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Protein footprinting

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https://www.readbyqxmd.com/read/28811350/defining-the-dna-binding-site-recognized-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#1
Beate Schwer, Ana M Sanchez, Angad Garg, Debashree Chatterjee, Stewart Shuman
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivoIMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28793397/the-carbon-footprint-of-integrated-milk-production-and-renewable-energy-systems-a-case-study
#2
Elisabetta Vida, Doriana Eurosia Angela Tedesco
Dairy farms have been widely acknowledged as a source of greenhouse gas (GHG) emissions. The need for a more environmentally friendly milk production system will likely be important going forward. Whereas methane (CH4) enteric emissions can only be reduced to a limited extent, CH4 manure emissions can be reduced by implementing mitigation strategies, such as the use of an anaerobic digestion (AD). Furthermore, implementing a photovoltaic (PV) electricity generation system could mitigate the fossil fuels used to cover the electrical needs of farms...
August 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28790174/multiple-dna-binding-modes-for-the-ets-family-transcription-factor-pu-1
#3
Shingo Esaki, Marina G Evich, Noa Erlitzki, Markus W Germann, Gregory M K Poon
The eponymous DNA-binding domain of ETS (E26 transformation specific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. While 10 bp of DNA was sufficient to support PU...
August 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28783075/design-of-a-new-ultracompact-resonant-plasmonic-multi-analyte-label-free-biosensing-platform
#4
Francesco Dell'Olio, Donato Conteduca, Maripina De Palo, Caterina Ciminelli
In this paper, we report on the design of a bio-multisensing platform for the selective label-free detection of protein biomarkers, carried out through a 3D numerical algorithm. The platform includes a number of biosensors, each of them is based on a plasmonic nanocavity, consisting of a periodic metal structure to be deposited on a silicon oxide substrate. Light is strongly confined in a region with extremely small size (=1.57 μm²), to enhance the light-matter interaction. A surface sensitivity Ss = 1.8 nm/nm has been calculated together with a detection limit of 128 pg/mm²...
August 6, 2017: Sensors
https://www.readbyqxmd.com/read/28771403/structural-insight-into-the-activation-of-a-class-b-g-protein-coupled-receptor-by-peptide-hormones-in-live-human-cells
#5
Lisa Seidel, Barbara Zarzycka, Saheem A Zaidi, Vsevolod Katritch, Irene Coin
The activation mechanism of class B G-protein-coupled receptors (GPCRs) remains largely unknown. To characterize conformational changes induced by peptide hormones, we investigated interactions of the class B corticotropin-releasing factor receptor type 1 (CRF1R) with two peptide agonists and three peptide antagonists obtained by N-truncation of the agonists. Surface mapping with genetically encoded photo-crosslinkers and pair-wise crosslinking revealed distinct footprints of agonists and antagonists on the transmembrane domain (TMD) of CRF1R and identified numerous ligand-receptor contact sites, directly from the intact receptor in live human cells...
August 3, 2017: ELife
https://www.readbyqxmd.com/read/28767700/environmental-impacts-of-food-consumption-by-dogs-and-cats
#6
Gregory S Okin
In the US, there are more than 163 million dogs and cats that consume, as a significant portion of their diet, animal products and therefore potentially constitute a considerable dietary footprint. Here, the energy and animal-derived product consumption of these pets in the US is evaluated for the first time, as are the environmental impacts from the animal products fed to them, including feces production. In the US, dogs and cats consume about 19% ± 2% of the amount of dietary energy that humans do (203 ± 15 PJ yr-1 vs...
2017: PloS One
https://www.readbyqxmd.com/read/28750283/evaluation-of-allocation-methods-for-calculation-of-carbon-footprint-of-grass-based-dairy-production
#7
P Rice, D O'Brien, L Shalloo, N M Holden
A major methodological issue for life cycle assessment, commonly used to quantify greenhouse gas emissions from livestock systems, is allocation from multifunctional processes. When a process produces more than one output, the environmental burden has to be assigned between the outputs, such as milk and meat from a dairy cow. In the absence of an objective function for choosing an allocation method, a decision must be made considering a range of factors, one of which is the availability and quality of necessary data...
July 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28748636/compact-cell-settlers-for-perfusion-cultures-of-microbial-and-mammalian-cells
#8
Cassandra A Freeman, Premsingh S D Samuel, Dhinakar S Kompala
As microbial secretory expression systems have become well developed for microbial yeast cells, such as Saccharomyces cerevisiae and Pichia pastoris, it is advantageous to develop high cell density continuous perfusion cultures of microbial yeast cells to retain the live and productive yeast cells inside the perfusion bioreactor while removing the dead cells and cell debris along with the secreted product protein in the harvest stream. While the previously demonstrated inclined or lamellar settlers can be used for such perfusion bioreactors for microbial cells, the size and footprint requirements of such inefficiently scaled up devices can be quite large in comparison to the bioreactor size...
July 27, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28743951/genome-wide-analysis-and-expression-divergence-of-the-trihelix-family-in-brassica-rapa-insight-into-the-evolutionary-patterns-in-plants
#9
Wenli Wang, Peng Wu, TongKong Liu, Haibo Ren, Ying Li, Xilin Hou
Trihelix gene family is an important transcription factor (TF) family involved in plants' growth and development. This extensive study of trihelix genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution in plants and support crop breeding. In this study, a total of 52 trihelix genes were identified in B.rapa. Whole-genome annotation, molecular-evolution and gene-expression analyses of all known trihelix genes were conducted. By statistics of the number of trihelix genes in each species, we found the expansion of trihelix gene family started with angiosperm evolution...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28736529/detection-of-ros-induced-proteomic-signatures-by-mass-spectrometry
#10
REVIEW
Brian McDonagh
Reversible and irreversible post-translational modifications (PTMs) induced by endogenously generated reactive oxygen species (ROS) in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28735898/genome-wide-single-molecule-footprinting-reveals-high-rna-polymerase-ii-turnover-at-paused-promoters
#11
Arnaud R Krebs, Dilek Imanci, Leslie Hoerner, Dimos Gaidatzis, Lukas Burger, Dirk Schübeler
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here, we harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy...
August 3, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28732013/the-kp1_4563-gene-is-regulated-by-the-camp-receptor-protein-and-controls-type-3-fimbrial-function-in-klebsiella-pneumoniae-ntuh-k2044
#12
Mei Luo, Shiya Yang, Xuan Li, Pin Liu, Jian Xue, Xipeng Zhou, Kewen Su, Xuan Xu, Ying Qing, Jingfu Qiu, Yingli Li
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen that can adhere to host cells or extracellular matrix via type 1 and type 3 fimbriae. KP1_4563 is a gene encoding a hypothetical protein in K. pneumoniae NTUH-K2044. KP1_4563 is located between the type 1 and type 3 fimbrial gene clusters and is likely associated with fimbrial function given its putative conserved domains of unknown function (DUF1471). Cyclic AMP receptor protein (CRP) regulates virulence-related gene expression and is a crucial transcriptional regulator in many bacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28715365/analysis-of-the-c-kit-ligand-promoter-using-chromatin-immunoprecipitation
#13
Pingyu Zhang, Andres Rojas, Boris Blechacz
Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin...
June 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28708998/profiling-ssb-nascent-chain-interactions-reveals-principles-of-hsp70-assisted-folding
#14
Kristina Döring, Nabeel Ahmed, Trine Riemer, Harsha Garadi Suresh, Yevhen Vainshtein, Markus Habich, Jan Riemer, Matthias P Mayer, Edward P O'Brien, Günter Kramer, Bernd Bukau
The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent polypeptides to assist protein folding. To reveal its working principle, we determined the nascent chain-binding pattern of Ssb at near-residue resolution by in vivo selective ribosome profiling. Ssb associates broadly with cytosolic, nuclear, and hitherto unknown substrate classes of mitochondrial and endoplasmic reticulum (ER) nascent proteins, supporting its general chaperone function. Ssb engages most substrates by multiple binding-release cycles to a degenerate sequence enriched in positively charged and aromatic amino acids...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28708131/a-clinicopathological-approach-to-the-diagnosis-of-dementia
#15
REVIEW
Fanny M Elahi, Bruce L Miller
The most definitive classification systems for dementia are based on the underlying pathology which, in turn, is categorized largely according to the observed accumulation of abnormal protein aggregates in neurons and glia. These aggregates perturb molecular processes, cellular functions and, ultimately, cell survival, with ensuing disruption of large-scale neural networks subserving cognitive, behavioural and sensorimotor functions. The functional domains affected and the evolution of deficits in these domains over time serve as footprints that the clinician can trace back with various levels of certainty to the underlying neuropathology...
August 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28674401/quantitative-protein-topography-measurements-by-high-resolution-hydroxyl-radical-protein-footprinting-enable-accurate-molecular-model-selection
#16
Boer Xie, Amika Sood, Robert J Woods, Joshua S Sharp
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28671673/ews-fli1-perturbs-mrtfb-yap-1-tead-target-gene-regulation-inhibiting-cytoskeletal-autoregulatory-feedback-in-ewing-sarcoma
#17
A M Katschnig, M O Kauer, R Schwentner, E M Tomazou, C N Mutz, M Linder, M Sibilia, J Alonso, D N T Aryee, H Kovar
Ewing sarcoma (EWS) is a paediatric bone cancer with high metastatic potential. Cellular plasticity resulting from dynamic cytoskeletal reorganization, typically regulated via the Rho pathway, is a prerequisite for metastasis initiation. Here, we interrogated the role of the Ewing sarcoma driver oncogene EWS-FLI1 in cytoskeletal reprogramming. We report that EWS-FLI1 strongly represses the activity of the Rho-F-actin signal pathway transcriptional effector MRTFB, affecting the expression of a large number of EWS-FLI1-anticorrelated genes including structural and regulatory cytoskeletal genes...
July 3, 2017: Oncogene
https://www.readbyqxmd.com/read/28667374/human-umbilical-cord-mesenchymal-stem-cells-protect-against-sca3-by-modulating-the-level-of-70-kd-heat-shock-protein
#18
Tan Li, Yi Liu, Linjie Yu, Jiamin Lao, Meijuan Zhang, Jiali Jin, Zhengjuan Lu, Zhuo Liu, Yun Xu
Spinocerebellar ataxia 3 (SCA3), which is a progressive neurodegenerative disease, is currently incurable. Emerging studies have reported that human umbilical cord mesenchymal stem cells (HUC-MSCs) transplantation could be a promising therapeutic strategy for cerebellar ataxias. However, few studies have evaluated the effects of HUC-MSCs on SCA3 transgenic mouse. Thus, we investigated the effects of HUC-MSCs on SCA3 mice and the underlying mechanisms in this study. SCA3 transgenic mice received systematic administration of 2 × 10(6) HUC-MSCs once per week for 12 continuous weeks...
June 30, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28663783/questions-on-unusual-mimivirus-like-structures-observed-in-human-cells
#19
Elena Angela Lusi, Dan Maloney, Federico Caicci, Paolo Guarascio
Background: Mimiviruses or giant viruses that infect amoebas have the ability to retain the Gram stain, which is usually used to colour bacteria. There is some evidence suggesting that Mimiviruses can also infect human cells. Guided by these premises, we performed a routine Gram stain on a variety of human specimens to see if we could detect the same Gram positive blue granules that identify Mimiviruses in the amoebas.  Methods: We analysed 24 different human specimens (liver, brain, kidney, lymph node and ovary) using Gram stain histochemistry, electron microscopy immunogold, high resolution mass spectrometry and protein identification...
2017: F1000Research
https://www.readbyqxmd.com/read/28662383/tracking-the-missing-footprints-of-idle-ribosomes
#20
Nicholas T Ingolia
Once inactive ribosomes are accounted for, ribosome footprint profiling data and pulse-labeled proteomics provide similar, accurate measurements of protein synthesis.
June 28, 2017: Cell Systems
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