Differential nuclear proteomes in response to N-methyl-N'-nitro-N-nitrosoguanidine exposure.

Abstract:

:As a model carcinogen in studying the mutagenicity and carcinogenicity of N-nitroso alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) can induce DNA damages and many cellular defensive events, such as DNA repair, G2/M-phase arrest and apoptosis. Noticeably, diverse cellular responses were observed to occur following MNNG treatment in our previous studies, including nontargeted mutations (NTM) at undamaged DNA bases, endoplasmic reticulum stress (ER stress) induction and the activation of several signal transduction pathways. In addition, whole cell proteome analysis also revealed that comprehensive and various changes were triggered by this mutagen. However, low-abundance proteins with key functions, such as nuclear proteins, are always underrepresented in proteomic studies. To reduce the complexity of protein samples and monitor subcellular alterations in response to MNNG exposure, nuclear extracts were fractionated from MNNG-treated cells and compared using two-dimensional fluorescence difference gel electrophoresis (2-D DIGE). Twenty-three differentially expressed protein spots were observed after 0.25 and 1 muM MNNG exposure, and 8 of them were shared between these two treatment groups. When MALDI-TOF MS was used, 17 nuclear proteins affected by MNNG were identified. These proteins were involved in regulation of RNA processing, signal transduction, metabolism, DNA repair, protein biosynthesis and microtubule or cytoskeleton organization. Among them, two nuclear proteins with nucleocytoplasmic shuttling activity, 14-3-3 zeta and hnRNP K, were further demonstrated to undergo different dynamic changes in response to MNNG exposure. These results will aid our understanding of the complicated mechanisms of MNNG-induced cellular responses.

journal_name

J Proteome Res

authors

Shen J,Zhu H,Xiang X,Yu Y

doi

10.1021/pr900008n

subject

Has Abstract

pub_date

2009-06-01 00:00:00

pages

2863-72

issue

6

eissn

1535-3893

issn

1535-3907

journal_volume

8

pub_type

杂志文章
  • Beyond linker histones and high mobility group proteins: global profiling of perchloric acid soluble proteins.

    abstract::Extraction with HClO(4) provides an easy method for efficient enrichment of both histone H1 and HMG proteins from a variety of tissues. Usually, the histone and the HMG proteins are the most abundant components of the extracts, however, other proteins have frequently been observed but only seldom studied in more detai...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050415p

    authors: Zougman A,Wiśniewski JR

    更新日期:2006-04-01 00:00:00

  • Selective Affinity Enrichment of Nitrotyrosine-Containing Peptides for Quantitative Analysis in Complex Samples.

    abstract::Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00275

    authors: Zhao Y,Zhang Y,Sun H,Maroto R,Brasier AR

    更新日期:2017-08-04 00:00:00

  • Effect of amphotericin B on the metabolic profiles of Candida albicans.

    abstract::Amphotericin B (AmB) is a polyene antifungal drug widely used for systemic fungal infections. In this study, a metabonomic method using gas chromatography-mass spectrometry (GC/MS) was developed to characterize the metabolic profiles of Candida albicans cells exposed to AmB. Thirty-one differentially produced metaboli...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr4002178

    authors: Cao Y,Zhu Z,Chen X,Yao X,Zhao L,Wang H,Yan L,Wu H,Chai Y,Jiang Y

    更新日期:2013-06-07 00:00:00

  • PTML Model for Proteome Mining of B-Cell Epitopes and Theoretical-Experimental Study of Bm86 Protein Sequences from Colima, Mexico.

    abstract::In this work, we developed a general perturbation theory and machine learning method for data mining of proteomes to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) under a set of experimental query conditions (cqj). The method u...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00477

    authors: Martínez-Arzate SG,Tenorio-Borroto E,Barbabosa Pliego A,Díaz-Albiter HM,Vázquez-Chagoyán JC,González-Díaz H

    更新日期:2017-11-03 00:00:00

  • Heat stabilization of the tissue proteome: a new technology for improved proteomics.

    abstract::After tissue or body fluid sampling, proteases and other protein-modifying enzymes can rapidly change composition of the proteome. As a direct consequence, analytical results will reflect a mix of in vivo proteome and ex vivo degradation products. Vital information about the presampling state may be destroyed or disto...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8006446

    authors: Svensson M,Boren M,Sköld K,Fälth M,Sjögren B,Andersson M,Svenningsson P,Andren PE

    更新日期:2009-02-01 00:00:00

  • Relative quantification of membrane proteins in wild-type and prion protein (PrP)-knockout cerebellar granule neurons.

    abstract::Approximately 25% of eukaryotic proteins possessing homology to at least two transmembrane domains are predicted to be embedded in biological membranes. Nevertheless, this group of proteins is not usually well represented in proteome-wide experiments due to their refractory nature. Here we present a quantitative mass ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200759m

    authors: Stella R,Cifani P,Peggion C,Hansson K,Lazzari C,Bendz M,Levander F,Sorgato MC,Bertoli A,James P

    更新日期:2012-02-03 00:00:00

  • Identification of Cytosolic Protein Targets of Catechol Estrogens in Breast Cancer Cells Using a Click Chemistry-Based Workflow.

    abstract::Catechol estrogens (CEs) are known to be toxic metabolites and the initiators of the oncogenesis of breast cancers via forming covalent adducts with DNAs. CEs shall also react with proteins, but their cellular protein targets remain unexplored. Here, we reported the identification of protein targets of CEs in the solu...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00578

    authors: Do QT,Huang TE,Liu YC,Tai JH,Chen SH

    更新日期:2021-01-01 00:00:00

  • Interactome of the amyloid precursor protein APP in brain reveals a protein network involved in synaptic vesicle turnover and a close association with Synaptotagmin-1.

    abstract::Knowledge of the protein networks interacting with the amyloid precursor protein (APP) in vivo can shed light on the physiological function of APP. To date, most proteins interacting with the APP intracellular domain (AICD) have been identified by Yeast Two Hybrid screens which only detect direct interaction partners....

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300123g

    authors: Kohli BM,Pflieger D,Mueller LN,Carbonetti G,Aebersold R,Nitsch RM,Konietzko U

    更新日期:2012-08-03 00:00:00

  • METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses.

    abstract::We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (meta...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00385

    authors: Saunders JK,Gaylord DA,Held NA,Symmonds N,Dupont CL,Shepherd A,Kinkade DB,Saito MA

    更新日期:2020-11-06 00:00:00

  • 193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes.

    abstract::Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00289

    authors: Robinson MR,Taliaferro JM,Dalby KN,Brodbelt JS

    更新日期:2016-08-05 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

  • A Comprehensive Investigation toward the Indicative Proteins of Bladder Cancer in Urine: From Surveying Cell Secretomes to Verifying Urine Proteins.

    abstract::Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00106

    authors: Guo J,Ren Y,Hou G,Wen B,Xian F,Chen Z,Cui P,Xie Y,Zi J,Lin L,Wu S,Li Z,Wu L,Lou X,Liu S

    更新日期:2016-07-01 00:00:00

  • Comparison of GC-MS and NMR for metabolite profiling of rice subjected to submergence stress.

    abstract::Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300953k

    authors: Barding GA Jr,Béni S,Fukao T,Bailey-Serres J,Larive CK

    更新日期:2013-02-01 00:00:00

  • Interaction between inducible nitric oxide synthase and calmodulin in Ca2+-free and -bound forms.

    abstract::We have obtained the first direct electrochemistry of full-length inducible nitric oxide synthase (iNOS) by entrapping the enzyme in polyethylenimine (PEI) film. The interaction between iNOS and calmodulin (CaM) was then studied, which revealed an enhanced electron-transfer reactivity of the enzyme facilitated by CaM....

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060544l

    authors: Xiao H,Zhou H,Chen G,Liu S,Li G

    更新日期:2007-04-01 00:00:00

  • Comprehensive Spectral Library from the Pathogenic Bacterium Streptococcus pneumoniae with Focus on Phosphoproteins.

    abstract::To understand bacterial reactions to environmental stress or infection-related processes, it is necessary to identify the involved proteins. In mass spectrometry-based proteomics, the method of choice for spectra-to-peptide-match is database search, but in recent times, spectral libraries have come into focus. Here, w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00615

    authors: Hentschker C,Maaß S,Junker S,Hecker M,Hammerschmidt S,Otto A,Becher D

    更新日期:2020-04-03 00:00:00

  • Proteomic characterization of human milk whey proteins during a twelve-month lactation period.

    abstract::Human milk is a rich source of bioactive proteins that support the early growth and development of the newborn. Although the major components of the protein fraction in human milk have been studied, the expression and relative abundance of minor components have received limited attention. We examined the expression of...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101028k

    authors: Liao Y,Alvarado R,Phinney B,Lönnerdal B

    更新日期:2011-04-01 00:00:00

  • Identification of protein fragments as pattern features in MALDI-MS analyses of serum.

    abstract::The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to acquire spectral profiles has become a common approach to detect proteomic biomarkers of disease. MALDI-MS signals may represent both intact proteins as well as proteolysis products. Liquid chromatography-tandem mass spectrometry (L...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050138m

    authors: Zimmerman LJ,Wernke GR,Caprioli RM,Liebler DC

    更新日期:2005-09-01 00:00:00

  • Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of Shewanella oneidensis to chromate exposure.

    abstract::Microbes are known to regulate both gene expression and protein activity through the use of post-translational modifications (PTMs). Common PTMs involved in cellular signaling and gene control include methylations, acetylations, and phosphorylations, whereas oxidations have been implicated as an indicator of stress. S...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070531n

    authors: Thompson MR,Thompson DK,Hettich RL

    更新日期:2008-02-01 00:00:00

  • Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics.

    abstract::Plastids are essential organelles because they contribute to primary and secondary metabolism and plant signaling networks. A high-quality inventory of the plastid proteome is therefore a critical tool in plant research. We present reference plastid proteomes for maize (Zea mays) and Arabidopsis (Arabidopsis thaliana)...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300952g

    authors: Huang M,Friso G,Nishimura K,Qu X,Olinares PD,Majeran W,Sun Q,van Wijk KJ

    更新日期:2013-01-04 00:00:00

  • Metabolomics in cerebrospinal fluid of patients with amyotrophic lateral sclerosis: an untargeted approach via high-resolution mass spectrometry.

    abstract::Amyotrophic lateral sclerosis (ALS) is characterized by the absence of reliable diagnostic biomarkers. The aim of the study was to (i) devise an untargeted metabolomics methodology that reliably compares cerebrospinal fluid (CSF) from ALS patients and controls by liquid chromatography coupled to high-resolution mass s...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400376e

    authors: Blasco H,Corcia P,Pradat PF,Bocca C,Gordon PH,Veyrat-Durebex C,Mavel S,Nadal-Desbarats L,Moreau C,Devos D,Andres CR,Emond P

    更新日期:2013-08-02 00:00:00

  • Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.

    abstract::Skeletal muscle has emerged as an important secretory organ that produces so-called myokines, regulating energy metabolism via autocrine, paracrine, and endocrine actions; however, the nature and extent of the muscle secretome has not been fully elucidated. Mass spectrometry (MS)-based proteomics, in principle, allows...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00720

    authors: Deshmukh AS,Cox J,Jensen LJ,Meissner F,Mann M

    更新日期:2015-11-06 00:00:00

  • Transcriptomic and Neuropeptidomic Analysis of the Stick Insect, Carausius morosus.

    abstract::One of the most thoroughly studied insect species, with respect to locomotion behavior, is the stick insect Carausius morosus. Although detailed information exists on premotor networks controlling walking, surprisingly little is known about neuropeptides, which are certainly involved in motor activity generation and m...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00155

    authors: Liessem S,Ragionieri L,Neupert S,Büschges A,Predel R

    更新日期:2018-06-01 00:00:00

  • Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date.

    abstract::The Biology/Disease-driven (B/D) working groups of the Human Proteome Project are alliances of research groups aimed at developing or improving proteomic tools to support specific biological or disease-related research areas. Here, we describe the activities and progress to date of the B/D working group focused on pro...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/acs.jproteome.8b00401

    authors: Boersema PJ,Melnik A,Hazenberg BPC,Rezeli M,Marko-Varga G,Kamiie J,Portelius E,Blennow K,Zubarev RA,Polymenidou M,Picotti P

    更新日期:2018-12-07 00:00:00

  • A protein processing filter method for bacterial identification by mass spectrometry-based proteomics.

    abstract::A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposab...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101086a

    authors: Jabbour RE,Deshpande SV,Stanford MF,Wick CH,Zulich AW,Snyder AP

    更新日期:2011-02-04 00:00:00

  • High-Resolution Mass Spectrometry Based Proteomic Analysis of the Response to Vancomycin-Induced Cell Wall Stress in Streptomyces coelicolor A3(2).

    abstract::Understanding how bacteria survive periods of cell wall stress is of fundamental interest and can help generate ideas for improved antibacterial treatments. In this study we use tandem mass tagging to characterize the proteomic response of vancomycin resistant Streptomyces coelicolor to the exposure to sublethal level...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00242

    authors: Hesketh A,Deery MJ,Hong HJ

    更新日期:2015-07-02 00:00:00

  • Introduction to the Food and Drug Administration (FDA) regulatory process.

    abstract::FDA oversight of medical devices, including in vitro diagnostic devices (IVDs or laboratory tests), in the United States was a direct result of the passage of the Medical Device Amendments of 1976. This law introduced a series of general controls for medical devices including registration and listing, requirements for...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr050059a

    authors: Hackett JL,Gutman SI

    更新日期:2005-07-01 00:00:00

  • Heterogeneous nuclear ribonucleoprotein A1 is identified as a potential biomarker for colorectal cancer based on differential proteomics technology.

    abstract::Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900365e

    authors: Ma YL,Peng JY,Zhang P,Huang L,Liu WJ,Shen TY,Chen HQ,Zhou YK,Zhang M,Chu ZX,Qin HL

    更新日期:2009-10-01 00:00:00

  • Impact of prenatal disorders on the metabolic profile of second trimester amniotic fluid: a nuclear magnetic resonance metabonomic study.

    abstract::This paper describes a metabonomic study of prenatal disorders using nuclear magnetic resonance (NMR) spectroscopy of amniotic fluid (AF) collected in the second trimester of pregnancy, to search for metabolite markers of fetal malformations, prediagnostic gestational diabetes (GD), preterm delivery (PTD), early ruptu...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100815q

    authors: Graca G,Duarte IF,Barros AS,Goodfellow BJ,Diaz SO,Pinto J,Carreira IM,Galhano E,Pita C,Gil AM

    更新日期:2010-11-05 00:00:00

  • Differential proteomic shotgun analysis elucidates involvement of water channel aquaporin 8 in presence of α-amylase in the colon.

    abstract::Aquaporin (AQP) family plays a pivotal role in fluid secretion and absorption, especially in the digestive system and secretory glands. Within this family, AQP8 was reported to be widely expressed in the epithelia of the digestive tract, liver, and pancreas. In two parallel experimental platforms with different analyt...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100789v

    authors: Magdeldin S,Li H,Yoshida Y,Satokata I,Maeda Y,Yokoyama M,Enany S,Zhang Y,Xu B,Fujinaka H,Yaoita E,Yamamoto T

    更新日期:2010-12-03 00:00:00

  • Domain graph of Arabidopsis proteome by comparative analysis.

    abstract::The domain graph of domains and domain combinations of Arabidopsis thaliana is established based on pfam 14.0 database and analyzed via comparison with 10 eukaryotic, 30 bacterial, and 16 archaeal proteomes. The comparative analysis of the domain graphs provides a useful platform for revealing global insights on the e...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049805m

    authors: Liu S,Zhang C,Zhou Y

    更新日期:2005-03-01 00:00:00