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Kbhb proteome in 293 cells

ABSTRACT: We performed an global Kbhb proteome screening and identified ~3000 Kbhb substrate.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: He Huang

LAB HEAD: Yingming Zhao

PROVIDER: PXD012328 | Pride | 2021-09-08

REPOSITORIES: Pride

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			Action	DRS
	Results.tar.gz	Other
	TD182.mzXML	Mzxml
	TD183.mzXML	Mzxml
	TD184.mzXML	Mzxml
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Publications

The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway.

Huang He H Zhang Di D Weng Yejing Y Delaney Kyle K Tang Zhanyun Z Yan Cong C Qi Shankang S Peng Chao C Cole Philip A PA Roeder Robert G RG Zhao Yingming Y

Science advances 20210224 9

Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyra ...[more]

PMID: 33627428

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Mouse Liver Lysine β-hydroxybutyrylome

Project description:Characterization of the lysine β-hydroxybutyrylome, proteome-wide, will start to define its cellular targets and enable investigation of its impact under ketogenesis. Here, we show the induction of global protein Kbhb in the liver. We identified 891 sites of Kbhb within 267 proteins belonging to macronutrient, detoxification and 1-carbon metabolic pathways, among others, in starved liver.

2021-09-08 | PXD016654 | Pride

Quantitative Proteomics Analysis Expands the Roles of Lysine -Hydroxybutyrylation Pathway in Response to Environmental β-Hydroxybutyrate

Project description:Lysine -hydroxybutyrylation (Kbhb) is a newly identified protein post-translational modification that derived from the ketone body β-hydroxybutyrate (BHB). BHB is synthesized in the liver from fatty acids and could be delivered to peripheral tissues when the supply of glucose is too low for the body’s energetic needs. The plasma concentration of BHB can increase up to 20 mM during starvation and in pathological conditions. Despite the progresses, how the cells that do not produce BHB respond to elevated environmental BHB remains largely unknown. Given that BHB significantly drives Kbhb, here we performed a quantitative proteomics study to characterize the BHB-induced lysine -hydroxybutyrylome and acetylome. A total of 840 unique Kbhb sites across 429 proteins were identified, with 42 sites from 39 proteins being increased by more than 50% in response to BHB. The upregulated β-hydroxybutyrylome induced by BHB are involved in aminoacyl-tRNA biosynthesis, 2-oxocarboxylic acid metabolism, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, and pyruvate metabolism pathways. Moreover, some BHB-targeted Kbhb substrates are potentially linked to diseases such as cancer. Taken together, this study revealed the dynamics of lysine -hydroxybutyrylome and acetylome in response to environmental BHB, which sheds light on the roles for Khib in regulation of diverse cellular processes and provides new insights into the biological functions of BHB.

2022-04-04 | PXD029481 | Pride

Khib proteome in response to p300 KO

Project description:We used quantitative proteomics to characterize the p300-regulated lysine 2-hydroxyisobutyrylome in wild type (WT) and p300 knockout (KO) cells.

2018-07-11 | PXD008525 | Pride

Identification and profiling of dynamic changes of site-specific histone acylations in HEK293T cells under metabolites treatment

Project description:1. Systematic survey of PTM site and stoichiometry on histone proteins has been lagged behind due to the lack of efficient quantitative peptide comparison methodology on histone proteins. Our quantitative mass spectrometry-based proteomics approach, Site-Profiling, used SILAC-based peptide ratio analysis on histone acylations with and without SCFA-derived metabolic treatment to directly compare the same peptide with the same modification and the same chain length. Different from the published methods that isotopically labeled metabolites, which might cause false-positive results and information lost, we only labelled all the lysines and arginines in histones and thus the same modification under native conditions would be kept, resulting that all modification peptides were comparable in parallel before and after metabolites stimulation. By a comprehensive analysis of all peptides containing the same histone marks, Site-Map can compare the abundance of each site-specific modification upon the treatment of the corresponding metabolite. 2. To reveal the site dependency of histone Kbhb distributed at the super enhancer region, we developed a method to isolate the super enhancer condensates by co-immunoprecipitation with coactivators BRD4. Same site-mapping method was utilized for comparasion the site dependency of histone Kbhb enriched with BRD4 or not.

2023-03-06 | PXD029508 | Pride

Proteome-wide analysis and functional identification of lysine β-hydroxybutyrylation in Ustilaginoidea virens

Project description:Lysine β-hydroxybutyrylation (Kbhb) is an evolutionarily conserved and widespread post-translational modification (PTM) in active gene transcription and cellular proliferation. However, its function remains unknown in phytopathogenic fungi. Here, we report a comprehensive identification of Kbhb in the rice false smut fungus Ustilaginoidea virens. Total 2,204 Kbhb sites were identified in 852 proteins. We found that β-hydroxybutyrylated proteins were enriched in mannose type O-glycan biosynthesis, citrate cycle (TCA cycle), ribosome, glycolysis/gluconeogenesis, proteasome, glyoxylate and dicarboxylate metabolism, alanine, aspartate and glutamate metabolism, pyruvate metabolism, biosynthesis of nucleotide sugars, butanoate metabolism, arginine biosynthesis, fructose and mannose metabolism, propanoate metabolism, methane metabolism, fatty acid degradation, β-alanine metabolism, valine, leucine and isoleucine degradation, phagosome, oxidative phosphorylation pathway. This suggests Kbhb might be involved in basic life functions of Ustilaginoidea virens.

2023-10-24 | PXD039304 | Pride

Toxic effects of BDE209 in human embryonic kidney 293 cells (HEK 293)

Project description:PBDEs are widely used in consumer and household products as flame retardants. Many studies have shown that PBDEs could disrupt thyroid hormone homeostasis and adversely affect brain development. Here, we explored the toxical effects of BDE209 on HEK 293 cells and found that BDE209 may have a role in nucleosome remodeling. Many gene sets involved in cancer are enriched at the BDE209-treated sample. This indicates the carcinogenicity of BDE209. Interestingly, the impacts of BDE209 dissoved in DMSO on gene expression are more pronounced than the simple additive effects of BDE209 and DMSO alone. Gene expression profiles of human embryonic kidney 293 cells (HEK 293) cultured in normal medium, and medium containing BDE209 or DMSO were generated by deep sequencing, using Illumina HighSeq2000, respectively..

2014-04-21 | E-GEOD-56361 | biostudies-arrayexpress

Transcription profiling of human 293 cells

Project description:A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets. Experiment Overall Design: In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid.

2009-06-23 | E-GEOD-12524 | biostudies-arrayexpress

BPA impacts on HEK 293 cells

Project description:Bisphenol A (BPA) is an environmental endocrine disruptor which has been detected in almost all human bodies. Many studies have implied that BPA exposure is harmful to human health. Previous studies mainly focused on BPA effects on ER-positive cells. Genome-wide impact of BPA on gene regulation in ER-negative cells is unclear. In the present study, we performed RNA-seq to characterize BPA-induced gene regulation on ER-negative HEK 293 cells.

2014-10-10 | E-MTAB-1959 | biostudies-arrayexpress

Gene expression of HEK 293 cells transfected with Vector (PCMV), Aire, or MBD-VP16

Project description:HEK 293 cells were transiently transfected with plasmids expressing Vector only(PCMV), Aire, or MBD-VP16 with the goal of comparing the global gene expression profiles in the Aire and MBD-VP16 groups We used microarrays to detail the global gene expression profile. HEK 293 cells were transiently transfected with plasmids expressing Vector only(PCMV), Aire, or MBD-VP16 and 72 hrs post transfection total RNA was collected for microarray analysis.

2013-11-21 | E-GEOD-52546 | biostudies-arrayexpress

Kcr proteome in response to p300 KO

Project description:We used quantitative proteomics to characterize the p300-regulated lysine crotonylome in wild type (WT) and p300 knockout (KO) cells.

2018-06-26 | PXD006407 | Pride