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

Authors: CHEN, YAO - Boyce Thompson Institute; WANG, XIN - Boyce Thompson Institute; Colantonio, Vincent; GAO, ZUHO - Sichuan University; PEI, YANGAN - Sichuan University; Fish, Tara; YI, JIE - Huazhong University Of Science And Technology; COURTNEY, LANCE - Boyce Thompson Institute; Thannhauser, Theodore; YE, ZHIBIAO - Huazhong University Of Science And Technology; LIU, YONGSHENG - Anhui Agricultural University; FEI, ZHANGJUN - Boyce Thompson Institute; LIU, MINGCHUNG - Sichuan University; Giovannoni, James

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2024
Publication Date: 2/10/2025
Citation: Chen, Y., Wang, X., Colantonio, V.N., Gao, Z., Pei, Y., Fish, T., Yi, J., Courtney, L., Thannhauser, T.W., Ye, Z., Liu, Y., Fei, Z., Liu, M., Giovannoni, J.J. 2025. Ethylene response factor SlERF. D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12. Proceedings of the National Academy of Sciences (PNAS). 12(7). https://doi.org/10.1073/pnas.2405894122.
DOI: https://doi.org/10.1073/pnas.2405894122

Interpretive Summary: Ripening in fleshy fruits is a complex and tightly controlled genetic program involving a range of changes in chemistry and physiology often typified by accumulation of nutritional compounds, synthesis and accrual of pigments, reduction in photosynthesis and photosynthetic pigments, texture modifications, and alterations in volatile aromatic profiles. Many genes underlying ripening control remain to be fully understood in terms of function. SlERF.D6 has previously been associated with fruit coloration and regulation of compounds making unripe fruit inedible. We used CRISPR/Cas9 gene-editing to generate loss-of-function mutants of SlERF.D6 and performed fruit gene expression profiling and DNA binding to clarify the role of SlERF.D6 in tomato fruit ripening. Our results suggest that SlERF.D6 is a positive regulator of fruit ripening and plays important roles in both flesh and locule (gel surrounding the seeds) tissues in part through regulation of at least two additional regulatory genes that operate with influence from additional ripening genes and the ripening hormone ethylene.

Technical 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.