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Online Journal of Bioinformatics ©
Volume 17(2):136-147, 2016
Molecular cloning and in-silico analysis of pectin lyase from Aspergillus niger MTCC 404
Amit Kumar Dubey1 (PhD), Sangeeta Yadav1 (PhD), Gautam Anand1 (MSc.), Vinay Kumar Singh2(MSc.) and Dinesh Yadav1*(PhD)
Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur (U.P.) 273 009 INDIA
Dubey AK, Yadav S, Anand G, Singh VK, Yadav D., Molecular cloning and in-silico analysis of pectin lyase from Aspergillus niger MTCC 404, Onl J Bioinform., 17(2):136-147, 2016. Pectin lyase does not produce toxic methanol as by-product and hence is preferred for food juice clarification. We describe cloned pectin lyase gene from Aspergillus niger MTCC 404 by PCR and in-silico sequence characterization. A pectin lyase gene was amplified using genomic DNA of A. niger MTCC404 as template DNA, gel eluted, cloned in pJET1.2/blunt vector and sequenced and assigned GenBank accession number KJ729121. The sequence of cloned pectin lyase gene of A. niger was subjected to homology search, multiple sequence alignment, motif search, phylogenetic tree construction and 3D structural prediction by homology modeling. A BLAST search revealed close identity with A. niger pectin lyase D (pelD) gene and FGENESH gene of 999 bp with 4 exons coding for a protein of 332 amino acid residues. Multiple sequence alignment of the 5 proteins of pectin lyase of A. niger with cloned pectin lyase of A. niger MTCC 404 showed maximum sequence homology. The phylogenetic tree showed two major clusters. The structural motifs observed for the pectin lyase protein of A. niger MTCC 404 revealed 4 sheets, 1β hairpin, 4β bulges, 16 strands, 8 helices, 1 helix-helix interaction, 33β turns , 5γ turns and 3 disulphide bonds. The cloned pectin lyase gene of A. niger needs to be expressed in a suitable vector.
KEY WORDS: Pectin lyase, Pectinases, Homology modelling, In-silico, Aspergillus niger, Gene.