Quantitative proteomic investigation employing stable isotope labeling by peptide dimethylation on proteins of strawberry fruit at different ripening stages

A quantitative proteomic investigation of strawberry fruit ripening employing stable isotope labeling by peptide dimethylation was conducted on 'Mira' and 'Honeoye' strawberry fruit. Postharvest physiological quality indices, including volatile production, total phenolics, total anthocyanins, antioxidant capacity, soluble solids and titratable acidity, were also characterized in white, pink and red fruit. More than 892 and 848 proteins were identified and quantified in the 'Mira' and 'Honeoye' fruit, respectively, using at least two peptides for each protein identification. Using the normalized ratio of protein abundance changes, proteins that changed two-fold or more were identified as proteins that are up- or down-regulated during fruit ripening. Among the quantified proteins, 111 proteins were common to both cultivars and represented five significant clusters based on quantitative changes. Among the up-regulated proteins were proteins involved in metabolic pathways including flavonoid/anthocyanin biosynthesis, volatile biosynthesis, antioxidant metabolism, stress responses and allergen formation. Proteins that decreased during fruit ripening were found to be responsible for methionine metabolism, antioxidant-redox, energy metabolism and protein synthesis. Our results show that strawberry ripening is a highly complex system involving multi-physiological processes made possible through changes in protein expression. This study provides new insights on the regulation of proteins during strawberry fruit ripening that lay the foundation for further targeted studies.

Biological significance: Research on the postharvest physiology and biochemistry of strawberry fruit as a model of non-climacteric fruit ripening has been conducted for many years. However, the mechanism(s) for the initiation and metabolic regulation of non-climacteric fruit ripening remains unknown. Little information on strawberry fruit ripening is available at the proteome level. This paper is the first report of a quantitative proteomic investigation of strawberry fruit ripening employing stable isotope labeling by peptide dimethylation. Postharvest physiological quality indices, including volatile production, total phenolics, total anthocyanins, antioxidant capacity, soluble solids and titratable acidity, were also characterized in ripening fruit. Significant biological changes associated with ripening were revealed and proteins that change significantly under these conditions were identified. Therefore, our study links the biological events of strawberry fruit ripening with proteomic information and provides insights into possible mechanisms of regulation. Proteins that changed during ripening were analyzed through function analysis, which provides new insights into metabolic changes occurring during ripening. Findings from this paper not only provide proteome information on fruit ripening, but also pave the way for further quantitative studies using SMR to investigate certain proteins and pathways involved in fruit ripening.