Research Projects

Project Origin, description and Importance: Drought is a major constraint in rice production, particularly in rainfed areas, which account for over 40% of global rice cultivation. As global temperatures rise and precipitation patterns become increasingly erratic due to climate change, drought events are growing in both frequency and intensity. This trend poses a major threat to food security in regions heavily dependent on rice as a staple crop. Traditional breeding aimed at improving drought tolerance have yielded limited success., largely due to the complex, quantitative nature of drought-related traits and their strong influence on genotype-environment interactions. In this context, epitranscriptomic regulation, especially through pseudouridylation (Ψ), emerges as a promising avenue for modulating stress-responsive gene networks. Ψ modifications can influence RNA stability, and splicing, highlighting pseudouridine synthase (PUS) enzymes as potential targets for precise enhancement of drought tolerance in rice. Post-transcriptional RNA modification Ψ, catalyzed by PUS enzymes, is one of the most abundant and evolutionarily conserved. PUS enzymes are essential for various biological processes, including growth, reproduction, and stress adaptations. For example, PUS members in Arabidopsis modulate chloroplast and mitochondrial translation, ABA signaling, drought responses, and overall plant development. Our preliminary work identified PUS9, a TRUA subfamily member in Arabidopsis, as a negative regulator of drought and ABA responses. Notably, knockout mutants of pus9 exhibit improved drought tolerance and increased ABA sensitivity, whereas its overexpression transgenics display the opposite phenotype (Dhingra et al., unpublished). Building on these insights, we have identified the rice ortholog OsTRUA3 based on sequence homology for functional characterization under drought conditions. We hypothesize that PUSs play a crucial role in enhancing abiotic stress resilience in plants, particularly under drought conditions. We propose to generate CRISPR/Cas9-mediated knockout lines of OsTRUA3 in rice, evaluate their physiological and molecular responses to drought stress. Our integrative approach will include transcriptomic profiling, Ψ-sequencing, RNA-immunoprecipitation (RNA-IP), and RNA structural analyses to elucidate the downstream targets and RNA modifications regulated by TRUA members in plants. Taken together, this project addresses a critical challenge in agriculture, enhancing drought resilience in rice. By targeting Ψ, a key RNA modification, we aim to uncover novel regulatory pathways in plant stress biology. Our findings on AtPUS9 offer a strong foundation for exploring OsTRUA3 and its RNA targets. Using CRISPR/Cas9 genome editing and integrative molecular tools, we aim to develop rice lines with improved drought tolerance and establish pseudouridylation as a novel mechanism for crop improvement.

RNA modifications, pseudouridylation, abiotic stresses, pseudouridine synthases, rice