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translational proteomics

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https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#1
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149817/high-density-lipoprotein-hdl-dysfunction-and-future-of-hdl
#2
Sibel Ertek
Although high density lipoprotein cholesterol (HDL-C) levels are inversely proportional to cardiovascular risk in many studies, recent pharmacological interventional studies with HDL-C raising strategies did not show a benefit in terms of vascular events. The HDL particle is heterogenous with anti-atherogenic functions and non-vascular effects. Many factors affect HDL components and may either cause compositional changes, post-translational modifications of proteins, or alter lipids and other cargo molecules; generally these factors cause more than one of these changes, resulting in functional differences...
November 16, 2017: Current Vascular Pharmacology
https://www.readbyqxmd.com/read/29147069/expression-profiling-of-long-noncoding-rna-splice-variants-in-human-microvascular-endothelial-cells-lipopolysaccharide-effects-in-vitro
#3
Imran H Chowdhury, Hema P Narra, Abha Sahni, Kamil Khanipov, Casey L C Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. We report on the expression profile of long noncoding (lnc) RNAs of human microvascular endothelial cells in response to LPS...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/29146174/proteome-level-analysis-indicates-global-mechanisms-for-post-translational-regulation-of-rrm-domains
#4
Roman Sloutsky, Kristen M Naegle
No abstract text is available yet for this article.
November 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29145655/paternal-exposure-to-environmental-chemical-stress-affectsmale-offspring-s-hepatic-mitochondria
#5
Roger Godschalk, Alex Remels, Camiel Hoogendoorn, Jan van Benthem, Mirjam Luijten, Nur Duale, Gunnar Brunborg, Ann-Karin Olsen, Freek G Bouwman, Armelle Munnia, Marco Peluso, Edwin Mariman, Frederik Jan van Schooten
Pre-conceptional paternal exposures may affect offspring's health, which cannot be explained by mutations in germ cells, but by persistent changes in the regulation of gene expression. Therefore, we investigated whether pre-conceptional paternal exposure to benzo[a]pyrene (B[a]P) could alter the offspring's phenotype. Male C57BL/6 mice were exposed to B[a]P by gavage for 6 weeks, 3x per week, and were crossed with unexposed BALB-c females 6 weeks after the final exposure. The offspring was kept under normal feeding conditions and was sacrificed at 3 weeks of age...
November 14, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29142256/quantitative-analysis-of-protein-protein-interactions-and-post-translational-modifications-in-rare-immune-populations
#6
Ayelet Avin, Maayan Levy, Ziv Porat, Jakub Abramson
In spite of recent advances in proteomics, quantitative analyses of protein-protein interactions (PPIs) or post-translational modifications (PTMs) in rare cell populations remain challenging. This is in particular true for analyses of rare immune and/or stem cell populations that are directly isolated from humans or animal models, and which are often characterized by multiple surface markers. To overcome these limitations, here we have developed proximity ligation imaging cytometry (PLIC), a protocol for proteomic analysis of rare cells...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142207/phosphorylation-dynamics-dominate-the-regulated-proteome-during-early-xenopus-development
#7
Elizabeth H Peuchen, Olivia F Cox, Liangliang Sun, Alex S Hebert, Joshua J Coon, Matthew M Champion, Norman J Dovichi, Paul W Huber
The earliest stages of animal development are largely controlled by changes in protein phosphorylation mediated by signaling pathways and cyclin-dependent kinases. In order to decipher these complex networks and to discover new aspects of regulation by this post-translational modification, we undertook an analysis of the X. laevis phosphoproteome at seven developmental stages beginning with stage VI oocytes and ending with two-cell embryos. Concurrent measurement of the proteome and phosphoproteome enabled measurement of phosphosite occupancy as a function of developmental stage...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142197/proteotoxicity-in-cardiac-amyloidosis-amyloidogenic-light-chains-affect-the-levels-of-intracellular-proteins-in-human-heart-cells
#8
Esther Imperlini, Massimiliano Gnecchi, Paola Rognoni, Eduard Sabidò, Maria Chiara Ciuffreda, Giovanni Palladini, Guadalupe Espadas, Francesco Mattia Mancuso, Margherita Bozzola, Giuseppe Malpasso, Veronica Valentini, Giuseppina Palladini, Stefania Orrù, Giovanni Ferraro, Paolo Milani, Stefano Perlini, Francesco Salvatore, Giampaolo Merlini, Francesca Lavatelli
AL amyloidosis is characterized by widespread deposition of immunoglobulin light chains (LCs) as amyloid fibrils. Cardiac involvement is frequent and leads to life-threatening cardiomyopathy. Besides the tissue alteration caused by fibrils, clinical and experimental evidence indicates that cardiac damage is also caused by proteotoxicity of prefibrillar amyloidogenic species. As in other amyloidoses, the damage mechanisms at cellular level are complex and largely undefined. We have characterized the molecular changes in primary human cardiac fibroblasts (hCFs) exposed in vitro to soluble amyloidogenic cardiotoxic LCs from AL cardiomyopathy patients...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141959/an-integrative-strategy-to-identify-the-entire-protein-coding-potential-of-prokaryotic-genomes-by-proteogenomics
#9
Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29141220/phosphorylation-and-ubiquitination-regulate-protein-phosphatase-5-activity-and-its-prosurvival-role-in-kidney-cancer
#10
Natela Dushukyan, Diana M Dunn, Rebecca A Sager, Mark R Woodford, David R Loiselle, Michael Daneshvar, Alexander J Baker-Williams, John D Chisholm, Andrew W Truman, Cara K Vaughan, Timothy A Haystead, Gennady Bratslavsky, Dimitra Bourboulia, Mehdi Mollapour
The serine/threonine protein phosphatase 5 (PP5) regulates multiple cellular signaling networks. A number of cellular factors, including heat shock protein 90 (Hsp90), promote the activation of PP5. However, it is unclear whether post-translational modifications also influence PP5 phosphatase activity. Here, we show an "on/off switch" mechanism for PP5 regulation. The casein kinase 1δ (CK1δ) phosphorylates T362 in the catalytic domain of PP5, which activates and enhances phosphatase activity independent of Hsp90...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29140531/an-update-on-sorfs-org-a-repository-of-small-orfs-identified-by-ribosome-profiling
#11
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138512/proteome-wide-identification-of-lysine-2-hydroxyisobutyrylation-reveals-conserved-and-novel-histone-modifications-in-physcomitrella-patens
#12
Zhiming Yu, Jun Ni, Wei Sheng, Zhikun Wang, Yuhuan Wu
Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly identified post-translational modification found in animal and yeast cells. Previous research suggested that histone Khib is involved in male cell differentiation and plays a critical role in the regulation of chromatin functions in animals. However, information regarding protein Khib in plants is still limited. In this study, using a specific antibody and LC-MS/MS methods, we identified 11,976 Khib sites in 3,001 proteins in Physcomitrella patens. The bioinformatics analysis indicated that these Khib-modified proteins were involved in a wide range of molecular functions and cellular processes, and showed diverse subcellular localizations...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137706/accurate-phosphorylation-site-localization-using-phospho-brackets
#13
Kaijie Xiao, Yun Shen, Shasha Li, Zhixin Tian
Phosphorylation is one of the most important and widely studied protein post-translational modifications. Tandem mass spectrometry using higher-energy collisional dissociation has evolved into a state-of-the-art analytical platform for both phosphorylation identification and site localization. Tens of thousands of phosphopeptides can now be routinely identified from a single shotgun proteomics study; site localization, however, is much more complicated and many challenges still exist. Here, we report our development of P-bracket using direct experimental evidence of phospho-containing site-determining product ions for accurate site localization without the need for additional FLR control...
December 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29136377/quantifying-missing-phospho-proteome-regions-with-the-broad-specificity-protease-subtilisin
#14
Humberto Gonczarowska-Jorge, Stefan Loroch, Margherita Dell'Aica, Albert Sickmann, Andreas Roos, René Peiman Zahedi
Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, non-unique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as Glu-C, Asp-N, Lys-N, Arg-C, LysArginase has been reported...
November 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29135940/comparative-proteomic-analysis-of-lysine-acetylation-in-fish-cik-cells-infected-with-aquareovirus
#15
Hong Guo, Jie Zhang, Yaping Wang, Chen Bu, Yanyan Zhou, Qin Fang
Grass carp (Ctenopharyngodon idellus) is an important worldwide commercial freshwater culture species. However, grass carp reovirus (GCRV) causes serious hemorrhagic disease in fingerlings and yearlings of fishes. To understand the molecular pathogenesis of host cells during GCRV infection, intensive proteomic quantification analysis of lysine acetylation in Ctenopharyngodon idella kidney (CIK) cells was performed. Using dimethylation labeling-based quantitative proteomics, 832 acetylated proteins with 1391 lysine acetylation sites were identified in response to GCRV infection, among which 792 proteins with 1323 sites were quantifiable...
November 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29134778/the-axonal-endoplasmic-reticulum-one-organelle-many-functions-in-development-maintenance-and-plasticity
#16
REVIEW
Alejandro Luarte, Víctor Hugo Cornejo, Francisca Bertin, Javiera Gallardo, Andrés Couve
The endoplasmic reticulum (ER) is highly conserved in eukaryotes and neurons. Indeed, the localization of the organelle in axons has been known for nearly half a century. However, the relevance of the axonal ER is only beginning to emerge. In this review, we discuss the structure of the ER in axons, examining the role of ER-shaping proteins and highlighting reticulons. We analyze the multiple functions of the ER and their potential contribution to axonal physiology. First, we examine the emerging roles of the axonal ER in lipid synthesis, protein translation, processing, quality control, and secretory trafficking of transmembrane proteins...
November 14, 2017: Developmental Neurobiology
https://www.readbyqxmd.com/read/29132214/chemical-probes-for-redox-signaling-and-oxidative-stress
#17
Masahiro Abo, Eranthie Weerapana
SIGNIFICANCE: Cellular reactive oxygen species (ROS) mediate redox signaling cascades that are critical to numerous physiological and pathological processes. Analytical methods to monitor cellular ROS levels and proteomic platforms to identify oxidative post-translational modifications (PTMs) of proteins are critical to understanding the triggers and consequences of redox signaling. Recent advances: The prevalence and significance of redox signaling has recently been illuminated through the use of chemical probes that allow for sensitive detection of cellular ROS levels and proteomic dissection of oxidative PTMs directly in living cells...
November 13, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29131144/top-down-characterization-of-endogenous-protein-complexes-with-native-proteomics
#18
Owen S Skinner, Nicole A Haverland, Luca Fornelli, Rafael D Melani, Luis H F Do Vale, Henrique S Seckler, Peter F Doubleday, Luis F Schachner, Kristina Srzentić, Neil L Kelleher, Philip D Compton
Protein complexes exhibit great diversity in protein membership, post-translational modifications and noncovalent cofactors, enabling them to function as the actuators of many important biological processes. The exposition of these molecular features using current methods lacks either throughput or molecular specificity, ultimately limiting the use of protein complexes as direct analytical targets in a wide range of applications. Here, we apply native proteomics, enabled by a multistage tandem MS approach, to characterize 125 intact endogenous complexes and 217 distinct proteoforms derived from mouse heart and human cancer cell lines in discovery mode...
November 13, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29130603/proteogenomic-re-annotation-of-coccidioides-posadasii-strain-silveira
#19
Natalie M Mitchell, Andrew L Sherrard, Surendra Dasari, D Mitchell Magee, Thomas E Grys, Douglas F Lake
The aims of this study were to provide protein-based evidence upon which to re-annotate of the genome of C. posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley Fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira were analyzed using a GeLC-MS/MS method. Acquired spectra were processed with a proteogenomics workflow comprising a Silveira proteome database, a 6-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs...
November 12, 2017: Proteomics
https://www.readbyqxmd.com/read/29129743/comprehensive-identification-of-proteins-binding-to-rna-g-quadruplex-motifs-in-the-5-utr-of-tumor-associated-mrnas
#20
Tatsuo Serikawa, Christos Spanos, Annekathrin von Hacht, Nediljko Budisa, Juri Rappsilber, Jens Kurreck
G-quadruplex structures in the 5' UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry...
November 9, 2017: Biochimie
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