National Institute of Plant Genome Research
 
Central Theme
Our major goal is to determine how proteins adapt to perform specific functions, and in particular, how they co-operate with each other to carry out their biological roles efficiently. A knowledge based computational approach is particularly appropriate to address complex problems in biology involving protein architecture, interactions and biosynthesis.
Terpenoid Diversity in Plants
The focus of this work is an analysis of plant terpenoid biosynthetic diversity based on a comprehensive computational study of the literature and available data on genes, proteins, and regulators of the terpene biosynthetic pathways. Despite the diversity in function and structure, all isoprenoids derive from the universal C5 precursors, isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). The cytoplasmic mevalonate pathway (MVA) and plastidial methyl erythritol pathway (MEP) together contribute to the formation of isoprene units (IPP) which are in turn, the precursors of numerous terpenoid compounds made by the terpene synthase enzymes (TPS). Terpenoids play a variety of crucial roles, such as in defense, and as components of membranes (sterols), pigments (carotenoids), hormones (gibberellins, abcissic acid, cytokinins), in the electron transport chain (quinines), and in the attraction of pollinators (volatile terpenes) as well. Key molecular features of terpene diversity are being investigated at the center through a detailed in-silico analysis of the terpene synthase enzymes and pathway interactions
Analysis of Molecular Interaction Networks
Biomolecular network comparisons have been carried out for Saccharomyces cerevisiae since it has the largest and most comprehensive amount of interaction data available. Superimposition of the physical protein interaction network over expression and regulatory networks (preliminary data) have revealed interesting clues towards understanding the mechanism of complex genetic interactions between superficially unrelated genes, mediated by long distance physical connections. Further analysis currently underway involves extraction of mRNA co-expression information for the pathway genes by microarray data normalization and multi-dimensional clustering techniques. A preliminary map of terpene pathways and its regulators is currently under construction. The interactors of various enzymes involved in isoprenoid pathways have been identified using information available in public interaction databases whereby putative interlogs are being extracted and verified using various strategies, from plant genomes.
Identification and Analysis of SSR Markers in Plant EST sequences
EST sequences and their assemblies available from the partially sequenced genomes of 35 different plants have been compiled on local servers using in-house scripts and programs. These are genomes having a substantial number of ESTs available, such as those of Cotton, Sugarcane, Tomato, Tobacco and several others. SSR markers have been identified for the EST sequences of Catharanthus roseus and Glycine max. Primers have been designed for these and mapping efforts are currently underway to construct genetic maps based on available data.
Mechanistic basis of differential activity of MIPS proteins in plants
Analysis of sequence level differences of two differentially expressing and differentially functioning L- myo inositol 1- phosphate synthase (MIPS) proteins in chick pea, and their structural mapping on to the three dimensional structure of the known salt tolerant MIPS protein from rice revealed that the differential activity is likely to be on account of variation in the inter-domain contact interfaces and variant protein-ligand interactions mediated by the respective proteins. One of the chick pea proteins, CAMIPS1, was found to have a relatively lower hydrophobicity in the inter-monomeric region, and was also more divergent at ten crucial positions identified in this analysis. Taken together, these features may explain why the second chick pea protein, CAMIPS2, would be more stable, and its activity less likely to be affected by destabilizing factors such as temperature and salt.
Design of Bacterial Hyaluronidases Inhibitors
Bacterial hyaluronidases are one of the major virulence factors, which facilitate the spreading of many severe and often fatal diseases in humans. The phenomenon of bacterial ‘spread’ is due to their ability to cleave the hyaluronan (HA) matrix, found predominantly in the extra cellular matrix (ECM) of all vertebrates, thus enabling greater microbial ingress, and migration between host tissues during the pathogenic process. These enzymes directly facilitate the spread of infection by degrading the HA matrix which constitutes a highly organized network in the extra cellular space in all vertebrates, acting as a diffusion barrier in vivo and regulating the transport of other substances through the intercellular space. The HA matrix in ECM is mainly composed of HA polymer, a negatively charged polysaccharide of repeating disaccharide units of D-glucuronic acid (β-1,3) and N-acetyl β-D-glucosamine, and is highly viscous in nature. Hyaluronidases are able to split this matrix, reducing its visco-elasticity and increasing membrane permeability, thereby allowing greater microbial access to, or promoting diffusion between host tissues for colonization. To control bacterial infection, it is necessary to design and develop a potent and specific hyaluronate lyase inhibitor that protects hyaluronan from degradation. Computational analyses have been carried out to identify prospective candidates as inhibitors and decipher the molecular mechanisms by which they function. Structural modeling of enzyme, substrate and the putative inhibitors are being used towards rational design of short peptides that mimic the inhibitory activity.
Analysis of plant lectin domains
Modern Glycobiology revolves, to a large extent, around the potential biological information stored in cell surface carbohydrates, whose roles in cell growth, differentiation and surface recognition are increasingly being investigated using Lectins, a large family of proteins with the ability to bind and agglutinate these sugars. Due to the huge diversity in sequence and carbohydrate specificity of Lectin domains across different organisms, methods that seek to improve glycoprotein detection, and/or predict their sugar binding specificity, can be of immediate interest to researchers working in this area. The work aims to elucidate the structure, sugar-binding activity, biological function and evolution of proteins in each of the plant lectin families as well as annotated sequences. Profile hidden markov models have been built for specific lection families enabling accurate identification and detection of domains. A structure-function relationship is being analysed for predicting specific sugar substrates of identified lectin domains.
Evolutionary studies of functional domain fusions spanning all organisms
We are trying to study the evolution of housekeeping genes across the major classes of organisms in direct contrast with the evolution of inducible genes. The objective is to identify genes having fused domains in lower organisnms, with homologs that have evolved as disjoint structures in higher organisms, i.e, individual alterations in group functions through the course of evolution. This effort also involves identification of functions that were separate originally but may have fused during evolution in higher organisms to form a new combined function. The goal is to understand the mechanistic basis of domain evolution, in the context of evolving organism complexity. Relevant data is being collected from several public databases containing domain structural information , and analysed using in house scripts and programs.