Four-Dimensional Data-Independent Acquisition-Based Proteomic Profiling Combined with Transcriptomic Analysis Reveals the Involvement of the Slym1-SlFHY3-CAB3C Module in Regulating Tomato Leaf Color

Peiwen Wang; Ziheng Li; Lin Zhu; Fulei Mo; Fengshuo Li; Rui Lv; Fanyue Meng; Huixin Zhang; Yuxin Zou; Haonan Qi; Lei Yu; Tianyue Yu; Siyu Ran; Yuanhang Xu; Mozhen Cheng; Yang Liu; Xiuling Chen; Xiaoxuan Zhang; Aoxue Wang

doi:10.1021/acs.jafc.4c07614

Four-Dimensional Data-Independent Acquisition-Based Proteomic Profiling Combined with Transcriptomic Analysis Reveals the Involvement of the Slym1-SlFHY3-CAB3C Module in Regulating Tomato Leaf Color

J Agric Food Chem. 2024 Dec 17. doi: 10.1021/acs.jafc.4c07614. Online ahead of print.

Authors

Peiwen Wang^{1

2}, Ziheng Li^{1

2}, Lin Zhu^{1

2}, Fulei Mo³, Fengshuo Li^{1

2}, Rui Lv^{1

2}, Fanyue Meng³, Huixin Zhang³, Yuxin Zou^{1

2}, Haonan Qi³, Lei Yu^{1

2}, Tianyue Yu^{1

2}, Siyu Ran^{1

2}, Yuanhang Xu^{1

2}, Mozhen Cheng^{1

2}, Yang Liu^{1

2}, Xiuling Chen^{1

2}, Xiaoxuan Zhang^{1

2}, Aoxue Wang^{1

2}

Affiliations

¹ College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
² Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China.
³ College of Life Science, Northeast Agricultural University, Harbin 150030, China.

PMID: 39688468
DOI: 10.1021/acs.jafc.4c07614

Abstract

In green plants, the chloroplast is responsible for light energy transition and organic assimilation. However, the molecular mechanisms underlying chloroplast development in horticultural crops remain unclear. Here, four-dimensional data-independent acquisition-based proteomic profiling identified 1,727 differentially expressed proteins between "Zhongshu 4" (ZS4) and yellowing mutant (ym) leaves, a considerable proportion of which were down-regulated chloroplast proteins. Functional analysis revealed that light harvesting and chlorophyll biosynthesis were correlated with ym leaf yellowing, validated by RNA sequencing. Quantitative PCR confirmed that chlorophyll a/b-binding protein 3C (CAB3C) related to light harvesting and NADPH:protochlorophyllide oxidoreductase 3 (POR3) involved in chlorophyll biosynthesis were repressed in ym leaves. Virus-induced gene silencing showed that suppressing CAB3C and POR3 decreased the net photosynthetic rate and chlorophyll content. Additionally, the F-box protein Slym1 negatively regulated the expression of CAB3C by depressing transcription factor SlFHY3 levels. Our findings offer insights into the regulatory mechanisms of chloroplast development in tomato.

Keywords: 4D-DIA proteomic analysis; chlorophyll biosynthesis; chloroplast development; leaf yellowing; light harvesting; photosynthetic antenna protein; tomato.