Global analysis of lysine succinylation in patchouli plant leaves

Xiaobing Wang,Liting Zhong,Hai Zheng,Jiyun Liu,Junren Li,Yun Tang,Xiuzhen Chen,Ruoting Zhan,Xuanxuan Zhou,Likai Chen,Yanting Liu

doi:10.1038/s41438-019-0216-5

Abstract

Lysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein−protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.

Highlights

Protein posttranslational modifications (PTMs) participate in diverse cellular events and biological processes in living organisms through various mechanisms[1,2,3]
A qualitative lysine succinylome analysis was conducted in patchouli plants in this study, with the purpose of uncovering the role of lysine succinylation in patchouli physiology and biology
1097 succinylation sites corresponding to 493 proteins were detected, among which 466 succinylation sites corresponding to 241 proteins were repeatedly identified in the three independent experiments (Fig. 1), indicating that lysine succinylation was a widespread PTM in various patchouli proteins

Summary

Introduction

Protein posttranslational modifications (PTMs) participate in diverse cellular events and biological processes in living organisms through various mechanisms[1,2,3]. With the development of mass spectrometry (MS) and bioinformatics, increasing novel PTMs have been identified, and their roles in cellular and metabolic processes have been studied[4]. More than 461 distinct PTMs have been reported in living organisms[5], among which lysine succinylation is a novel naturally occurring PTM in eukaryotes and prokaryotes affecting various cellular events and metabolism processes[6,7]. The identification of global lysine succinylation sites at the proteomic level, namely, protein succinylome, was performed in diverse organisms, including microorganisms, animals, and plants[7,8]. Hundreds and even thousands of succinylated sites and proteins have been identified in

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