Comparative proteomic profiles of tropical seagrass Thalassia hemprichii under contrasting nutrient and light conditions based on optimized protein extraction and identification

Limitations in efficient protein extraction and identification hinder proteomic studies in seagrasses. Using optimized extraction and identification methods, comparative proteomic profiles of tropical seagrass T. hemprichii under contrasting nutrient and light conditions were examined. An extraction buffer with lower PVPP content yielded more protein and improved band profiles. The T. hemprichii proteome from a de novo transcriptome assembly identified over twice as many proteins as the Zostera marina database, offering an effective proteomics approach for genome-limited seagrasses. Seagrass in high nutrient and light environments showed up-regulation of RuBisCO, oxygen-evolving complex subunits (PsbO, PsbP, PsbQ), ferredoxin:NADP(H) oxidoreductases, PSI_PsaF, PSI_PsaE, and chlorophyll a/b-binding proteins, suggesting enhanced photosynthetic activity provided more carbon and energy for excess nitrogen metabolism. This was supported by up-regulation of fructose-1,6-bisphosphate aldolase, phosphoglycerate kinase, and glyceraldehyde-3-phosphate dehydrogenase. High-affinity nitrate transporter was down-regulated under high nutrient and light conditions, whereas glutamine synthetase and glutaredoxins were up-regulated. The reduction of nitrogen uptake and enhancement of nitrogen assimilation could alleviate the toxic effects of high nutrients. Furthermore, key stress-related proteins, including glutaredoxins, calmodulin, Ca²⁺-dependent lipid binding proteins, and HSP70s, were up-regulated under high nutrient and light conditions, while enoyl-CoA hydratase, RNA recognition motif, and tubulin proteins linked to growth were down-regulated. Therefore, elevated ROS and toxic compounds under stress conditions may suppress seagrass growth. In conclusion, this study identified distinct proteomic profiles of T. hemprichii under contrasting nutrient and light conditions using optimized protein extraction and identification. These findings enhance understanding of seagrass molecular adaptation and support the development of stress indicators for conservation and management.