Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ketone Bodies-mediated Cysteine Modifications Discovered by Chemical Proteomics

ABSTRACT: All the studies of ketone body-dependent post-translational modifications (PTMs), notably those mediated by ketone bodies, β-hydroxybutyrate (Bhb) and acetoacetate (Acac), have focused on lysine acylations. However, given the chemically diverse and reactive nature of metabolites generated, it remains unclear whether non-lysine modifications can also happen. Here, we report the synthesis of an acetoacetate-alkyne (Acac-alkyne) chemical probe that enables efficient metabolic labeling, robust fluorescent visualization, and mass spectrometry-based identification of Acac-modified proteins. By combining chemical proteomics with open-search strategy, we showed that Acac will induce previously uncharacterized cysteine modifications in mammalian cells. Notably, cysteine S-crotonation (Ccr) is validated by employing both probe-based and standard peptide-based co-elution assays. Metabolic pathway tracing further identifies BDH1 and ECHS1 as key enzymes that generate Ccr formation. Together, these findings establish ketone metabolism as a novel source of cysteine modifications and provide an alternative mechanistic pathway to explain the profound biological effects of ketone body.

ORGANISM(S): Homo Sapiens

SUBMITTER: Zhipeng Wang

PROVIDER: PXD066371 | iProX | Tue Jul 22 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Chemical Proteomic Profiling of Lysine Crotonylation by Bioorthogonal Probes in Mammalian Cells

Project description:we report an alkynyl-functionalized bioorthogonal chemical probe, Cr-alkyne, for the detection and identification of protein lysine crotonylation in mammalian cells.

2024-07-04 | PXD053632 |

DYn-2 based identification of Arabidopsis sulfenomes

Project description:Identifying the sulfenylation state (-SOH) of stressed cells. Here, we optimized an in vivo trapping method of sulfenic acids in hydrogen peroxide (H2O2) stressed plant cells. With click chemistry, the dimedone based alkyne functionalized DYn-2 probe was biotinylated for subsequent streptavidin enrichment of sulfenylated proteins. the DYn-2 modification and DYn-2-Biotin-azide modification were unknown modifications, we therefore chose N-D-glucuronylglycine [MOD00067] and N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine [MOD00444]

2016-06-27 | PXD001562 | Pride

NAIA for cysteine profiling in HepG2 cells, protein target identification of covalent ligand and studying cysteine oxidative modifications

Project description:New cysteine probes, N-acryloylindole-alkynes (NAIAs), have been developed. We have applied NAIA-5 for cysteine profiling in HepG2 cell lysates, and the results have been compared to the conventional cysteine probe iodoacetamide-alkyne (IAA). NAIA-5 allows identification of more ligandable Cys than IAA in our experiment, and more interesting, a unique pool of Cys which have not been profiled previously by any reported cysteine probe. We have further utilized NAIA-5 for covalent ligand screening experiment. This allows us to discover hit compounds targeting the newly identified cysteines and proteins. One of the hit compounds, CL1, demonstrated good bioactivity by arresting cell cycle at G1 phase through targeting proteins associated with cell cycle and regulations. In addition, NAIA-5 has been successfully coupled with NAI compound for studying cysteine oxidative modifications in HepG2 cells by MS experiments.

2023-06-14 | PXD041264 | Pride

Competition of PG-DA vs PA-DA probes in mammalian cell and brain lysates

Project description:Here we aim to find the protein targets of monoacylglyerol lipids by competing the 1-palmitoyl-glycerol diazirine alkyne (PGDA) vs palmitic acid diazirine alkyne (PGDA) the probe usinc chemical proteomics approaches in mammalian cell and mouse brain lysates.

2025-06-23 | PXD051399 | Pride

Protein target identification of CL16 in HCT116 cells by an alkyne probe, CL16-alkyne

Project description:By coupling activity-based protein profiling (ABPP) with covalent ligand screening experiment, we have identified a cysteine-reactive covalent ligand, CL16, which can bind strongly and selectively with RhoA in vitro. In this experiment, we investigated the protein targets of CL16 in colorectal cancer HCT116 cells by a molecular probe of CL16, CL16-alkyne. HCT116 cells were pretreated with solvent vehicle or CL16, followed by CL16-alkyne. The cells were lysed, and the CL16-alkyne-labeled proteins were then installed with desthiobiotin through copper-catalyzed azide-alkyne cycloaddition (CuAAC), enriched, tryptic digested and profiled by LC-MS/MS. Peptides with fold change (Control/CL16)>4 and p<0.05 (i.e. at least 75% occupancy and statistical significance) were considered as targets bound with CL16.

2025-08-30 | PXD053041 | Pride

Validation of PA-DA probe in mammalian cell and brain lysates

Project description:Here we aim to characterize the palmitic acid diazirine alkyne (PA-DA) probe using chemical proteomics approaches in mammalian cell and mouse brain lysates.

2025-06-24 | PXD051775 | Pride

Validation of PG-DA probe in mammalian cell and brain lysates

Project description:Here we aim to characterize the 1-palmitoyl-glycerol diazirine alkyne (PGDA) probe using chemical proteomics approaches in mammalian cell and mouse brain lysates.

2025-06-24 | PXD051332 | Pride

Reversible histone deacetylase activity catalyzes lysine acylation

Project description:The dynamic modification of proteins by many metabolites suggests an intimate link between energy metabolism and post-translational modifications (PTM). For instance, starvation and low-carbohydrate diets lead to the accumulation of the ketone body, β-hydroxybutyrate (BHB), whose blood concentrations increase more than 10-fold into the millimolar range, concomitant with the accumulation of lysine β-hydroxybutyrylation (Kbhb) of proteins. As with other lysine acylations, Kbhb marks can be removed by histone deacetylases (HDACs). Here, we report that class I HDACs unexpectedly catalyze a reverse reaction that generates the Kbhb modification on target proteins. Through mutational analysis, we show a shared reliance on key active site amino acids for classical deacetylation and non-canonical HDAC-catalyzed β-hydroxybutyrylation. Based on these data, we propose that HDACs catalyze a condensation reaction between the free amine group on lysine and BHB, thereby generating the amide bond required for covalent attachment of BHB. Also consistent with reversible HDAC activity, Kbhb formation is driven by mass action and substrate availability. This reversible HDAC activity is not limited to BHB but also extends to multiple short-chain fatty acids and represents a novel mechanism of PTM deposition relevant to metabolically-sensitive proteome modifications.

2025-04-16 | PXD058840 | Pride

The muscle-specific MEF2D⍺2 isoform promotes muscle ketolysis and running capacity in mice

Project description:Ketone bodies are an alternate fuel source generated by the liver in response to low carbohydrate availability in neonates and after starvation and exhausting exercise in adulthood. The postnatal alternative splicing generates a highly conserved muscle-specific MEF2D⍺2 protein isoform of the transcription factor MEF2D. Here, we discovered that compared to WT mice, MEF2D⍺2 exon knockout (Eko) mice displayed reduced running capacity and muscle expression of all three ketolytic genes, BDH1, OXCT1, and ACAT1. Consistent with reduced muscle utilization of ketone bodies, MEF2D⍺2 Eko mice also showed increased ketone body levels in a tolerance test, after exercise, and upon feeding a ketogenic diet. Lastly, using mitochondria isolated from skeletal muscle, we showed reduced ketone body utilization and respiration in Eko compared to WT mice. Thus, we identified a new role of MEF2D⍺2 protein isoform in regulating skeletal muscle ketone body oxidation, exercise capacity, and its effect on systemic ketone body levels.

2025-07-18 | GSE302518 | GEO

Ethynylation of Cysteines from Peptides to Proteins in Living Cells

Project description:Efficient methods to introduce bioorthogonal groups, such as terminal alkynes, into biomolecules are important tools for chemical biology. State-of-the-art approaches are based on the introduction of a linker between the targeted amino acid and the alkyne, and still present limitations of either reactivity, selectivity or adduct stability. Herein, we present a new ethynylation method of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. In contrast to other approaches, the acetylene group is directly introduced onto the thiol group of cysteine and can be used in one-pot in a copper-catalyzed alkyne-azide cycloaddition (CuAAC) for further functionalization. Labeling proceeded with reaction rates comparable or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab. Under optimized conditions, high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed a much-improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine-reagent based probes. Fine-tuning of the EBX reagents allowed optimization of their reactivity and physical properties for the desired application.

2020-04-07 | PXD018165 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data