Comparative proteomic and ultrastructural analysis shed light on fruit pigmentation distinct in two Lycium species

Abstract Lycium barbarum L. (LB) and L. ruthenicum Murr. (LR) are the two closet species in Lycium genus phylogenetically. The LB fruit (LBF) contains high level of carotenoids and undetectable anthocyanins, while LR fruit (LRF) has abundant anthocyanins and very low amount of carotenoids. Although the causes of the pigmentation difference in term of gene expression and metabolites were previously investigated in the two species, the underlying mechanism remains unclear at protein level. In this study, the ripening fruits of LB, LR and their hybrid were harvested for comparative proteomic and ultrastructural analysis. Ultrastructural analysis indicates that LBF successfully form abundant tubular chromoplasts, and that LRF fail to develop chromoplasts. This result is confirmed by the expression ratio of rbcLs/PDS as an indicator of plastid number. Proteomic results uncover that the number of photosynthesis-related proteins undetectable in LRF is significant higher than in LBF. Chromoplast-biogenesis protein OR and plastoglobules-localized ABC1K1 is abundant in LBF but undetectable in LRF. Meanwhile, anthocyanin enzyme localizing ER vesiculate seriously in LRF while failed in LBF. The abundance of vacuole-localized anthocyanin trafficking protein SYP22 and vacuolar formation protein VPS4 increased in LRF and decreased/undetectable in LBF. Proteomic results also reveal that differentially expressed proteins related to anthocyanin synthesis and accumulation are enriched and increased in ripening LRF with undetectable certain proteins involved in carotenoid pathway and vice versus for LBF. Altogether, our data provide new insight on ER and vacuole formation and plastid differentiation, which contribute largely to the pigmentation distinct in Lycium fruits.