Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation

Meng, Xiaoxi; Lv, Yuanda; Mujahid, Hana; Edelmann, Mariola J.; Zhao, Han; Peng, Xiaojun; Peng, Zhaohua

doi:10.1016/j.bbapap.2017.12.001

Cited by 32 publications

(48 citation statements)

References 94 publications

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“…Regarding the cellular component category, 38% of the Khib proteins were located in the cell, 28% in organelles, 15% in the membrane, and 14% in macromolecular complexes. The classification of Khib proteins is very similar to those that undergo other acylations in rice, such as acetylation (Ashburner et al 2000;Meng et al 2018;Xue et al 2018), succinylation (He et al 2016), and crotonylation (Liu et al 2018), suggesting that various acylations may be involved in these molecular functions or biological processes. The subcellular localization prediction for the modified proteins was performed using WoLF PSORT software (Fig.…”

Section: Functional Annotation and Subcellular Localization Analyses mentioning

confidence: 86%

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

Xue

Zhang

Chen

et al. 2020

Rice

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Background: Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. Results: In this study, using LC-MS/MS qualitative proteomics strategies, we identified 4163 Khib sites on 1596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalk of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms. Conclusions: In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.

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Section: Functional Annotation and Subcellular Localization Analyses mentioning

confidence: 86%

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

Xue

Zhang

Chen

et al. 2020

Rice

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“…In an effort to discover the PKA in rice anthers in the stage of meiosis, Li et al (2018) identified a total of 1354 PKA sites in 676 proteins, which are mostly related to chromatin silencing, protein folding, and fatty acid biosynthetic processes [ 27 ]. There were also 44 and 692 lysine acetylated proteins that were identified from suspension cells and grain-filling stage seeds [ 24 , 28 ]. With a special focus on the seed development, Wang et al (2017) carried out a quantitative acetylproteomic study on pistil and early developing seeds.…”

Section: Discussionmentioning

confidence: 99%

“…This also intrigued researchers to explore PKAs in rice. So far, at least 8 independent cases have been reported regarding the profiling of PKA sites, peptides, and proteins in rice seedlings, reproductive organs, and leaves under oxidative stress, which yielded the identification of over 8599 PKA sites and 4990 proteins [ 7 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. Despite efforts being made on rice, the previous studies only explored the tip of the iceberg of rice acetylome, given that rice genome contains over 56,000 protein coding genes [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)

Wang

Bello

et al. 2018

Molecules

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PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.

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“…Multiple protein PTMs are reported in plants (Friso and van Wijk, 2015 ; Canut et al, 2016 ), and their study poses challenges inherent to the chemical nature and abundance of each PTM. Targeted approaches are not yet widely used in the plant field, even though plant acetylation, SUMOylation, and methylation have been studied successfully using discovery proteomics (Deng et al, 2010 ; Miller et al, 2010 ; Song and Walley, 2016 ; Meng et al, 2018 ), and targeted proteomics on multiple protein PTMs has been performed in other organisms outside the plant kingdom (Schilling et al, 2012 ; Lamoliatte et al, 2013 ; Tang et al, 2014 )…”

Section: Potential For the Use Of Targeted Proteomics In The Analysismentioning

confidence: 99%

Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics

2018

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Protein post-translational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined.

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Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation

Cited by 32 publications

References 94 publications

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa

Construction of a Quantitative Acetylomic Tissue Atlas in Rice (Oryza sativa L.)

Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics

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