Time-resolved transcriptomics of single Vitis vinifera fruits: membrane transporters as switches of the double sigmoidal growth

By revealing that the grape berry loses one H+ per accumulated sucrose at the inception of ripening, adopting a single fruit paradigm elucidates the fundamentals of the malate-sugar nexus, previously obscured by asynchrony in population-based models of ripening. More broadly, the development of the individual fruit was revisited from scratch to capture the simultaneous changes in gene expression and metabolic fluxes in a kinetically relevant way from flowering to overripening. Dynamics in water, tartrate, malate, hexoses, and K+ fluxes obtained by combining individual single fruit growth and concentration data allowed to define eleven sub-phases in fruit development, which distributed on a rigorous curve in RNAseq PCA. WGCNA achieved unprecedented time resolutions in exploring transcript level-metabolic rate associations. A comprehensive set of membrane transporters was found specifically expressed during the first growth phase related to vacuolar over-acidification. Unlike in slightly more acidic citrus, H+ V-PPase transcripts were predominantly expressed, followed by V-ATPase, clarifying the thermodynamic limit beyond which their replacement by the tonoplast P3A/P3B ATPase (PH5/PH1) complex turns compulsory. Puzzlingly, bona fide aluminum-activated malate transporter (ALMT) kept a low profile at this stage, possibly replaced by a predominating uncharacterized anion channel. At the onset of ripening, the switch role of hexose transporter HT6 in sugar accumulation is confirmed, electroneutralized by malate vacuolar leakage and H+ pumps activation.