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phosphoproteome

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https://www.readbyqxmd.com/read/28545444/site-specific-his-asp-phosphoproteomic-analysis-of-prokaryotes-reveals-putative-targets-for-drug-resistance
#1
Shu-Jung Lai, I-Fan Tu, Wan-Ling Wu, Jhih-Tian Yang, Louis Y P Luk, Mei-Chin Lai, Yu-Hsuan Tsai, Shih-Hsiung Wu
BACKGROUND: Phosphorylation of amino acid residues on proteins is an important and common post-translational modification in both eukaryotes and prokaryotes. Most research work has been focused on phosphorylation of serine, threonine or tyrosine residues, whereas phosphorylation of other amino acids are significantly less clear due to the controversy on their stability under standard bioanalytical conditions. RESULTS: Here we applied a shotgun strategy to analyze the histidine and aspartate phosphorylations in different microbes...
May 25, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28542873/a-map-of-the-phosphoproteomic-alterations-that-occur-after-a-bout-of-maximal-intensity-contractions
#2
Gregory K Potts, Rachel M McNally, Rocky Blanco, Jae-Sung You, Alexander S Hebert, Michael S Westphall, Joshua J Coon, Troy A Hornberger
The maintenance of skeletal muscle mass is essential for health and quality of life. It is well recognized that maximal-intensity contractions, such as those which occur during resistance exercise, promote an increase in muscle mass. Yet, the molecules that sense the mechanical information and convert it into the signalling events (e.g. phosphorylation) that drive the increase in muscle mass remain undefined. Here we describe a phosphoproteomics workflow to examine the effects of electrically evoked maximal-intensity contractions (MIC) on protein phosphorylation in mouse skeletal muscle...
May 25, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28542436/stress-induced-release-of-oct-1-from-the-nuclear-envelope-is-mediated-by-jnk-phosphorylation-of-lamin-b1
#3
Ivan I Boubriak, Ashraf N Malhas, Marek M Drozdz, Lior Pytowski, David J Vaux
The nuclear lamina can bind and sequester transcription factors (TFs), a function lost if the lamina is abnormal, with missing or mutant lamin proteins. We now show that TF sequestration is not all-or-nothing, but a dynamic physiological response to external signals. We show that the binding of the ubiquitous TF, Oct-1, to lamin B1 was reversed under conditions of cellular stress caused, inter alia, by the chemical methylating agent methylmethanesulfonate (MMS). A search for lamin B1 post-translational modifications that might mediate changes in Oct-1 binding using kinase inhibitors uncovered a role for c-Jun N-terminal kinase (JNK)...
2017: PloS One
https://www.readbyqxmd.com/read/28539364/integrative-proteomics-and-biochemical-analyses-define-ptc6p-as-the-saccharomyces-cerevisiae-pyruvate-dehydrogenase-phosphatase
#4
Xiao Guo, Natalie M Niemi, Joshua J Coon, Dave J Pagliarini
The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation, and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue approximately 50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28539327/quantitative-phospho-proteomic-analysis-of-tnf%C3%AE-nf%C3%AE%C2%BAb-signaling-reveals-a-role-for-ripk1-phosphorylation-in-suppressing-necrotic-cell-death
#5
Firaz Mohideen, Joao Paolo, Alban Ordureau, Steve P Gygi, J Wade Harper
TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level...
May 24, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28537707/the-tyrosine-kinase-inhibitor-gefitinib-restricts-mycobacterium-tuberculosis-growth-through-increased-lysosomal-biogenesis-and-modulation-of-cytokine-signaling
#6
Kimberly M Sogi, Katie A Lien, Jeffrey Johnson, Nevan J Krogan, Sarah Stanley
Host-directed therapeutics have the potential to combat the global tuberculosis pandemic. We previously identified gefitinib, an inhibitor of EGFR, as a potential host-targeted therapeutic effective against M. tuberculosis infection of macrophages and mice. Here we examine the functional consequences of gefitinib treatment on M. tuberculosis infected macrophages. Using phosphoproteomic and transcriptional profiling, we identify two mechanisms by which gefitinib influences macrophage responses to infection to impact cytokine responses and limit replication of M...
May 24, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28533032/design-and-synthesis-of-an-immobilized-metal-affinity-chromatography-and-metal-oxide-affinity-chromatography-hybrid-material-for-improved-phosphopeptide-enrichment
#7
Da-Song Yang, Xi-Ying Ding, Hong-Ping Min, Bo Li, Meng-Xiang Su, Miao-Miao Niu, Bin Di, Fang Yan
Reversible phosphorylation of proteins is one of the most important post-translational modifications, while the detection of phosphopeptides is difficult due to their low abundance and the signal suppression of nonphosphorylated peptides. Therefore, selective enrichment of phosphopeptides from highly complicated mixtures is vital for MS-based phosphoproteome analysis. Despite various strategies have been developed, there is no single method that is capable of providing full coverage of the whole phosphoproteome...
May 10, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28520795/birc6-mediates-imatinib-resistance-independently-of-mcl-1
#8
Denis O Okumu, Michael P East, Merlin Levine, Laura E Herring, Raymond Zhang, Thomas S K Gilbert, David W Litchfield, Yanping Zhang, Lee M Graves
Baculoviral IAP repeat containing 6 (BIRC6) is a member of the inhibitors of apoptosis proteins (IAPs), a family of functionally and structurally related proteins that inhibit apoptosis. BIRC6 has been implicated in drug resistance in several different human cancers, however mechanisms regulating BIRC6 have not been extensively explored. Our phosphoproteomic analysis of an imatinib-resistant chronic myelogenous leukemia (CML) cell line (MYL-R) identified increased amounts of a BIRC6 peptide phosphorylated at S480, S482, and S486 compared to imatinib-sensitive CML cells (MYL)...
2017: PloS One
https://www.readbyqxmd.com/read/28512345/phosphoproteome-analysis-reveals-phosphorylation-underpinnings-in-the-brains-of-nurse-and-forager-honeybees-apis-mellifera
#9
Gebreamlak Bezabih, Han Cheng, Bin Han, Mao Feng, Yu Xue, Han Hu, Jianke Li
The honeybee brain is a central organ in regulating wide ranges of honeybee biology, including life transition from nurse to forager bees. Knowledge is still lacking on how protein phosphorylation governs the neural activity to drive the age-specific labor division. The cerebral phosphoproteome of nurse and forager honeybees was characterized using Ti(4+)-IMAC phosphopeptide enrichment mass-spectrometry-based proteomics and protein kinases (PKs) were predicted. There were 3,077 phosphosites residing on 3,234 phosphopeptides from 1004 phosphoproteins in the nurse bees...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28509920/insights-into-chemoselectivity-principles-in-metal-oxide-affinity-chromatography-using-tailored-nanocast-metal-oxide-microspheres-and-mass-spectrometry-based-phosphoproteomics
#10
Alexander Leitner, Motolani Sakeye, Christian Eugen Zimmerli, Jan-Henrik Smått
The ability to comprehensively characterize biological samples, including tissues and body fluids, opens up new possibilities to diagnose and treat diseases and to better understand fundamental biological processes. For this purpose, suitable experimental workflows need to be designed. In this context, materials with particular chemoselective properties are used for the enrichment of certain classes of (bio)molecules. Metal oxides such as titanium dioxide have become the materials of choice for the large-scale study of protein phosphorylation in phosphoproteomics...
May 16, 2017: Analyst
https://www.readbyqxmd.com/read/28509555/differential-phosphoproteomic-analysis-of-recombinant-chinese-hamster-ovary-cells-following-temperature-shift
#11
Michael Henry, Martin Power, Prashant Kaushik, Orla Coleman, Martin Clynes, Paula Meleady
Phosphorylation is one of the most important post-translational modifications, playing a crucial role in regulating many cellular processes including transcription, cytoskeletal rearrangement, cell proliferation, differentiation, apoptosis and signal transduction. However, to date little work has been carried out on the phosphoproteome in CHO cells. In this study we have carried out a large scale differential phosphoproteomic analysis of recombinant CHO cells following a reduction of culture temperature (temperature shift)...
May 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28508642/identification-of-alternative-splice-variants-using-unique-tryptic-peptide-sequences-for-database-searches
#12
Trung T Tran, Ravi C Bollineni, Margarita Strozynski, Christian J Koehler, Bernd Thiede
Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot...
May 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28508362/quantitative-phosphoproteomic-analysis-of-brain-tissues
#13
Bing Bai, Haiyan Tan, Junmin Peng
Protein phosphorylation regulates brain development and neuronal activities; and dysregulation of phosphorylation contributes to neurobiological disorders. Phosphoproteomic analysis provides comprehensive modification maps for measuring protein activities in cellular pathways and biological processes. Here, we introduce a mass spectrometry (MS)-based protocol to quantitatively analyze the phosphoproteome of human postmortem brains of Alzheimer's disease. In this isobaric labeling protocol, up to ten brain samples are selected from control and diseased cases for comparison...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507225/phosphorylation-of-pkp1-by-ripk4-regulates-epidermal-differentiation-and-skin-tumorigenesis
#14
Philbert Lee, Shangwen Jiang, Yuanyuan Li, Jiping Yue, Xuewen Gou, Shao-Yu Chen, Yingming Zhao, Markus Schober, Minjia Tan, Xiaoyang Wu
Tissue homeostasis of skin is sustained by epidermal progenitor cells localized within the basal layer of the skin epithelium. Post-translational modification of the proteome, such as protein phosphorylation, plays a fundamental role in the regulation of stemness and differentiation of somatic stem cells. However, it remains unclear how phosphoproteomic changes occur and contribute to epidermal differentiation. In this study, we survey the epidermal cell differentiation in a systematic manner by combining quantitative phosphoproteomics with mammalian kinome cDNA library screen...
May 15, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28501616/identification-of-phosphorylation-sites-on-%C3%AE-1-adrenergic-receptor-in-the-mouse-heart
#15
Kozo Hayashi, Masamitsu Gotou, Toshikatsu Matsui, Kenichi Imahashi, Tomoyuki Nishimoto, Hiroyuki Kobayashi
β1-adrenergic receptor (Adrb1) belongs to the superfamily of G-protein-coupled receptors (GPCRs) and plays a critical role in the regulation of heart rate and myocardial contraction force. GPCRs are phosphorylated at multiple sites to regulate distinct signal transduction pathways in different tissues. However, little is known about the location and function of distinct phosphorylation sites of Adrb1 in vivo. To clarify the mechanisms underlying functional regulation associated with Adrb1 phosphorylation in vivo, we aimed to identify Adrb1 phosphorylation sites in the mouse heart using phosphoproteomics techniques with nano-flow liquid chromatography/tandem mass spectrometry (LC-MS/MS)...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28500843/bmpr2-promotes-invasion-and-metastasis-via-the-rhoa-rock-limk2-pathway-in-human-osteosarcoma-cells
#16
Shidong Wang, Tingting Ren, Guangjun Jiao, Yi Huang, Xing Bao, Fan Zhang, Kuisheng Liu, Bingxin Zheng, Kunkun Sun, Wei Guo
Bone morphogenetic protein receptor 2 (BMPR2) has been identified in several types of cancer. However, its role in osteosarcoma is largely unknown. We systematically investigated the role of BMPR2 in osteosarcoma cell lines, human tissue samples and xenograft models. The relationship between BMPR2 expression and osteosarcoma patients' survival was investigated by bioinformatics and clinical data. Wound healing assay and transwell assay were used to detect the changes of cell migration and invasion ability after BMPR2 transfection...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28494245/global-reprogramming-of-host-kinase-signaling-in-response-to-fungal-infection
#17
Aseem Pandey, Sheng Li Ding, Qing-Ming Qin, Rahul Gupta, Gabriel Gomez, Furong Lin, Xuehuan Feng, Luciana Fachini da Costa, Sankar P Chaki, Madhu Katepalli, Elizabeth D Case, Erin J van Schaik, Tabasum Sidiq, Omar Khalaf, Angela Arenas, Koichi S Kobayashi, James E Samuel, Gonzalo M Rivera, Robert C Alaniz, Sing-Hoi Sze, Xiaoning Qian, William J Brown, Allison Rice-Ficht, William K Russell, Thomas A Ficht, Paul de Figueiredo
Cryptococcus neoformans (Cn) is a deadly fungal pathogen whose intracellular lifestyle is important for virulence. Host mechanisms controlling fungal phagocytosis and replication remain obscure. Here, we perform a global phosphoproteomic analysis of the host response to Cryptococcus infection. Our analysis reveals numerous and diverse host proteins that are differentially phosphorylated following fungal ingestion by macrophages, thereby indicating global reprogramming of host kinase signaling. Notably, phagocytosis of the pathogen activates the host autophagy initiation complex (AIC) and the upstream regulatory components LKB1 and AMPKα, which regulate autophagy induction through their kinase activities...
May 10, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28493823/hepatitis-c-virus-core-protein-targets-4e-bp1-expression-and-phosphorylation-and-potentiates-myc-induced-liver-carcinogenesis-in-transgenic-mice
#18
Cosette Abdallah, Charlène Lejamtel, Nassima Benzoubir, Serena Battaglia, Nazha Sidahmed-Adrar, Christophe Desterke, Matthieu Lemasson, Arielle R Rosenberg, Didier Samuel, Christian Bréchot, Delphine Pflieger, François Le Naour, Marie-Françoise Bourgeade
Hepatitis C virus (HCV) is a leading cause of liver diseases including the development of hepatocellular carcinoma (HCC). Particularly, core protein has been involved in HCV-related liver pathologies. However, the impact of HCV core on signaling pathways supporting the genesis of HCC remains largely elusive. To decipher the host cell signaling pathways involved in the oncogenic potential of HCV core, a global quantitative phosphoproteomic approach was carried out. This study shed light on novel differentially phosphorylated proteins, in particular several components involved in translation...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28493132/phosphopeptide-enrichment-and-lc-ms-ms-analysis-to-study-the-phosphoproteome-of-recombinant-chinese-hamster-ovary-cells
#19
Michael Henry, Orla Coleman, Prashant, Martin Clynes, Paula Meleady
The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is one of the most important post-translational modifications that regulates many biological processes. The phosphoproteome has not been studied in any great detail in recombinant Chinese hamster ovary (CHO) cells to date despite phosphorylation playing a crucial role in regulating many molecular and cellular processes relevant to bioprocess phenotypes including, for example, transcription, translation, growth, apoptosis, and signal transduction...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28492659/ensemble-clustering-of-phosphoproteomic-data-identifies-differences-in-protein-interactions-and-cell-cell-junction-integrity-of-her2-overexpressing-cells
#20
Katherine E Schaberg, Venktesh S Shirure, Elizabeth A Worley, Steven C George, Kristen M Naegle
Overexpression of HER2, a receptor tyrosine kinase of the ERBB family, in breast cancer is related to increased cancer progression and aggressiveness. A breast epithelial cell model with the single perturbation of HER2 overexpression is capable of replicating the increased aggressiveness of HER2 overexpressing cancers. In previous work, Wolf-Yadlin and colleagues (Wolf-Yadlin et al., Mol. Syst. Biol., 2006, 2) measured the proximal tyrosine phosphorylation dynamics of the parental and HER2 overexpressing cells (24H) in response to EGF...
May 11, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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