Transcription factor NtELF3 promotes the polyphenol accumulation by targeting NtFLS-1 and NtCHIL-2 genes in tobacco

Tobacco (Nicotiana tabacum L.) is an important economic crop, from which polyphenols are crucial for regulating its growth and development as well as shaping its quality. However, few genes associated with polyphenol accumulation have been cloned from tobacco, and the molecular mechanisms underlying this process remain poorly understood. Here, we found that the tobacco transcription factor EARLY FLOWERING 3 (NtELF3), which is highly expressed in tobacco leaves, positively regulates the accumulation of chlorogenic acid, neochlorogenic acid, cryptochlorogenic acid, rutin, scopoletin, and total polyphenols in tobacco middle leaves. The metabolomic and transcriptomic analyses of middle leaves showed that a total of 177 differentially accumulated metabolites and 7409 differentially expressed genes (DEGs) were identified in ntelf3-1 mutant versus wild type, respectively. Further investigation identified that 17 DEGs were involved in phenylpropanoid metabolic and flavonoid metabolic processes. Combined analysis indicated that the phenylpropanoid and flavonoid biosynthesis pathways were also co-enriched in kyoto encyclopedia of genes and genomes enrichment analysis. Molecular biology experiment demonstrated that NtELF3 directly binds to the promoters of NtFLS-1 and NtCHIL-2 that are both associated with phenylpropanoid and flavonoid biosynthesis, and promotes their expression. Taken together, our results not only provide new theoretical support for in-depth understanding of the regulatory mechanisms underlying polyphenol accumulation in tobacco, but also offer excellent genes and germplasm resources for tobacco quality breeding.