Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model

Wenfang Zeng,Mingqiao Wang,Zhaohui Wang,Xun Meng,Zhenhua Lu,Yan Wang,Liang Niu,Zhiqiang Wang,Weining Weng,Xiaobei Wang,Lei Pan,Guochao Cui

doi:10.1038/s41438-020-0249-9

Abstract

Peach (Prunus persica) is a typical climacteric fruit that produces ethylene rapidly during ripening, and its fruit softens quickly. Stony hard peach cultivars, however, do not produce large amounts of ethylene, and the fruit remains firm until fully ripe, thus differing from melting flesh peach cultivars. To identify the key proteins involved in peach fruit ripening, an antibody-based proteomic analysis was conducted. A mega-monoclonal antibody (mAb) library was generated and arrayed on a chip (mAbArray) at a high density, covering ~4950 different proteins of peach. Through the screening of peach fruit proteins with the mAbArray chip, differentially expressed proteins recognized by 1587 mAbs were identified, and 33 corresponding antigens were ultimately identified by immunoprecipitation and mass spectrometry. These proteins included not only important enzymes involved in ethylene biosynthesis, such as ACO1, SAHH, SAMS, and MetE, but also novel factors such as NUDT2. Furthermore, protein–protein interaction analysis identified a metabolon containing SAHH and MetE. By combining the antibody-based proteomic data with the transcriptomic and metabolic data, a mathematical model of ethylene biosynthesis in peach was constructed. Simulation results showed that MetE is an important regulator during peach ripening, partially through interaction with SAHH.

Highlights

Peach (Prunus persica L.), which belongs to the Rosaceae family, is an important fruit tree species worldwide
Proteins were extracted from the mesocarps of fruit from the melting flesh (MF) cultivar CN13 and the stony hard (SH) cultivar CN16 harvested between fruitripening stages S3 and S4 III (Fig. 1a)
By combining mAbArray-based proteomics and RNA-seqbased transcriptomics with a systems biology approach, we obtained functional networks based on measured differences and a parameterized mathematic model

Summary

Introduction

Peach (Prunus persica L.), which belongs to the Rosaceae family, is an important fruit tree species worldwide. According to their fruit texture and firmness, peach cultivars are classified into one of three groups: the melting flesh (MF), nonmelting flesh (NMF), and stony hard (SH) types[1,2]. The induction of ACS1 is responsible for climacteric ethylene production[6]. The fruit of MF peach cultivars produces large amounts of ethylene via system-2 ethylene production during the fruit-ripening stage, which results in rapid fruit softening. System-2 ethylene production is caused by the high induction of PpACS1 at the late-ripening stage. The fruit of SH peach cultivars only produces basal levels of ethylene due to a low expression level of PpACS17,8

Methods

Results

Conclusion