Abstract
Ubiquitination is a critical post-translational modification machinery that governs a wide range of cellular functions by regulating protein homeostasis. Identification of ubiquitinated proteins and lysine residues can help researchers better understand the physiological roles of ubiquitin modification in different biological systems. In this study, we report the first comprehensive analysis of the peach ubiquitome by liquid chromatography-tandem mass spectrometry-based diglycine remnant affinity proteomics. Our systematic profiling revealed a total of 544 ubiquitination sites on a total of 352 protein substrates. Protein annotation and functional analysis suggested that ubiquitination is involved in modulating a variety of essential cellular and physiological processes in peach, including but not limited to carbon metabolism, histone assembly, translation and vesicular trafficking. Our results could facilitate future studies on how ubiquitination regulates the agricultural traits of different peach cultivars and other crop species.
Highlights
Ubiquitination is a critical post-translational modification machinery that governs a wide range of cellular functions by regulating protein homeostasis
After digesting the proteins extracted from Okubo peach leaves with trypsin, ubiquitin-conjugated peptide fragments were enriched by immunoaffinity purification (IAP) using antibodies that selectively recognize lysine residues carrying a diglycine-modified ε-amino group
The analysis revealed 544 ubiquitination sites on 507 peptide fragments that represented 352 proteins based on the Uniprot Prunus persica proteome (Supplementary Table S1)
Summary
Ubiquitination is a critical post-translational modification machinery that governs a wide range of cellular functions by regulating protein homeostasis. Protein annotation and functional analysis suggested that ubiquitination is involved in modulating a variety of essential cellular and physiological processes in peach, including but not limited to carbon metabolism, histone assembly, translation and vesicular trafficking. Functional analysis suggested that ubiquitination could be involved in regulating essential metabolic pathways and key cellular functions such as histone assembly, translation and vesicular trafficking. These findings could allow agricultural researchers to better understand the roles of ubiquitination in peach physiology and identify novel ubiquitin-driven regulatory mechanisms that could be exploited for peach improvement
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