Proteome analysis of a hepatocyte-specific BIRC5 (survivin)-knockout mouse model during liver regeneration.

Abstract:

:The Baculoviral IAP repeat-containing protein 5 (BIRC5), also known as inhibitor of apoptosis protein survivin, is a member of the chromosomal passenger complex and a key player in mitosis. To investigate the function of BIRC5 in liver regeneration, we analyzed a hepatocyte-specific BIRC5-knockout mouse model using a quantitative label-free proteomics approach. Here, we present the analyses of the proteome changes in hepatocyte-specific BIRC5-knockout mice compared to wildtype mice, as well as proteome changes during liver regeneration induced by partial hepatectomy in wildtype mice and mice lacking hepatic BIRC5, respectively. The BIRC5-knockout mice showed an extensive overexpression of proteins related to cellular maintenance, organization and protein synthesis. Key regulators of cell growth, transcription and translation MTOR and STAT1/STAT2 were found to be overexpressed. During liver regeneration proteome changes representing a response to the mitotic stimulus were detected in wildtype mice. Mainly proteins corresponding to proliferation, cell cycle and cytokinesis were up-regulated. The hepatocyte-specific BIRC5-knockout mice showed impaired liver regeneration, which had severe consequences on the proteome level. However, several proteins with function in mitosis were found to be up-regulated upon the proliferative stimulus. Our results show that the E3 ubiquitin-protein ligase UHRF1 is strongly up-regulated during liver regeneration independently of BIRC5.

journal_name

J Proteome Res

authors

Bracht T,Hagemann S,Loscha M,Megger DA,Padden J,Eisenacher M,Kuhlmann K,Meyer HE,Baba HA,Sitek B

doi

10.1021/pr401188r

subject

Has Abstract

pub_date

2014-06-06 00:00:00

pages

2771-82

issue

6

eissn

1535-3893

issn

1535-3907

journal_volume

13

pub_type

杂志文章
  • Analysis of detergent-insoluble and whole cell lysate fractions of resting neutrophils using high-resolution mass spectrometry.

    abstract::Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1000253

    authors: Tomazella GG,daSilva I,Thomé CH,Greene LJ,Koehler CJ,Thiede B,Wiker HG,de Souza GA

    更新日期:2010-04-05 00:00:00

  • Proteome Changes during Transition from Human Embryonic to Vascular Progenitor Cells.

    abstract::Human embryonic stem cells (hESCs) are promising in regenerative medicine (RM) due to their differentiation plasticity and proliferation potential. However, a major challenge in RM is the generation of a vascular system to support nutrient flow to newly synthesized tissues. Here we refined an existing method to genera...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00180

    authors: Tsolis KC,Bagli E,Kanaki K,Zografou S,Carpentier S,Bei ES,Christoforidis S,Zervakis M,Murphy C,Fotsis T,Economou A

    更新日期:2016-06-03 00:00:00

  • ¹H NMR metabolic profiling of plasma reveals additional phenotypes in knockout mouse models.

    abstract::The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr501039k

    authors: Probert F,Rice P,Scudamore CL,Wells S,Williams R,Hough TA,Cox IJ

    更新日期:2015-05-01 00:00:00

  • Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats).

    abstract::Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively exp...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr060623x

    authors: Miller MG

    更新日期:2007-02-01 00:00:00

  • Aptamer microarray mediated capture and mass spectrometry identification of biomarker in serum samples.

    abstract::Sensitive detection of molecular biomarkers in clinical samples is crucially important in disease diagnostics. This paper reports the development of an aptamer microarray platform combined with sol-gel technology to identify low-abundance targets in complex serum samples. Because of the nanoporous structure of the sol...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100300t

    authors: Ahn JY,Lee SW,Kang HS,Jo M,Lee DK,Laurell T,Kim S

    更新日期:2010-11-05 00:00:00

  • Snake venomics of Bothriechis nigroviridis reveals extreme variability among palm pitviper venoms: different evolutionary solutions for the same trophic purpose.

    abstract::We report the proteomic characterization and biological activities of the venom of the black-speckled palm pitviper, Bothriechis nigroviridis, a neotropical arboreal pitviper from Costa Rica. In marked contrast to other Bothriechis species investigated, the venom of B. nigroviridis does not possess detectable Zn(2+)-d...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100545d

    authors: Fernández J,Lomonte B,Sanz L,Angulo Y,Gutiérrez JM,Calvete JJ

    更新日期:2010-08-06 00:00:00

  • Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers.

    abstract::Clostridioides difficile-associated infection (CDI) is a health-care-associated infection caused, as the name suggests, by obligate anaerobic pathogen C. difficile and thus mainly transmitted via highly resistant endospores from one person to the other. In vivo, the spores need to germinate into cells prior to establi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00413

    authors: Abhyankar WR,Zheng L,Brul S,de Koster CG,de Koning LJ

    更新日期:2019-11-01 00:00:00

  • Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation.

    abstract::Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer's disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1009096

    authors: Virok DP,Simon D,Bozsó Z,Rajkó R,Datki Z,Bálint É,Szegedi V,Janáky T,Penke B,Fülöp L

    更新日期:2011-04-01 00:00:00

  • CREB Signaling Mediates Dose-Dependent Radiation Response in the Murine Hippocampus Two Years after Total Body Exposure.

    abstract::The impact of low-dose ionizing radiation (IR) on the human brain has recently attracted attention due to the increased use of IR for diagnostic purposes. The aim of this study was to investigate low-dose radiation response in the hippocampus. Female B6C3F1 mice were exposed to total body irradiation with 0 (control),...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00552

    authors: Hladik D,Dalke C,von Toerne C,Hauck SM,Azimzadeh O,Philipp J,Ung MC,Schlattl H,Rößler U,Graw J,Atkinson MJ,Tapio S

    更新日期:2020-01-03 00:00:00

  • Altered fatty acid metabolism in long duration road transport: An NMR-based metabonomics study in sheep.

    abstract::The physical, endocrine, and metabolic responses of livestock to road transport have been evaluated by conventional hematological and biochemistry parameters for more than 20 years. However, these measures are relatively insensitive to subtle metabolic adaptations. We applied NMR-based metabonomics to assess system-wi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100862t

    authors: Li J,Wijffels G,Yu Y,Nielsen LK,Niemeyer DO,Fisher AD,Ferguson DM,Schirra HJ

    更新日期:2011-03-04 00:00:00

  • MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity.

    abstract::Arabidopsis MAP kinase 4 (MPK4) has been proposed to be a negative player in plant immunity, and it is also activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and regulates plant defense remain elusive. In this study, we investigated Arabidop...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00345

    authors: Zhang T,Schneider JD,Lin C,Geng S,Ma T,Lawrence SR,Dufresne CP,Harmon AC,Chen S

    更新日期:2019-03-01 00:00:00

  • Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update.

    abstract::The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 protei...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00400

    authors: Vandenbrouck Y,Lane L,Carapito C,Duek P,Rondel K,Bruley C,Macron C,Gonzalez de Peredo A,Couté Y,Chaoui K,Com E,Gateau A,Hesse AM,Marcellin M,Méar L,Mouton-Barbosa E,Robin T,Burlet-Schiltz O,Cianferani S,Ferro M,Fr

    更新日期:2016-11-04 00:00:00

  • Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer.

    abstract::Advances in proteomics are continually driven by the introduction of new mass spectrometric instrumentation with improved performances. The recently introduced quadrupole Orbitrap (Q Exactive) tandem mass spectrometer allows fast acquisition of high-resolution higher-energy collisional dissociation (HCD) tandem mass s...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr3000249

    authors: Kelstrup CD,Young C,Lavallee R,Nielsen ML,Olsen JV

    更新日期:2012-06-01 00:00:00

  • Proteomic analysis and identification of the structural and regulatory proteins of the Rhodobacter capsulatus gene transfer agent.

    abstract::The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To fac...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8006045

    authors: Chen F,Spano A,Goodman BE,Blasier KR,Sabat A,Jeffery E,Norris A,Shabanowitz J,Hunt DF,Lebedev N

    更新日期:2009-02-01 00:00:00

  • Experimental metabonomic model of dietary variation and stress interactions.

    abstract::Stress in the form of moderate periods of maternal separation of newborn rats has been postulated to cause permanent changes in the central nervous system and diseases in later life. It is also considered that dietary supplementation with long chain polyunsaturated fatty acids (LC-PUFAs) can potentially ameliorate the...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0504182

    authors: Wang Y,Holmes E,Tang H,Lindon JC,Sprenger N,Turini ME,Bergonzelli G,Fay LB,Kochhar S,Nicholson JK

    更新日期:2006-07-01 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

  • Interactive feature finding in liquid chromatography mass spectrometry data.

    abstract::We propose a method for finding features in liquid chromatography mass spectrometry data that is based on the isotopic pattern of peaks. Our interactive approach to feature finding is carried out across many samples simultaneously and aligns features concurrently. Our scale-independent approach prioritises potential f...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060226m

    authors: Clifford D,Buckley M,Fung KY,Cosgrove L

    更新日期:2006-11-01 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

  • Muscle metabolic modulation by chronic hypoxia.

    abstract::De Palma et al. published a research paper in which they describe the effect of chronic hypoxia on rat skeletal muscle metabolism by means of a comparative proteomic analysis (J. Proteome Res. 2007, 6(5), 1974-1984). For this, relatively young animals were used. In our communication, we note that, based on other liter...

    journal_title:Journal of proteome research

    pub_type: 评论,杂志文章

    doi:10.1021/pr070315e

    authors: Gosker HR,Schols AM

    更新日期:2007-09-01 00:00:00

  • Biomarker discovery for arsenic exposure using functional data. Analysis and feature learning of mass spectrometry proteomic data.

    abstract::Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070491n

    authors: Harezlak J,Wu MC,Wang M,Schwartzman A,Christiani DC,Lin X

    更新日期:2008-01-01 00:00:00

  • Sputum proteomics identifies elevated PIGR levels in smokers and mild-to-moderate COPD.

    abstract::Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and mortality around the world. However, the exact mechanisms leading to COPD and its progression are still poorly understood. In this study, induced sputum was analyzed by cysteine-specific two-dimensional difference gel electropho...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr2006395

    authors: Ohlmeier S,Mazur W,Linja-Aho A,Louhelainen N,Rönty M,Toljamo T,Bergmann U,Kinnula VL

    更新日期:2012-02-03 00:00:00

  • Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    abstract::Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b01035

    authors: Shah AD,Inder KL,Shah AK,Cristino AS,McKie AB,Gabra H,Davis MJ,Hill MM

    更新日期:2016-10-07 00:00:00

  • Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome.

    abstract::Recent advances in genome editing technologies have enabled the insertion of epitope tags at endogenous loci with relative efficiency. We describe an approach for investigation of protein interaction dynamics of the AMP-activated kinase complex AMPK using a catalytic subunit AMPKα2 (PRKAA2 gene) as the bait, based on ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00378

    authors: Stein BD,Herzig S,Martínez-Bartolomé S,Lavallée-Adam M,Shaw RJ,Yates JR 3rd

    更新日期:2019-10-04 00:00:00

  • Prediction of membrane protein types in a hybrid space.

    abstract::Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr700715c

    authors: Jia P,Qian Z,Feng K,Lu W,Li Y,Cai Y

    更新日期:2008-03-01 00:00:00

  • Proteome-driven elucidation of adaptive responses to combined vitamin E and C deficiency in zebrafish.

    abstract::The purpose of this study was to determine the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome using zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C. We describe a label-free proteomics workflow t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr401108d

    authors: Motorykin I,Traber MG,Tanguay RL,Maier CS

    更新日期:2014-03-07 00:00:00

  • Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches.

    abstract::Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200092z

    authors: Zarei M,Sprenger A,Metzger F,Gretzmeier C,Dengjel J

    更新日期:2011-08-05 00:00:00

  • Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation.

    abstract::The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00445

    authors: Woo J,Han D,Wang JI,Park J,Kim H,Kim Y

    更新日期:2017-09-01 00:00:00

  • Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem.

    abstract::A method for the rapid correlation of tandem mass spectra to a list of protein sequences in a database has been developed. The combination of the fast and accurate computational search algorithm, X!Tandem, and a Linux cluster parallel computing environment with PVM or MPI, significantly reduces the time required to pe...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050058i

    authors: Duncan DT,Craig R,Link AJ

    更新日期:2005-09-01 00:00:00

  • Investigating the impact of elevated levels of ozone on tropical wheat using integrated phenotypical, physiological, biochemical, and proteomics approaches.

    abstract::Ozone (O3), a potent air pollutant and a significant greenhouse gas, has been recognized as a major component of global climate change. However, current increasing trends in its background level are projecting a more severe threat to natural and cultivated plants in the near future. The present study has been designed...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1002824

    authors: Sarkar A,Rakwal R,Bhushan Agrawal S,Shibato J,Ogawa Y,Yoshida Y,Kumar Agrawal G,Agrawal M

    更新日期:2010-09-03 00:00:00

  • Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus.

    abstract::Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in huma...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00485

    authors: Pan J,Chen R,Li C,Li W,Ye Z

    更新日期:2015-10-02 00:00:00