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Background  The phytohormone ethylene (ET) is a key signaling molecule for inducing the biosynthesis of shikonin and its derivatives, which are secondary metabolites in  Lithospermum erythrorhizon . Although ETHYLENE INSENSITIVE3 (EIN3)/EIN3-like proteins (EILs) are crucial transcription factors in ET signal transduction pathway, the possible function of EIN3/EIL1 in shikonin biosynthesis remains unknown. In this study, by targeting  LeEIL-1  ( L. erythrorhizon  EIN3-like protein gene 1) at the expression level, we revealed the positive regulatory effect of  LeEIL-1  on shikonin formation.    Results  The mRNA level of  LeEIL-1  was significantly up-regulated and down-regulated in the  LeEIL-1 -overexpressing hairy root lines and  LeEIL-1 -RNAi hairy root lines, respectively. Specifically,  LeEIL-1  overexpression resulted in increased transcript levels of the downstream gene of ET signal transduction pathway ( LeERF-1 ) and a subset of genes for shikonin formation, excretion and/or transportation ( LePAL ,  LeC4H-2 ,  Le4CL-1 ,  HMGR ,  LePGT-1 ,  LeDI-2 , and  LePS-2 ), which was consistent with the enhanced shikonin contents in the  LeEIL-1- overexpressing hairy root lines. Conversely,  LeEIL-1 -RNAi dramatically repressed the expression of the above genes and significantly reduced shikonin production.    Conclusions  The results revealed that  LeEIL-1  is a positive regulator of the biosynthesis of shikonin and its derivatives in  L. erythrorhizon  hairy roots. Our findings gave new insights into the molecular regulatory mechanism of ET in shikonin biosynthesis.  LeEIL-1  could be a crucial target gene for the genetic engineering of shikonin biosynthesis .Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0812-6) contains supplementary material, which is available to authorized users.

Transgenic studies reveal the positive role of LeEIL-1 in regulating shikonin biosynthesis in Lithospermum erythrorhizon hairy roots