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Journal of Proteome Research

Sunhee Jung, Jeffrey R Whiteaker, Lei Zhao, Han-Wook Yoo, Amanda G Paulovich, Si Houn Hahn
Wilson's Disease (WD), a copper transport disorder caused by a genetic defect in the ATP7B gene, has been a long time strong candidate for newborn screening (NBS), since early interventions can give better results by preventing irreversible neurological disability or liver cirrhosis. Several previous pilot studies measuring ceruloplasmin (CP) in infants or children showed that this marker alone was insufficient to meet the universal screening for WD. WD results from mutations that cause absent or markedly diminished levels of ATP7B...
December 9, 2016: Journal of Proteome Research
Johanna M Smeekens, Haopeng Xiao, Ronghu Wu
Protein secretion is essential for numerous cellular activities, and secreted proteins in bodily fluids are a promising and non-invasive source of biomarkers for disease detection. Systematic analysis of secreted proteins and glycoproteins will provide insight into protein function and cellular activities. Yeast (Saccharomyces cerevisiae) is an excellent model system for eukaryotic cells, but global analysis of secreted proteins and glycoproteins in yeast is challenging due to the low abundances of secreted proteins and contamination from high-abundance intracellular proteins...
December 9, 2016: Journal of Proteome Research
Mohammad Zeeshan, Inderjeet Kaur, Joseph Joy, Ekta Saini, Gourab Paul, Abhinav Kaushik, Surbhi Dabral, Asif Mohmmed, Dinesh Gupta, Pawan Malhotra
Plasmodium falciparum undergoes a tightly regulated developmental process in human erythrocytes, and recent studies suggest an important regulatory role of post-translational modifications (PTMs). As compared to Plasmodium phosphoproteome, little is known about other PTMs in the parasite. In the present study, we performed a global analysis of asexual blood stages of Plasmodium falciparum to identify arginine-methylated proteins. Using two different methyl arginine-specific antibodies we immunoprecipitated the arginine-methylated proteins from the stage-specific parasite lysates and identified 843 putative arginine methylated proteins by LC-MS/MS...
December 9, 2016: Journal of Proteome Research
Erik Richter, Manuela Harms, Katharina Ventz, Rolf Nölker, Martin J Fraunholz, Jörg Mostertz, Falko Hochgräfe
Internalization of Staphylococcus aureus by nonprofessional phagocytic cells is a major suspected cause of persistent and difficult-to-treat infections, including pneumonia. In this study, we established an infection model with 16HBE14o- human bronchial epithelial cells and demonstrated internalization, escape from phagosomal clearance, and intracellular replication of S. aureus HG001 within the first 4 h postinfection. We used quantitative phosphoproteomics to identify characteristic signaling networks in the host at different infection stages...
November 4, 2016: Journal of Proteome Research
Di Liu, Cheng Chang, Ning Lu, Xing Wang, Qian Lu, Xiaojie Ren, Peng Ren, Dianyuan Zhao, Lijing Wang, Yunping Zhu, Fuchu He, Li Tang
Tumor-associated macrophages (TAMs) are major components of the tumor microenvironment. Although a role for TAMs in promoting tumor progression has been revealed, the differentiation mechanisms and intrinsic signals of TAMs regulated by the tumor microenvironment remain unclear. Here we constructed an in vitro TAMs cell model, TES-TAMs, which is from tumor-extract-stimulated bone-marrow-derived macrophages. We performed a comparative proteomics analysis of bone-marrow-derived macrophages and TES-TAMs, which indicated that TES-TAMs possessed characteristic molecular expression of TAMs...
November 3, 2016: Journal of Proteome Research
Erik Leonardus de Graaf, Davide Pelligrini, Liam A McDonnell
Here we assessed the ability of an automated sample preparation device equipped with disposable microcolumns to prepare mass-limited samples for high-sensitivity quantitative proteomics, using both label-free and isobaric labeling approaches. Firstly, we compared peptide label-free quantification reproducibility for 1.5-150 µg of cell lysates and found that labware preconditioning was essential for reproducible quantification of <7.5 µg digest. Secondly, in-solution and on-column TMT-labeling protocols were compared and optimized for 1 µg of sample...
November 3, 2016: Journal of Proteome Research
Ghazala Mustafa, Setsuko Komatsu
Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. For possible interactions between NPs and crops under flooding stress to be investigated, the molecular mechanisms in soybeans affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of the root including hypocotyl was increased, and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway...
November 3, 2016: Journal of Proteome Research
Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
In the postgenomic era, the number of unreviewed protein sequences is remarkably larger and grows tremendously faster than that of reviewed ones. However, existing methods for protein subchloroplast localization often ignore the information from these unlabeled proteins. This paper proposes a multi-label predictor based on ensemble linear neighborhood propagation (LNP), namely, LNP-Chlo, which leverages hybrid sequence-based feature information from both labeled and unlabeled proteins for predicting localization of both single- and multi-label chloroplast proteins...
November 3, 2016: Journal of Proteome Research
Mie R Rasmussen, Kirstine L Nielsen, Mia R Laursen, Camilla B Nielsen, Pia Svendsen, Henrik Dimke, Erik I Christensen, Mogens Johannsen, Søren K Moestrup
Loss-of-function mutations in the transmembrane ABCC6 transport protein cause pseudoxanthoma elasticum (PXE), an ectopic, metabolic mineralization disorder that affects the skin, eye, and vessels. ABCC6 is assumed to mediate efflux of one or several small molecule compounds from the liver cytosol to the circulation. Untargeted metabolomics using liquid chromatography-mass spectrometry was employed to inspect liver cytosolic extracts from mice with targeted disruption of the Abcc6 gene. Absence of the ABCC6 protein induced an altered profile of metabolites in the liver causing accumulation of compounds as more features were upregulated than downregulated in ABCC6-deficient mice...
November 3, 2016: Journal of Proteome Research
Fengchao Yu, Ning Li, Weichuan Yu
In computational proteomics, the identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process...
November 3, 2016: Journal of Proteome Research
Julia H Roberts, Fang Liu, Jaret M Karnuta, Michael C Fitzgerald
Described here is the application of thermodynamic stability measurements to study age-related differences in the protein folding and stability of proteins in a rodent model of ageing. Thermodynamic stability profiles were generated for 809 proteins in brain cell lysates from mice, aged 6- (n=7) and 18-months (n=9) using the Stability of Proteins from Rates of Oxidation (SPROX) technique. The biological variability of the protein stability measurements was low and within the experimental error of SPROX. A total of 83 protein hits was detected with age-related stability differences in the brain samples...
November 2, 2016: Journal of Proteome Research
Vikram Subramanian, Ingar Seemann, Juliane Merl-Pham, Stefanie M Hauck, Fiona Anne Stewart, Michael J Atkinson, Soile Tapio, Omid Azimzadeh
Epidemiological data from patients undergoing radiotherapy for thoracic tumours clearly show the damaging effect of ionising radiation on cardiovascular system. The long-term impairment of heart function and structure after local high-dose irradiation is associated with systemic inflammatory response, contraction impairment, microvascular damage and cardiac fibrosis. The goal of the present study was to investigate molecular mechanisms involved in this process. C57BL/6J mice received a single X-ray dose of 16 Gy given locally to the heart at the age of 8 weeks...
November 2, 2016: Journal of Proteome Research
Mingwei Sun, Jun-Yu Xu, Zhixiang Wu, Linhui Zhai, Chengxi Liu, Zhongyi Cheng, Guofeng Xu, Shengce Tao, Bang-Ce Ye, Yingming Zhao, Minjia Tan
Propionylation at protein lysine residue is characterized to be present in both eukaryotic and prokaryotic species. However, the majority of lysine propionylation substrates still remain largely unknown. Using affinity enrichment and mass spectrometric based proteomics, we identified 1467 lysine propionylation sites in 603 proteins in E. coli. Quantitative propionylome analysis further revealed that global lysine propionylation level was drastically increased in response to propionate treatment, a carbon source for many microorganisms and also a common food preservative...
November 2, 2016: Journal of Proteome Research
Karuna P Karunakaran, Hong Yu, Xiaozhou Jiang, Queenie Chan, Michael F Goldberg, Marc K Jenkins, Leonard J Foster, Robert C Brunham
Worldwide Salmonella enterica infections result in substantial morbidity and mortality and is the major cause of infant bacteremia in sub Saharan Africa. Diseases caused by Salmonella are treatable with antibiotics but successful antibiotic treatment has become difficult due to antimicrobial resistance and collateral effects on the microbiome. An effective vaccine together with public health efforts may be a better strategy to control these infections. Protective immunity against Salmonella depends primarily on CD4 T cell-mediated immune responses and therefore identifying relevant T cell antigens is necessary for Salmonella vaccine development...
November 1, 2016: Journal of Proteome Research
Malwina Michalak, Uwe Warnken, Sabine André, Martina Schnölzer, Hans-Joachim Gabius, Juergen Kopitz
Endogenous lectins have the capacity to translate glycan-encoded information on the cell surface into effects on cell growth. As test case to examine changes in protein presence associated with tumor growth inhibition, we applied SILAC-based proteomics on human colon carcinoma cells treated with galectin-4 (Gal-4). The five tested lines LS 180, Vaco 432, Colo 205, CX 1 and HCT 116 responded with differentiation and reduced proliferation to Gal-4 binding. In proteomic analysis (mass spectral data deposited with PRIDE - PXD003489), 2654 proteins were quantified: 190 down- and 115 up-regulated (>2-fold)...
November 1, 2016: Journal of Proteome Research
Owen E Branson, Michael Alan Freitas
Label-free quantitative methods are advantageous in bottom-up (shotgun) proteomics because they are robust and can easily be applied to different workflows without additional cost. Both label-based and label-free approaches are routinely applied to discovery based proteomics experiments and are widely accepted as semi-quantitative. Label-free quantitation approaches are segregated into two distinct approaches: peak abundance based approaches and spectral counting (SpC). Peak abundance approaches like MaxLFQ, which is integrated into the MaxQuant environment, require precursor peak alignment that is computationally intensive and cannot be routinely applied to low-resolution data...
October 31, 2016: Journal of Proteome Research
Karl Mumm, Kadi Ainsaar, Sergo Kasvandik, Tanel Tenson, Rita Hõrak
Zinc is an important micronutrient for bacteria but its excess is toxic. Recently, the ColRS two-component system was shown to detect and respond to zinc excess and to contribute to zinc tolerance of Pseudomonas putida. Here, we applied a label-free whole-cell proteome analysis to compare the zinc-induced responses of P. putida and colR knockout. We identified dozens of proteins that responded to zinc in a ColR-independent manner, among others, known metal efflux systems CzcCBA1, CzcCBA2, CadA2 and CzcD. Nine proteins were affected in a ColR-dependent manner and besides known ColR targets, four new candidates for ColR regulon were identified...
October 31, 2016: Journal of Proteome Research
Geison Cambri, Mirta Mittelstedt Leal de Sousa, Davi de Miranda Fonseca, Fabricio Marchini, Joana Lea Meira da Silveira, Jaime Paba
Analysis of fungal secretomes is a prospection tool for the discovery of new catalysts with biotechnological application. Since enzyme secretion is strongly modulated by environmental factors, evaluation of growth conditions is of utmost importance to achieve optimal enzyme production. Here, a non-sequenced wood-rotting fungus, L. crinitus, was used for secretome analysis by enzymatic assays and a proteomics approach. Enzyme production was assessed after culturing the fungus in five different carbon sources and three nitrogen containing compounds...
October 31, 2016: Journal of Proteome Research
Lucie Beresova, Eva Vesela, Ivo Chamrád, Jiri Voller, Masayuki Yamada, Tomas Furst, Rene Lenobel, Katarina Chroma, Jan Gursky, Katerina Krizova, Martin Mistrik, Jiri Bartek
Replication stress (RS) fuels genomic instability and cancer development and may contribute to ageing, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait...
October 30, 2016: Journal of Proteome Research
Heiner Koch, Mathias Wilhelm, Benjamin Ruprecht, Scarlet Beck, Martin Frejno, Susan Klaeger, Bernhard Kuster
Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. The tumor microenvironment can rescue cancer cells from kinase inhibitors by growth factor mediated induction of pro-survival pathways. Here, we show that EGFR inhibition by Gefitinib is counteracted by growth factors notably FGF2 and we assessed the global molecular consequences of this resistance at the proteome and phosphoproteome level in A431 cells...
October 30, 2016: Journal of Proteome Research
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