Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya. Bioinformatic analysis on Maize sugary1 gene (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Budding Researchers, pp. 173

1. Bioinformatic analysis on Maize sugary 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 combination of both α(1->4) and α(1->6) linkages. The polydisperse molecules of starch are generally classified as belonging to two component fractions, known as amylose and amylopectin, on the basis of their degree of polymerization (DP) and the ratio of α(1->6) to α(1->4) linkages. Typically, amylose molecules constitute 20–30% of the mass of starch, have a DP of between 500 and 5000, and contain less than 1% α(1->6) linkages. By contrast, amylopectin contributes 70–80% of the dry weight of starch, is a much larger molecule with DP ranging from 5000 to 50 000 and contains 4–5% α(1->6) linkages. The sugary-l (sul) mutant of maize, Zea mays L., which is the usual sweet corn of commerce, has been known and utilized and specific efforts to improve particular varieties of sweet . OBJECTIVE OF THE STUDY Maize sugary 1 (su1) gene encodes an essential starch debranching enzyme (SBEIIb) which hydrolysis α-(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 from Zea mays to find neighbor genera using BLAST provided grass plant (remote homolog) but manual inspection on the region of alignment drew in entropical regions i.e repeated base pairs at the 3’end of the su1 gene (Fig. A). Genome-wide comparison was made using plant genomes available in GRAMENE database (PG 2011 release) yielded alignment over Oryza indica (Indian Rice; Fig B) with built-in BLAT program. Examination over alignment was encompassed in repeated sequences. We further masked the repeat sequence using engineered Repeat Masker which ultimately gave no similarity. Hence, search for CpG island was carried out using CpG Island Searcher & resulted in CpG island at the 5’ end of the su1 gene (Fig C and D). To explore the contribution of sequence-based complexity of su1 gene, we retrieved corresponding 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 known Zea mays cultivars around 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 of Zea mays in the starch biosynthesis. BLAST search on GenBank NR Database excluding Zea mays MAJOR CITATIONS : 1. James et al., 1995 Plant Cell 7: 417-429. 2. Prasanna & Hoisington, 2001 IJBT 1: 85-98 3. Gonzales et al., 1976 Plant Physiol 58: 28-32. 4. Pan & Nelson, 1984 Plant Physiol 74: 324-328. 5. Cobe & Hannah, 1988 Plant Phyiol 88: 1219-1221. 6. Rahman et al., 1998 Plant Physiol 117: 425-435. Programs used in the Study Sequence based Genome Comparison: Oryza indica genome in GRAMENE database using BLAT algorithm A B Sequence logo of su1 gene showing high 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 divergence of su1 gene product Zea mays cultivars around the globe. Disorderness prediction of su1 protein Helical protein predicted by secondary structure analysis using PSIPRED E F G