Study of Bioinformatics Criteria of Ocimum basilicum L. Phenylalanine Ammonia Lyase Gene

Phenylpropanoids are volatile secondary metabolites which comprise the main part of essential oil of some Ocimum basilicum L. (O.b). These compounds have remarkable medicinal and aromatic importance, and are synthesized in a complex pathway in plants [1,2]. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the first regulating and rate-limiting enzyme of the phenylpropanoids metabolism pathway. This enzyme acts as a branch point of primary and secondary metabolites synthesis [2, 3]. We intended to study bioinformatics criteria of ObPAL cDNA sequence (Gene bank accession number, KU375119) and gained more knowledge about this critical enzyme.Online sequence homology tools (Blast N and P) and multiple alignment programs were used for comparing the sequence similarities. ORF finder, ScanSite, ProtParam, PROSITE, InterProScan, ProDom, TrEMBL programs were utilized for finding ORF, physicochemical properties, structural and functionally important regions of predicted PAL protein. ObPAL cDNA (almost full length) had 2229 nt size with 5ʹ UTR (165 nt), 3ʹ UTR (133 nt) and an ORF region (2064 nt) witch encoded a 687 amino acid poly peptide chain. Sequence similarity evaluation showed high identity with other PAL cDNA and predicted protein sequences such as Perilla frutescens (86%, 89%), Melissa officinalis (85%, 89%) and, Salvia miltiorrhiza (82%, 89%). Estimated molecular weight and pI of PAL protein were about 74.64 kDa and 8.64, respectively. PAL protein sequence revealed a conserved active site motif that could be found in all PAL enzymes. In addition, it showed two main motifs including histidine ammonia-lyase and phenylalanine and histidine ammonia-lyases signatures. It also contained several conserved domains consisting of active site catalytic domain, deamination domain (L203, V169, A248) and pentapeptide domain(HNQDV, 493-497). Several catalytic domains were recognized by MotifScan program, most important of which were N-glycosylation site, cAMP- and cGMP-dependent protein kinase phosphorylation site, Casein kinase II phosphorylation site, Protein kinase C phosphorylation site, Tyrosine kinase phosphorylation site, Histidine ammonia-lyase and, Phenylalanine and histidine ammonia-lyases signatures. Existing different phosphorylation sites could point to various regulation pathways of this enzyme. PORTER program demonstrated that most parts of protein were placed in α-helices secondary structures (52.26%) and random coil regions (27.22%). Other parts of the protein comprised extended strands (10.63%) and, β-turns (9.90%). Hydrophobicity analysis proposed that PAL protein could anchor to endoplasmic reticulum organelle. Characterizing the PAL protein in more details could be beneficial for a better understanding of its function and molecular regulation.

کلیدواژه ها:

Bioinformatics criteria ، Phenylalanine ammonia lyase ، Ocimum basilicum L.