Steroidal glycoalkaloids (SGA) are an important defensive secondary metabolite in Solanaceae plants. They mainly exist in the form of α-tomatine in immature fruits such as tomatoes, and play an important role in resisting pests and diseases. Since α-tomatine has a bitter taste and certain toxicity, it is not conducive to the spread of seeds through animal feeding. Therefore, during the fruit ripening process, α-tomatine will be converted into non-toxic and non-bitter aescin through multi-step enzymatic reactions.
This metabolic transformation process is very important for seed propagation, fruit taste and edible safety, and is the key to driving the transformation of tomatoes from bitter to delicious during tomato domestication. Although there have been many studies on the SGA metabolic pathway, the regulatory mechanism and molecular network that regulate the detoxification and debittering of tomato fruits during ripening still need to be systematically analyzed.
On February 19, 2025, Mingchun Liu's research team at Sichuan University published a research paper titled "Removal of toxic steroidal glycoalkaloids and bitterness in tomato is controlled by a complex epigenetic and genetic network" in Science Advances. The multi-level molecular network of epigenetic modification, plant hormones and key transcription factors that synergistically regulate SGA metabolic reprogramming during tomato fruit ripening was deeply analyzed, and it was found that the network was naturally selected during tomato domestication, driving the rapid directional transformation of toxic SGA during fruit ripening.
This discovery clarifies the balance mechanism between maintaining resistance and improving edible quality of tomato fruits from the perspective of molecular interaction and evolution, and provides a theoretical basis for understanding how human domestication improves wild highly toxic germplasm into palatable cultivated varieties through gene network reprogramming.
The study found that the promoter region of a key transporter (GORKY) of four key structural genes (GAME31, GAME36, GAME40 and GAME5) involved in the conversion of α-tomatine to aescin A significantly decreased in methylation during fruit ripening. Further studies showed that this demethylation process was mainly mediated by DNA demethylase DML2, whose expression was significantly upregulated during the fruit ripening stage, promoting the conversion of α-tomatine to aescin A during ripening.
As the main regulator of respiratory climacteric fruit ripening, plant hormone ethylene also plays an important role in SGA metabolism. Experiments showed that exogenous ethylene treatment significantly induced the expression of GAME31, GAME40, GAME5 and GORKY, while the expression levels of these genes were significantly downregulated in ethylene signaling pathway-deficient materials (such as ein2 and EBF3-OE). Interestingly, another key GAME gene, GAME36, showed a different expression pattern from other genes related to SGA transformation. It was not induced by ethylene, but was induced by methyl jasmonate.
The study also found that ethylene further affected SGA metabolism by positively regulating the expression of DML2, indicating that the ethylene signaling pathway and DNA demethylation can form a synergistic network in the regulation of SGA metabolism.
The key transcription factors NOR, RIN and FUL1 downstream of ethylene also play a key regulatory role in the regulation of SGA metabolism. Chromatin immunoprecipitation and gel migration blocking experiments revealed that NOR, RIN and FUL1 directly bind to the promoter regions of the key SGA metabolic GAME genes GAME31, GAME40 and GAME5 to activate their expression. At the same time, RIN and FUL1 form heterodimers to synergistically enhance the transcriptional activity of GAME genes and GORKY, further enhancing the regulatory efficiency of SGA metabolism.
Studies have found that MYC2, a core transcription factor of the jasmonic acid signaling pathway, is also involved in the fine regulation of SGA metabolism. MYC2 activates the transcription of GAME36 by binding to the G-box cis-element in the promoter region of GAME36 and recruiting histone acetyltransferases to mediate H3K9ac and H3K27ac modifications. This finding suggests that MYC2 not only regulates the biosynthesis of SGA during fruit development to maintain defense function, but also participates in the detoxification process of SGA during maturity, and is a key regulatory factor that balances SGA metabolism at different stages of fruit development.
During the domestication of tomatoes, the SGA content showed a step-by-step decline from wild tomatoes (PIM) to cherry tomatoes (CER) and then to modern cultivated tomatoes (BIG). Through the analysis of metabolome and transcriptome data of 342 tomato germplasm resources, it was found that from PIM to CER to BIG, the content of α-tomatine and its downstream metabolites decreased significantly, while the content of aescin A gradually increased. This change is closely related to the selection of DML2 and downstream GAME genes. In addition, the expression of upstream SGA synthesis genes was inhibited during domestication, while the expression of downstream detoxification genes was significantly enhanced, further promoting the transformation of toxic SGA.
This "saving money and increasing income" strategy was preferentially selected during the domestication process, which enabled cultivated tomatoes to significantly improve the edible quality and safety of the fruit while retaining a certain degree of disease resistance. It is worth noting that the genomic regions of key transcription factors (such as MYC2, NOR and FUL1) also underwent selection during the domestication process, and the changes in their expression levels were highly consistent with the expression patterns of GAME genes, further supporting the important role of these transcription factors in the regulation of SGA metabolism.
Figure 1. During the green fruit stage, the target gene is in a very low expression state due to high DNA methylation and low ethylene synthesis levels; During the ripening stage, the decreased DNA methylation, increased ethylene, and histone acetylation recruited by MYC2 jointly drive the conversion of toxic α-tomatine into non-toxic and non-bitter aescin. (Bai, et al., 2025)
In summary, this study revealed the multi-level coordinated regulatory mechanism of epigenetic modification (DNA demethylation, histone acetylation), plant hormones (ethylene, JA) and transcription factor networks in SGA metabolic reprogramming.
DNA demethylation activates transcription through DML2-mediated demethylation of the GAME gene promoter region, the ethylene signaling pathway directly regulates the expression of multiple GAME genes through NOR, RIN and FUL1, and the JA signaling pathway finely regulates the expression of GAME36 through MYC2-mediated histone acetylation modification.
In addition, from the perspective of molecular evolution, it also explains how the domestication process reshapes the gene network, inhibits the synthesis of upstream toxic substances and enhances the expression of downstream detoxification genes, significantly reduces the SGA content in tomato fruits, and improves their edible safety and palatability. This study not only deepens the understanding of the SGA metabolic regulatory network, but also provides an important theoretical basis for optimizing the resistance and quality balance of Solanaceae crops through molecular breeding.
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