©1996-2019. All
Rights Reserved. Online Journal of Bioinformatics . You may not store
these pages in any form except for your own personal use. All other usage or
distribution is illegal under international copyright treaties. Permission to
use any of these pages in any other way besides the
before mentioned must be gained in writing from the publisher. This
article is exclusively copyrighted in its entirety to OJB publications. This
article may be copied once but may not be, reproduced or
re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements
(DEST) for the Higher Education Research Data Collection (Australia). Linking: To link to this page or any
pages linking to this page you must link directly to this page only here rather
than put up your own page.
OJBTM
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
ABSTRACT
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.
FULL-TEXT (SUBSCRIPTION OR PURCHASE
TITLE $25USD)