Predictive Modelling of the Rice (Oryza sativa) metabolic network

This project began with a research collaboration agreement between Oxford Brookes University and the University of Calcutta. As a result, our group was contacted by Dr Sudip Kundu of the Department of Biophysics, Molecular Biology & Bioinformatics and we began a project to use the techniques we had developed for the construction of a genome-scale metabolic model of Arabidopsis to build a similar model for rice.

After an initial visit of Dr Kundu to Oxford funded by Oxford Brookes University, we were successful in obtaining a grant from the BBSRC as part of their India Partnering Awards scheme.

This was for:

• Completion of a rice genome-scale metabolic network predicted from annotated sequences (checking pathways for minor biomass components; incorporating compartmental information).
• Flux balance analysis modelling (linear programming) to determine constraints on the network, the significance of network difference between different genotypes, and precursor availability for engineered metabolic modifications (additional carotenoid and lysine content of seeds).
• Experimental flux analysis of wild-type and transgenic rice to calibrate the model and validate predictions.
• Integration of rice transcriptomic and proteomic data with the model, e.g. producing tissue-specific variants.
• Method development to automate more of the steps in generating genome-scale metabolic networks from annotated sequences.

In addition, the Department of Biotechnology (DBT), India, awarded a CREST Fellowship to Dr Kundu to enable hime to make an extended visit to Oxford Brookes University in 2012.

The BBSRC grant (BB/G530317/1) runs from 2009 to 2013. In December 2009, there was an opening workshop in Kolkata, and the final event was a closing workshop in Kolkata in January 2013.

A major outcome of this project was a paper describing a Genome Scale Model of Rice, details of which can be found here