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translational proteomics

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https://www.readbyqxmd.com/read/28220989/global-and-local-mechanisms-sustain-axonal-proteostasis-of-transmembrane-proteins
#1
REVIEW
Víctor Hugo Cornejo, Alejandro Luarte, Andrés Couve
The control of neuronal protein homeostasis or proteostasis is tightly regulated both spatially and temporally, assuring accurate and integrated responses to external or intrinsic stimuli. Local or autonomous responses in dendritic and axonal compartments are crucial to sustain function during development, physiology and in response to damage or disease. Axons are responsible for generating and propagating electrical impulses in neurons, and the establishment and maintenance of their molecular composition are subject to extreme constraints exerted by length and size...
February 21, 2017: Traffic
https://www.readbyqxmd.com/read/28220896/mitochondrial-dysregulation-secondary-to-endoplasmic-reticulum-stress-in-autosomal-dominant-tubulointerstitial-kidney-disease-umod-adtkd-umod
#2
Elisabeth Kemter, Thomas Fröhlich, Georg J Arnold, Eckhard Wolf, Rüdiger Wanke
'Autosomal dominant tubulointerstitial kidney disease - UMOD' (ADTKD-UMOD) is caused by impaired maturation and secretion of mutant uromodulin (UMOD) in thick ascending limb of Henle loop (TAL) cells, resulting in endoplasmic reticulum (ER) stress and unfolded protein response (UPR). To gain insight into pathophysiology, we analysed proteome profiles of TAL-enriched outer renal medulla samples from ADTKD-UMOD and control mice by quantitative LC-MS/MS. In total, 212 differentially abundant proteins were identified...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28218735/aurora-kinase-a-regulates-survivin-stability-through-targeting-fbxl7-in-gastric-cancer-drug-resistance-and-prognosis
#3
M Kamran, Z-J Long, D Xu, S-S Lv, B Liu, C-L Wang, J Xu, E W-F Lam, Q Liu
Aurora kinase A (AURKA) has been implicated in the regulation of cell cycle progression, mitosis and a key number of oncogenic signaling pathways in various malignancies. However, little is known about its role in gastric cancer prognosis and genotoxic resistance. Here we found that AURKA was highly overexpressed in gastric cancer and inversely correlated with disease prognosis. Overexpression of AURKA exacerbated gastric cancer drug resistance through upregulating the expression of the anti-apoptotic protein Survivin...
February 20, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28217912/cold-adaptation-of-the-antarctic-haloarchaea-halohasta-litchfieldiae-and-halorubrum-lacusprofundi
#4
Timothy J Williams, Yan Liao, Jun Ye, Rhiannon P Kuchel, Anne Poljak, Mark J Raftery, Ricardo Cavicchioli
Halohasta litchfieldiae represents ∼ 44% and Halorubrum lacusprofundi ∼ 10% of the hypersaline, perennially cold (≥ -20°C) Deep Lake community in Antarctica. We used proteomics and microscopy to define physiological responses of these haloarchaea to growth at high (30°C) and low (10 and 4°C) temperatures. The proteomic data indicate that both species responded to low temperature by modifying their cell envelope including protein N-glycosylation, maintaining osmotic balance and translation initiation, and modifying RNA turnover and tRNA modification...
February 20, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28217095/endogenous-protein-interactome-of-human-udp-glucuronosyltransferases-exposed-by-untargeted-proteomics
#5
Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock, Chantal Guillemette
The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, transcriptional, post-transcriptional and post-translational levels. However, the UGT protein interaction network, which is likely to influence glucuronidation, has received little attention...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28216224/targeted-proteomics-driven-verification-of-biomarker-candidates-associated-with-breast-cancer-aggressiveness
#6
Iva Procházková, Juraj Lenčo, Alena Fučíková, Jiří Dresler, Lenka Čápková, Roman Hrstka, Rudolf Nenutil, Pavel Bouchal
Breast cancer is the most common and molecularly relatively well characterized malignant disease in women, however, its progression to metastatic cancer remains lethal for 78% of patients 5years after diagnosis. Novel markers could identify the high risk patients and their verification using quantitative methods is essential to overcome genetic, inter-tumor and intra-tumor variability and translate novel findings into cancer diagnosis and treatment. We recently identified 13 proteins associated with estrogen receptor, tumor grade and lymph node status, the key factors of breast cancer aggressiveness, using untargeted proteomics...
February 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#7
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28211672/proteomic-analysis-of-post-synaptic-protein-complexes-underlying-neuronal-plasticity
#8
Anthony J Baucum
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies...
February 17, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28208668/redox-proteomics-and-platelet-activation-understanding-the-redox-proteome-to-improve-platelet-quality-for-transfusion
#9
REVIEW
Giona Sonego, Mélanie Abonnenc, Jean-Daniel Tissot, Michel Prudent, Niels Lion
Blood banks use pathogen inactivation (PI) technologies to increase the safety of platelet concentrates (PCs). The characteristics of PI-treated PCs slightly differ from those of untreated PCs, but the underlying reasons are not well understood. One possible cause is the generation of oxidative stress during the PI process. This is of great interest since reactive oxygen species (ROS) act as second messengers in platelet functions. Furthermore, there are links between protein oxidation and phosphorylation, another mechanism that is critical for cell regulation...
February 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208305/predicting-electrophoretic-mobility-of-tryptic-peptides-for-high-throughput-cze-ms-analysis
#10
Oleg V Krokhin, Geoffrey Anderson, Vic Spicer, Liangliang Sun, Norman J Dovichi
A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28207764/didehydrophenylalanine-an-abundant-modification-in-the-beta-subunit-of-plant-polygalacturonases
#11
Kjell Sergeant, Bruno Printz, Annelie Gutsch, Marc Behr, Jenny Renaut, Jean-Francois Hausman
The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described...
2017: PloS One
https://www.readbyqxmd.com/read/28202229/requirement-of-the-rna-binding-protein-smpb-during-intracellular-growth-of-listeria-monocytogenes
#12
Mobarak Abu Mraheil, Renate Frantz, Lisa Teubner, Heiko Wendt, Uwe Linne, Jessica Wingerath, Thomas Wirth, Trinad Chakraborty
Bacterial trans-translation is the main quality control mechanism employed to relieve stalled ribosomes. Trans-translation is mediated by the small protein B (SmpB) and transfer-mRNA (tmRNA) ribonucleoprotein complex, which interacts with translational complexes stalled at the 3' end of non-stop mRNAs to release the stalled ribosomes thereby targeting the nascent polypeptides and truncated mRNAs for degradation. The trans-translation system exists with a few exceptions in all bacteria. In the present study, we assessed the contribution of SmpB to the growth and virulence of Listeria monocytogenes, a human intracellular food-borne pathogen that colonizes host tissues to cause severe invasive infections...
February 1, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28199320/the-use-of-urinary-proteomics-in-the-assessment-of-suitability-of-mouse-models-for-ageing
#13
Esther Nkuipou-Kenfack, Joost P Schanstra, Seerat Bajwa, Martin Pejchinovski, Claire Vinel, Cédric Dray, Philippe Valet, Jean-Loup Bascands, Antonia Vlahou, Thomas Koeck, Melanie Borries, Hauke Busch, Wibke Bechtel-Walz, Tobias B Huber, Karl L Rudolph, Andreas Pich, Harald Mischak, Petra Zürbig
Ageing is a complex process characterised by a systemic and progressive deterioration of biological functions. As ageing is associated with an increased prevalence of age-related chronic disorders, understanding its underlying molecular mechanisms can pave the way for therapeutic interventions and managing complications. Animal models such as mice are commonly used in ageing research as they have a shorter lifespan in comparison to humans and are also genetically close to humans. To assess the translatability of mouse ageing to human ageing, the urinary proteome in 89 wild-type (C57BL/6) mice aged between 8-96 weeks was investigated using capillary electrophoresis coupled to mass spectrometry (CE-MS)...
2017: PloS One
https://www.readbyqxmd.com/read/28197924/sumoylation-as-an-integral-mechanism-in-bacterial-infection-and-disease-progression
#14
Chittur V Srikanth, Smriti Verma
Post translational modification pathways regulate fundamental processes of cells and thus govern vital functions. Among these, particularly the modification with Small Ubiquitin-like Modifiers (SUMO) is being recognized as a pathway crucial for cell homeostasis and health. Understandably, bacterial pathogens intervene with the SUMO pathway of the host for ensuring successful infection. Among the bacterial pathogens known to target host sumoylation varied points of intervention are utilized. Majority of them including Salmonella Typhimurium, Shigella flexneri and Listeria monocytogenes target the E2 conjugating enzyme Ubc9...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28196878/global-characterization-of-protein-secretion-from-human-macrophages-following-non-canonical-caspase-4-5-inflammasome-activation
#15
Martina B Lorey, Katariina Rossi, Kari K Eklund, Tuula A Nyman, Sampsa Matikainen
Gram-negative bacteria are associated with a wide spectrum of infectious diseases in humans. Inflammasomes are cytosolic protein complexes that are assembled when the cell encounters pathogens or other harmful agents. The non-canonical caspase-4/5 inflammasome is activated by gram-negative bacteria-derived lipopolysaccharide (LPS) and by endogenous oxidized phospholipids. Protein secretion is a critical component of the innate immune response. Here we have used label-free quantitative proteomics to characterize global protein secretion in response to non-canonical inflammasome activation upon intracellular LPS recognition in human primary macrophages...
February 14, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28194967/multicellular-tumor-spheroids-combined-with-mass-spectrometric-histone-analysis-to-evaluate-epigenetic-drugs
#16
Peter E Feist, Simone Sidoli, Xin Liu, Monica M Schroll, Sharif Rahmy, Rina Fujiwara, Benjamin A Garcia, Amanda B Hummon
Multicellular tumor spheroids (MCTS) are valuable in vitro tumor models frequently used to evaluate the penetration and efficacy of therapeutics. In this study, we evaluated potential differences in epigenetic markers, i.e., histone post-translational modifications (PTMs), in the layers of the HCT116 colon carcinoma MCTS. Cells were grown in agarose-coated 96 well plates, forming reproducible 1-mm-diameter MCTS. The MCTS were fractionated into three radially concentric portions, generating samples containing cells from the core, the mid and the external layers...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193903/structural-analysis-of-mycobacterium-tuberculosis-homologues-of-the-eukaryotic-proteasome-assembly-chaperone-2-pac2
#17
Lin Bai, Jordan B Jastrab, Marta Isasa, Kuan Hu, Hongjun Yu, Steven P Gygi, K Heran Darwin, Huilin Li
A previous bioinformatics analysis identified the Mycobacterium tuberculosis (M. tuberculosis) proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 could function in proteasome assembly. We solved the crystal structure of Rv2125 at 3.0 Å resolution, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2...
February 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28191785/impact-of-the-secretome-of-human-mesenchymal-stem-cells-on-brain-structure-and-animal-behavior-in-a-rat-model-of-parkinson-s-disease
#18
Fábio G Teixeira, Miguel M Carvalho, Krishna M Panchalingam, Ana J Rodrigues, Bárbara Mendes-Pinheiro, Sandra Anjo, Bruno Manadas, Leo A Behie, Nuno Sousa, António J Salgado
Research in the last decade strongly suggests that mesenchymal stem cell (MSC)-mediated therapeutic benefits are mainly due to their secretome, which has been proposed as a possible therapeutic tool for the treatment of Parkinson's disease (PD). Indeed, it has been shown that the MSC secretome increases neurogenesis and cell survival, and has numerous neuroprotective actions under different conditions. Additionally, using dynamic culturing conditions (through computer-controlled bioreactors) can further modulate the MSC secretome, thereby generating a more potent neurotrophic factor cocktail (i...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28191734/integrative-proteomics-genomics-and-translational-immunology-approaches-reveal-mutated-forms-of-proteolipid-protein-1-plp1-and-mutant-specific-immune-response-in-multiple-sclerosis
#19
Veneta Qendro, Grace A Bugos, Debbie H Lundgren, John Glynn, May H Han, David K Han
In order to gain mechanistic insights into multiple sclerosis (MS) pathogenesis, we utilized a multi-dimensional approach to test the hypothesis that mutations in myelin proteins lead to immune activation and central nervous system autoimmunity in MS. Mass spectrometry-based proteomic analysis of human MS brain lesions revealed seven unique mutations of PLP1; a key myelin protein that is known to be destroyed in MS. Surprisingly, in-depth genomic analysis of two MS patients at the genomic DNA and mRNA confirmed mutated PLP1 in RNA, but not in the genomic DNA...
February 12, 2017: Proteomics
https://www.readbyqxmd.com/read/28191457/the-copper-transport-associated-protein-ctr4-can-form-prion-like-epigenetic-determinants-in-schizosaccharomyces-pombe
#20
Theodora Sideri, Yoko Yashiroda, David A Ellis, María Rodríguez-López, Minoru Yoshida, Mick F Tuite, Jürg Bähler
Prions are protein-based infectious entities associated with fatal brain diseases in animals, but also modify a range of host-cell phenotypes in the budding yeast, Saccharomyces cerevisiae. Many questions remain about the evolution and biology of prions. Although several functionally distinct prion-forming proteins exist in S. cerevisiae, [HET-s] of Podospora anserina is the only other known fungal prion. Here we investigated prion-like, protein-based epigenetic transmission in the fission yeast Schizosaccharomyces pombe...
January 2017: Microbial Cell
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