Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in <i>Oryza Sativa</i>

Xue, Cong; Liu, Shuai; Chen, Chen; Zhu, Jun; Yang, Xiaobo; Liang, Guohua; Guo, Rui; Liu, Xiaoyu; Gong, Zhiyun

doi:10.1002/pmic.201700036

Cited by 40 publications

(54 citation statements)

References 57 publications

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“…Protein Extraction, Trypsin Digestion, and HPLC Fractionation-Protein extraction, trypsin digestion and HPLC fractionation were conducted using a procedure described by Xue et al (34). Leaf samples were ground under liquid nitrogen and sonicated three times on ice using a high intensity ultrasonic processor (Scientz) in lysis buffer (8 M urea, 1% Triton-100, 65 mM DTT, and 0.1% Protease Inhibitor Mixture).…”

Section: Methodsmentioning

confidence: 99%

“…The resulting peptides were cleaned with C18 ZipTips (Millipore) according to the manufacturer's instructions prior to LC-MS/MS analysis. Enrichment of lysine peptides were analyzed using LC-MS/MS as described by Xue et al (34). Briefly, peptides were dissolved in 0.1% formic acid and directly loaded onto a reversed-phase precolumn (Acclaim PepMap 100, Thermo Scientific).…”

Section: Affinity Enrichment Of Kcr Peptides and Enrichment Of Lysinementioning

confidence: 99%

“…Functional Annotation of Proteins-Gene ontology (GO) annotation of the proteome was achieved with reference to the UniProt-gene ontology annotation (GOA) database (www. http://www.ebi.ac.uk/ GOA/) using a procedure described by Xue et al (34). Proteins were classified by GO annotation based on three categories: biological process, cellular component, and molecular function.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

“…Functional Enrichment Analysis-The Encyclopedia of Genes and Genomes (KEGG) database was used to identify enriched pathways using the Functional Annotation Tool of database for annotation, visualization and integrated discovery (DAVID) against the background of Nipponbare, following a detailed procedure described by Xue et al (34). GO annotation and enriched pathways with a corrected p value Ͻ0.05 were considered to be statistically significant.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

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Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice

Liu

Xue

Fang

et al. 2018

Molecular & Cellular Proteomics

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Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice ( L. ) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. In addition, a genomic localization analysis of histone Kcr by ChIP-seq was performed to assess the relevance between histone Kcr and the genome. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in gene body, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr-facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome and might mark other cis-regulatory DNA elements that are different from IPA1, a transcription activator in rice seedlings. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.

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Section: Methodsmentioning

confidence: 99%

Section: Affinity Enrichment Of Kcr Peptides and Enrichment Of Lysinementioning

confidence: 99%

Section: Bioinformatics Analysismentioning

confidence: 99%

Section: Bioinformatics Analysismentioning

confidence: 99%

See 2 more Smart Citations

Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice

Liu

Xue

Fang

et al. 2018

Molecular & Cellular Proteomics

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“…Histones are prone to reversible posttranslational modifications such as phosphorylation, ubiquitination, acetylation, methylation, and glycosylation, which allow the proteins to respond flexibly to stimuli [63]. They are DNA-binding proteins of nucleoids or nucleomorph, while may possibly be posttranslationally modified and perform the role in chloroplasts [64,65].…”

Section: Discussionmentioning

confidence: 99%

The iTRAQ-based chloroplast proteomic analysis of Triticum aestivum L. leaves subjected to drought stress and 5-aminolevulinic acid alleviation reveals several proteins involved in the protection of photosynthesis

Wang

Liu

et al. 2020

BMC Plant Biol

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Backgrounds: The perturbance of chloroplast proteins is a major cause of photosynthesis inhibition under drought stress. The exogenous application of 5-aminolevulinic acid (ALA) mitigates the damage caused by drought stress, protecting plant growth and development, but the regulatory mechanism behind this process remains obscure.Results: Wheat seedlings were drought treated, and the iTRAQ-based proteomic approach was employed to assess the difference in chloroplast protein content caused by exogenous ALA. A total of 9499 peptides, which could be classified into 2442 protein groups, were identified with ≤0.01 FDR. Moreover, the contents of 87 chloroplast proteins was changed by drought stress alone compared to that of the drought-free control, while the contents of 469 was changed by exogenous ALA application under drought stress compared to that of drought stress alone. The Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results suggested that the ALA pretreatment adjusted some biological pathways, such as metabolic pathways and pathways involved in photosynthesis and ribosomes, to enhance the drought resistance of chloroplasts. Furthermore, the drought-promoted H 2 O 2 accumulation and O 2 − production in chloroplasts were alleviated by the exogenous pretreatment of ALA, while peroxidase (POD) and glutathione peroxidase (GPX) activities were upregulated, which agreed with the chloroplast proteomic data. We suggested that ALA promoted reactive oxygen species (ROS) scavenging in chloroplasts by regulating enzymatic processes. Conclusions:Our results from chloroplast proteomics extend the understanding of the mechanisms employed by exogenous ALA to defend against drought stress in wheat.

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Quantitative Proteomic Analysis of Global Protein Acetylation in PRRSV‐Infected Pulmonary Alveolar Macrophages

et al. 2020

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Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a serious viral disease affecting global swine industry. Due to the lack of effective vaccines, new antiviral strategies to compensate for the inefficacy of available vaccines are urgently required. Lysine acetylation, as an important post‐translational modification during infection, plays a key regulatory role in host antiviral responses. In this study, the global acetylome is profiled using acetylation specific antibody‐based enrichment and tandem mass tag label high‐affinity purification liquid chromatography‐mass spectrometry in PRRSV‐infected pulmonary alveolar macrophages (PAMs). As a result, 3731 lysine acetylation sites on 1421 cellular proteins are identified. Bioinformatics analysis of the different acetylated proteins revealed their involvement in various biological processes, including the host immune response and energy metabolism. These findings will contribute to the understanding of PRRSV pathogenesis and identify new cellular targets for anti‐PPRSV therapeutics.

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Global Proteome Analysis Links Lysine Acetylation to Diverse Functions in Oryza Sativa

Cited by 40 publications

References 57 publications

Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice

Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice

The iTRAQ-based chloroplast proteomic analysis of Triticum aestivum L. leaves subjected to drought stress and 5-aminolevulinic acid alleviation reveals several proteins involved in the protection of photosynthesis

Quantitative Proteomic Analysis of Global Protein Acetylation in PRRSV‐Infected Pulmonary Alveolar Macrophages

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