Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress.

Abstract:

:O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting the cellular stress response and thus survival. The aim of this study was to identify proteins that are differentially O-GlcNAcylated upon acute oxidative stress (H2O2) to provide insight into the mechanisms by which O-GlcNAc promotes survival. We achieved this goal by employing Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC) and a novel "G5-lectibody" immunoprecipitation strategy that combines four O-GlcNAc-specific antibodies (CTD110.6, RL2, HGAC39, and HGAC85) and the lectin WGA. Using the G5-lectibody column in combination with basic reversed phase chromatography and C18 RPLC-MS/MS, 990 proteins were identified and quantified. Hundreds of proteins that were identified demonstrated increased (>250) or decreased (>110) association with the G5-lectibody column upon oxidative stress, of which we validated the O-GlcNAcylation status of 24 proteins. Analysis of proteins with altered glycosylation suggests that stress-induced changes in O-GlcNAcylation cluster into pathways known to regulate the cell's response to injury and include protein folding, transcriptional regulation, epigenetics, and proteins involved in RNA biogenesis. Together, these data suggest that stress-induced O-GlcNAcylation regulates numerous and diverse cellular pathways to promote cell and tissue survival.

journal_name

J Proteome Res

authors

Lee A,Miller D,Henry R,Paruchuri VD,O'Meally RN,Boronina T,Cole RN,Zachara NE

doi

10.1021/acs.jproteome.6b00369

subject

Has Abstract

pub_date

2016-12-02 00:00:00

pages

4318-4336

issue

12

eissn

1535-3893

issn

1535-3907

journal_volume

15

pub_type

杂志文章
  • Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.

    abstract::A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00474

    authors: Díez P,Droste C,Dégano RM,González-Muñoz M,Ibarrola N,Pérez-Andrés M,Garin-Muga A,Segura V,Marko-Varga G,LaBaer J,Orfao A,Corrales FJ,De Las Rivas J,Fuentes M

    更新日期:2015-09-04 00:00:00

  • A metabonomic investigation on the biochemical perturbation in liver failure patients caused by hepatitis B virus.

    abstract::A metabonomic study was performed to investigate the biochemical perturbation of the serum samples from liver failure patients induced by hepatitis B virus (HBV; n=24) and control normal subjects (n=23). The serum metabonome was detected using gas chromatography-mass spectrometry (GC-MS) technique integrated with a co...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060591d

    authors: Yu K,Sheng G,Sheng J,Chen Y,Xu W,Liu X,Cao H,Qu H,Cheng Y,Li L

    更新日期:2007-07-01 00:00:00

  • Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down To 50 000 Cells as Starting Material.

    abstract::Histone post-translational modifications (PTMs) are fundamental players of chromatin regulation, as they contribute to editing histone chemical properties and recruiting proteins for gene transcription and DNA repair. Mass spectrometry (MS)-based proteomics is currently the most widely adopted strategy for high-throug...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00544

    authors: Guo Q,Sidoli S,Garcia BA,Zhao X

    更新日期:2018-01-05 00:00:00

  • Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment.

    abstract::T lymphocytes mediate cellular and humoral defense against foreign bodies or autoantigens. An understanding of T-cell information processing furthers studies of the immunological response. We describe a large-scale phosphorylation analysis of primary T cells using a multidimensional separation strategy, involving prep...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800500r

    authors: Carrascal M,Ovelleiro D,Casas V,Gay M,Abian J

    更新日期:2008-12-01 00:00:00

  • Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development.

    abstract::During asexual intraerythrocytic development, Plasmodium falciparum diverges from the paradigm of the eukaryotic cell cycles by undergoing multiple rounds of DNA replication and nuclear division without cytokinesis. A better understanding of the molecular switches that coordinate a myriad of events for the progression...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400394g

    authors: Pease BN,Huttlin EL,Jedrychowski MP,Talevich E,Harmon J,Dillman T,Kannan N,Doerig C,Chakrabarti R,Gygi SP,Chakrabarti D

    更新日期:2013-09-06 00:00:00

  • Label-Free LC-MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis.

    abstract::Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00804

    authors: Collins MA,An J,Hood BL,Conrads TP,Bowser RP

    更新日期:2015-11-06 00:00:00

  • System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

    abstract::Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00815

    authors: Terfve C,Sabidó E,Wu Y,Gonçalves E,Choi M,Vaga S,Vitek O,Saez-Rodriguez J,Aebersold R

    更新日期:2017-02-03 00:00:00

  • Proteomics reveals that redox regulation is disrupted in patients with ethylmalonic encephalopathy.

    abstract::Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and re...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101218d

    authors: Palmfeldt J,Vang S,Stenbroen V,Pavlou E,Baycheva M,Buchal G,Monavari AA,Augoustides-Savvopoulou P,Mandel H,Gregersen N

    更新日期:2011-05-06 00:00:00

  • Dissolving Peptides in 0.1% Formic Acid Brings Risk of Artificial Formylation.

    abstract::The ability of concentrated formic acid to formylate reactive amino acid residues is known from previous reports. In contrast, solvents containing a low concentration of formic acid are generally recognized as a safe environment for proteomic applications. The primary objective of this study was to explain the excessi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00823

    authors: Lenčo J,Khalikova MA,Švec F

    更新日期:2020-03-06 00:00:00

  • Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics.

    abstract::Defined as proteins actively transported via secretion systems, secreted proteins can have radically different subcellular destinations in monoderm (Gram-positive) bacteria. From degradative enzymes in saprophytes to virulence factors in pathogens, secreted proteins are the main tools used by bacteria to interact with...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1003642

    authors: Desvaux M,Dumas E,Chafsey I,Chambon C,Hébraud M

    更新日期:2010-10-01 00:00:00

  • Advances in Higher Order Multiplexing Techniques in Proteomics.

    abstract::Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statis...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/acs.jproteome.9b00228

    authors: Aggarwal S,Talukdar NC,Yadav AK

    更新日期:2019-06-07 00:00:00

  • Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation.

    abstract::Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400446z

    authors: Hayakawa E,Menschaert G,De Bock PJ,Luyten W,Gevaert K,Baggerman G,Schoofs L

    更新日期:2013-12-06 00:00:00

  • The Muscle Metabolome Differs between Healthy and Frail Older Adults.

    abstract::Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00840

    authors: Fazelzadeh P,Hangelbroek RW,Tieland M,de Groot LC,Verdijk LB,van Loon LJ,Smilde AK,Alves RD,Vervoort J,Müller M,van Duynhoven JP,Boekschoten MV

    更新日期:2016-02-05 00:00:00

  • Multiplexed Quantitative Proteomic Analysis of HEK293 Provides Insights into Molecular Changes Associated with the Cell Density Effect, Transient Transfection, and Virus-Like Particle Production.

    abstract::The production of virus-like particles (VLPs) has gained importance over the last few years owing to the benefits they provide compared to conventional vaccines. The biopharmaceutical industry is currently searching for safer candidates based on VLPs for new and existing vaccines and implementing new methods of manufa...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00601

    authors: Lavado-García J,Jorge I,Cervera L,Vázquez J,Gòdia F

    更新日期:2020-03-06 00:00:00

  • Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated α-fibrinogen in plasma for pancreatic cancer diagnosis.

    abstract::Pancreatic cancer is a devastating disease and early diagnosis and treatment are essential to improve the prognosis. We previously showed that α-fibrinogen containing hydroxylated proline residues at positions 530 and 565 is increased in plasma of pancreatic cancer patients. However, no antibody specific for hydroxyla...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr3008144

    authors: Yoneyama T,Ohtsuki S,Ono M,Ohmine K,Uchida Y,Yamada T,Tachikawa M,Terasaki T

    更新日期:2013-02-01 00:00:00

  • Proteomics and leukocytes: an approach to understanding potential molecular mechanisms of inflammatory responses.

    abstract::Leukocytes play an important role in the progression of disease and leukocyte-derived proteins are associated with the pathogenesis of the disease. Leukocyte activation causes production of inflammatory mediators, over-expression of cell surface adhesion molecules, and an increase in migration and infiltration, phagoc...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr0499601

    authors: Wang X,Zhao H,Andersson R

    更新日期:2004-09-01 00:00:00

  • Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration.

    abstract::Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hier...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00066

    authors: Postic G,Marcoux J,Reys V,Andreani J,Vandenbrouck Y,Bousquet MP,Mouton-Barbosa E,Cianférani S,Burlet-Schiltz O,Guerois R,Labesse G,Tufféry P

    更新日期:2020-07-02 00:00:00

  • Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability.

    abstract::We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the grea...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0502525

    authors: Thongboonkerd V,Chutipongtanate S,Kanlaya R

    更新日期:2006-01-01 00:00:00

  • Challenges in Peptide-Spectrum Matching: A Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits.

    abstract::Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide-spectrum matches (PSMs). To improve the robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that hav...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00478

    authors: Hubler SL,Kumar P,Mehta S,Easterly C,Johnson JE,Jagtap PD,Griffin TJ

    更新日期:2020-01-03 00:00:00

  • Identification of hepatocellular-carcinoma-associated antigens and autoantibodies by serological proteome analysis combined with protein microarray.

    abstract::To comprehensively study autoantibodies in patients with hepatocellular carcinoma (HCC), we used an approach-based serology and proteomics technologies. Total proteins extracted from HepG2 cells and HepG2.2.15 cells were separated by two-dimensional gel electrophoresis (2DE) and then transferred onto polyvinylidene di...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070525r

    authors: Li L,Chen SH,Yu CH,Li YM,Wang SQ

    更新日期:2008-02-01 00:00:00

  • Metabolic regulatory network alterations in response to acute cold stress and ginsenoside intervention.

    abstract::Acute stress may trigger systemic biochemical and physiological changes in living organisms, leading to a rapid loss of homeostasis, which can be gradually reinstated by self-regulatory mechanisms and/or drug intervention strategy. However, such a sophisticated metabolic regulatory process has so far been poorly under...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070051w

    authors: Wang X,Su M,Qiu Y,Ni Y,Zhao T,Zhou M,Zhao A,Yang S,Zhao L,Jia W

    更新日期:2007-09-01 00:00:00

  • Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

    abstract::Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visuali...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b01031

    authors: Mai TL,Hu GM,Chen CM

    更新日期:2016-07-01 00:00:00

  • Site-specific IGFBP-1 hyper-phosphorylation in fetal growth restriction: clinical and functional relevance.

    abstract::Phosphorylation enhances IGFBP-1 binding to IGF-I, thereby limiting the bioavailability of IGF-I that may be important in fetal growth. Our goal in this study was to determine whether changes in site-specific IGFBP-1 phosphorylation were unique to fetal growth restriction. To establish a link, we compared IGFBP-1 phos...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900987n

    authors: Abu Shehab M,Khosravi J,Han VK,Shilton BH,Gupta MB

    更新日期:2010-04-05 00:00:00

  • PhosphoScore: an open-source phosphorylation site assignment tool for MSn data.

    abstract::Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800169k

    authors: Ruttenberg BE,Pisitkun T,Knepper MA,Hoffert JD

    更新日期:2008-07-01 00:00:00

  • Proteomic approach to identify champagne wine proteins as modified by Botrytis cinerea infection.

    abstract::The presence of the fungal pathogen, Botrytis cinerea, in the vineyard causes reductions in both quality and quantity of grapes and wine. Because proteins are involved in the foam stabilization of sparkling wines, we have undertaken, for the first time, a thorough proteomic analysis of two champagne base wines prepare...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070419p

    authors: Cilindre C,Jégou S,Hovasse A,Schaeffer C,Castro AJ,Clément C,Van Dorsselaer A,Jeandet P,Marchal R

    更新日期:2008-03-01 00:00:00

  • Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus.

    abstract::Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity ha...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr9010684

    authors: Teutschbein J,Albrecht D,Pötsch M,Guthke R,Aimanianda V,Clavaud C,Latgé JP,Brakhage AA,Kniemeyer O

    更新日期:2010-07-02 00:00:00

  • Improved Integrated Whole Proteomic and Phosphoproteomic Profiles of Severe Acute Pancreatitis.

    abstract::Severe acute pancreatitis (SAP) is caused by complicated biological factors, and revealing its complex pathogenesis by single-target analysis is difficult. Systematic studies have developed slowly because extraction of degradable pancreatic proteins exposed to multiple proteases is challenging. We present integrated w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00229

    authors: Wang C,Zhang Y,Tan J,Chen B,Sun L

    更新日期:2020-06-05 00:00:00

  • Direct protein detection from biological media through electrospray-assisted laser desorption ionization/mass spectrometry.

    abstract::We report here using a novel technology-electrospray-assisted laser desorption ionization (ELDI)/mass spectrometry-for the rapid and sensitive detection of the major proteins that exist in dried biological fluids (e.g., blood, tears, saliva, serum), bacterial cultures, and tissues (e.g., porcine liver and heart) under...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050442f

    authors: Huang MZ,Hsu HJ,Lee JY,Jeng J,Shiea J

    更新日期:2006-05-01 00:00:00

  • Nontargeted urinary metabolite profiling of a mouse model of Crohn's disease.

    abstract::Crohn's disease is an inflammatory disorder of the bowel, believed to arise from the dysregulation of intestinal mucosal immunity. The interleukin-10-deficient (IL10-/-) mouse, which develops intestinal inflammation in the presence of gut microflora, serves as a mouse model of Crohn's disease. Nontargeted urinary meta...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800999t

    authors: Lin HM,Edmunds SI,Helsby NA,Ferguson LR,Rowan DD

    更新日期:2009-04-01 00:00:00

  • B. subtilis ribosomal proteins: structural homology and post-translational modifications.

    abstract::Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identifica...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr801114k

    authors: Lauber MA,Running WE,Reilly JP

    更新日期:2009-09-01 00:00:00