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Molecular & Cellular Proteomics: MCP

Kehilwe C Nakedi, Bridget Calder, Mousumi Barnejee, Alexander Giddey, Andrew Jm Nel, Shaun Garnett, Jonathan M Blackburn, Nelson A Da Cruz Soares
Mycobacterial Ser/Thr kinases play a critical role in bacterial physiology and pathogenesis. Linking kinases to the substrates they phosphorylate in vivo, thereby elucidating their exact functions, is still a challenge. The aim of this work was to associate protein phosphorylation in mycobacteria with important subsequent macro cellular events by identifying the physiological substrates of PknG in Mycobacterium bovis BCG.  The study compared the phosphoproteome dynamics during the batch growth of M. bovis BGC versus the respective PknG knock-out mutant (ΔPknG-BCG) strains...
March 16, 2018: Molecular & Cellular Proteomics: MCP
Mohamed Ali Maroui, Ghizlane Maarifi, Francis P McManus, Frederic Lamoliatte, Pierre Thibault, Mounira K Chelbi-Alix
We report that interferon (IFN) a treatment at short and long periods increases the global cellular SUMOylation and requires the presence of the SUMO E3 ligase promyelocytic leukemia protein (PML), the organizer of PML nuclear bodies (NBs). Several PML isoforms (PMLI-PMLVII) derived from a single PML gene by alternative splicing, share the same N-terminal region but differ in their C-terminal sequences. Introducing each of the human PML isoform in PML-negative cells revealed that enhanced SUMOylation in response to IFN is orchestrated by PMLIII and PMLIV...
March 13, 2018: Molecular & Cellular Proteomics: MCP
Jinho Lee, Gary K Geiss, Gokhan Demirkan, Christopher P Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y Bogatzki, Warren E Carter, Rhonda K Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M Beechem, Gordon Mills
Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy.  Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application.  Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples...
March 12, 2018: Molecular & Cellular Proteomics: MCP
Marie Duhamel, Mélanie Rose, Franck Rodet, Adriana-Nathalia Murgoci, Lea Zografidou, Anne Régnier-Vigouroux, Fabien Vanden Abeele, Firas Kobeissy, Serge Nataf, Laurent Pays, Maxence Wisztorski, Dasa Cizkova, Isabelle Fournier, Michel Salzet
High grade gliomas are the most common brain tumors in adult. These tumors are characterized by a high infiltration in microglial cells and macrophages. The immunosuppressive tumor environment is known to orient immune cells towards a pro-tumoral and anti-inflammatory phenotype. Therefore, the current challenge for cancer therapy is to find a way to reorient macrophages toward an anti-tumoral phenotype. Previously, we demonstrated that macrophages secreted anti-tumoral factors when they were invalidated for the proprotein converstase 1/3 (PC1/3) and treated with LPS...
March 12, 2018: Molecular & Cellular Proteomics: MCP
Jun-Yu Xu, Zhen Xu, Xin-Xin Liu, Minjia Tan, Bang-Ce Ye
Clostridium acetobutylicum is a strict anaerobic, endospore-forming bacterium, which is used for the production of the high energy biofuel butanol in metabolic engineering. The life cycle of C. acetobutylicum can be divided into two phases, with acetic and butyric acids being produced in the exponential phase (acidogenesis) and butanol formed in the stationary phase (solventogenesis). During the transitional phase from acidogenesis to solventogenesis and latter stationary phase, concentration peaks of the<br />metabolic intermediates butyryl phosphate and acetyl phosphate are observed...
March 9, 2018: Molecular & Cellular Proteomics: MCP
Marc Planas, Martí Bernardo-Faura, Judith Katharina Paulus, Farnusch Kaschani, Markus Kaiser, Marc Valls, Renier van der Hoorn, Nuria Sanchez Coll
Activity-based protein profiling (ABPP) is a powerful proteomic technique to display protein activities in a proteome. It is based on the use of small molecular probes that react with the active site of proteins in an activity-dependent manner. We used ABPP to dissect the protein activity changes that occur in the intercellular spaces of tolerant (Hawaii 7996) and susceptible (Marmande) tomato plants in response to R. solanacearum, the causing agent of bacterial wilt, one of the most destructive bacterial diseases in plants...
March 9, 2018: Molecular & Cellular Proteomics: MCP
Dior Kelley
Ubiquitin-mediated control of protein stability is central to most aspects of plant hormone signaling. Attachment of ubiquitin to target proteins occurs via an enzymatic cascade with the final step being catalyzed by a family of enzymes known as E3 ubiquitin ligases, which have been classified based on their protein domains and structures. While E3 ubiquitin ligases are conserved among eukaryotes, in plants they are well-known to fulfill unique roles as central regulators of phytohormone signaling, including hormone perception and regulation of hormone biosynthesis...
March 7, 2018: Molecular & Cellular Proteomics: MCP
Christofer A Q Karlsson, Sofia Järnum, Lena Winstedt, Christian Kjellman, Lars Bjorck, Adam Linder, Johan Malmström
Infectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a combined mass spectrometry based proteomics strategy to investigate how the human proteome is transiently modified by the pathogen Streptococcus pyogenes , with a particular focus on bacterial cleavage of IgG in vivo In invasive diseases, S. pyogenes evokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG...
March 6, 2018: Molecular & Cellular Proteomics: MCP
Hella Schmidt, Sebastian Vlaic, Thomas Krüger, Franziska Schmidt, Johannes Balkenhohl, Thomas Dandekar, Reinhard Guthke, Olaf Kniemeyer, Thorsten Heinekamp, Axel A Brakhage
Invasive infections by the human pathogenic fungus Aspergillus fumigatus start with the outgrowth of asexual, airborne spores (conidia) into the lung tissue of immunocompromised patients. The resident alveolar macrophages phagocytose conidia, which end up in phagolysosomes. However, A. fumigatus conidia resist phagocytic degradation to a certain degree. This is mainly attributable to the pigment 1,8-dihydroxynaphthalene (DHN) melanin located in the cell wall of conidia, which manipulates the phagolysosomal maturation and prevents their intracellular killing...
March 5, 2018: Molecular & Cellular Proteomics: MCP
Erxu Pi, Chengmin Zhu, Wei Fan, Yingying Huang, Liqun Qu, Yangyang Li, Qinyi Zhao, Feng Ding, Lijuan Qiu, Huizhong Wang, B W Poovaiah, Liqun Du
Salinity causes osmotic stress to crops and limits their productivity. To understand the mechanism underlying soybean salt tolerance, proteomics approach was used to identify phosphoproteins altered by NaCl treatment. Results revealed that 412 of the 4698 quantitatively analyzed phosphopeptides were significantly up-regulated upon salt treatment, including a phosphopeptide covering the serine 59 in the transcription factor GmMYB173. Our data showed that GmMYB173 is one of the three MYB proteins differentially phosphorylated upon salt treatment, and a substrate of the casein kinase-II...
March 1, 2018: Molecular & Cellular Proteomics: MCP
Raghuveera Kumar Goel, Marta Paczkowska, Juri Reimand, Scott Napper, Kiven Erique Lukong
SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites), also known as PTK 70 (Protein tyrosine kinase 70), is a non-receptor tyrosine kinase that belongs to the BRK family of kinases (BFKs). To date less is known about the cellular role of SRMS primarily due to the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS...
March 1, 2018: Molecular & Cellular Proteomics: MCP
Susanne Sievers, Silvia Dittmann, Tim Jordt, Andreas Otto, Falko Hochgräfe, Katharina Riedel
The strictly anaerobic bacterium C. difficile has become one of the most problematic hospital acquired pathogens and a major burden for health care systems. Although antibiotics work effectively in most C. difficile infections (CDIs), their detrimental effect on the intestinal microbiome paves the way for recurrent episodes of CDI. To develop alternative, non-antibiotics-based treatment strategies, deeper knowledge on the physiology of C. difficile , stress adaptation mechanisms and regulation of virulence factors is mandatory...
March 1, 2018: Molecular & Cellular Proteomics: MCP
Vagisha Sharma, Josh Eckels, Birgit Schilling, Christina Ludwig, Jacob D Jaffe, Michael J MacCoss, Brendan MacLean
To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers and readers immediate visual access to the data behind published conclusions, we present Panorama Public (, a repository of Skyline documents supporting published results.  Panorama Public is built on Panorama, an open source data management system for mass spectrometry data processed with the Skyline targeted mass spectrometry environment...
February 27, 2018: Molecular & Cellular Proteomics: MCP
Emna Ouni, Didier Vertommen, Maria Costanza Chiti, Marie-Madeleine Dolmans, Christiani Andrade Amorim
Fertility preservation research in women today is increasingly taking advantage of bioengineering techniques to develop new biomimetic materials and solutions to safeguard ovarian cell function and microenvironment in vitro and in vivo. However, available data on the human ovary are limited and fundamental differences between animal models and humans are hampering researchers in their quest for more extensive knowledge of human ovarian physiology and key reproductive proteins that need to be preserved. We therefore turned to multi-dimensional label-free mass spectrometry to analyze human ovarian cortex, as it is a high-throughput and conclusive technique providing information on the proteomic composition of complex tissues like the ovary...
February 23, 2018: Molecular & Cellular Proteomics: MCP
Liangliang Ren, Chaoying Li, Youliang Wang, Yan Teng, Huichuan Sun, Baocai Xing, Xiao Yang, Ying Jiang, Fuchu He
Aberrant kinases contribute to cancer survival and proliferation. Here, we quantitatively characterized phosphoproteomic changes in an HBx-transgenic mouse model of hepatocellular carcinoma (HCC) using high-resolution mass spectrometry, profiled 22,539 phosphorylation sites on 5,431 proteins. Utilizing a strategy to interpret kinase-substrate relations in HCC and to uncover predominant kinases in tumors, our results, revealed elevated kinase activities of Src family kinases (SFKs), PKCs, MAPKs, and ROCK2 in HCC, representatives of which were further validated in cell models and clinical HBV-positive HCC samples...
February 22, 2018: Molecular & Cellular Proteomics: MCP
Twishi Gulati, Cheng Huang, Franco Caramia, Dinesh Raghu, Piotr Jan Paul, Robert J A Goode, Simon Paul Keam, Scott G Williams, Sue Haupt, Oded Kleifeld, Ralf B Schittenhelm, Cristina Gamell, Ygal Haupt
Prostate cancer is a common cause of cancer-related death in men. E6AP (E6-Associated Protein), an E3 ubiquitin ligase and a transcription cofactor, is elevated in a subset of prostate cancer patients. Genetic manipulations of E6AP in prostate cancer cells expose a role of E6AP in promoting growth and survival of prostate cancer cells in vitro and in vivo. However, the effect of E6AP on prostate cancer cells is broad and it cannot be explained fully by previously identified tumour suppressor targets of E6AP, promyelocytic leukemia protein and p27...
February 20, 2018: Molecular & Cellular Proteomics: MCP
Clement M Potel, Miao-Hsia Lin, Albert J R Heck, Simone Lemeer
Here we demonstrate that biomolecular contaminants, such as nucleic acid molecules, can seriously interfere with IMAC based phosphopeptide enrichments. We address and largely solve this issue, developing a robust protocol implementing methanol/chloroform protein precipitation and enzymatic digestion using benzonase, which degrades all forms of DNA and RNA, prior to IMAC-column loading. This simple procedure resulted in a drastic increase of enrichment sensitivity, enabling the identification of around 17,000 unique phosphopeptides and 12,500 unambiguously localized phosphosites in human cell-lines from a single LC-MS/MS run, constituting a 50% increase when compared to the standard protocol...
February 15, 2018: Molecular & Cellular Proteomics: MCP
Mylène Da Silva, Clara Dombre, Aurélien Brionne, Philippe Monget, Magali Chessé, Marion De Pauw, Maryse Mills, Lucie Combes-Soia, Valérie Labas, Nicolas Guyot, Yves Nys, Sophie Rehault-Godbert
In many amniotes, the amniotic fluid is depicted as a dynamic milieu that participates in the protection of the embryo (cushioning, hydration, and immunity). However, in birds, the protein profile of the amniotic fluid remains unexplored, even though its proteomic signature is predicted to differ compared to human's. In fact, unlike humans, chicken amniotic fluid does not collect excretory products and its protein composition strikingly changes at mid-development due to the massive inflow of egg white proteins, which are thereafter swallowed by the embryo to support its growth...
February 14, 2018: Molecular & Cellular Proteomics: MCP
Yesica R Nievas, Ajay A Vashisht, Maria M Corvi, Sebastian Metz, Patricia J Johnson, James A Wohlschlegel, Natalia de Miguel
The flagellated protozoan parasite Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common non-viral sexually transmitted infection worldwide. As an obligate extracellular pathogen, adherence to epithelial cells is critical for parasite survival within the human host and a better understanding of this process is a prerequisite for the development of therapies to combat infection. In this sense, recent work has shown S-acylation as a key modification that regulates pathogenesis in different protozoan parasites...
February 14, 2018: Molecular & Cellular Proteomics: MCP
Shichang Liu, Fengchao Yu, Zhu Yang, Tingliang Wang, Hairong Xiong, Caren Chang, Weichuan Yu, Ning Li
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we describe a dimethyl-labelling-based extracted ion chromatogram (XIC) quantitation protocol, which was applied to study dynamic acetylproteomic changes in Arabidopsis. The workflow integrates dimethyl labelling with chromatography-based acetylpeptide enrichment followed by mass spectrometry (MS) analysis. A software program named <span style="text-decoration: underline;">S</span>table isotope-based <span style="text-decoration: underline;">Qua</span>ntitation-Dimethyl labelling (SQUA-D) was developed to measure dynamic changes in acetylpeptide levels...
February 13, 2018: Molecular & Cellular Proteomics: MCP
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