Ethylene response factor SlERF.D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12

Yao Chen, Xin Wang, Vincent Colantonio, Zhuo Gao, Yangang Pei, Tara Fish, Jie Ye, Lance Courtney, Theodore W. Thannhauser, Zhibiao Ye, Yongsheng Liu, Zhangjun Fei , Mingchun Liu, and James J. Giovannoni

PNAS; February 10, 2025; 122 (7) e2405894122

https://doi.org/10.1073/pnas.2405894122

Significance

A tomato ETHYLENE RESPONSE FACTOR gene, SlERF.D6, encodes a positive and primary regulator of tomato fruit ripening, influencing all measured ripening changes and numerous corresponding known genes contributing to ripening phenotypes with evidence for effects via a cascade of multiple transcription factors (TFs). Based on our results, the proposed SlERF.D6 ripening regulatory module was positioned in the context of known ripening regulators including ethylene and previously described essential ripening TFs.

Abstract

Ripening is crucial for the development of fleshy fruits that release their seeds following consumption by frugivores and are important contributors to human health and nutritional security. Many genetic ripening regulators have been identified, especially in the model system tomato, yet more remain to be discovered and integrated into comprehensive regulatory models. Most tomato ripening genes have been studied in pericarp tissue, though recent evidence indicates that locule tissue is a site of early ripening-gene activities. Here, we identified and functionally characterized an Ethylene Response Factor (ERF) gene, SlERF.D6, by investigating tomato transcriptome data throughout plant development, emphasizing genes elevated in the locule during fruit development and ripening. SlERF.D6 loss-of-function mutants resulting from CRISPR/Cas9 gene editing delayed ripening initiation and carotenoid accumulation in both pericarp and locule tissues. Transcriptome analysis of lines altered in SlERF.D6 expression revealed multiple classes of altered genes including ripening regulators, in addition to carotenoid, cell wall, and ethylene pathway genes, suggesting comprehensive ripening control. Distinct regulatory patterns in pericarp versus locule tissues were observed, indicating tissue-specific activity of this transcription factor (TF). Analysis of SlERF.D6 interaction with target promoters revealed an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) TF (SlDEAR2) as a target of SlERF.D6. Furthermore, we show that a third TF gene, SlTCP12, is a target of SlDEAR2, presenting a tricomponent module of ripening control residing in the larger SlERF.D6 regulatory network.

See https://www.pnas.org/doi/10.1073/pnas.2405894122

Figure 1:

Images and ripening onset of CRISPR/Cas9 tomato mutants. (A–M) Representative fruit phenotypes of (A) Ailsa Craig WT and edited mutants of 12 TFs at 40 DPA. (B) CR-BLH1, Solyc01g007070; (C) CR-MYC6, Solyc01g102300; (D) CR-bZIP8, Solyc01g104650; (E) CR-WOX14, Solyc02g082670; (F) CR-HZL2, Solyc02g087840; (G) CR-VAH1, Solyc03g113270; (H) CR-ERF.D6, Solyc04g071770; (I) CR-NAC39, Solyc05g007770; (J) CR-HsfA6b, Solyc06g053960; (K) CR-ARR11, Solyc08g077230; (L) CR-ZHD23, Solyc09g065670; (M) CR-JA2, Solyc12g013620. (N) Time from anthesis to the breaker stage of Ailsa Craig WT (AC) and edited mutants. Statistical significance was determined by Student’s t test: *0.01 < P < 0.05; ***P < 0.001. Error bars indicate SE.