Title : Modulating TPP riboswitch activity simultaneously enhances crop yield, nutritional quality and stress tolerance
Abstract:
Global food security faces growing pressures from climate change, population expansion, and widespread micronutrient deficiency. Coordinately improving crop yield, nutritional value, and stress resilience is a core objective of sustainable agriculture, yet is frequently constrained by inherent trait trade-offs. Thiamine Pyrophosphate (TPP), the active coenzyme form of vitamin B1, plays a central role in primary metabolism as a cofactor for key enzymes in the tricarboxylic acid cycle, Calvin-Benson cycle, and nitrogen assimilation. In higher plants, endogenous TPP biosynthesis is subject to tight negative feedback regulation via a conserved TPP riboswitch residing in the 3'-untranslated region of the THIC gene. However, the potential of targeting this cis-regulatory element to achieve synergistic improvement of multiple agronomically important traits remains underexploited.In this study, we employed CRISPR-Cas9-mediated genome editing to precisely disrupt the TPP riboswitch in rice (Oryza sativa) and tomato (Solanum lycopersicum), thereby relieving the feedback inhibition of TPP production. We performed comprehensive phenotypic, metabolic, and molecular characterizations of the edited lines under both normal field growth and controlled stress conditions. Our results showed that riboswitch editing significantly elevated endogenous TPP levels in both vegetative and reproductive tissues. The edited plants exhibited enhanced photosynthetic capacity and nitrogen use efficiency, driven by upregulated activities of core metabolic enzymes. Field trials revealed that rice edited lines achieved approximately 9% higher grain yield relative to wild type, along with notably increased contents of vitamin B1, essential amino acids, and grain protein. Tomato edited lines similarly showed improved fruit yield and enhanced nutritional quality including higher soluble solids and vitamin levels. Furthermore, the edited lines displayed substantially enhanced tolerance to cold stress and resistance to pathogen infection, with improved reactive oxygen species scavenging capacity and cell membrane integrity, resulting in markedly reduced yield penalty under adverse conditions. The consistent phenotypic effects observed in both rice and tomato demonstrate the cross-species universality of this strategy. Collectively, our findings establish that precise modulation of TPP riboswitch activity represents an efficient metabolic engineering strategy to simultaneously boost crop yield, nutritional quality, and multi-stress tolerance through reprogramming central carbon and nitrogen metabolism. This work provides a novel and broadly applicable approach for breeding high-yield, nutrient-dense, and stress-resilient crops, with significant implications for advancing sustainable agriculture and global food and nutrition security.
