Identification and bioinformatics analysis of lactate dehydrogenase genes from Echinococcus granulosus

ObjectiveTo identify full length cDNA sequence of lactate dehydrogenase (LDH) from adult Echinococcus granulosus (E. granulosus) and to predict the structure and function of its encoding protein using bioinformatics methods.MethodsWith the help of NCBI, EMBI, Expasy and other online sites, the open reading frame (ORF), conserved domain, physical and chemical parameters, signal peptide, epitope, topological structures of the protein sequences were predicted and a homology tertiary structure model was created; Vector NTI software was used for sequence alignment, phylogenetic tree construction and tertiary structure prediction.ResultsThe target sequence was 1 233 bp length with a 996 bp biggest ORF encoding 331 amino acids protein with typical L-LDH conserved domain. It was confirmed as full length c DNA of LDH from E. granulosus and named as EgLDH (GenBank accession number: HM748917). The predicted molecular weight and isoelectric point of the deduced protein were 3 5516.2D a and 6.32 respectively. Compared with LDH s from Taenia solium, Taenia saginata asiatica, Spirometra erinaceieuropaei, Schistosoma japonicum, Clonorchis sinensis and human, it showed similarity of 86%, 85%, 55%, 58%, 58% and 53%, respectively. Eg LDH contained 3 putative transmembrane regions and 4 major epitopes (54aa-59aa, 81aa-87aa, 97aa-102aa, 307aa-313aa), the latter were significant different from the corresponding regions of human LDH. In addition, some NAD and substrate binding sites located on epitopes 54aa-59aa and 97aa-102aa, respectively. Tertiary structure prediction showed that 3 key catalytic residues 105R, 165D and 192H forming a catalytic center near the epitope 97aa-102aa, most NAD and substrate binding sites located around the center.ConclusionsThe full length c DNA sequences of Eg LDH were identified. It encoded a putative transmembrane protein which might be an ideal target molecule for vaccine and drugs.