How a tiny mutation turns red tomatoes yellow

Researchers have identified a single mutation in the YFT3 gene that disrupts a key enzymatic function in tomato carotenoid biosynthesis, resulting in strikingly yellow fruits. This gene encodes the isopentenyl diphosphate isomerase enzyme, which regulates the critical balance between IPP and DMAPP, two C5 precursors essential for isoprenoid production. A single amino acid change—Serine to Arginine at position 126—impairs this balance, leading to reduced enzymatic activity, compromised chromoplast development, and severely diminished lycopene levels in the fruit. These findings not only reveal a fundamental mechanism underlying tomato pigmentation but also highlight Ser126 as a crucial catalytic residue, offering new targets for improving fruit quality through molecular breeding.

Tomato fruit color is largely dictated by the accumulation of carotenoids—natural pigments critical for plant reproduction and human nutrition. These compounds are synthesized from the isoprenoid pathway, which relies on a precise balance of its C5 building blocks, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The interconversion between them, mediated by the isomerase enzyme IDI1, is essential for maintaining metabolic flow. Disruptions in this process can alter chromoplast formation and pigment biosynthesis, leading to changes in fruit color and nutritional value. Despite advances in understanding carotenoid pathways, the specific amino acid residues crucial for IDI1 function have remained elusive. Due to these unresolved questions, a deeper investigation into YFT3’s role was needed.

A research team from Shanghai Jiao Tong University has identified a single-point mutation in the YFT3 gene responsible for yellow fruit coloration in tomatoes. Their findings (DOI: 10.1093/hr/uhae202), published on July 24, 2024 in Horticulture Research, reveal that the mutation disrupts a critical enzyme in the isoprenoid pathway, impairing carotenoid accumulation. Through map-based cloning, molecular assays, and in vivo functional analyses, the team demonstrated that a Ser126Arg substitution in YFT3 undermines its enzymatic activity, providing new insight into the molecular control of fruit pigmentation.

The researchers discovered that the yellow-fruited tomato mutant (yft3) carries a recessive allele of YFT3, encoding a mutated version of SlIDI1, a plastid-localized isomerase responsible for converting IPP to DMAPP. The mutation—an A→C transversion at nucleotide 2117—leads to a Ser126Arg substitution. Despite unchanged protein levels and plastid localization, enzymatic activity was drastically reduced. Functional complementation restored red color, while knockout lines mimicked the yellow phenotype, confirming YFT3’s essential role.

Detailed expression analyses showed upregulation of carotenoid pathway genes (DXS, DXR, HDR, PSY1, CRTISO, CYCB, CYP97A, NCED) in yft3 and CRISPR knockout lines. However, biochemical assays revealed severely reduced lycopene and total carotenoid levels, indicating that the gene upregulation could not compensate for enzymatic deficiency. Molecular docking revealed that the Ser126 mutation alters the active site conformation, impairs Mg²⁺ cofactor binding, and diminishes catalytic efficiency. These findings suggest Ser126 is critical for the correct positioning and function of substrate-enzyme interactions in carotenoid biosynthesis. Moreover, the impaired chromoplast ultrastructure in yft3 and YFT3-KO lines further underscores YFT3's role in fruit color development and quality.

“This study elegantly connects a single amino acid change to large-scale phenotypic effects,” said Dr. Lingxia Zhao, senior author of the paper. “By dissecting the enzymatic mechanism of YFT3 and demonstrating its crucial role in balancing IPP and DMAPP in plastids, we've uncovered a molecular bottleneck that determines tomato color. The identification of Ser126 as a key catalytic residue opens the door to targeted manipulation of carotenoid content in fruit. It's a promising target not only for improving aesthetic and nutritional value in tomatoes but also for broader isoprenoid-related crop traits.”

This discovery holds significant potential for agricultural biotechnology and breeding programs. Understanding the role of YFT3 in regulating the isoprenoid pathway offers breeders a precise genetic handle to enhance fruit pigmentation and carotenoid content—key traits for market appeal and nutrition. Beyond tomato, these insights may extend to other carotenoid-rich crops, aiding efforts to fortify foods with pro-vitamin A compounds. Future work could explore gene editing strategies to modulate YFT3 activity or optimize isomerase function in different metabolic contexts. Ultimately, this research lays the groundwork for metabolic engineering approaches that balance yield, visual appeal, and nutritional quality in fruit crops.

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References

DOI

10.1093/hr/uhae202

Original Source URL

https://doi.org/10.1093/hr/uhae202

Funding information

This work was supported by the National Natural Science Foundation of China (32072583, 32372694), Shanghai Collaborative Innovation Center of Agri-Seeds Foundation (ZXWH2150201/010), Shanghai and Kunshan Creation Center of Tomato Novel Germplasm Foundation (SJYY2022-T001), and Collection and Conservation of the Characteristic Crop Germplasm Resource in Kunshan City (Kunshan-AGR-001).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.