Plant systems biology: Application to rice for understanding metabolic and regulatory characteristics under biotic stress conditions (bacterial leaf blight)

Rice is one of the major global food crops. Although the overall yield of rice has been increasing, the growing population and adverse climatic changes pose huge challenges for their sustained production in the future. Xanthomonas oryzae pathovar oryzae (Xoo) is a vascular pathogen that causes leaf blight in rice leading to severe yield losses. Since the usage of chemical control methods has not been very promising for the future disease management, it is of high importance to systematically gain new insights about Xoo virulence and pathogenesis. Therefore, systematic approaches are highly required to explore their effects on rice phenotypic and cellular responses. It could be achieved by combining the available multiple high throughput data such as genomics, metabolomics, proteomics and transcriptomics, thereby analysing the possible biochemical adaptations to several abiotic and biotic stresses, and subsequently improving the crop yield. We have employed similar systems biology approach to reconstruct a fully compartmentalized genome scale metabolic model of rice. Subsequently, transcriptomics data were systematically integrated with the model to identify the potential candidate regulatory genes. In addition, we also reconstructed a genome-scale metabolic model of Xoo (iXOO673) and validated the model predictions using culture experiments. Constraintbased modeling approach was then utilized to highlight the critical role of gluconeogenesis, glycogen biosynthesis and degradation pathways of Xoo in the exacerbation of leaf blight in rice exposed to nitrogenous fertilizers, which are remarkably consistent with published experimental literature. Moreover, using model based interrogation of transcriptomic data, we reveal the metabolic components under the DSF regulon that are crucial for virulence and survival in Xoo. Finally, we identified promising antibacterial targets for the control of leaf blight in rice by gene essentiality analysis. In future, the current in silico model guided framework can be further extended by including comprehensive genome scale model of rice and its leaf microbiome for characterizing their interactions with Xoo and host. As such, this will allow us to systematically devise new strategies to effectively control leaf blight in rice.

Bijayalaxmi Mohanty received her MSc and MPhil degree from Utkal University, Bhubaneswar, India in 1983 and 1985 respectively and PhD degree from the University of Cambridge, UK in 1991. She is currently a Visiting Research Scientist at the NUS Environmental Research Institute, National University of Singapore, Singapore. Her main research interests focus on the abiotic stress tolerance in rice and other plants, plant genomics, metabolic and transcriptional regulation, integrative omics approaches to different abiotic stress conditions and plant modeling. She is the Associate Editor for Current Plant Biology, Plant Biophysics and Modeling, Frontiers in Plant Science, Crop Design and Review Editor for more than 30 internationally referred journals.