Cloning and Bioinformatics Analysis of RiPAL1 Gene of Raspberry
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Abstract:
Phenylalanine ammonia-lyase (PAL) is a key enzyme in the metabolism of phenylpropane that regulates the biosynthesis of flavonoids in raspberry. To elucidate the function and regulation mechanism of the RiPAL1 gene in raspberry, total RNA was extracted from raspberry fruits to synthesize first-strand cDNA. The gene was successfully cloned, and related bioinformatics analyses were carried out. Our results showed that the coding sequence (CDS) of the RiPAL1 gene was 2 133 bp in length, encoding 710 amino acids, with a molecular weight of 77.5 ku and an isoelectric point of 6.21. The maximum hydrophobicity of RiPAL1 protein was 4.50, its minimum hydrophobicity was -4.50, and its average hydrophobicity index was -0.49. Based on these, it was determined that it is a hydrophilic protein with no transmembrane structure and no signal peptide. The RiPAL1 protein contained 4 N-glycosylation sites and 67 specific kinase sites. Its secondary structure was mainly composed of α-helices, while its tertiary structure was a homotetramer. Multiple sequence alignment showed that the RiPAL1 protein has a typical conserved domain of phenylalanine ammonia-lyase. Phylogenetic analysis indicated that the RiPAL1 protein is closely related to that of strawberry. This study provides a reference for further research on the molecular mechanism of the RiPAL1 gene in the biosynthesis of flavonoids in raspberry fruit.
