Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, <em>Camelus dromedarius</em>

• Main Authors: Dalia Fouad, Hesham Mahmoud Saeed, Farid Shokry Ataya, Ajamaluddin Malik
• Format: Article
• Language: English
• Published: MDPI AG 2012-07-01
• Series: International Journal of Molecular Sciences
• Subjects: Ape1/Ref-1/APEX1; 3D structure modeling; DNA repair; BER; cloning; molecular characterization; qPCR; one-humped camel
• Online Access: http://www.mdpi.com/1422-0067/13/7/8578

The domesticated one-humped camel, <em>Camelus dromedarius</em>, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative <em>cAPEX1 </em>gene was amplified for the first time from <em>C. dromedarius </em>by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of <em>cAPEX1 </em>in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of <em>cAPEX1</em> transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of<em> S. scrofa</em>. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.