新西兰白兔SOD1基因编码区克隆及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2019.08.006

Abstract

Abstract:

This study was aimed to clone and analyze the CDS region of SOD1 gene in New Zealand White rabbits.Specific primers were designed according to the SOD1 gene sequence of Oryctolagus cuniculus (accession No.:NM_001082627.2) in GenBank, then the complete CDS region of SOD1 gene in New Zealand White rabbits was amplified by RT-PCR and cloned into T vector.After sequencing and identification, the homology was compared with other species and phylogenetic tree was constructed.SOPMA, SWISS-MODEL, ExPASy, ProtParam and other software and online tools were used to analyze the protein sequence, the subcellular localization and interaction network of SOD1 protein were predicted.The results showed that the CDS region of SOD1 gene in New Zealand White rabbits was 459 bp in length, the contents of A, T, C and G bases were 24.84%, 18.95%, 23.09% and 33.12%, respectively, and the content of GC was higher than that of AT, which coding 153 amino acids.The homologies of SOD1 gene CDS between New Zealand White rabbit and Oryctolagus cuniculus, Cebus apella, Homo sapiens, Pan troglodytes, Callithrix jacchus, Camelus dromedarius, Canis lupus familiaris, Macaca mulatta, Sus scrofa and Mus musculus were 99.8%, 85.2%, 85.0%, 84.7%, 84.1%, 83.9%, 83.9%, 83.7%, 83.2% and 81.3%, respectively.The phylogenetic tree results showed that New Zealand White rabbits and Oryctolagus cuniculus had the closest evolutionary relationship, and clustered into a single branch.The molecular weight of SOD1 protein in New Zealand White rabbits was 15.7 ku, the theoretical isoelectric point (pI) was 5.86, the formula was C₆₇₂H₁₀₈₄N₂₀₀O₂₂₁S₅, the instability index, fat coefficient and average hydrophilic index (GRAVY) were 23.79, 78.89 and -0.276, respectively.SOD1 was a hydrophilic protein, with no signal peptide and transmembrane region.SOD1 protein contained 5 potential phosphorylation modification sites and 3 potential glycosylation sites, and there was a conserved active site at 45-120 amino acids.The secondary structure was mainly random coil, accounting for 53.59%.The tertiary structure modeling showed that the protein was easy to form homologous dimer.Subcellular localization results showed that the cytoplasm, nucleus and mitochondria accounted for 65.2%, 26.1% and 8.7%, respectively.SOD1 protein could interact with SOD2, PRDX1, PRDX3, PRDX4 and DERL1 molecules in vivo.The results provided a reference for further study of the function of SOD1 gene and the relationship between SOD1 gene and related diseases.

Key words: New Zealand White rabbit; SOD1 gene; cloning; bioinformatics; prediction

CLC Number:

DENG Xiaoliang, MA Wenkang, HONG Wei, FU Xin, TAN Yin. Cloning and Bioinformatics Analysis of SOD1 Gene in New Zealand White Rabbits[J]. , 2019, 46(8): 2236-2245.

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Cloning and Bioinformatics Analysis of SOD1 Gene in New Zealand White Rabbits

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