# Comprehensive Genome-Wide Analysis of the AP2/ERF Transcription Factor Family and Examination of Potential Regulators CpERF140 and CpERF138 in the Biosynthesis of Lobetyolin in Codonopsis pilosula

## TL;DR

This study explores how specific transcription factors regulate the production of a key compound in Codonopsis pilosula, using genome-wide analysis and hairy root cultures.

## Contribution

The first genome-wide characterization of AP2/ERF transcription factors in Codonopsis pilosula and identification of CpERF140 and CpERF138 as regulators of lobetyolin biosynthesis.

## Key findings

- 175 AP2/ERF transcription factors were identified and categorized into subfamilies in Codonopsis pilosula.
- MeJA treatment increased lobetyolin accumulation and activated jasmonate signaling and secondary metabolism pathways.
- CpERF140 and CpERF138 were confirmed as nuclear-localized TFs with GCC-box binding affinity.

## Abstract

Lobetyolin is a key bioactive compound in Codonopsis pilosula, but the existing literature has not well explored the regulatory mechanisms governing its biosynthesis. This study performed a genome-wide identification of 175 AP2/ERF transcription factors (TFs), categorizing them into the AP2, ERF, and RAV subfamilies. Promoter analysis revealed numerous hormone- and stress-responsive cis-elements, with a notable prevalence of methyl jasmonate (MeJA)-related motifs. In MeJA-treated hairy root cultures, we observed a significant increase in lobetyolin accumulation. Integrated transcriptomic and metabolomic analyses demonstrated the activation of jasmonate signaling and secondary metabolism pathways. Two MeJA-induced TFs, CpERF140 and CpERF138, were identified as key regulatory candidates. Subsequent experiments confirmed their nuclear localization and specific binding affinity for GCC-box motifs. This study constitutes the inaugural genome-wide characterization of the AP2/ERF family in C. pilosula, employing hairy root culture as an effective platform for functional investigation. Our findings offer novel perspectives on the transcriptional regulation of lobetyolin biosynthesis, providing a foundation for the future metabolic engineering of this medicinal plant.