Isolation and molecular molecular characterization of VPS39/VAM6 from olive
VPS39/VAM6 promotes aggregating and fusing of endosomesand lysosomes. It is a component of a protein complex that isfound in vacuole membranes. This gene has been studied fromvarious organisms including humans,Drosophila,Arabidopsisandrice. No studies on olive VPS39/VAM6, however, have beenreported. The aim of this study is to report information of oliveVPS39/VAM6 including expression pattern and biochemicalcharacterization.VPS39/VAM6 was isolated from a cDNA library we con-structed from fruited olive leaves in July. To determine the puta-tive name of the cDNA, BLAST analyses were conducted fornucleotide, open reading frame and amino acid sequence compar-isons. BioEdit program was used to determine the nucleotide andamino acid composition along with its molecular weight and iso-electric point (pI). Hydropathy analysis was conducted usingKyte and Doolittle program. Phylogenetic analysis was doneusing MEGA7. Cellular localization of the product was predictedusing SOSUI GRAMN. The three dimentional structure of theprotein was calculated using I-TASSER and compared to previ-ously known structures using Cn3D.The BLAST and BioEdit analyses revealed VPS39/VAM6 had836 base pairs coding 120 amino acids with a molecular weightof 13.38 kDa, and pI of 6.39. The AT/GC ratio was very high(1.5) comparing to its homologs from other plants suggesting toexpect significant differences of this gene’s function from theothers. Amino acid composition analysis revealed high rates of Serine, Leusine and Isoleucine indicating a hydrophobic propertyof the protein. The hydrophobic feature was confirmed by Kyteand Doolittle analysis while the cellular location was revealed tobe extracellular. The hydrophobic nature despite extracellularlocation suggests it is a membrane associated protein which wasconfirmed by transmembrane domain analysis. As expected nosignal peptide was detected. The 3D structure of the protein wassimilar to its previously reported homologs.