of 255 nt, including a putative polyadenylation signal sequence (AATAAA) and ploy A tail. The nucleotide sequence conserves poorly with other PGRPs by BLASTN. The free energy of the mRNA second structure is -194.3 kkal/mol. The ORF of Zhikong scallop PGRP-S1 gene encodes a protein of 252 aa. Its MW is 27.88 kDa, and its PI is 8.255. It has a signal peptide sequence of 22 aa. It also has a Zn2+ binding sites (H112, H221 and C229), two conserved cysteines (C119 and C125) to engage in the formation of the disulfide bond that is required for proper tertiary structure. PGRP-S1 contains a PGRP domain (83-225) and an Ami2 domain (100-231). The PGRP domain of PGRP-S1 has three conserved PGRP sub-domains (PGRP-I, PGRP-II and PGRP-III). This domain also has 4 alpha-helixes and 5 be...
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