Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Low-input redoxomics facilitates global identification of metabolic regulators of oxidative stress in the gut

ABSTRACT: we developed a low-input and user-friendly pipeline for the simultaneous profiling of five distinct Cys states with regional resolution in the gut of monkeys, including free SH, total Cys oxidation (Sto), sulfenic acid (SOH), S-nitrosylation (SNO), and S-glutathionylation (SSG), shedding light on redox modification stoichiometries and redox signaling of gut aging.Furthermore, redox-modification and proteomic analysis of colonic tissues of calorie-restricted aged mice revealed that CR can reduce oxidative stress and highlight the protective effect of CR on intestinal health.

ORGANISM(S): Macaca Fascicularis Fascicularis Homo Sapiens Mus Musculus

SUBMITTER: Lunzhi Dai

PROVIDER: PXD053818 | iProX | Mon Dec 16 00:00:00 GMT 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Proteome-wide detection of cysteine nitrosylation targets and motifs using bio-orthogonal cleavable linker based enrichment and switch technique (Cys-BOOST)

Project description:Cysteine (Cys) reversible post-translational modifications (PTMs) are emerging as important players in cellular signaling and redox homeostasis. Here we present Cys-BOOST a novel strategy for LC-MS/MS based quantitative analysis of reversibly modified Cys using switch technique, enrichment via bio-orthogonal cleavable linker and quantification using tandem mas tag (TMT) reagents. We performed direct comparison of Cys-BOOST (n=3) with iodo-TMT (n=3) by analyzing the total CysCys from HeLa cell extracts. As a result higher sensitivity (25,019 vs 9,966 Cys peptides), specificity (98 vs 74 %) and technical reproducibility were obtained by Cys-BOOST. In addition, the application of Cys-BOOST for the analysis of Cys nitrosylation (SNO) in S-nitrosoglutathione (GSNO) treated and non-treated HeLa cell extracts lead to the identification of unprecedented number of SNO proteins (3,537), SNO peptides (9,314) and unique SNO sites (8,304). Based on the quantitative data we describe SNO consensus motifs for endogenous SNO and SNO sites with differential reactivity to GSNO. Collectively, our findings suggest Cys-BOOST as a concurrent method of choice for Cys PTM analysis.

2019-05-21 | PXD011131 | Pride

S-nitrosation of proteins relevant to Alzheimer’s disease during early stages of neurodegeneration

Project description:Protein S-nitrosation (SNO-protein) is a post-translational modification in which a cysteine (Cys) residue is modified by nitric oxide (SNO-Cys). SNO-proteins impact many biological systems, but their identification has been technically challenging. We developed a chemical proteomic strategy - SNOTRAP (SNO trapping by triaryl phosphine) -that allows improved identification of SNO-proteins by mass spectrometry. We found that S-nitrosation is elevated during early stages of neurodegeneration, preceding cognitive decline. We identified changes in the SNOproteome during early neurodegeneration that are potentially relevant for synapse function, metabolism, and Alzheimer’s disease pathology. SNO-proteome analysis further reveals a potential linear motif for SNO-Cys sites that are altered during neurodegeneration. Our strategy can be applied to multiple cellular and disease contexts and can reveal signaling networks that aid drug development.

2016-03-31 | PXD003802 | Pride

NTRC controls chloroplast redox homeostasis through the regulation of the redox balance of 2-Cys Prxs in Arabidopsis

Project description:Thiol-dependent redox regulation is essential for the rapid adaptation of chloroplast metabolism to unpredictable changes of light intensity. The disulfide reductase activity of thioredoxins (Trxs), which relies on photo-reduced ferredoxin (Fdx) and a Fdx-dependent Trx reductase (FTR), constitutes the Fdx-FTR-Trxs system, which links chloroplast redox regulation to light. In addition, chloroplasts harbor an NADPH-dependent Trx reductase (NTR) with a joint Trx domain, NTRC. The activity of these two redox systems is integrated by the balance of the hydrogen peroxide scavenging enzyme 2-Cys peroxiredoxin (2-Cys Prx), which thus plays a key role in maintaining the reducing capacity of chloroplast Trxs in response to light intensity. Based on the severe phenotype of mutant lines lacking NTRC, it is clear that this enzyme plays an essential role in chloroplast redox homeostasis. However, whether the function of NTRC depends on its capacity of reduce 2-Cys Prxs or has additional targets remains unknown. Here, we have addressed this issue by a comparative analysis of the triple mutant of Arabidopsis thaliana, ntrc-2cpab, simultaneously lacking 2-Cys Prxs and NTRC, and the double mutant 2cpab lacking 2-Cys Prxs. The phenotype of the ntrc-2cpab mutant is indistinguishable of the 2cpab mutant, as shown by growth rate, photosynthesis performance, light-dependent redox regulation of enzyme activity and comparative transcriptomics based RNA-Seq. Based on these results, we propose that the function of NTRC in chloroplast redox homeostasis is exerted by the regulation of the redox balance of 2-Cys Prxs rather than by the direct reduction of additional targets.

2021-09-09 | GSE147793 | GEO

Elucidation of molecular and functional networks linked to sarcopenia prevention by caloric restriction in rhesus monkeys

Project description:Caloric restriction (CR) improves survival in nonhuman primates and delays the onset of age-related morbidities including sarcopenia, the age-related loss of muscle mass and function. A shift in metabolism anticipates the onset of muscle aging phenotypes in nonhuman primates suggesting a potential role for metabolism in CR’s protective effects. Here we show that CR induced profound changes in muscle composition and the cellular metabolic environment. Bioinformatic analysis linked these adaptations to proteostasis, RNA processing, and lipid synthetic pathways. At the tissue level, CR maintained contractile content and attenuated age-related metabolic shifts among individual fiber types with higher mitochondrial activity, altered redox metabolism, and smaller lipid droplet size. Biometric and metabolic rate data confirm preserved metabolic efficiency in CR animals that correlated with attenuation of age-related muscle mass and physical activity. These data suggest that CR-induced reprogramming of metabolism plays a role in delayed aging of skeletal muscle in rhesus monkeys.

2019-12-11 | GSE139081 | GEO

Detection of SNO by cysTMT switch

Project description:HAPEC treated with SNO-Cys or control compounds

2012-01-16 | PRD000410 | Pride

gut metagenome

Project description:LotuS: an efficient and user-friendly OTU processing pipeline

| PRJNA259602 | ENA

An Easy Operating Pathogen Microarray (EOPM) Platform for Rapid Screening of Vertebrate Pathogens

Project description:An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface.

2013-07-01 | GSE45860 | GEO

Drosophila melanogaster

Project description:A user-friendly chromatographic method to purify small regulatory RNAs

| PRJNA174816 | ENA

S-bacillithiolation of the OhrR repressor and the methionine synthase MetE protect against hypochlorite stress in Bacillus subtilis

Project description:Protein S-thiolation is a post-translational thiol-modification that controls redox-sensing transcription factors and protects active site cysteine residues against irreversible oxidation. In B. subtilis, the MarR-type repressor OhrR was shown to sense organic hydroperoxides via formation of mixed disulfides with the redox buffer bacillithiol (Cys-GlcN-Malate) termed as S-bacillithiolation. We have studied changes in the transcriptome and redox proteome caused by the strong oxidant hypochloric acid (NaOCl), the active component of house-hold bleach. The OhrR-controlled peroxiredoxin OhrA was most strongly up-regulated by NaOCl stress and conferred specific protection against NaOCl. Inactivation of the OhrR repressor was caused by S-bacillithiolation of the redox-sensing Cys15 residue in response to NaOCl. Two cobalamin-independent methionine synthases MetE and YxjG were identified as S-bacillithiolated at their essential active site cysteines resulting in hypochlorite-induced methionine limitation. In summary, our studies show that S-bacillithiolation of OhrR and the methionine synthases is the major mechanism in protection against hypochlorite stress in B. subtilis. The B. subtilis 168 wild type strain was grown in minimal medium to OD500 of 0.4 and harvested before and 10 minutes after exposure to 50 µM NaOCl. Microarray hybridizations were performed in triplicate using RNA isolated from independent cultures.

2011-07-04 | E-GEOD-27637 | biostudies-arrayexpress

Interactive analysis of single-cell epigenomic landscapes with ChromSCape

Project description:Here, we present ChromSCape, a user-friendly interactive Shiny/R application that processes single-cell epigenomic data to help the biological interpretation of chromatin landscapes within cell populations. ChromSCape successfully analyses the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets.

2020-06-16 | GSE152502 | GEO

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