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Identification and analysis of histone lysine 2-hydroxyisobutyrylation in Arabidopsis

ABSTRACT: Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation in eukaryotes, but its prevalence and genomic function in higher plants remain unclear. Using mass spectrometry, we identified histone lysine 2-hydroxyisobutyrylation in Arabidopsis

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling

SUBMITTER: Yonghong Zhang

LAB HEAD: Yonghong Zhang

PROVIDER: PXD018017 | Pride | 2021-06-09

REPOSITORIES: Pride

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Salt-inhibited protein 2-hydroxyisobutyrylation affects silique development of Arabidopsis thaliana

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distribute in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that this highly conserved modification was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: 3810 normalized 2-hydroxyisobutyrylation sites on 1254 proteins were identified in siliques under salt stress, and lysine 2-hydroxyisobutyrylation was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants.

2021-12-30 | PXD026643 | Pride

Landscape of the Regulatory Elements for Lysine 2-Hydroxyisobutyrylation Pathway

Project description:This project reported a comprehensive global lysine 2-hydroxyisobutyrylome that provided a dataset of 6548 reliable lysine 2-hydroxyisobutyrylation (Khib) sites on 1725 proteins in HeLa cells. This dataset represents the first Khib proteome in mammalian cell to date, and illustrates a broad landscape of the Khib pathway.

2017-12-06 | PXD005414 | Pride

Proteomic analyses of lysine 2-hydroxyisobutyrylation in Fusarium graminearum in response to tebuconazole and carbendazim

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification in some prokaryotic and eukaryotic organisms. Here, we carried out proteome-wide analysis of Khib in Fusarium graminearum, identifying the reshaping of lysine 2-hydroxyisobutyrylome by tebuconazole or carbendazim, using the most recently-developed high-resolution LC-MS/MS in combination with high-specific affinity enrichment. In total, 3035 quantifiable Khib sites on 937 proteins were identified. With the criteria of fold changes over 1.3, normalized with total proteins, 1083 Khib sites of 509 proteins were considered as significantly affected by tebuconazole treatment, while 344 Khib sites of 227 proteins were significantly affacted by carbendazim. Furthermore, bioinformatics analysis were conducted.

2022-04-04 | PXD022499 | Pride

Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques

Project description:In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that Khib was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: Totally 3,810 normalized Khib sites on 1,254 proteins were identified in siliques under salt stress, and Khib was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss silique. Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation Khib modification. Bioinformatics analysis suggests that Khib mainly participates in glycolysis/gluconeogenesis and endocytosis. In particular, there were 117 Khib-modified proteins that were mapped to the protein interaction database, and the proteins with the most significant up-regulation of Khib sites were on P46422, O82514, Q38970, Q9LD57, and Q9STW6, while the most down-regulated sites were on Q9M9K1, Q9SF16, O24456, P83484, Q9FWA3, and P54609. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism.

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Expression data from arabidopsis root in response to boron toxicity

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2013-05-18 | E-GEOD-45212 | biostudies-arrayexpress

Expression data in whole Arabidopsis seedlings after treatment with the herbicide dicamba

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Project description:The goal of the microarray experiment was to identify genes that are differentially expressed among the Arabidopsis mutant med14, med16, npr1, and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that the induction of a large group of defense genes was suppressed in the med14 mutant compared with both med16 and the wild type. Three biological replicates with leaves from 8 plants per sample were collected at 0 and 4 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

2013-05-18 | E-GEOD-45214 | biostudies-arrayexpress

Microarray analyses of pathogen-induced transcriptome changes in the Arabidopsis mutant med14

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-05-18 | E-GEOD-45215 | biostudies-arrayexpress

Transcript profiling of the wild type Arabidopsis grown under different photoperiods

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2012-07-27 | E-MEXP-3331 | biostudies-arrayexpress

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