Combined Transcriptomic and Proteomic Analyses Uncover Molecular Basis of Heat Tolerance in Pakchoi (Brassica rapa subsp. chinensis)

Abstract

Introduction: High temperature posed a significant abiotic stress, severely limiting plant growth and development. As a cool-loving vegetable, pakchoi (Brassica rapa subsp. chinensis) is highly sensitive to high temperatures, yet its molecular mechanisms underlying heat stress tolerance in pakchoi are not well explored. Methods: This study employed an integrated approach combining physiological assessments with extensive transcriptomic and proteomic profiling of leaves from a heat-tolerant pakchoi line. Results: Our physiological analyses revealed that 5 days of heat stress (39/32℃, day/night) significantly impaired plant performance, resulting in a significant reduction in plant fresh weight, chlorophyll content, and critical Chl fluorescence parameters, including Fv/Fm and PIABS. Furthermore, the activities of key antioxidant enzymes, peroxidase and catalase, were significantly reduced, suggesting a reduced reliance on these antioxidant enzymes for mitigating oxidative stress in heat-tolerant varieties. Subsequent integrated transcriptomic and proteomic analysis identified 4414 differentially expressed genes (DEGs) and 506 differentially abundant proteins (DAPs) under heat stress. Functional enrichment analysis demonstrated that up-regulated DEGs/DAPs were significantly enriched in pathways essential for cellular protection and energy metabolism, including protein processing in endoplasmic reticulum, starch and sucrose metabolism, glycolysis/gluconeogenesis. Conversely, down-regulated DEGs/DAPs were mainly involved in plant hormones and signaling pathway (e.g. ABA pathway, MAPK signaling), as well as secondary metabolic processes (e.g. phenylpropanoid and flavonoid biosynthesis), suggesting a strategic reallocation of cellular resources and a shift in metabolic priorities under stress. Notably, integrated omics and protein-protein interaction (PPI) analysis highlighted the privotal role of the heat shock proteins (HSPs) in mediating heat tolerance, particularly heat shock protein 70s (HSP70s), with four HSP70s identified as hub nodes in the PPI network, three of which were involved in protein processing in the endoplasmic reticulum. Dissusion: This study not only provides novel and comprehensive insights into the multi-level physiological and adaptations of pakchoi to heat stress, but also lays a robust foundation for the development of more heat-tolerant pakchoi through targeted breeding strategies.