Ocimum kilimandscharicum 4-Coumarate CoA ligase 11 negatively regulates root formation by inhibiting polar auxin transport via flavonoids accumulation

4-Coumarate-CoA Ligase (4CL), is a key enzyme for phenylpropanoid biosynthesis. Multiple isoforms of 4CLs are identified in Ocimum species; however, their in planta functions remain enigmatic. To characterize in planta functions, we overexpressed three Ok4CL isoforms (Ok4CL7, -11 and -15) in Nicotiana benthamiana. Interestingly, Ok4CL11 overexpression (OE) caused a rootless or reduced root growth phenotype, while other two isoforms showed normal adventitious root growth. To understand the molecular basis of rootless phenotype, we performed RNA-sequencing of Ok4CL11-OE lines and wild-type (WT) Nicotiana benthamianausing whole plants. Our analysis revealed down-regulation of several auxin transport and signaling genes in Ok4CL11-OE lines compared to WT. Further, metabolites profiling of Ok4CL11-OE lines showed over-accumulation of flavonoid-glycosides including kaempferol-3,7-O-bis-alpha-L-rhamnoside (K3,7R), and reduced auxin levels. In silico analysis suggested that K3,7R has a higher binding affinity towards auxin transporters (PINs/LAXs) and it could function as auxin transport inhibitor. Overall, our study reveals a conserved and unique function of Ok4CL11 as a negative regulator of root growth development by inhibiting polar auxin transport via the accumulation of specific flavonoid-glycosides.