Transporters within cellular compartments,including proton pumps and secondary metabolite transporters,are essential for many physiological processes.Vacuoles are moderately acidic in most plant cells due to the role of V-ATPase and/or pyrophosphatase proton pumps,however,the regulator of these proton pumps that mediate cell pH is largely unknown.Here,we identify a transcription factor(TF)MdMYB1,which binds to the promoters of MdVHA-B1 and MdVHA-B2,but not to that of MdVHA-B3.MdMYB1 activates MdVHA-B1 and MdVHA-B2 to enhance the activity of V-ATPase.A series of transgenic analyses in different tissues and organs of apples demonstrate that MdMYB1 controls cell pH,malate content and anthocyanin coloration by regulating MdVHA-B1 and MdVHA-B2.Meanwhile,a series of target genes of MdMYB1 are identified by RNA-Seq analysis,which is used to support MdMYB1 directly or indirectly binding to malate and anthocyanin-associated target genes to mediate the apple fruit acidity and coloration process.Finally,we demonstrate that the mechanism through which MYB TF controls the cell pH and coloration formation via the regulation of V-ATPase is conserved in different species.In summary,our research provides a novel viewpoint to determine how pigment-related MYB transcription factors mediate the organ coloration and cell pH in plants.