A dual-function transcription factor SlJAF13 promotes anthocyanin biosynthesis in tomato

Unlike modern tomato (Solanum lycopersicum) cultivars, cv. LA1996 harbors the dominant Aft allele, which is associated with anthocyanin synthesis in the tomato fruit peel. However, the control of Aft anthocyanin biosynthesis remains unclear. Here, we used ethyl methanesulfonate (EMS)-induced and CRISPR/Cas9-mediated mutation of LA1996 to show, respectively, that two class IIIf basic helix-loop-helix (bHLH) transcription factors (TFs), SlJAF13 and SlAN1, are involved in the control of anthocyanin synthesis. These TFs are key components of the MYB-bHLH-WD40 (MBW) complex, which positively regulates anthocyanin synthesis. Molecular and genetic analyses showed that SlJAF13 functions as an upstream activation factor of SlAN1 by binding directly to the G-Box motif of its promoter region. On the other hand, SlJAZ2, a JA signaling repressor, interferes with formation of the MBW complex to suppress anthocyanin synthesis by directly binding these two bHLH components. Unexpectedly, the transcript level of SlJAZ2 was in turn repressed in an SlJAF13-dependent manner. Mechanistically, SlJAF13 interacts with SlMYC2 and inhibiting SlMYC2 activation of SlJAZ2 transcription, thus constituting a negative feedback loop governing anthocyanin accumulation. Taken together, our findings support a sophisticated regulatory network, in which SlJAF13 acts as an upstream dual-function regulator that fine tunes anthocyanin biosynthesis in tomato.