Analysis of Chloroplast Proteome of Shandan Huangshen (Sphallerocarpus gracilis) During the Tuberous Root Formation

Shandan Huangshen (Sphallerocarpus gracilis) is a drought- and alkali-tolerant perennial herb. However, due to overharvesting and habitat degradation, highlighting the urgent need for conservation and artificial cultivation. To elucidate the mechanisms underlying its high adaptability and value, this study investigated the chloroplast proteome during its tuberous root formation using a mass spectrometry-based proteomic approach integrated with LC-MS/MS and bioinformatic analyses. A total of 1,616 chloroplast proteins were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the most significantly enriched pathways included metabolic pathways, biosynthesis of amino acids, carbon metabolism, oxidative phosphorylation, photosynthesis, biosynthesis of secondary metabolites, the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, ribosome function, and proteasome activity. Furthermore, protein-protein interaction network analysis indicated that the core 25-node subnetwork primarily consists of proteins involved in small molecule metabolic processes, single-organism biosynthesis, organic acid metabolism, and oxoacid metabolism. This study provides a comprehensive dataset of the Sphallerocarpus gracilis chloroplast proteome, along with detailed functional annotations, Gene Ontology (GO) enrichment, and KEGG pathway analysis. These findings offer crucial insights into key biological processes in Sphallerocarpus gracilis, advance proteomic research on its high photosynthetic efficiency, and serve as a valuable resource for future functional studies and utilization based on its proteomic profile.