1.Bioinformatic analysis on Maizesugary 1(su1) gene Vishal H.
Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, Yogesh
T. Jasrai* and Himanshu A. Pandya Bioinformatics Laboratory,
Department of Botany, University School of Sciences, Gujarat
University, Ahmedabad-380009, Gujarat, India*Corresponding author:
[email protected] INTRODUCTION Maize (Zea mays) is a major world
crop and important model monocot for plant for studying genetics,
genomics and molecular biology. Many maize mutants are known that
alter the composition of endosperm carbohydrates. The sugary (su)
genotype commonly known as sweet corn, has more sucrose than
starchy maize. Two isoforms of starch branching enzyme have been
identified in starch storing organs of maize. In maize, two
isoforms of SBE II exist (SBE IIa and SBE IIb). Starch is composed
of a single monomer type glucose,polymerized into large molecules
through a combinationof both (1->4) and (1->6) linkages. The
polydispersemolecules of starch are generally classified as
belongingto two component fractions, known as amylose
andamylopectin, on the basis of their degree of polymerization(DP)
and the ratio of (1->6) to (1->4) linkages. Typically,amylose
molecules constitute 2030% of the mass ofstarch, have a DP of
between 500 and 5000, and containless than 1% (1->6) linkages.
By contrast, amylopectincontributes 7080% of the dry weight of
starch, is a muchlarger molecule with DP ranging from 5000 to 50
000 andcontains 45% (1->6) linkages. The sugary-l (sul) mutant
ofmaize, Zea mays L., which is the usual sweet corn ofcommerce, has
been known and utilized and specific effortsto improve particular
varieties of sweet . OBJECTIVE OF THE STUDY Maizesugary 1(su1) gene
encodes an essential starchdebranching enzyme (SBEIIb) which
hydrolysis -(1->6) glycosidic bonds involved in starch
biosynthesis. Genetic mutations in this gene contributes for the
shrunken and immature kernel phenotypically and accumulation of
simple sugars genotypically. In the present study, su1 gene was
analyzed using Bioinformatics approaches. We made attempts to
search for homologs in other carbohydrate-rich plants. The maize
su1 gene was predicted to be the characteristic feature promoting
starch content and no evolutionary trace was identified. Further,
maize cultivars distributed throughout the world showed a conserved
pattern. We also noticed that the contents of GC bases are found to
be relatively higher showing signs of highly de-regularized gene
structure (CpG island). Conceptual translation of gene sequence
provided an insight of ordered structure with a single stretch of
disorderness at its N-terminal. Thus, we emphasize that the
de-regularized gene structure of su1 makes its own way to diverge
from other plant genera and the protein (enzyme) secondary
structure level information showed that it is dense with high
helix- rich content and a member of isoamylase enzyme
family.METHODOLOGY OVERVIEW RESULTS AND DISCUSSION DISCUSSION
Sequence-based homolog search of su1 gene fromZea maysto find
neighbor genera using BLASTprovided grass plant (remote homolog)
but manualinspection on the region of alignment drew inentropical
regions i.e repeated base pairs at the 3endof the su1 gene (Fig.
A). Genome-wide comparisonwas made using plant genomes available
inGRAMENE database (PG 2011 release) yieldedalignment overOryza
indica(Indian Rice; Fig B) withbuilt-in BLAT program. Examination
over alignmentwas encompassed in repeated sequences. We
furthermasked the repeat sequence using engineered RepeatMasker
which ultimately gave no similarity. Hence,search for CpG island
was carried out using CpGIsland Searcher & resulted in CpG
island at the 5 end ofthe su1 gene (Fig C and D). To explore the
contributionof sequence-based complexity of su1 gene, we
retrievedcorresponding gene products (protein) from UCSC and
analyzed how much extent of complexity dense region contributes for
its tertiary structure. UCL Disopred predicted su1 protein sequence
as globular protein and found to be helical protein with long
coiled conformation at both of its terminals, respectively (Fig. E
& F). Phylogenetic analysis was performed with su1 gene
sequences obtained from knownZea mays cultivarsaround the world
from UCSC leading to a relationship of evolutionary divergence (Fig
G). Moreover, multiple sequence alignment showed that alignment was
conserved in the complexity regions.CONCLUSION We emphasize that
su1 gene and protein sequence are conserved among their own
species/isolates. The relationship with other carbohydrate-rich
plants gave no insight. Additionally, gene- and protein-based
sequence analysis revealed that genetic evolution is conserved in
their genera following protein biochemical function (debranching
enzymatic activity) remains unaffected. Hence, su1 is a
characteristic feature ofZea maysin the starch biosynthesis. BLAST
search on GenBank NR DatabaseexcludingZea mays MAJOR CITATIONS : 1.
James et al., 1995Plant Cell7: 417-429. 2. Prasanna &
Hoisington, 2001IJBT1: 85-98 3. Gonzales et al., 1976Plant
Physiol58: 28-32. 4. Pan & Nelson, 1984Plant Physiol74:
324-328. 5. Cobe & Hannah, 1988Plant Phyiol88: 1219-1221. 6.
Rahman et al., 1998Plant Physiol117: 425-435. Programs used in the
Study Sequence based Genome Comparison:Oryza indicagenome in
GRAMENE database using BLAT algorithm A B Sequence logo of su1 gene
showinghigh magnitude of CG dinucleotides(first 100 nts shown fro
clarity) C D CpG Island Detection at 5 end of the su 1 gene
Phylogenetic tree (NJ algorithm) depicting the divergenceof su1
gene productZea mayscultivars around the globe.Disorderness
prediction ofsu1 protein Helical protein predicted by secondary
structure analysis using PSIPRED E F G