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translational proteomics

Paolo Cifani, Alex Kentsis
Given superior analytical features, mass spectrometry proteomics is well suited for the basic investigation and clinical diagnosis of human disease. Modern mass spectrometry enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy mass spectrometry in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner...
October 24, 2016: Proteomics
Daria Matyushkina, Olga Pobeguts, Ivan Butenko, Anna Vanyushkina, Nicolay Anikanov, Olga Bukato, Daria Evsyutina, Alexandra Bogomazova, Maria Lagarkova, Tatiana Semashko, Irina Garanina, Vladislav Babenko, Maria Vakhitova, Valentina Ladygina, Gleb Fisunov, Vadim Govorun
What strategies do bacteria employ for adaptation to their hosts and are these strategies different for varied hosts? To date, many studies on the interaction of the bacterium and its host have been published. However, global changes in the bacterial cell in the process of invasion and persistence, remain poorly understood. In this study, we demonstrated phase transition of the avian pathogen Mycoplasma gallisepticum upon invasion of the various types of eukaryotic cells (human, chicken, and mouse) which was stable during several passages after isolation of intracellular clones and recultivation in a culture medium...
October 24, 2016: Scientific Reports
Christoph T Schanzenbächer, Sivakumar Sambandan, Julian D Langer, Erin M Schuman
Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation...
October 19, 2016: Neuron
Stacy L DeBlasio, Richard S Johnson, Michael J MacCoss, Stewart M Gray, Michelle Cilia
Phloem localization of plant viruses is advantageous for acquisition by sap-sucking vectors but hampers host-virus protein interaction studies. In this study, Potato leafroll virus (PLRV)-host protein complexes were isolated from systemically infected potato, a natural host of the virus. Comparing two different co-immunoprecipitation support matrices coupled to mass spectrometry, we identified 44 potato proteins and one viral protein (P1) specifically associated with virus isolated from infected phloem. An additional 142 proteins interact in complex with virus at varying degrees of confidence...
October 20, 2016: Journal of Proteome Research
Darren M Hutt, Daniela Martino Roth, Christelle Marchal, Marion Bouchecareilh
Gene expression is regulated in part through the reversible acetylation of histones, by the action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). HAT activity results in the addition of acetyl groups on the lysine residues of histone tails leading to decondensation of the chromatin, and increased gene transcription in general, whereas HDACs remove these acetyl groups, thus leading to an overall suppression of gene transcription. Recent evidence has elucidated that histones are not the only components of the proteome that are targeted by HATs and HDACs...
2017: Methods in Molecular Biology
Camille Lombard-Banek, Sally A Moody, Peter Nemes
Direct measurement of protein expression with single-cell resolution promises to deepen the understanding of the basic molecular processes during normal and impaired development. High-resolution mass spectrometry provides detailed coverage of the proteomic composition of large numbers of cells. Here we discuss recent mass spectrometry developments based on single-cell capillary electrophoresis that extend discovery proteomics to sufficient sensitivity to enable the measurement of proteins in single cells. The single-cell mass spectrometry system is used to detect a large number of proteins in single embryonic cells in the 16-cell embryo of the South African clawed frog (Xenopus laevis) that give rise to distinct tissue types...
2016: Frontiers in Cell and Developmental Biology
Caiyun He, Guori Gao, Jianguo Zhang, Aiguo Duan, Hongmei Luo
BACKGROUND: Low temperature is one of the crucial environmental factors limiting the productivity and distribution of plants. Sea buckthorn (Hippophae rhamnoides L.), a well recognized multipurpose plant species, live successfully in in cold desert regions. But their molecular mechanisms underlying cold tolerance are not well understood. METHODS: Physiological and biochemical responses to low-temperature stress were studied in seedlings of sea buckthorn. Differentially expressed protein spots were analyzed using multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption/ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry (MS), the concentration of phytohormone was measured using enzyme-linked immunosorbent assay, and a spectrophotometric assay was used to measure enzymatic reactions...
2016: Proteome Science
Barbara Kathage, Sebastian Gehlert, Anna Ulbricht, Laura Lüdecke, Victor E Tapia, Zacharias Orfanos, Daniela Wenzel, Wilhelm Bloch, Rudolf Volkmer, Bernd K Fleischmann, Dieter O Fürst, Jörg Höhfeld
The cochaperone BAG3 is a central protein homeostasis factor in mechanically strained mammalian cells. It mediates the degradation of unfolded and damaged forms of the actin-crosslinker filamin through chaperone-assisted selective autophagy (CASA). In addition, BAG3 stimulates filamin transcription in order to compensate autophagic disposal and to maintain the actin cytoskeleton under strain. Here we demonstrate that BAG3 coordinates protein synthesis and autophagy through spatial regulation of the mammalian target of rapamycin complex 1 (mTORC1)...
October 15, 2016: Biochimica et Biophysica Acta
Hye Yeon Koh, Hyun Park, Jun Hyuck Lee, Se Jong Han, Young Chang Sohn, Sung Gu Lee
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ 2 fold, p <0...
October 17, 2016: Environmental Microbiology
Clizia Chinello, Vincenzo L'Imperio, Martina Stella, Andrew James Smith, Giorgio Bovo, Angelica Grasso, Marco Grasso, Francesca Raimondo, Marina Pitto, Fabio Pagni, Fulvio Magni
Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids...
October 17, 2016: Expert Review of Proteomics
Fengchao Yu, Ning Li, Weichuan Yu
In computational proteomics, 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...
October 17, 2016: Journal of Proteome Research
Mar Margalef-Català, Isabel Araque, Albert Bordons, Cristina Reguant, Joaquín Bautista-Gallego
Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM) was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins...
2016: Frontiers in Microbiology
Martin Gamerdinger
The biogenesis of new polypeptides by ribosomes and their subsequent correct folding and localization to the appropriate cellular compartments are essential key processes to maintain protein homoeostasis. These complex mechanisms are governed by a repertoire of protein biogenesis factors that directly bind to the ribosome and chaperone nascent polypeptide chains as soon as they emerge from the ribosomal tunnel exit. This nascent chain 'welcoming committee' regulates multiple co-translational processes including protein modifications, folding, targeting and degradation...
October 15, 2016: Essays in Biochemistry
John S Bett
Cells have developed an evolutionary obligation to survey and maintain proteome fidelity and avoid the possible toxic consequences of protein misfolding and aggregation. Disturbances to protein homoeostasis (proteostasis) can result in severe cellular phenotypes and are closely linked with the accumulation of microscopically visible deposits of aggregated proteins. These include inclusion bodies found in AD (Alzheimer's disease), HD (Huntington's disease) and ALS (amyotrophic lateral sclerosis) patient neurons...
October 15, 2016: Essays in Biochemistry
Arnav Mehta, Ketan Ghaghada, Srinivasan Mukundan
The first generation of cross-sectional brain imaging using computed tomography (CT), ultrasonography, and eventually MR imaging focused on determining structural or anatomic changes associated with brain disorders. The current state-of-the-art imaging, functional imaging, uses techniques such as CT and MR perfusion that allow determination of physiologic parameters in vivo. In parallel, tissue-based genomic, transcriptomic, and proteomic profiling of brain tumors has created several novel and exciting possibilities for molecular targeting of brain tumors...
November 2016: Magnetic Resonance Imaging Clinics of North America
Priyakshi Kalita-de Croft, Fares Al-Ejeh, Amy E McCart Reed, Jodi M Saunus, Sunil R Lakhani
Our understanding of the natural history of breast cancer has evolved alongside technologies to study its genomic, transcriptomic, proteomic, and metabolomics landscapes. These technologies have helped decipher multiple molecular pathways dysregulated in breast cancer. First-generation 'omics analyses considered each of these dimensions individually, but it is becoming increasingly clear that more holistic, integrative approaches are required to fully understand complex biological systems. The 'omics represent an exciting era of discovery in breast cancer research, although important issues need to be addressed to realize the clinical utility of these data through precision cancer care...
November 2016: Advances in Anatomic Pathology
Sang C Lee, Jack Zhang, Josh Strom, Danzhou Yang, Thai Nho Dinh, Kyle Kappeler, Qin M Chen
Inhibition of protein synthesis serves as a general measure of cellular consequence to chemical stress. A few proteins are translated selectively and influence cell fate. How these proteins can bypass the general control of translation remains unknown. We found that low to mild doses of oxidants induce de novo translation of NRF2 protein. Here we demonstrate the presence of a G-quadruplex structure in 5' Untranslated Region (5' UTR) of NRF2 mRNA, as measured by Circular Dichroism, Nuclear Magnetic Resonance, and Dimethylsulfate Footprinting...
October 10, 2016: Molecular and Cellular Biology
Daniel Köhler, Stefan Helm, Birgit Agne, Sacha Baginsky
Toc159-containing complexes at the outer chloroplast envelope membrane form stable super-complexes with a 1-MDa translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo-lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins...
October 12, 2016: Plant Physiology
Mi Suk Lee, Hyo-Jung Choi, Eui-Jung Park, Hye-Jeong Park, Tae-Hwan Kwon
Carboxyl-terminus of AQP2 (AQP2c) undergoes post-translational modifications, including phosphorylation and ubiquitination, for the regulation of aquaporin-2 (AQP2) translocation and protein abundance. We aimed to identify novel proteins interacting with AQP2c. Recombinant AQP2c protein was made in E. coli BL21 (DE3) by exploiting the pET32 TrxA fusion system. Lysates of rat kidney inner medullary collecting duct (IMCD) tubule suspensions interacted with rat AQP2c bound to Ni(2+)-resin were subjected to LC-MS/MS proteomic analysis...
October 12, 2016: American Journal of Physiology. Renal Physiology
Elena Pazos, Manuel Garcia Algar, Cristina Penas, Moritz Nazarenus, Arnau Torruella, Nicolas Pazos-Perez, Luca Guerrini, M Eugenio Vázquez, Eduardo Garcia-Rico, José L Mascareñas, Ramon A Alvarez-Puebla
Blood-based biomarkers (liquid biopsy) offer extremely valua-ble tools for the non-invasive diagnosis and monitoring of tumors. The protein c-MYC, a transcription factor that has been shown to be deregulated in up to 70% of human cancers, can be used as a robust proteomic signature for cancer. Herein, we developed a rapid, highly specific and sensitive SERS assay for the quantification of c-MYC in real blood samples. The sensing scheme relies on the use of specifically designed hybrid plasmonic materials and their bioderivatization with a selective peptidic receptor modified with a SERS transducer...
October 12, 2016: Journal of the American Chemical Society
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