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https://www.readbyqxmd.com/read/28345137/a-comparative-analysis-of-phosphoproteome-in-ovine-muscle-at-early-postmortem-in-relationship-to-tenderness-%C3%A2
#1
Xin Li, Lijuan Chen, Fan He, Meng Li, Qingwu Shen, Dequan Zhang
BACKGROUND: Tenderness is considered to be the most important quality characteristic of meat as it is the main cause of unacceptability of meat. Post-translational modification regulates protein functions that involve in postmortem changes in muscle and meat quality formation. Specifically, phosphorylation was proved to regulate postmortem glycolytic rates and meat tenderization. However, the relationship between protein phosphorylation and meat tenderness remains unclear. This study examined the phosphoproteomes found in ovine muscle with different degrees of tenderness over time (at 0...
March 26, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#2
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331895/data-on-interleukin-il-2-and-il-15-dependent-changes-in-il-2r%C3%AE-and-il-2r%C3%AE-complexes
#3
Nerea Osinalde, Virginia Sánchez-Quiles, Blagoy Blagoev, Irina Kratchmarova
We provide detailed datasets from our analysis of the proteins that associate with IL-2Rβ and IL-2Rγ in T-cells stimulated with IL-2 or IL-15 compared with resting T-cells, as identified by SILAC-based quantitative proteomics. We also include quantitative data regarding site-specific phosphorylation events observed both in IL-2Rβ and IL-2Rγ. Moreover, we provide results demonstrating the specific protein recruitment capacity of four of those site-specific phosphorylations. The proteomics and phosphoproteomics data described in this article is associated with a research article entitled "Characterization of receptor-associated protein complex assembly in Interleukin (IL)-2- and IL-15-activated T-lymphocytes" (Osinalde et al...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28331001/quantitative-tyrosine-phosphoproteomics-of-egfr-tyrosine-kinase-inhibitor-treated-lung-adenocarcinoma-cells-reveals-potential-novel-biomarkers-of-therapeutic-response
#4
Xu Zhang, Tapan Maity, Manoj K Kashyap, Mukesh Bansal, Abhilash Venugopalan, Sahib Singh, Shivangi Awasthi, Arivusudar Marimuthu, Harrys Kishore Charles Jacob, Natalya Belkina, Stephanie Pitts, Constance M Cultraro, Shaojian Gao, Fatos Kirkali, Romi Biswas, Raghothama Chaerkady, Andrea Califano, Akhilesh Pandey, Udayan Guha
Mutations in the Epidermal growth factor receptor (EGFR) kinase domain, such as the L858R missense mutation and deletions spanning the conserved sequence 747LREA750, are sensitive to tyrosine kinase inhibitors (TKIs). The gatekeeper site residue mutation, T790M accounts for around 60% of acquired resistance to EGFR TKIs. The first generation EGFR TKIs, erlotinib and gefitinib, and the second generation inhibitor, afatinib are FDA approved for initial treatment of EGFR mutated lung adenocarcinoma. The predominant biomarker of EGFR TKI responsiveness is the presence of EGFR TKI-sensitizing mutations...
March 22, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28327990/estimating-the-total-number-of-phosphoproteins-and-phosphorylation-sites-in-eukaryotic-proteomes
#5
Panayotis Vlastaridis, Pelagia Kyriakidou, Anargyros Chaliotis, Yves Van de Peer, Stephen G Oliver, Grigoris D Amoutzias
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and phosphorylation sites (p-sites), for four eukaryotes (human, mouse, Arabidopsis, and yeast)...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28326294/the-eukaryote-like-serine-threonine-kinase-stk-regulates-the-growth-and-metabolism-of-zoonotic-streptococcus-suis
#6
Chunyan Zhang, Wen Sun, Meifang Tan, Mengmeng Dong, Wanquan Liu, Ting Gao, Lu Li, Zhuofei Xu, Rui Zhou
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28325837/threonine-eliminylation-by-bacterial-phosphothreonine-lyases-rapidly-causes-crosslinking-of-mapk-in-live-cells
#7
Benoit M Meijer, Suk Min Jang, Ida C Guerrera, Cerina Chhuon, Joanna Lipecka, Caroline Reisacher, Françoise Baleux, Philippe Sansonetti, Christian Muchardt, Laurence Arbibe
Old long-lived proteins contain dehydroalanine (Dha) and dehydrobutyrine (Dhb), two amino acids engendered by dehydration of serines and threonines respectively. While these residues have a suspected role in protein crosslink and aggregation, their direct implication has yet to be determined. Here, we have taken advantage of the ability of the enteropathogen Shigella to convert the phosphothreonine residue of the pT-X-pY consensus sequence of ERK and p38 into Dhb, and followed the impact of dehydration on the fate of the two MAPKs...
March 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28302921/deciphering-the-acute-cellular-phosphoproteome-response-to-irradiation-with-x-rays-protons-and-carbon-ions
#8
Martin Winter, Ivana Dokic, Julian Schlegel, Uwe Warnken, Jürgen Debus, Amir Abdollahi, Martina Schnölzer
Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions...
March 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28298517/phosphoproteomics-of-fgf1-signaling-in-chondrocytes-identifying-the-signature-of-inhibitory-response
#9
Jessica R Chapman, Olga Katsara, Rachel Ruoff, David Morgenstern, Shruti Nayak, Claudio Basilico, Beatrix Ueberheide, Victoria Kolupaeva
Fibroblast growth factor (FGF) signaling is vital for many biological processes, beginning with development. The importance of FGF signaling for skeleton formation was first discovered by the analysis of genetic FGFR mutations which cause several bone morphogenetic disorders, including achondroplasia, the most common form of human dwarfism. The formation of the long bones is mediated through proliferation and differentiation of highly specialized cells - chondrocytes. Chondrocytes respond to FGF with growth inhibition, a unique response which differs from the proliferative response of the majority of cell types; however its molecular determinants are still unclear...
March 15, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28296561/tyr-less-kinase-signalling-during-mitosis
#10
Sabine Elowe
Tyrosine phosphorylation is rare, representing only about 0.5% of phosphorylations in the cell under basal conditions. While mitogenic tyrosine kinase signalling has been extensively explored, the role of phosphotyrosine signaling across the cell cycle and in particular during mitosis is poorly understood. Two recent, independent studies tackled this question from different angles to reveal exciting new insights into the role of this modification during cell division. Caron et al. (1) exploited mitotic phosphoproteomics datasets to determine the extent of mitotic tyrosine phosphorylation, and St-Denis et al...
March 15, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28295753/identification-of-stn7-stn8-kinase-targets-reveals-connections-between-electron-transport-metabolism-and-gene-expression
#11
Anna Schönberg, Anja Rödiger, Wiebke Mehwald, Johann Galonska, Gideon Christ, Stefan Helm, Domenika Thieme, Petra Majovsky, Wolfgang Hoehenwarter, Sacha Baginsky
The thylakoid-associated kinases STN7 and STN8 are involved in short- and long-term acclimation of photosynthetic electron transport to changing light conditions. Here we report the identification of STN7/STN8 in vivo targets that connect photosynthetic electron transport with metabolism and gene expression. Comparative phosphoproteomics with the stn7 and stn8 single and double mutants identified two proteases, one RNA-binding protein, a ribosomal protein, the large subunit of rubisco and a ferredoxin-NADP reductase as targets for the thylakoid-associated kinases...
March 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28290473/phosphoproteomics-reveals-hmga1-a-ck2-substrate-as-a-drug-resistant-target-in-non-small-cell-lung-cancer
#12
Yi-Ting Wang, Szu-Hua Pan, Chia-Feng Tsai, Ting-Chun Kuo, Yuan-Ling Hsu, Hsin-Yung Yen, Wai-Kok Choong, Hsin-Yi Wu, Yen-Chen Liao, Tse-Ming Hong, Ting-Yi Sung, Pan-Chyr Yang, Yu-Ju Chen
Although EGFR tyrosine kinase inhibitors (TKIs) have demonstrated good efficacy in non-small-cell lung cancer (NSCLC) patients harboring EGFR mutations, most patients develop intrinsic and acquired resistance. We quantitatively profiled the phosphoproteome and proteome of drug-sensitive and drug-resistant NSCLC cells under gefitinib treatment. The construction of a dose-dependent responsive kinase-substrate network of 1548 phosphoproteins and 3834 proteins revealed CK2-centric modules as the dominant core network for the potential gefitinib resistance-associated proteins...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28288883/insights-regarding-fungal-phosphoproteomic-analysis
#13
REVIEW
Liliane F C Ribeiro, Cynthia L Chelius, Steven D Harris, Mark R Marten
Protein phosphorylation is a major means of regulation for cellular processes, and is important in cell signaling, growth, and cell proliferation. To study phosphorylated proteins, high throughput phosphoproteomic technologies, such as reverse phase protein array, phospho-specific flow cytometry, and mass spectrometry (MS) based technologies, have been developed. Among them, mass spectrometry has become the primary tool employed for the identification of phosphoproteins and phosphosites in fungi, leading to an improved understanding of a number of signaling pathways...
March 10, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28287266/identifications-of-putative-pka-substrates-with-quantitative-phosphoproteomics-and-primary-sequence-based-scoring
#14
Haruna Imamura, Omar Wagih, Tomoya Niinae, Naoyuki Sugiyama, Pedro Beltrao, Yasushi Ishihama
Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation and apoptosis. To better understand the functions of PKA, it is necessary to elucidate the direct interplay between PKA and their substrates in living human cells. In order to identify kinase target substrates in a high-throughput manner, we firstly quantified the change of phosphoproteome in the cells of which PKA activity was perturbed by drug stimulations...
March 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28285833/integrative-proteomics-and-phosphoproteomics-profiling-reveals-dynamic-signaling-networks-and-bioenergetics-pathways-underlying-t-cell-activation
#15
Haiyan Tan, Kai Yang, Yuxin Li, Timothy I Shaw, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng, Hongbo Chi
The molecular circuits by which antigens activate quiescent T cells remain poorly understood. We combined temporal profiling of the whole proteome and phosphoproteome via multiplexed isobaric labeling proteomics technology, computational pipelines for integrating multi-omics datasets, and functional perturbation to systemically reconstruct regulatory networks underlying T cell activation. T cell receptors activated the T cell proteome and phosphoproteome with discrete kinetics, marked by early dynamics of phosphorylation and delayed ribosome biogenesis and mitochondrial activation...
March 21, 2017: Immunity
https://www.readbyqxmd.com/read/28283928/estimating-the-efficiency-of-phosphopeptide-identification-by-tandem-mass-spectrometry
#16
Chuan-Chih Hsu, Liang Xue, Justine V Arrington, Pengcheng Wang, Juan Sebastian Paez Paez, Yuan Zhou, Jian-Kang Zhu, W Andy Tao
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events...
March 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28270605/phosphoproteins-in-extracellular-vesicles-as-candidate-markers-for-breast-cancer
#17
I-Hsuan Chen, Liang Xue, Chuan-Chih Hsu, Juan Sebastian Paez Paez, Li Pan, Hillary Andaluz, Michael K Wendt, Anton B Iliuk, Jian-Kang Zhu, W Andy Tao
The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28270554/identifying-protein-kinase-specific-effectors-of-the-osmostress-response-in-yeast
#18
Natalie Romanov, David Maria Hollenstein, Marion Janschitz, Gustav Ammerer, Dorothea Anrather, Wolfgang Reiter
The budding yeast Saccharomyces cerevisiae reacts to increased external osmolarity by modifying many cellular processes. Adaptive signaling relies primarily on the high-osmolarity glycerol (HOG) pathway, which is closely related to the mammalian p38 mitogen-activated protein kinase (MAPK) pathway in core architecture. To identify target proteins of the MAPK Hog1, we designed a mass spectrometry-based high-throughput experiment to measure the impact of Hog1 activation or inhibition on the Scerevisiae phosphoproteome...
March 7, 2017: Science Signaling
https://www.readbyqxmd.com/read/28265048/machine-learning-of-global-phosphoproteomic-profiles-enables-discrimination-of-direct-versus-indirect-kinase-substrates
#19
Evgeny Kanshin, Sebastien Giguere, Jing Cheng, Michael D Tyers, Pierre Thibault
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is not possible to deconvolute substrate phosphorylation that is directly mediated by a particular kinase versus phosphorylation that is mediated by downstream kinases. Here, we describe a framework for assignment of direct in-vivo kinase substrates using a combination of selective chemical inhibition, quantitative phosphoproteomics, and machine learning techniques...
March 6, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28261963/phosphoproteome-analysis-of-synoviocytes-from-patients-with-rheumatoid-arthritis
#20
Masayoshi Katano, Manae S Kurokawa, Kosuke Matsuo, Kayo Masuko, Naoya Suematsu, Kazuki Okamoto, Toshikazu Kamada, Hiroshi Nakamura, Tomohiro Kato
AIM: To explore disease-associated molecules in rheumatoid arthritis (RA), we comprehensively analyzed phosphoproteins purified from RA synoviocytes. METHOD: Synoviocytes were obtained from three patients with RA and three patients with osteoarthritis (OA). Profiles of phosphoproteins purified from the synoviocytes were compared by two-dimensional differential gel electrophoresis (2D-DIGE) between the RA and OA groups. Protein spots with significantly different phosphorylation levels were identified by mass spectrometry...
March 5, 2017: International Journal of Rheumatic Diseases
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