Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis

Abstract

Background: Photorespiration, a highly wasteful process of energy dissipation, depresses the productivity of C3 plants such as rice (Oryza sativa) under dry and hot conditions. Thus, it is highly required to understand the cellular physiology and relevant metabolic states under photorespiration using systems approaches, thereby devising strategies for improving rice production. Findings: In silico model-driven gene deletion analysis was performed on photorespiring leaf cells under ambient and stressed environmental conditions using our central metabolic network of rice cells. As a result, we identified a number of essential genes for the cell growth across various functional pathways such as photorespiratory cycle, Calvin cycle, GS-GOGAT cycle and sucrose metabolism as well as certain inter-compartmental transporters, which are mostly in good agreement with previous experiments. Synthetic lethal (SL) screening was also performed to identify the pair of non-essential genes whose simultaneous deletion become lethal, revealing the existence of more than 220 pairs of SLs on rice central metabolism. Conclusions: The gene deletion and synthetic lethal analyses highlighted the rigid nature of rice photosynthetic pathways and characterized functional interactions between central metabolic genes, respectively. The biological roles of such reported essential genes should be further explored to better understand the rice photorespiration in future. © 2013 Lakshmanan et al.; licensee Springer.