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Molecular & Cellular Proteomics: MCP

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https://www.readbyqxmd.com/read/28814509/chemoproteomics-reveals-chemical-diversity-and-dynamics-of-4-oxo-2-nonenal-modifications-in-cells
#1
Rui Sun, Ling Fu, Ke-Ke Liu, Cai-Ping Tian, Yong Yang, Keri A Tallman, Ned A Porter, Daniel C Liebler, Jing Yang
4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adducts to cysteine...
August 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28798222/an-integrated-approach-to-explore-composition-and-dynamics-of-cholesterol-rich-membrane-microdomains-in-sexual-stages-of-malaria-parasite
#2
Federica Fratini, Carla Raggi, Gabriella Sferra, Cecilia Birago, Anna Sansone, Felicia Grasso, Chiara Curr Agrave, Anna Olivieri, Tomasino Pace, Stefania Mochi, Leonardo Picci, Carla Ferreri, Antonella Di Biase, Elisabetta Pizzi, Marta Ponzi
Membrane microdomains that include lipid rafts, are involved in key physiological and pathological processes and participate in the entry of endocellular pathogens. These assemblies, enriched in cholesterol and sphingolipids, form highly dynamic, liquid-ordered phases that can be separated from the bulk membranes thanks to their resistance to solubilization by non-ionic detergents. To characterize complexity and dynamics of detergent-resistant membranes of sexual stages of the rodent malaria parasite Plasmodium berghei, here we propose an integrated study of raft components based on proteomics, lipid analysis and bioinformatics...
August 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28794006/identification-of-the-sox2-interactome-by-bioid-reveals-ep300-as-a-mediator-of-sox2-dependent-squamous-differentiation-and-lung-squamous-cell-carcinoma-growth
#3
Bo Ram Kim, Etienne Coyaud, Estelle Laurent, Jonathan St-Germain, Emily Van de Laar, Ming Sound Tsao, Brian Raught, Nadeem Moghal
Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in SOX2 in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma...
August 9, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#4
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28733429/proteogenomic-analysis-and-discovery-of-immune-antigens-in-mycobacterium-vaccae
#5
Jianhua Zheng, Lihong Chen, Liguo Liu, Haifeng Li, Bo Liu, Dandan Zheng, Tao Liu, Jie Dong, Lilian Sun, Yafang Zhu, Jian Yang, Xiaobing Zhang, Qi Jin
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M...
July 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28729386/dormancy-in-embryos-insight-from-hydrated-encysted-embryos-of-an-aquatic-invertebrate
#6
Tamar Ziv, Vered Chalifa-Caspi, Nadav Denekamp, Inbar Plaschkes, Sylwiya Sylwia Kierszniowska, Idit Blais, Arie Admon, Esther Lubzens
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with non-dormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilis</p> <p>A total of 2,631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p=0...
July 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28729385/pyqms-enables-universal-and-accurate-quantification-of-mass-spectrometry-data
#7
Johannes Leufken, Anna Niehues, Peter Sarin, Florian Wessel, Michael Hippler, Sebastian A Leidel, Christian Fufezan
Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching which offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy...
July 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28706005/a-cell-wall-proteome-and-targeted-cell-wall-analyses-provide-novel-information-on-hemicellulose-metabolism-in-flax
#8
Malika Chabi, Estelle Goulas, Celine Leclercq, Isabelle de Waele, Christophe Rihouey, Ugo Cenci, Arnaud Day, Anne-Sophie Blervacq, Godfrey Neutelings, Ludovic Duponchel, Patrice Lerouge, Jean-François Hausman, Jenny Renaut, Simon Hawkins
Experimentally-generated (nanoLC-MS/MS) proteomic analyses of four different flax organs/tissues (inner-stem, outer-stem, leaves and roots) enriched in proteins from 3 different sub-compartments (soluble-, membrane-, and cell wall-proteins) was combined with publically available data on flax seed and whole-stem proteins to generate a flax protein database containing 2996 non-redundant total proteins. Subsequent multiple analyses (MapMan, CAZy, WallProtDB and expert curation) of this database were then used to identify a flax cell wall proteome consisting of 456 non-redundant proteins localized in the cell wall and/or associated with cell wall biosynthesis, remodeling and other cell wall related processes...
July 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28706004/feedback-microtubule-control-and-microtubule-actin-cross-talk-in-arabidopsis-revealed-by-integrative-proteomic-and-cell-biology-analysis-of-katanin-1-mutants
#9
Tomáš Takáč, Olga Šamajová, Tibor Pechan, Ivan Luptovčiak, Jozef Šamaj
Microtubule organization and dynamics are critical for key developmental processes such as cell division, elongation and morphogenesis. Microtubule severing is an essential regulator of microtubules, and is exclusively executed by KATANIN 1 in Arabidopsis. In this study we comparatively studied the proteome-wide effects in two KATANIN 1 mutants. Thus, shot-gun proteomic analysis of roots and aerial parts of single nucleotide mutant fra2 and T-DNA insertion mutant ktn1-2 was carried out. We have detected 42 proteins differentially abundant in both fra2 and ktn1-2 KATANIN 1 dysfunction altered abundances of proteins involved in development, metabolism and stress responses...
July 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28706003/phosphorylation-mediated-regulatory-networks-in-mycelia-of-pyricularia-oryzae-revealed-by-phosphoproteomic-analyses
#10
Ruijin Wang, Junbo Peng, Qing X Li, You-Liang Peng
Protein phosphorylation is known to regulate pathogenesis, mycelial growth, conidiation and stress response in Pyricularia oryzae However, phosphorylation mediated regulatory networks in the fungal pathogen remain largely to be uncovered. In this study, we identified 1621 phosphorylation sites of 799 proteins in mycelia of P. oryzae, including 899 new p-sites of 536 proteins and 47 new p-sites of 31 pathogenesis-relation proteins. From the sequences flanking the phosphorylation sites, 19 conserved phosphorylation motifs were identified...
July 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28687556/spatiotemporal-proteomic-profiling-of-human-cerebral-development
#11
Ugljesa Djuric, Deivid C Rodrigues, Ihor Batruch, James Ellis, Patrick Shannon, Phedias Diamandis
Mass spectrometry (MS) analysis of human post-mortem central nervous system (CNS) tissue and induced pluripotent stem cell (iPSC)-based directed differentiations offer complementary avenues to define protein signatures of neurodevelopment. Methodological improvements of formalin-fixed, paraffin-embedded (FFPE) protein isolation now enable widespread proteomic analysis of well-annotated archival tissue samples in the context of development and disease. Here, we utilize a shotgun label-free quantification (LFQ) MS method to profile magnetically enriched human cortical neurons and neural progenitor cells (NPCs) derived from iPSCs...
July 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28684633/metaproteomics-reveals-functional-differences-in-intestinal-microbiota-development-of-preterm-infants
#12
Romy D Zwittink, Diny van Zoeren-Grobben, Rocio Martin, Richard A van Lingen, Liesbeth J Groot Jebbink, Sjef Boeren, Ingrid B Renes, Ruurd M van Elburg, Clara Belzer, Jan Knol
Development of the gastrointestinal tract and immune system can be modulated by the gut microbiota. Establishment of the intestinal microbiota, in its turn, is affected by host- and environmental factors. As such, development of the gut microbiota is greatly impacted in preterm infants, who have an immature gut and are exposed to factors like hospitalisation, caesarean section, antibiotics, and respiratory support.</p> <p>Design: We analysed faecal microbiota composition and activity of ten preterm infants (gestational age 25-30 weeks; birthweight 630-1750 gram) during the first six postnatal weeks through metaproteomics (LC-MS/MS) and 16S-rRNA gene sequencing...
July 6, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28679685/changes-of-protein-turnover-in-aging-caenorhabditis-elegans
#13
Ineke Dhondt, Vladislav A Petyuk, Sophie Bauer, Heather M Brewer, Richard D Smith, Geert Depuydt, Bart P Braeckman
Protein turnover rates severely decline in aging organisms, including C. elegans However, limited information is available on turnover dynamics at the individual protein level during aging. We followed changes in protein turnover at one-day resolution using a multiple-pulse (15)N-labeling and accurate mass spectrometry approach. Forty percent of the proteome shows gradual slowdown in turnover with age, while only few proteins show increased turnover. Decrease in protein turnover was consistent for only a minority of functionally related protein subsets, including tubulins and vitellogenins, while randomly diverging turnover patterns with age were the norm...
July 5, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28679684/study-of-the-plasma-membrane-proteome-dynamics-reveals-novel-targets-of-nitrogen-regulation-in-yeast
#14
Jennifer Villers, Jérôme Savocco, Aleksandra Szopinska, Hervé Degand, Sylvain Nootens, Pierre Morsomme
Yeast cells, to be able to grow on a wide variety of nitrogen sources, regulate the set of nitrogen transporters present at their plasma membrane. Such regulation relies on both transcriptional and post-translational events. While microarray studies have identified most nitrogen-sensitive genes, nitrogen-induced post-translational regulation has only been studied for very few proteins among which the general amino acid permease Gap1. Adding a preferred nitrogen source to proline-grown cells triggers Gap1 endocytosis and vacuolar degradation in an Rsp5-Bul1/2-dependent manner...
July 5, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28674151/kinase-activity-ranking-using-phosphoproteomics-data-karp-quantifies-the-contribution-of-protein-kinases-to-the-regulation-of-cell-viability
#15
Edmund Wilkes, Pedro Casado, Vinothini Rajeeve, Pedro Rodriguez Cutillas
Cell survival is regulated by a signaling network driven by the activity of protein kinases; however, determining the contribution that each kinase in the network makes to such regulation remains challenging. Here, we report a computational approach that uses mass spectrometry-based phosphoproteomics data to rank protein kinases based on their contribution to cell regulation. We found that the scores returned by this algorithm, which we have termed Kinase Activity Ranking using Phosphoproteomics data (KARP), were a quantitative measure of the contribution that individual kinases make to the signaling output...
July 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28674150/temporal-regulation-of-a-salmonella-typhimurium-virulence-factor-by-the-transcriptional-regulator-ydcr
#16
Yanhua Liu, Qian Liu, Linlu Qi, Tao Ding, Zhen Wang, Jiaqi Fu, Mo Hu, Min Li, Jeongmin Song, Xiaoyun Liu
We previously examined Salmonella proteome within infected host cells and found differential expression of many proteins with defined functional roles such as metabolism or virulence. However, the precise roles of other altered proteins in Salmonella pathogenesis are largely unknown. A putative transcriptional regulator, YdcR, was highly induced intracellularly while barely expressed in vitro, implicating potential relevance to bacterial infection. To unveil its physiological functions, we exploited quantitative proteomics of intracellular Salmonella and found that genetic ablation of ydcR resulted in severe repression of SrfN, a known virulence factor...
July 3, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28663172/mettl21b-is-a-novel-human-lysine-methyltransferase-of-translation-elongation-factor-1a-discovery-by-crispr-cas9-knock-out
#17
Joshua J Hamey, Beeke Wienert, Kate G R Quinlan, Marc R Wilkins
Lysine methylation is widespread on human proteins, however the enzymes that catalyse its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knock out putative protein methyltransferases METTL21B and METTL23 in K562 cells, to determine if they methylate elongation factor eEF1A. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knock out of METTL21B, and the expected loss of lysine 79 methylation on knock out of EEF1AKMT1...
June 29, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28637836/bacterial-cellulose-shifts-transcriptome-and-proteome-of-cultured-endothelial-cells-towards-native-differentiation
#18
Gerhard Feil, Ralf Horres, Julia Schulte, Andreas F Mack, Svenja Petzoldt, Caroline Arnold, Chen Meng, Lukas Jost, Jochen Boxleitner, Nicole Kiessling-Wolf, Ender Serbest, Dominic Helm, Bernhard Kuster, Isabel Hartmann, Thomas Korff, Hannes Hahne
Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation...
June 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28576848/identification-of-fc-gamma-receptor-glycoforms-that-produce-differential-binding-kinetics-for-rituximab
#19
Jerrard M Hayes, Asa Frostell, Robert Karlsson, Steffen Müller, Silvia Millan-Martin, Martin Pauers, Franziska Reuss, Eoin Cosgrave, Cecilia Anneren, Gavin P Davey, Pauline M Rudd
Fc gamma receptors (FcyR) bind the Fc region of antibodies and therefore play a prominent role in antibody-dependent cell-based immune responses such as ADCC, CDC and ADCP. The immune effector cell activity is directly linked to a productive molecular engagement of FcyRs where both the protein and glycan moiety of antibody and receptor can affect the interaction and in the present study we focus on the role of the FcyR glycans in this interaction. We provide a complete description of the glycan composition of Chinese hamster ovary (CHO) expressed human Fcy receptors RI (CD64), RIIa Arg131/His131 (CD32a), RIIb (CD32b) and RIIIa Phe158/Val158 (CD16a) and analyze the role of the glycans in the binding mechanism with IgG...
June 2, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28550165/the-clasp2-protein-interaction-network-in-adipocytes-links-clip2-to-agap3-clasp2-to-g2l1-mark2-and-soga1-and-identifies-soga1-as-a-microtubule-associated-protein
#20
Rikke Kruse, James Krantz, Natalie Barker, Richard Coletta, Ruslan Rafikov, Moulun Luo, Kurt Hoejlund, Lawrence J Mandarino, Paul R Langlais
CLASP2 is a microtubule-associated protein that undergoes insulin-stimulated phosphorylation and co-localization with reorganized actin and GLUT4 at the plasma membrane. To gain insight to the role of CLASP2 in this system, we developed and successfully executed a streamlined interactome approach and built a CLASP2 protein network in 3T3-L1 adipocytes. Using two different commercially available antibodies for CLASP2 and an antibody for epitope-tagged, overexpressed CLASP2, we performed multiple affinity purification coupled with mass spectrometry (AP-MS) experiments in combination with label-free quantitative proteomics and analyzed the data with the bioinformatics tool Significance Analysis of Interactome (SAINT)...
May 26, 2017: Molecular & Cellular Proteomics: MCP
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