Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit

Wenzhen Li; Lulu Chen; Weihua Zhao; Yuhang Li; Ying Chen; Tengjian Wen; Zhengjun Liu; Chao Huang; Lida Zhang; Lingxia Zhao

doi:10.1093/hr/uhae202

Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit

Hortic Res. 2024 Jul 24;11(9):uhae202. doi: 10.1093/hr/uhae202. eCollection 2024 Sep.

Authors

Wenzhen Li^{1

2}, Lulu Chen^{1

3}, Weihua Zhao^{1

2}, Yuhang Li^{1

2}, Ying Chen⁴, Tengjian Wen^{1

2}, Zhengjun Liu⁵, Chao Huang⁶, Lida Zhang^{1

2}, Lingxia Zhao^{1

2}

Affiliations

¹ Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
² Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
³ Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, 2 South Xiwang Avenue, Yancheng 224002, China.
⁴ Youlaigu Science and Technology Innovation Center, 588 West Chenfeng, Yushan town, Agriculture Service Center, Kunshan 215300, China.
⁵ National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 2708 South Huaxi Avenue, Guiyang 550025, China.
⁶ Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, College of Pharmaceutical Science, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou 310053, China.

Abstract

Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, tomato fruit color formation is an intricate biological process that remains elusive. In this work we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in the YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme, which may function in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allelic (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were upregulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35 and 47 days post-anthesis compared with the red-fruit tomato cultivar (M82). In vitro and in vivo biochemical analyses indicated that YFT3 (S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that the S126R mutation can impair YFT3 activity. Molecular docking analysis showed that the YFT3 allele has higher ability to recruit isopentenyl pyrophosphate (IPP), but abolishes attachment of the Mg²⁺ cofactor to IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.