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Background  Melatonin ( N -acetyl-5-methoxytryptamine) in plants, regulates shoot and root growth and alleviates environmental stresses. Melatonin and the phyto-hormone auxin are tryptophan-derived compounds. However, it largely remains controversial as to whether melatonin and auxin act through similar or overlapping signalling and regulatory pathways.    Results  Here, we have used a promoter-activation study to demonstrate that, unlike auxin (1-naphthalene acetic acid, NAA), melatonin neither induces  Direct repeat 5 DR5  expression in  Arabidopsis thaliana  roots under normal growth conditions nor suppresses the induction of  Alternative oxidase 1a AOX1a  in leaves upon Antimycin A treatment, both of which are the hallmarks of auxin action. Additionally, comparative global transcriptome analysis conducted on Arabidopsis treated with melatonin or NAA revealed differences in the number and types of differentially expressed genes. Auxin (4.5 μM) altered the expression of a diverse and large number of genes whereas melatonin at 5 μM had no significant effect but melatonin at 100 μM had a modest effect on transcriptome compared to solvent-treated control. Interestingly, the prominent category of genes differentially expressed upon exposure to melatonin trended towards biotic stress defence pathways while downregulation of key genes related to photosynthesis was observed.    Conclusion  Together these findings indicate that though they are both indolic compounds, melatonin and auxin act through different pathways to alter gene expression in  Arabidopsis thaliana . Furthermore, it appears that effects of melatonin enable  Arabidopsis thaliana  to prioritize biotic stress defence signalling rather than growth. These findings clear the current confusion in the literature regarding the relationship of melatonin and auxin and also have greater implications of utilizing melatonin for improved plant protection.

Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin