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Analysis of reversibly oxidized cysteines from the Chlamydomonas proteome with yeast spike-in

ABSTRACT: Benchmarking dataset for the objective evaluation of quantitative and statistical workflows.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Chlamydomonas Reinhardtii

SUBMITTER: Evan McConnell

LAB HEAD: Leslie M. Hicks

PROVIDER: PXD009693 | Pride | 2019-03-19

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20161007_EWM47_ER_100ng_1_5-35_7uL.wiff	Wiff
	20161007_EWM47_ER_100ng_1_5-35_7uL.wiff.scan	Wiff
	20161007_EWM47_ER_100ng_2_5-35_7uL.wiff	Wiff
	20161007_EWM47_ER_100ng_2_5-35_7uL.wiff.scan	Wiff
	20161007_EWM47_ER_100ng_3_5-35_7uL.wiff	Wiff

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Publications

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics.

Berg Philip P McConnell Evan W EW Hicks Leslie M LM Popescu Sorina C SC Popescu George V GV

BMC bioinformatics 20190314 Suppl 2

<h4>Background</h4>Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data.<h4>Results</h4>Our methodology includes variance stabilization, nor ...[more]

PMID: 30871482

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Chemical inhibition of the target of rapamycin kinase in Chlamydomonas reinhardtii leads to rapid cysteine oxidation and sustained physiological changes.

Project description:The target of rapamycin (TOR) kinase is a key metabolic regulator with a role in diverse processes, including nutritional sensing, protein translation, and autophagy. In the green alga Chlamydomonas reinhardtii, TOR maintains these responsibilities and is additionally linked to the regulation of increased triacylglycerol accumulation. In this study, we used an ATP-competitive inhibitor (AZD8055) to inactivate TOR kinase in vivo and quantified any accompanying changes in global protein abundance and reversible cysteine oxidation.

2019-10-04 | PXD014819 | Pride

Proteome-wide analysis of cysteine reactivity in Arabidopsis associated with biotic stress response

Project description:We used a method for the enrichment of proteins with oxidative post-translational modifications that enabled the comprehensive identification and label-free quantification of reversibly oxidized thiols across the plant proteome. The redoxomes were characterized in wild-type and the top1top2 null mutants in the early stages of effector-triggered immunity.

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Analysis of the Chlamydomonas proteome with UPS1 spike-in

Project description:Benchmarking dataset for the objective evaluation of quantitative and statistical workflows.

2020-10-20 | PXD009694 | Pride

Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles

Project description:Silver nanoparticles (AgNPs) are widely used nanomaterials in both commercial and clinical biomedical applications, but the molecular mechanisms underlying their activity remain elusive. In this work we profiled proteomics and redox proteomics changes induced by AgNPs in two lung cancer cell lines: AgNPs sensitive Calu-1 and AgNPs resistant NCI-H358. We show that AgNPs induce changes in protein abundance and reversible oxidation in a time and cell line dependent manner impacting key cellular processes such as protein translation and modification, lipid metabolism, bioenergetics and mitochondrial dynamics. Supporting confocal microscopy and transmission electron microscopy (TEM) data further emphasize mitochondria as a target of AgNPs toxicity differentially impacting mitochondrial networks and morphology in Calu-1 and NCI-H358 lung cells.

2021-04-01 | PXD021493 | Pride

IDH3 serves as a redox switch that regulates mitochondrial energy metabolism and contractility in the heart under oxidative stress

Project description:Redox signaling and cardiac function are tightly linked. Still, it is largely unknown which specific protein targets are affected by reactive oxygen species (ROS) that underly the impaired inotropic effect in oxidative stress. Here, we combined a new chemogenetic mouse model (HMC HyPer-DAO transgenic mice) and a redox proteomics approach to identify cellular redox switches and their functional role. Using the HyPer-DAO mice, we prove that increased endogenous production of H2O2 in cardiomyocytes is leading to a reversible cardiac contractility in vivo. We identified the -subunit of the TCA cycle enzyme isocitrate dehydrogenase (IDH)3 as a redox switch and linked this modification to mitochondrial metabolism and glutathione synthesis. Molecular dynamics simulations combined with experimental evidence from cysteine-gene-edited point mutations revealed that IDH3 Cys148 and 284 are critically involved in oxidant-dependent alterations of IDH3 function. Together, our results demonstrate a specific link between ROS, IDH3 and mitochondrial metabolism. Cardiac phenotyping of the chemogenetic mice reveal the biological significance of these ROS-induced modifications.

2023-04-21 | PXD037987 | Pride

Reversible oxidative signaling in Chlamydomonas following nitrogen deprivation

Project description:As global temperatures climb to historic highs, the far-reaching effects of climate change have impacted agricultural nutrient availability. This has extended to low latitude oceans, where a deficit in both nitrogen and phosphorus stores has led to dramatic decreases in carbon sequestration in oceanic phytoplankton. Although Chlamydomonas reinhardtii, a freshwater model green alga, has shown drastic systems-level alterations following nitrogen deprivation, the mechanism(s) through which these alterations are triggered and regulated are unclear. This study examined the role of reversible oxidative signaling in the nitrogen stress response of C. reinhardtii. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 7,889 unique oxidized cysteine thiol identifiers were quantified, with 231 significantly changing peptides from 184 proteins following 2 h of nitrogen deprivation. These results demonstrate proteins affected by oxidation involved in nitrogen assimilation, amino acid metabolism, photosynthesis, and other metabolic processes. An enhanced role of non-damaging oxidative pathways is observed throughout the photosynthetic apparatus that provides a framework for further analysis in phototrophs.

2020-06-28 | PXD019491 | Pride

Sequential enrichment of phosphorylation on reversibly oxidized proteoforms – part 1

Project description:Post-translational modifications (PTMs) are necessary for the regulation of critical processes including metabolism, signaling, and overall homeostasis. While proteins PTMs have been largely investigated independently in bottom-up proteomics methodologies, examination into how different PTMs interact, or crosstalk, will reveal a more complete understanding of the reciprocity of signaling cascades across numerous pathways. Combinatorial reversible thiol oxidation and phosphorylation in eukaryotes is largely recognized, but rigorous approaches for experimental verification are underdeveloped and must be advanced to begin meaningful definition of crosstalk in targeted pathway and systems biology research. Herein, we applied protein-level enrichment of reversibly oxidized proteoforms in Chlamydomonas reinhardtii with subsequent phosphopeptide analysis to determine the extent of phosphorylation in the redox thiol proteome.

2018-04-23 | PXD008370 | Pride

Sequential enrichment of phosphorylation on reversibly oxidized proteoforms – part 2

2018-04-23 | PXD008371 | Pride

S-acylated and S-palmitoylated proteins in HeLa

Project description:S-fatty-acylation is the covalent attachment of long chain fatty acids, predominately palmitate (C16:0, S-palmitoylation), to cysteine (Cys) residues via a thioester linkage on proteins. This post-translational and reversible lipid modification regulates protein function and localization in eukaryotes and is important in mammalian physiology and human disease. While chemical labeling methods have improved the detection and enrichment of S-fatty-acylated proteins, mapping sites of modification and characterization of endogenously attached fatty acids is still challenging. here, we optimized and compared two methods widely employed to identify S-fatty-acylated proteins by MS-based proteomics. While these methods identified an overlapping list of fatty-acylated proteins, only alk-16 chemical reporter combined with NH2OH specifically and robustly identified S-fatty-acylated proteins. Alk-16 chemical reporter labeling alone gave a list of S/N/O-fatty acylated proteins, while acyl-RAC provided a list of S-acylated proteins. Acyl-RAC identifies any proteins with a thioester modification and is often misused in the literature to validate S-fatty-acylated proteins. It would be preferable, when validating new S-fatty-acylated proteins, to use acyl-RAC and alk-16 (+/-NH2OH) in combination.

2018-03-28 | PXD008398 | Pride

Redox proteomics analysis of E.coli biofilms

Project description:Proteomics analysis of planktonic and biofilm E.coli, in aerobic an anaerobic conditions. The proteomics analysis is aimed to detect the different pattern of s-nitrosylation and cysteine oxidation in the two life-styles.

2021-05-06 | PXD020249 | Pride

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