scholarly journals High-throughput living-cell protein crosslinking analysis uncovers the physiological relevance of forming the “inserted” state of the ATP synthase ε-subunit

2019 ◽  
Author(s):  
Yang Liu ◽  
Jiayu Yu ◽  
Mengyuan Wang ◽  
Qingfang Zeng ◽  
Xinmiao Fu ◽  
...  
Keyword(s):  
Atp Synthase ◽  
High Throughput ◽  
Living Cell ◽  
Polyacrylamide Gel Electrophoresis ◽  
Unnatural Amino Acid ◽  
Fine Tuning ◽  
Cell Protein ◽  
Experimental Conditions ◽  
Physiological Relevance ◽  
In Cells

AbstractATP synthase, a highly conserved multi-subunit enzyme complex having a common stoichiometry of α3β3γδεab2c8-15, functions to supply ATP as the universal energy currency for cells. It comprises of the peripheral F1 sector (α3β3γδε) and the membrane-integrated Fo sector (ab2c8-15). In vitro structural analyses revealed that the C-terminal domain of the ε-subunit could adopt either an “inserted” or “non-inserted” state (with or without interacting with the α/β-subunits), with the former being viewed as inhibitory for the ATP hydrolysis activity of ATP synthase. Nevertheless, as common in current protein researches, the physiological relevance of such an “inserted” state for ATP synthase functioning is hardly known. To decipher this, designed an unnatural amino acid-mediated living-cell protein photocrosslinking analysis pipeline by developing the scarless genome-targeted site-directed mutagenesis and the high-throughput gel polyacrylamide gel electrophoresis (HT-PAGE) techniques. Employing this powerful approach, we systematically examined the interactions involving the C-terminal helix of the ε-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the “inserted” and “non-inserted” states of the ε-subunit exist as an equilibrium in cells cultured under common experimental conditions, shifting to the former upon the appearance of unfavorable conditions, acting as a low-gear state to strengthen the ATP synthesis function. Such a fine-tuning mechanism allows the ATP synthase to reversibly and instantly switch between two functional states. Further, the two powerful techniques that we developed here might be applied to many aspects of protein researches.

scholarly journals Fate of surface proteins of rabbit polymorphonuclear leukocytes during phagocytosis. II. Internalization of proteins.

1979 ◽  
Vol 82 (1) ◽  
pp. 45-56 ◽  
Author(s):  
M Willinger ◽  
N Gonatas ◽  
F R Frankel
Keyword(s):  
Plasma Membrane ◽  
Polymorphonuclear Leukocytes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Surface Proteins ◽  
Cell Protein ◽  
Resting Cells ◽  
Experimental Conditions ◽  
Particle Uptake ◽  
Differentiated Cells ◽  
Free Iodine

The distribution of surface proteins during phagocytosis by rabbit peritoneal polymorphonuclear leukocytes was studied to determine whether the proteins of the phagocytic vesicles of these differentiated cells were representative of the entire set of plasma membrane proteins. Phagocytosis of bovine serum albumin-diisodecylphthalate emulsion by lactoperoxidase-iodinated rabbit neutrophils was linear over 15-20 min at a rate of 96 microgram oil/min/mg cell protein. This rate was similar to that of unlabeled cells. Incorporation of cell-associated free iodine by endogenous myeloperoxidase during phagocytosis was inhibited by 1 mM cyanide, which had no effect on the rate of particle uptake. The surface of intact neutrophils contained at least 13 iodinated proteins distinguishable by polyacrylamide gel electrophoresis followed by autoradiography. Isolated phagosomes were deficient in six of these proteins. The plasma membrane fraction of these cells was missing five of these same proteins which, however, were enriched in a dense surface fraction (Willinger, M., and F. R. Frankel. J. Cell Biol. 82: 32-44). When experimental conditions were reversed, and the PMNs were labeled after phagocytosis, these five proteins remained on the cell surface, while at least three of the major proteins found on resting cells were depleted. Incubating the cells with colchicine, which has been shown to affect the distribution of some plasma membrane constituents during phagocytosis, had no effect on the distribution of surface proteins in our system. These results indicate that a nonrandom interiorization of lactoperoxidase-labeled surface proteins of polymorphonuclear leukocytes occurs during phagocytosis.

scholarly journals Simple and Rapid High-Throughput Assay to Identify HSV-1 ICP0 Transactivation Inhibitors

2021 ◽  
Author(s):  
Cindy Y. Ly ◽  
Chunmiao Yu ◽  
Peter McDonald ◽  
Anuradha Roy ◽  
David Johnson ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Viral Gene Expression ◽  
Lytic Replication ◽  
Cell Protein ◽  
Viral Gene ◽  
Herpes Simplex Virus 1 ◽  
Cellular Factors ◽  
In Cells ◽  
Hsv 1

AbstractHerpes simplex virus 1 (HSV-1) is a ubiquitous virus that results in lifelong infections due to it’s ability to cycle between lytic replication and latency. As an obligate intracellular pathogen, HSV-1 exploits host cellular factors to replicate and aid in its life cycle. HSV-1 expresses infected cell protein 0 (ICP0), an immediate-early regulator, to stimulate the transcription of all classes of viral genes via its E3 ubiquitin ligase activity. Mechanisms by which ICP0 activates viral gene expression and the cellular factors involved are largely unknown. Here we report an automated, inexpensive, and rapid high-throughput approach to examine the effects of small molecule compounds on ICP0 transactivator function in cells. Two HSV-1 reporter viruses, KOS6β (wt) and dlx3.1-6β (ICP0-null mutant), were used to monitor ICP0 transactivation activity through the HSV-1 ICP6 promoter::lacz expression cassette. A ≥10-fold difference in β-galactosidase activity was observed in cells infected with KOS6β compared to dlx3.1-6β, demonstrating that ICP0 potently transactivates the ICP6 promoter. We established the robustness and reproducibility with a Z′- factor score of ≥0.69, an important criterium for high-throughput analyses. Approximately 19,000 structurally diverse compounds were screened and 76 potential inhibitors of the HSV-1 transactivator ICP0 were identified. We expect this assay will aid in the discovery of novel inhibitors and tools against HSV-1 ICP0. Using well-annotated compounds could identify potential novel factors and pathways that interact with ICP0 to promote HSV-1 gene expression.

scholarly journals Carbon and Nitrogen Sources Have No Impact on the Organization and Composition of Ustilago maydis Respiratory Supercomplexes

2021 ◽  
Vol 7 (1) ◽  
pp. 42
Author(s):  
Deyamira Matuz-Mares ◽  
Oscar Flores-Herrera ◽  
Guadalupe Guerra-Sánchez ◽  
Lucero Romero-Aguilar ◽  
Héctor Vázquez-Meza ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Polyacrylamide Gel Electrophoresis ◽  
Atp Synthesis ◽  
Nitrogen Sources ◽  
Growth Conditions ◽  
Energy Conditions ◽  
Respiratory Complexes ◽  
Respiratory Supercomplexes ◽  
Nadh Dehydrogenases ◽  
Reduced Nicotinamide Adenine Dinucleotide

Respiratory supercomplexes are found in mitochondria of eukaryotic cells and some bacteria. A hypothetical role of these supercomplexes is electron channeling, which in principle should increase the respiratory chain efficiency and ATP synthesis. In addition to the four classic respiratory complexes and the ATP synthase, U. maydis mitochondria contain three type II NADH dehydrogenases (NADH for reduced nicotinamide adenine dinucleotide) and the alternative oxidase. Changes in the composition of the respiratory supercomplexes due to energy requirements have been reported in certain organisms. In this study, we addressed the organization of the mitochondrial respiratory complexes in U. maydis under diverse energy conditions. Supercomplexes were obtained by solubilization of U. maydis mitochondria with digitonin and separated by blue native polyacrylamide gel electrophoresis (BN-PAGE). The molecular mass of supercomplexes and their probable stoichiometries were 1200 kDa (I1:IV1), 1400 kDa (I1:III2), 1600 kDa (I1:III2:IV1), and 1800 kDa (I1:III2:IV2). Concerning the ATP synthase, approximately half of the protein is present as a dimer and half as a monomer. The distribution of respiratory supercomplexes was the same in all growth conditions. We did not find evidence for the association of complex II and the alternative NADH dehydrogenases with other respiratory complexes.

scholarly journals Macromolecular properties and polymeric structure of canine tracheal mucins

1991 ◽  
Vol 276 (2) ◽  
pp. 525-532 ◽  
Author(s):  
V Shankar ◽  
A K Virmani ◽  
B Naziruddin ◽  
G P Sachdev
Keyword(s):  
Gel Electrophoresis ◽  
Guanidine Hydrochloride ◽  
Polyacrylamide Gel Electrophoresis ◽  
Hydrophobic Properties ◽  
Experimental Conditions ◽  
Protein Core ◽  
Polymeric Structure ◽  
Composite Gel ◽  
Self Association ◽  
Static Laser Light Scattering

Two high-Mr mucus glycoproteins (mucins), CTM-A and CTM-B, were highly purified from canine tracheal pouch secretions, and their macromolecular properties as well as polymeric structure were investigated. On SDS/composite-gel electrophoresis, a diffuse band was observed for each mucin. Polyacrylamide-gel electrophoresis using 6% gels also showed the absence of low-Mr contaminants in the mucins. Comparison of chemical and amino acid compositions revealed significant differences between the two mucins. Using a static-laser-light-scattering technique, CTM-A and CTM-B were found to have weight-average Mr values of about 11.0 x 10(6) and 1.4 x 10(6) respectively. Both mucins showed concentration-dependent aggregation in buffer containing 6 M-guanidine hydrochloride. Under similar experimental conditions, reduced-alkylated CTM-A had an Mr of 5.48 x 10(6) and showed no concentration-dependent aggregation. Hydrophobic properties of the mucins, investigated by the fluorescent probe technique using mansylphenylalanine as the probe, showed the presence of a large number of low-affinity (KD approx. 10(5) M) binding sites. These sites appeared to be located on the non-glycosylated regions of the protein core, since Pronase digestion of the mucins almost completely eliminated probe binding. Reduction of disulphide bonds of CTM-A and CTM-B did not significantly alter the probe-binding properties. Also, addition of increasing NaCl concentrations (0.03-1.0 M) to the buffer caused only a small change in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable degradation, using a combination of chemical and enzymic methods. On SDS/PAGE the protein core was estimated to have an Mr of approx. 60,000. On the basis of the protein and carbohydrate contents of the major mucin CTM-A, the mucin monomer was calculated to have an Mr of approx. 140,000. The high Mr (11 x 10(6] observed by physical methods is therefore due to self-association of the mucin monomer subunits.

Apical control of band elongation in Antithamnion defectum (Ceramiaceae, Rhodophyta)

1988 ◽  
Vol 66 (7) ◽  
pp. 1308-1315 ◽  
Author(s):  
David Garbary ◽  
Daniel Belliveau ◽  
Robert Irwin
Keyword(s):  
Cell Elongation ◽  
Experimental Conditions ◽  
Axial Cell ◽  
Wall Deposition ◽  
Apical Control ◽  
Band Position ◽  
Apical Cells ◽  
In Cells

Cell elongation in the Ceramiaceae typically occurs by means of one or two bands located apically and (or) basally in each cell. In axial cells of Antithamnion defectum two bands are present; however, most cell elongation occurs as a result of new wall deposition in bands at the base of each axial cell. In cells of determinate branches, only the basal band is present. In experimental conditions in which apical cells of indeterminate branches are differentially excised, location of the primary elongation band can be reestablished in relation to remaining indeterminate axes. Thus, the primary elongation band in axial cells is always basal with respect to indeterminate apical cells. When all indeterminate apices are removed, band growth becomes highly disrupted, and diffuse, irregularly located bands are formed. These results suggest that regulation of band position and elongation is through apical control.

scholarly journals Automated Sample Preparation and Data Collection Workflow for High-Throughput In Vitro Metabolomics

Metabolites ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 52
Author(s):  
Julia M. Malinowska ◽  
Taina Palosaari ◽  
Jukka Sund ◽  
Donatella Carpi ◽  
Gavin R. Lloyd ◽  
...  
Keyword(s):  
Sample Preparation ◽  
High Throughput ◽  
High Throughput Screening ◽  
In Vitro Screening ◽  
Chemical Safety ◽  
Experimental Conditions ◽  
Well Location ◽  
Relative Standard ◽  
Automated Sample Preparation

Regulatory bodies have started to recognise the value of in vitro screening and metabolomics as two types of new approach methodologies (NAMs) for chemical risk assessments, yet few high-throughput in vitro toxicometabolomics studies have been reported. A significant challenge is to implement automated sample preparation of the low biomass samples typically used for in vitro screening. Building on previous work, we have developed, characterised and demonstrated an automated sample preparation and analysis workflow for in vitro metabolomics of HepaRG cells in 96-well microplates using a Biomek i7 Hybrid Workstation (Beckman Coulter) and Orbitrap Elite (Thermo Scientific) high-resolution nanoelectrospray direct infusion mass spectrometry (nESI-DIMS), across polar metabolites and lipids. The experimental conditions evaluated included the day of metabolite extraction, order of extraction of samples in 96-well microplates, position of the 96-well microplate on the instrument’s deck and well location within a microplate. By using the median relative standard deviation (mRSD (%)) of spectral features, we have demonstrated good repeatability of the workflow (final mRSD < 30%) with a low percentage of features outside the threshold applied for statistical analysis. To improve the quality of the automated workflow further, small method modifications were made and then applied to a large cohort study (4860 sample infusions across three nESI-DIMS assays), which confirmed very high repeatability of the whole workflow from cell culturing to metabolite measurements, whilst providing a significant improvement in sample throughput. It is envisioned that the automated in vitro metabolomics workflow will help to advance the application of metabolomics (as a part of NAMs) in chemical safety, primarily as an approach for high throughput screening and prioritisation.

scholarly journals The Transcriptional landscape of Streptococcus pneumoniae reveals a complex operon architecture and abundant riboregulation critical for growth and virulence

2018 ◽  
Author(s):  
Indu Warrier ◽  
Nikhil Ram-Mohan ◽  
Zeyu Zhu ◽  
Ariana Hazery ◽  
Michelle M Meyer ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
High Throughput ◽  
Transcription Initiation ◽  
High Throughput Sequencing ◽  
Regulatory Element ◽  
Fine Tuning ◽  
Transcriptional Units ◽  
Rna Elements ◽  
Transcriptional Landscape

AbstractEfficient and highly organized transcription initiation and termination is fundamental to an organism’s ability to survive, proliferate, and quickly respond to its environment. Over the last decade, our simplistic outlook of bacterial transcriptional regulation and architecture has evolved to include stimulus-responsive regulation by untranslated RNA and the formation of alternate transcriptional units. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae by applying a combination of high-throughput RNA-sequencing techniques. Our study reveals a complex transcriptome wherein environment-respondent alternate transcriptional units are observed within operons stemming from internal transcription start sites (TSS) and transcription terminators (TTS) suggesting that more fine-tuning of regulation occurs than previously thought. Additionally, we identify many putative cis-regulatory RNA elements and riboswitches within 5’-untranslated regions (5’-UTR) of genes. By integrating TSSs and TTSs with independently collected RNA-Seq datasets from a variety of conditions, we establish the response of these regulators to changes in growth conditions and validate several of them. Furthermore, to determine the importance of ribo-regulation by 5’-UTR elements for in vivo virulence, we show that the pyrR regulatory element is essential for survival, successful colonization and infection in mice suggesting that such RNA elements are potential drug targets. Importantly, we show that our approach of combining high-throughput sequencing with in vivo experiments can reconstruct a global understanding of regulation, but also pave the way for discovery of compounds that target (ribo-) regulators to mitigate virulence and antibiotic resistance.

scholarly journals A Novel H+ Conductance in Eosinophils

1999 ◽  
Vol 190 (2) ◽  
pp. 183-194 ◽  
Author(s):  
Botond Bánfi ◽  
Jacques Schrenzel ◽  
Oliver Nüsse ◽  
Daniel P. Lew ◽  
Erzsébet Ligeti ◽  
...  
Keyword(s):  
Nadph Oxidase ◽  
The Novel ◽  
Experimental Conditions ◽  
Intact Cells ◽  
Electrophysiological Studies ◽  
Dependent Signal ◽  
Low Threshold ◽  
Nadph Oxidase Activation ◽  
In Cells

Efficient mechanisms of H+ ion extrusion are crucial for normal NADPH oxidase function. However, whether the NADPH oxidase—in analogy with mitochondrial cytochromes—has an inherent H+ channel activity remains uncertain: electrophysiological studies did not find altered H+ currents in cells from patients with chronic granulomatous disease (CGD), challenging earlier reports in intact cells. In this study, we describe the presence of two different types of H+ currents in human eosinophils. The “classical” H+ current had properties similar to previously described H+ conductances and was present in CGD cells. In contrast, the “novel” type of H+ current had not been described previously and displayed unique properties: (a) it was absent in cells from gp91- or p47-deficient CGD patients; (b) it was only observed under experimental conditions that allowed NADPH oxidase activation; (c) because of its low threshold of voltage activation, it allowed proton influx and cytosolic acidification; (d) it activated faster and deactivated with slower and distinct kinetics than the classical H+ currents; and (e) it was ∼20-fold more sensitive to Zn2+ and was blocked by the histidine-reactive agent, diethylpyrocarbonate (DEPC). In summary, our results demonstrate that the NADPH oxidase or a closely associated protein provides a novel type of H+ conductance during phagocyte activation. The unique properties of this conductance suggest that its physiological function is not restricted to H+ extrusion and repolarization, but might include depolarization, pH-dependent signal termination, and determination of the phagosomal pH set point.

scholarly journals Fine Tuning of Redox Networks on Multiheme Cytochromes fromGeobacter sulfurreducensDrives Physiological Electron/Proton Energy Transduction

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Leonor Morgado ◽  
Joana M. Dantas ◽  
Marta Bruix ◽  
Yuri Y. Londer ◽  
Carlos A. Salgueiro
Keyword(s):  
Microbial Fuel Cells ◽  
Geobacter Sulfurreducens ◽  
Cellular Growth ◽  
Bohr Effect ◽  
Fine Tuning ◽  
Physiological Relevance ◽  
Ph Range ◽  
Coupling Mechanisms ◽  
Redox Bohr Effect

The bacteriumGeobacter sulfurreducens (Gs)can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified inGs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e−/H+coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e−/H+transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e−/H+transfer at the physiological pH range for cellular growth.

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