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Molecular & Cellular Proteomics: MCP

Louise Hetherington, Elena Schneider, Caroline Scott, David DeKretser, Charles H Muller, Hubert Hondermarck, Tony Velkov, Mark A Baker
Globally, approximately 1 in 15 men of reproductive age are infertile, yet the precise mechanisms underlying their gamete failure are unknown. Although a semen-analysis is performed to determine fertilizing potential, the diagnostic suitability of this analysis has been questioned in several reports, as many men, classified as "infertile" according to their semen analysis, subsequently turn out to be fertile. Herein, we have used a quantitative (phospho)-proteomic analysis, using enrichment on titanium dioxide followed by ion-trap mass spectrometry (LC-MS/MS), to compare the semen of infertile versus fertile males...
October 21, 2016: Molecular & Cellular Proteomics: MCP
Kevin A Welle, Tian Zhang, Jennifer R Hyrohorenko, Shichen Shen, Jun Qu, Sina Ghaemmaghami
Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples...
October 20, 2016: Molecular & Cellular Proteomics: MCP
Dayoung Park, Narine Arabyan, Cynthia C Williams, Ting Song, Anupam Mitra, Bart C Weimer, Emanual Maverakis, Carlito B Lebrilla
Although gut host-pathogen interactions are glycan-mediated processes, few details are known about the participating structures. Here we employ high-resolution mass spectrometric profiling to comprehensively identify and quantitatively measure the exact modifications of native intestinal epithelial cell surface N-glycans induced by S. Typhimurium infection. Sixty minutes post-infection, select sialylated structures showed decreases in terms of total number and abundances. To assess the effect of cell surface mannosylation, we selectively rerouted glycan expression on the host using the alpha-mannosidase inhibitor, kifunensine, toward overexpression of high mannose...
October 17, 2016: Molecular & Cellular Proteomics: MCP
Tino W Sanchez, Guangyu Zhang, Jitian Li, Liping Dai, Saied Mirshahidi, Nathan R Wall, Clayton Yates, Colwick Wilson, Susanne Montgomery, Jian-Ying Zhang, Carlos A Casiano
African American (AA) men suffer from a disproportionately high incidence and mortality of prostate cancer (PCa) compared to other racial/ethnic groups. Despite these disparities, African American men are underrepresented in clinical trials and in studies on PCa biology and biomarker discovery. We used immunoseroproteomics to profile anti-tumor autoantibody responses in AA and European American (EA) men with PCa, and explored differences in these responses. This minimally invasive approach detects autoantibodies to tumor-associated antigens that could serve as clinical biomarkers and immunotherapeutic agents...
October 14, 2016: Molecular & Cellular Proteomics: MCP
Sophie Braga-Lagache, Natasha Buchs, Mircea-Ioan Iacovache, Benoit Zuber, Christopher Benjamin Jackson, Manfred Heller
BACKGROUND: Cells of the vascular system release spherical vesicles, called microparticles, in the size range of 0.1-1μm induced by a variety of stress factors resulting in variable concentrations between health and disease. Furthermore, microparticles have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today's most used analytical technology for mecroparticle characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past...
October 12, 2016: Molecular & Cellular Proteomics: MCP
Wim Jonckheere, Wannes Dermauw, Vladimir Zhurov, Nicky Wybouw, Jan Van den Bulcke, Carlos A Villarroel, Robert Greenhalgh, Mike Grbić, Rob C Schuurink, Luc Tirry, Geert Baggerman, Richard M Clark, Merijn R Kant, Bartel Vanholme, Gerben Menschaert, Thomas Van Leeuwen
The two-spotted spider mite Tetranychus urticae is an extremely polyphagous crop pest. Alongside an unparalleled detoxification potential for plant secondary metabolites, it has recently been shown that spider mites can attenuate or even suppress plant defenses. Salivary constituents, notably effectors, have been proposed to play an important role in manipulating plant defenses and might determine the outcome of plant-mite interactions. Here, the proteomic composition of saliva from T. urticae lines adapted to various host plants - bean, maize, soy, and tomato - was analyzed using a custom-developed feeding assay coupled with nano-LC tandem mass spectrometry...
October 4, 2016: Molecular & Cellular Proteomics: MCP
Matthew Torres, Henry Dewhurst, Niveda Sundararaman
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function &- a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) &- a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al...
October 3, 2016: Molecular & Cellular Proteomics: MCP
Petra Van Damme, Thomas V Kalvik, Kristian K Starheim, Veronique Jonckheere, Line M Myklebust, Gerben Menschaert, Jan Erik Varhaug, Kris Gevaert, Thomas Arnesen
N-terminal acetylation (Nt-acetylation) by N-terminal acetyltransferases (NATs) is one of the most common protein modifications in eukaryotes. The NatC complex represents one of three major NATs of which the substrate profile remains largely unexplored. Here, we defined the in vivo human NatC Nt-acetylome on a proteome-wide scale by combining knockdown of its catalytic subunit Naa30 with positional proteomics. We identified 46 human NatC substrates, expanding our current knowledge on the substrate repertoire of NatC which now includes proteins harboring Met-Leu, Met-Ile, Met-Phe, Met-Trp, Met-Val, Met-Met, Met-His and Met-Lys N-termini...
September 30, 2016: Molecular & Cellular Proteomics: MCP
Kristin E Burnum-Johnson, Song Nie, Cameron P Casey, Matthew E Monroe, Daniel J Orton, Yehia M Ibrahim, Marina A Gritsenko, Therese R W Clauss, Anil K Shukla, Ronald J Moore, Samuel O Purvine, Tujin Shi, Weijun Qian, Tao Liu, Erin S Baker, Richard D Smith
Current proteomic approaches are comprised of both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g., candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, while targeted measurements are significantly more sensitive but only sample a limited portion of the proteome...
September 25, 2016: Molecular & Cellular Proteomics: MCP
Aaron R Goldman, Benjamin G Bitler, Zachary Schug, Jose R Conejo-Garcia, Rugang Zhang, David W Speicher
Inactivating mutations in ARID1A, which encodes a subunit of the SWI/SNF chromatin-remodeling complex, are found in over half of ovarian clear cell carcinoma cases and more broadly across most types of cancers. To identify ARID1A-dependent changes in intracellular signaling pathways, we performed proteome analyses of isogenic ovarian clear cell carcinoma cell lines with or without ARID1A expression. Knockout of ARID1A in an ovarian clear cell carcinoma cell line with wild-type ARID1A, OVCA429, primarily resulted in downregulation of the mevalonate pathway, an important metabolic pathway involved in isoprenoid synthesis, cholesterol synthesis, and other downstream pathways...
September 21, 2016: Molecular & Cellular Proteomics: MCP
Thuyen Truong, Guisheng Zeng, Qingsong Lin, Teck Kwang Lim, Tong Cao, Fong Yee Chan, Yue Wang, Chaminda Jayampath Seneviratne
Candida albicans is a major fungal pathogen causing lethal infections in immunocompromised patients. C. albicans forms antifungal tolerant biofilms contributing significantly to therapeutic failure. The recently established haploid C. albicans biofilm model provides a new toolbox to uncover the mechanism governing the higher antifungal tolerance of biofilms. Here, we comprehensively examined the proteomics and antifungal susceptibility of standard diploid (SC5314 and BWP17) and stable haploid (GZY792 and GZY803) strains of C...
September 19, 2016: Molecular & Cellular Proteomics: MCP
Jun-Mu Lin, Yu-Ting Tsai, Yu-Hsuan Liu, Yun Lin, Hwan-Ching Tai, Chien-Sheng Chen
Cellular proteins are constantly damaged by reactive oxygen species generated by cellular respiration. Due to its metal-chelating property, the histidine residue is easily oxidized in the presence of Cu/Fe ions and H2O2 via metal-catalyzed oxidation, usually converted to 2-oxohistidine. We hypothesized that cells may have evolved antioxidant defenses against the generation of 2-oxohistidine residues on proteins, and therefore there would be cellular proteins which specifically interact with this oxidized side chain...
September 19, 2016: Molecular & Cellular Proteomics: MCP
Giorgio Oliviero, Gerard L Brien, Ariane Watson, Gundula Streubel, Emilia Jerman, Darrell Andrews, Benjamin Doyle, Nayla Munawar, Kieran Wynne, John Crean, Adrian P Bracken, Gerard Cagney
Polycomb proteins assemble to form complexes with important roles in epigenetic regulation. The Polycomb Repressive Complex 2 (PRC2) modulates the di- and tri-methylation of lysine 27 on histone H3, each of which are associated with gene repression. Although three subunits, EZH1/2, SUZ12 and EED, form the catalytic core of PRC2, a wider group of proteins associate with low stoichiometry. This raises the question of whether dynamic variation of the PRC2 interactome results in alternative forms of the complex during differentiation...
September 15, 2016: Molecular & Cellular Proteomics: MCP
Jia Zhang, Ming-Kun Yang, Honghui Zeng, Feng Ge
While the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of posttranslational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases...
September 14, 2016: Molecular & Cellular Proteomics: MCP
Ryan C Smith, Jonas G King, Dingyin Tao, Oana A Zeleznik, Clara Brando, Gerhard G Thallinger, Rhoel R Dinglasan
The innate immune response is highly conserved across all eukaryotes and has been studied in great detail in several model organisms. Hemocytes, the primary immune cell population in mosquitoes, are important components of the mosquito innate immune response, yet critical aspects of their biology have remained uncharacterized. Using a novel method of enrichment, we isolated phagocytic granulocytes and quantified their proteomes by mass spectrometry. The data demonstrate that phagocytosis, blood-feeding, and Plasmodium falciparum infection promote dramatic shifts in the proteomic profiles of An...
September 13, 2016: Molecular & Cellular Proteomics: MCP
Thea King, Chawalit Kocharunchitt, Kari Gobius, John P Bowman, Tom Ross
Enterohaemorrhagic Escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. Currently, no completely effective method for controlling this pathogen during carcass processing exists. Understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. Therefore, we studied the growth kinetics and physiological response of exponential phase E...
September 11, 2016: Molecular & Cellular Proteomics: MCP
Jorge Bellati, Chloé Champeyroux, Sonia Hem, Valérie Rofidal, Gabriel Krouk, Christophe Maurel, Véronique Santoni
PIP1;2 and PIP2;1 are aquaporins which are highly expressed in roots and bring a major contribution to root water transport and its regulation by hormonal and abiotic factors. Interactions between cellular proteins or with other macromolecules contribute to forming molecular machines. Proteins that molecularly interact with PIP1;2 and PIP2;1 were searched to get new insights into regulatory mechanisms of root water transport. For that, a immunopurification strategy coupled to protein identification and quantification by mass spectrometry (IP-MS) of PIPs was combined with data from the literature, to build thorough PIP1;2 and PIP2;1 interactomes, sharing about 400 interacting proteins...
September 8, 2016: Molecular & Cellular Proteomics: MCP
Charles A S Banks, Gina Boanca, Zachary T Lee, Cassandra G Eubanks, Gaye L Hattem, Allison Peak, Lauren E Weems, Juliana J Conkright, Laurence Florens, Michael P Washburn
The NF-κB family of transcription factors is pivotal in controlling cellular responses to environmental stresses; abnormal NF-κB signaling features in many autoimmune diseases and cancers. Several components of the NF-κB signaling pathway have been reported to interact with the protein TNIP2 (also known as ABIN2), and TNIP2 can both positively and negatively regulate NF-κB- dependent transcription of target genes. However, the function of TNIP2 remains elusive and the cellular machinery associating with TNIP2 has not been systematically defined...
September 8, 2016: Molecular & Cellular Proteomics: MCP
Seungjin Na, Samuel H Payne, Nuno Bandeira
Peptide and protein identification remains challenging in organisms with poorly annotated or rapidly evolving genomes, as are commonly encountered in environmental or biofuels research. Such limitations render tandem mass spectrometry (MS/MS) database search algorithms ineffective as they lack corresponding sequences required for peptide-spectrum matching. We address this challenge with the spectral networks approach to a) match spectra of orthologous peptides across multiple related species and then b) propagate peptide annotations from identified to unidentified spectra...
September 8, 2016: Molecular & Cellular Proteomics: MCP
Martijn J C van Herwijnen, Marijke I Zonneveld, Soenita Goerdayal, Esther N M Nolte-'t Hoen, Johan Garssen, Bernd Stahl, A F Maarten Altelaar, Frank A Redegeld, Marca H M Wauben
Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, while whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids and proteins...
September 6, 2016: Molecular & Cellular Proteomics: MCP
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