Overexpression of Solanum Lycopersicum DDB1 Interacting Protein 4 (slddi4) Extends Tomato Shelf Life by Methylation-Mediated Suppression of Softening-Related Genes Expression

Prolonging the fruit storage period is strategically important due to the limitation of postharvest life determined by excessive softening. Efforts have been made to alleviate the issue of fruit softening in transgenic fruit by suppressing genes that encode cell wall-degrading proteins. However, individual genes related to the degradation of cell walls have limited ability, resulting in minimal success. SET domain-containing protein (SET protein) is widely expressed in most plant organs and crucial in plant growth and development. A tomato SET protein was previously identified as SlDDI4 (Solanum lycopersicum DDB1 interacting protein 4) with a H3K9 methyltransferase activity involving cell proliferation and organ size regulation. In this study, we demonstrated that SlDDI4 overexpression (SlDDI4-OE) promotes fruit firmness in addition to increased fruit size. Further experimental investigations revealed that the increased expression of SlDDI4 inhibited cellulase and pectinase activities, consequently increasing the proportion of cellulose and insoluble pectin. RNA-seq profiling indicated the genes involved in cell wall metabolism in SlDDI4-OE fruit were significantly down-regulated. DNA methylation and McrBC-PCR analysis at the SlCEL2, SlPG2, and SlEXP12 loci revealed that their down-regulation was associated with the elevated methylation level in the individual promoter regions. Furthermore, up-regulation of SlDDI4 generated fruit with increased lycopene content and prolonging shelf-life by approximately 20 d without adverse impacts on the flavor indicators. Thus, our results suggest that manipulation of SlDDI4 expression enables broad favorable effects on postharvest life as well as fruit size and quality through chromatin remodeling.