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: yjasrai@yahoo.com 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