Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds

Meng, Xiaoxi; Xing, Shihai; Perez, Loida M.; Peng, Xiaojun; QingYong, Zhao; Redoña, Edilberto D.; Wang, Cailin; Peng, Zhaohua

doi:10.1038/s41598-017-17756-6

Cited by 59 publications

(117 citation statements)

References 63 publications

(72 reference statements)

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“…Also in ubiquitin of wheat ( Triticum sp.) and rice, lysines were targeted by acetylation (Wang et al ., ) and by PTMs metabolically related to acetylation, such as 2‐hydroxyisobutyrylation (Meng et al ., ), succinylation (He et al ., ) and malonylation (Mujahid et al ., ). In rice, all ubiquitin lysines, except Lys29, are modified by acetylation, malonylation, butyrylation, and/or succinylation (Figure a).…”

Section: Resultsmentioning

confidence: 99%

“…For instance, in plants, this post-translational N-terminal acetylation often occurs on plastid protein N-termini exposed after transit peptide cleavage (Bienvenut et al, 2012;K€ ohler et al, 2015;Rowland et al, 2015). In addition to phosphorylation and acetylation, PTMs reported of late include N-terminal myristoylation (Majeran et al, 2018), Olinked N-acetylglucosaminylation (O-GlcNAcylation) (Xu et al, 2017a) in Arabidopsis, lysine modifications, such as 2-hydroxyisobuturylation (Meng et al, 2017) and malonylation (Mujahid et al, 2018) in rice (O. sativa spp. japonica), and SUMOylation in Arabidopsis (Rytz et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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The Plant PTM Viewer, a central resource for exploring plant protein modifications

et al. 2019

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Summary Post‐translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Plant PTM Viewer, a central resource for exploring plant protein modifications

et al. 2019

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“…To reveal the conservation and uniqueness of Khib among rice (Oryza sativa) [23], 234 Physcomitrella patens [41], and wheat, we utilized a BLAST search to estimate the 235 degree of conservation and uniqueness of the Khib proteins [42]. As shown in 236 Figure 5A, 752 (70.0%) of the Khib proteins were orthologous proteins between wheat 237 and the other two species (Supplemental Table S10; Figure 5A).…”

Section: Conservation and Uniqueness Of The Khib Proteins 233mentioning

confidence: 99%

“…Khib is known to occur on nuclear, cytoplasmic, mitochondrial, and chloroplast 277 proteins [23,39,40]. As a result, this PTM could be crucial for processes inside the 278 nucleus and could be important for regulating different cellular and metabolic processes.…”

Section: Khib Proteins Involved In Photosynthesis 276mentioning

confidence: 99%

Global Profiling of 2-hydroxyisobutyrylome in Common Wheat

Zhang

et al. 2020

Preprint

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33As a novel post-translational modification (PTM), lysine 2-hydroxyisobutyrylation 34 (Khib) has been found to play a role in active gene transcription in mammalian cells 35 and yeast, but the function of Khib proteins in plants remains unknown. In this study, 36 we used western blot to demonstrate that Khib is an evolutionarily-conserved PTM in 37 wheat and its donators, with the highest Khib abundance occurring in hexaploidy wheat. 38 Additionally, global profiling using affinity purification and mass spectroscopy of 2-39 hydroxyisobutyrylome revealed that there were 3348 lysine modification sites from 40 1074 proteins in common wheat (Triticum aestivum L.). Moreover, bioinformatic data 41 indicated that Khib proteins participate in a wide variety of biological and metabolic 42 pathways. Immunoprecipitation and western blot confirmed that Khib proteins had an 43 in vivo origin. A comparison of Khib and other major PTMs revealed that Khib proteins 44 were simultaneously modified by multiple PTMs. Using mutagenesis experiments and 45Co-IP, we demonstrated that Khib on K206 is a key regulatory modification of 46 phosphoglycerate kinase enzymatic activity and found that de-Khib on K206 affects 47 protein interactions. Furthermore, Khib production of low-molecular-weight proteins 48 was a response to the deacetylase inhibitors nicotinamide and trichostatin A. This study 49 provides evidence that enhances our current understanding of Khib in wheat plants, 50 including the cooperation between this PTM and metabolic regulation. 51 Introduction 54 Protein post-translational modification (PTM) can change the charge, conformation, 55 and molecular weight of proteins by adding chemical groups to the amino acid residues 56 of a protein that can also expand the biological functions of the protein [1]. PTMs have 57 been found to play a vital role in diverse biological processes by regulating protein 58 function [2]. Lysine acetylation (Kac) is an important PTM that neutralizes positively-59 charged lysine residues; previous studies of Kac have mainly focused on nuclear 60 proteins [3, 4]. Using mass spectrometry, a high abundance of non-histone proteins has 61 been extensively characterized recently [5−9]. Kac is currently known to regulate 62 diverse protein properties, including subcellular localization, DNA-protein interactions, 63 protein stability, protein-protein interactions, and enzymatic activity [7, 8, 10, 11]. With 64 the help of high sensitivity mass spectrometry, there are currently 9 novel lysine PTMs 65 reported, including formylation (Kfor), crotonylation (Kcr), butyrylation (Kbu), 66 succinylation (Ksu), malonylation (Kma), propionylation (Kpr), glutarylation (Kglu), 67 β-hydroxybutyrylation (Kbhb), and 2-hydroxyisobutyrylation (Khib), and the catalog 68 is still growing [12−18]. These novel PTMs have been mainly found in mammalian and 69 yeast cells, and also in plants, such as Arabidopsis thaliana [19], rice [20−23], and 70 tobacco [19, 24]. Increasing evidence suggests that these new types of PTMs are 71 ...

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“…For example, for Arabidopsis thaliana (Arabidopsis), approximately 57,000 phosphorylation sites are available in PhosPhAt 4.0 (Heazlewood et al, 2008). Besides phosphorylation, recently reported PTMs include N-terminal myristoylation (Majeran et al, 2018) and O -linked N-acetylglucosaminylation ( O -GlcNAcylation) (Xu et al, 2017) in Arabidopsis, and lysine 2-hydroxyisobuturylation (Meng et al, 2017) and malonylation (Mujahid et al, 2018) in rice ( Oryza sativa spp. japonica ).…”

Section: Introductionmentioning

confidence: 99%

The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function

Willems

Horne

Goormachtig

et al. 2018

Preprint

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2 SUMMARY Posttranslational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased number and types of mapped protein modifications, a database is necessary that simultaneouly integrates and compares sitespecific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 200,000 PTM sites for 17 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools facilitate to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.

show abstract

Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds

Cited by 59 publications

References 63 publications

The Plant PTM Viewer, a central resource for exploring plant protein modifications

The Plant PTM Viewer, a central resource for exploring plant protein modifications

Global Profiling of 2-hydroxyisobutyrylome in Common Wheat

The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function

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