Isolation, Identification and in silico Analysis of Alpha-amylase Gene of Aspergillus niger strain CSA35 Obtained from cassava Undergoing Spoilage
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Date
2018
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ELSEVIER Biochemistry and Biophysics Reports
Abstract
In this investigation, a gene (CDF_Amyl) encoding extracellular α-amylase in Aspergillus niger
strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in
silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues
with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was
located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40,
respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or
animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction
enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product
had a hydrophobicity score of − 0.43 but no transmembrane helix. The CDF_Amyl protein was
subcellularly localized in the secretory pathway, an indication of its release into extracellular space after
secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic
of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was
concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find
applications in biotechnological, food and pharmaceutical industries where cloning and further
modification of this gene would be required for product development and improvement.
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Keywords
Aspergillus niger, Alpha-amylase gene, Bioinformatics characterization, Restriction enzymes Phylogenetics, Evolution