Cytoplasm Of Mammalian Cells Research Articles

Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING

The presence of microbial or self DNA in the cytoplasm of mammalian cells is a danger signal detected by the DNA sensor cyclic-GMP-AMP (cGAMP) synthase (cGAS), which catalyzes the production of cGAMP that in turn serves as a second messenger to activate innate immune responses. Here we show that endogenous cGAMP in mammalian cells contains two distinct phosphodiester linkages, one between 2'-OH of GMP and 5'-phosphate of AMP, and the other between 3'-OH of AMP and 5'-phosphate of GMP. This molecule, termed 2'3'-cGAMP, is unique in that it binds to the adaptor protein STING with a much greater affinity than cGAMP molecules containing other combinations of phosphodiester linkages. The crystal structure of STING bound to 2'3'-cGAMPrevealed the structural basis of this high-affinitybinding and a ligand-induced conformational change in STING that may underlie its activation.

Cyclic GMP-AMP Synthase (cGAS) is a cytosolic DNA sensor that activates type I interferon pathway by generating a second messenger (P1346)

Abstract The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers the host immune responses such as the production of type-I interferons (IFN). This DNA signaling pathway requires the adaptor protein STING and the transcription factor IRF3, but the mechanism of DNA sensing is unclear. Here we showed that mammalian cytosolic extracts synthesized cyclic-GMP-AMP (cGAMP) in vitro from ATP and GTP in the presence of DNA but not RNA. DNA transfection or DNA virus infection of mammalian cells also triggered cGAMP production in vivo. cGAMP bound to STING, leading to the activation of IRF3 and induction of interferon-β. Thus, cGAMP represents the first cyclic di-nucleotide in metazoa and it functions as an endogenous second messenger that triggers interferon production in response to cytosolic DNA. Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family. Overexpression of cGAS activated the transcription factor IRF3 and induced IFNβ in a STING-dependent manner. Knockdown of cGAS inhibited IRF3 activation and IFNβ induction by DNA transfection or DNA virus infection. cGAS bound to DNA in the cytoplasm and catalyzed cGAMP synthesis. These results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP.

Inside GPCR signalling

von Zastrow and colleagues provide direct evidence that G protein-coupled receptor (GPCR) signalling occurs at endosomes, in addition to the plasma membrane. They generated a conformation-specific antibody (nanobody (Nb80)) that functions as a biosensor for activated (that is, agonist-bound) β2 adrenergic receptor (β2AR), a prototypical GPCR. Without agonist, Nb80–GFP localized to the cytoplasm in mammalian cells. After the addition of the agonist isoprenaline, Nb80–GFP was rapidly recruited to the plasma membrane, where it colocalized with β2ARs. β2ARs are known to be internalized after activation. Importantly, the authors observed that internalized β2ARs were not bound to Nb80–GFP; Nb80–GFP was later recruited to activated β2ARs at early endosomes. Use of another nanobody, Nb37, that is specific for activated G proteins, showed that G protein activation occurred at β2AR-containing endosomes, which contributed to the cellular cyclic AMP response. This directly shows that GPCRs signal from endosomes and the plasma membrane.

Reconstituted plant viral capsids can release genes to mammalian cells

The nucleocapsids of many plant viruses are significantly more robust and protective of their RNA contents than those of enveloped animal viruses. In particular, the capsid protein (CP) of the plant virus Cowpea Chlorotic Mottle Virus (CCMV) is of special interest because it has been shown to spontaneously package, with high efficiency, a large range of lengths and sequences of single-stranded RNA molecules. In this work we demonstrate that hybrid virus-like particles, assembled in vitro from CCMV CP and a heterologous RNA derived from a mammalian virus (Sindbis), are capable of releasing their RNA in the cytoplasm of mammalian cells. This result establishes the first step in the use of plant viral capsids as vectors for gene delivery and expression in mammalian cells. Furthermore, the CCMV capsid protects the packaged RNA against nuclease degradation and serves as a robust external scaffold with many possibilities for further functionalization and cell targeting.

GPI-anchored carbonic anhydrase IV displays both intra- and extracellular activity in cRNA-injected oocytes and in mouse neurons

Soluble cytosolic carbonic anhydrases (CAs) are well known to participate in pH regulation of the cytoplasm of mammalian cells. Membrane-bound CA isoforms--such as isoforms IV, IX, XII, XIV, and XV--also catalyze the reversible conversion of carbon dioxide to protons and bicarbonate, but at the extracellular face of the cell membrane. When human CA isoform IV was heterologously expressed in Xenopus oocytes, we observed, by measuring H(+) at the outer face of the cell membrane and in the cytosol with ion-selective microelectrodes, not only extracellular catalytic CA activity but also robust intracellular activity. CA IV expression in oocytes was confirmed by immunocytochemistry, and CA IV activity measured by mass spectrometry. Extra- and intracellular catalytic activity of CA IV could be pharmacologically dissected using benzolamide, the CA inhibitor, which is relatively slowly membrane-permeable. In acute cerebellar slices of mutant mice lacking CA IV, cytosolic H(+) shifts of granule cells following CO(2) removal/addition were significantly slower than in wild-type mice. Our results suggest that membrane-associated CA IV contributes robust catalytic activity intracellularly, and that this activity participates in regulating H(+) dynamics in the cytosol, both in injected oocytes and in mouse neurons.

Structural Characterization of the Helicobacter Pylori VacA Toxin by Single Particle Em and X-Ray Crystallography

Helicobacter pylori is a Gram-negative bacterium that infects the human stomach and contributes to the pathogenesis of peptic ulceration, gastric adenocarcinoma and gastric lymphoma. H. pylori secretes an exotoxin called vacuolating toxin (VacA), known for its ability to induce vacuolation in the cytoplasm of mammalian cells. VacA can cause depolarization of membrane potential, alteration of mitochondrial membrane permeability, apoptosis, activation of mitogen-activated protein kinases, inhibition of T cell activation and proliferation, and autophagy. The mechanisms by which these processes occur are not yet fully understood but many of these toxic effects depend on the capacity of VacA to form anion-selective membrane channels. VacA is an 88 kDa protein that contains two distinct domains, p55 and p33. The 88 kDa monomers can assemble into large water-soluble oligomeric “flower”-shaped structures. Using single particle electron microscopy and the random conical tilt approach, we have determined three-dimensional (3D) structures of six distinct VacA oligomeric conformations at ∼15 A resolution. This analysis shows that VacA can organize into a number oligomeric conformations that include both single and double layer hexamers and heptamers. The structures, regardless of oligomeric type, contain two prominent features: extended straight “legs” with a slight kink at the distal end and a central “spoke-like” density that contains two distinct globular domains separated by a thin connecting density. We have also generated structures of three VacA mutant proteins that all form oligomers but differ in activity. Overall, these studies provide the most detailed analysis of p33 structure to date and also provide a more thorough understanding of how VacA forms oligomers.

Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway.

The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons. Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate-adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor protein STING. Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family. Overexpression of cGAS activated the transcription factor IRF3 and induced interferon-β in a STING-dependent manner. Knockdown of cGAS inhibited IRF3 activation and interferon-β induction by DNA transfection or DNA virus infection. cGAS bound to DNA in the cytoplasm and catalyzed cGAMP synthesis. These results indicate that cGAS is a cytosolic DNA sensor that induces interferons by producing the second messenger cGAMP.

Detection of micro‐ and nano‐particles in animal cells by ToF‐SIMS 3D analysis

The present study describes the detection and localization of silica particles with diameters between 2 µm and 150 nm within the cytoplasm of mammalian cells by means of ToF‐SIMS 3D analysis. The particles were selected as model objects for non‐luminescent, unlabeled particles that are hard to localize by other experimental approaches. ToF‐SIMS analysis proved the uptake of the particles into the cell body, provided images of their distribution around the cell nucleus and indications that the cell membranes are undulated by the µm‐sized particles beneath the membrane. Two ion sources (Cs+ and O2+) were applied for sputtering the organic material and expose deeper sections of the cells. The resulting images are presented and compared. Copyright © 2012 John Wiley & Sons, Ltd.

Cellular Uptake Mechanisms and Endosomal Trafficking of Supercharged Proteins

Supercharged proteins (SCPs) can deliver functional macromolecules into the cytoplasm of mammalian cells more potently than unstructured cationic peptides. Thus far, neither the structural features of SCPs that determine their delivery effectiveness nor their intracellular fate postendocytosis, has been studied. Using a large set of supercharged GFP (scGFP) variants, we found that the level of cellular uptake is sigmoidally related to net charge and that scGFPs enter cells through multiple pathways, including clathrin-dependent endocytosis and macropinocytosis. SCPs activate Rho and ERK1/2 and also alter the endocytosis of transferrin and EGF. Finally, we discovered that the intracellular trafficking of endosomes containing scGFPs is altered in a manner that correlates with protein delivery potency. Collectively, our findings establish basic structure-activity relationships of SCPs and implicate the modulation of endosomal trafficking as a determinant of macromolecule delivery efficiency.

Translation Initiation on mRNAs Bound by Nuclear Cap-binding Protein Complex CBP80/20 Requires Interaction between CBP80/20-dependent Translation Initiation Factor and Eukaryotic Translation Initiation Factor 3g

In the cytoplasm of mammalian cells, either cap-binding proteins 80 and 20 (CBP80/20) or eukaryotic translation initiation factor (eIF) 4E can direct the initiation of translation. Although the recruitment of ribosomes to mRNAs during eIF4E-dependent translation (ET) is well characterized, the molecular mechanism for CBP80/20-dependent translation (CT) remains obscure. Here, we show that CBP80/20-dependent translation initiation factor (CTIF), which has been shown to be preferentially involved in CT but not ET, specifically interacts with eIF3g, a component of the eIF3 complex involved in ribosome recruitment. By interacting with eIF3g, CTIF serves as an adaptor protein to bridge the CBP80/20 and the eIF3 complex, leading to efficient ribosome recruitment during CT. Accordingly, down-regulation of CTIF using a small interfering RNA causes a redistribution of CBP80 from polysome fractions to subpolysome fractions, without significant consequence to eIF4E distribution. In addition, down-regulation of eIF3g inhibits the efficiency of nonsense-mediated mRNA decay, which is tightly coupled to CT but not to ET. Moreover, the artificial tethering of CTIF to an intercistronic region of dicistronic mRNA results in translation of the downstream cistron in an eIF3-dependent manner. These findings support the idea that CT mechanistically differs from ET.

Infectivity study of Streptococcus phocae to seven fish and mammalian cell lines by confocal microscopy

Streptococcus phocae is a beta-haemolytic bacterium that causes systemic infections in Atlantic salmon, Salmo salar L., cultured in southern Chile and also in seals. In this study, the host-pathogen interaction between S. phocae and seven types of cell lines (fish and mammalian) was examined using an indirect fluorescent antibody and confocal microscopy (CM). Chinook salmon embryo (CHSE-214), epithelioma papulosum cyprini (EPC), salmon head kidney (SHK-1) and Atlantic salmon kidney were used as the fish cell lines, while human cervix epithelial adenocarcinoma (HeLa), African green monkey kidney fibroblast (Cos-7) and mouse leukaemic monocyte macrophage (Raw 264.7) were included as mammalian cell lines. Streptococcus phocae type strain ATCC 51973(T) and isolates LM-08-Sp and P23 were selected as representatives from the salmon and seal host, respectively. For the CM examination, monolayers seeded on round coverslips were studied at 2- and 20-h post-inoculation (pi). The results showed that there is no common infectivity pattern between the three S. phocae strains at 2-h pi and the cell lines tested, regardless of the source of isolation (seal or salmon). All S. phocae strains could internalize and were found inside the fish and mammalian cell cytoplasm after 20-h pi. Regardless of the cells studied (fish or mammal) and incubation (2 and 20 h), S. phocae was never observed inside the nuclei. Seal and salmon isolates showed the highest number of bacteria entering into the primate cell lines (HeLa and Cos-7) from 2-h pi, while ATCC 51973(T) was not found outside or inside the HeLa and Cos-7 cells.

Down-regulation of Fer induces ROS levels accompanied by ATM and p53 activation in colon carcinoma cells

Fer is an intracellular tyrosine kinase which resides in both the cytoplasm and nucleus of mammalian cells. This kinase was also found in all malignant cell-lines analyzed and was shown to support cell-cycle progression in cancer cells. Herein we show that knock-down of Fer, both, impairs cell-cycle progression and imposes programmed cell death in colon carcinoma (CC) cells. The cell-cycle arrest and apoptotic death invoked by the depletion of Fer were found to depend on the activity of p53. Accordingly, down regulation of Fer led to the activation of the Ataxia Telangiectasia Mutated protein (ATM) and its down-stream effector-p53. Knock-down of Fer also increased the level of Reactive-Oxygen Species (ROS) in CC cells, and subjection of Fer depleted cells to ROS neutralizing scavengers significantly decreased the induced phosphorylation and activation of ATM and p53. Notably, over-expression of Fer opposed the Doxorubicin driven activation of ATM and p53, which can be mediated by ROS.Collectively, our findings imply that Fer sustains low ROS levels in CC cells, thereby restraining the activation of ATM and p53 in these cells.

Brightness Characterization of Cytoplasmic & Membrane-Bound Protein Mixtures by Z-Scan Fluorescence Fluctuation Spectroscopy

Fluorescence fluctuation spectroscopy (FFS) has been employed to quantify the stoichiometry of soluble proteins in the nucleus and cytoplasm of mammalian cells. However, some proteins have both cytoplasmic and membrane-bound components which render traditional FFS methods inapplicable due to coexcitation of the spatially distributed protein mixture. In this work, we apply z-scan FFS to characterize the brightness of both the membrane-bound and cytoplasmic populations of a protein. Experimentally, we choose HRas-EGFP as our membrane-bound/cytoplasmic model system. We use a combination of stationary FFS measurements to determine the brightness of membrane-bound and cytoplasmic HRas-EGFP and z-scan intensity profiles to correct for brightness bias due to thin layer geometry and coexcitation of membrane and cytoplasmic layers. Our data show HRas-EGFP to be monomeric at both the upper and lower plasma membrane and also in the cytoplasm. We further examine the brightness statistics of proteins by comparing the experimental brightness distribution of a membrane-bound protein system with that of a soluble protein system. This work is extended by creating a dimeric membrane protein system in order to establish a model for calibrating brightness and stoichiometry. The z-scan FFS measurement technique along with a reliable monomer/dimer calibration system will be important for future membrane protein stoichiometry studies. This research was supported by grants from the National Institutes of Health (GM64589) and the National Science Foundation (PHY 0346782).

Modeling of Particle Number Fluctuations in Entire Cells

In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane illumination spectroscopy (SPIM).Here we introduce a new, efficient method for modeling FCS-type measurements, based on the digital model cell mentioned above, that can reproduce the local particle number fluctuations at the level of imaging resolution. This method allows local variations in, e.g., the diffusion coefficients, average particle numbers, and binding/dissociation coefficients. In combination with FCS-type experiments, and with SPIM in particular, this method can be used to map the parameters important to protein dynamics in an entire cell. Furthermore, in contrast with traditional analytical models currently applied, it can also be used to model non-equilibrium situations.[1] Kuhn T, Ihalainen T O, Hyvaluoma J, Dross N, Willman S F, Langowski J, Vihinen-Ranta M and Timonen J. 2011 Protein Diffusion in Mammalian Cell Cytoplasm. PLoS ONE 6(8): e22962

Computational Modeling of Protein Dynamics in Eukaryotic Cells

Proteins have important functions inside the cell, traveling diffusively or being actively transported to various cellular sites where their activity is needed. Protein motion in the cellular environment is therefore an important topic to understand. However, the cell provides a very complex environment for that motion, which poses problems especially for any modeling effort designed to interpret experimentally observed features. So as to gain a realistic picture of protein dynamics inside the cell, we have recently introduced advanced numerical methods for describing that dynamics [1]. The starting point is an accurate numerical duplicate of the cell determined by LSCM, which can be used as a simulation geometry. Interpreting the internal cellular structures that obstruct the protein motion as the solid component of a porous structure, and treating the motion in the same way as in the case of a porous medium (distinction between effective and apparent diffusion), we can rather accurately take into account the cellular environment in which the motion takes place. The numerical simulations of protein motion in the model cell are based on the lattice-Boltzmann method. Here we use these methods to exactly reproduce photobleaching experiments on the diffusion of Enhanced Yellow Fluorescent Protein (EYFP) in HeLa cells. Comparison of simulated and real experiments can be used to characterize protein motion and the related diffusion coefficients. We pay particular attention to the nuclear translocation of EYFP in these cells.[1] Kuhn T., Ihalainen T. O., Hyvaluoma J., Dross N., Willman S. F., Langovski J., Vihinen-Ranta M. and Timonen J. 2011 Protein Diffusion in Mammalian Cell Cytoplasm. PLoS ONE 6(8): e22962.

Sumoylation of human translationally controlled tumor protein is important for its nuclear transport.

Translationally controlled tumor protein (TCTP) lacks nuclear bipartite localization signal sequence; yet TCTP is present abundantly in the nucleus. At present it is not known how TCTP gets transported to the nucleus. Sequence analyses showed that all TCTPs described to date have putative small ubiquitin-like modifier (SUMO) motifs. Since SUMO modification plays an important role in the nuclear transport of proteins, we evaluated whether SUMO motifs are important for transport of TCTP into the nucleus. We show that TCTP exists in sumoylated form in cytoplasm and nucleus of mammalian cells. Point mutation of lysine residue in the SUMO motif compromised the ability of TCTP to get sumoylated in vitro. When cells were transfected with FLAG-tagged mutated TCTP, nuclear transport of TCTP was inhibited confirming that sumoylation is critical for the nuclear transport of TCTP. Our previous studies demonstrated that TCTP can function as an antioxidant protein in the nucleus. When we mutated TCTP at the SUMO motif the antioxidant function of TCTP was compromised. Results presented in this study thus show that sumoylation plays an important role in the transport of TCTP into the nucleus where they function as antioxidant protein.

Critical importance of the de novo pyrimidine biosynthesis pathway for Trypanosoma cruzi growth in the mammalian host cell cytoplasm

The intracellular parasitic protist Trypanosoma cruzi is the causative agent of Chagas disease in Latin America. In general, pyrimidine nucleotides are supplied by both de novo biosynthesis and salvage pathways. While epimastigotes—an insect form—possess both activities, amastigotes—an intracellular replicating form of T. cruzi—are unable to mediate the uptake of pyrimidine. However, the requirement of de novo pyrimidine biosynthesis for parasite growth and survival has not yet been elucidated. Carbamoyl-phosphate synthetase II (CPSII) is the first and rate-limiting enzyme of the de novo biosynthetic pathway, and increased CPSII activity is associated with the rapid proliferation of tumor cells. In the present study, we showed that disruption of the T. cruzicpsII gene significantly reduced parasite growth. In particular, the growth of amastigotes lacking the cpsII gene was severely suppressed. Thus, the de novo pyrimidine pathway is important for proliferation of T. cruzi in the host cell cytoplasm and represents a promising target for chemotherapy against Chagas disease.

Trehalose transporter from African chironomid larvae improves desiccation tolerance of Chinese hamster ovary cells

Dry preservation has been explored as an energy-efficient alternative to cryopreservation, but the high sensitivity of mammalian cells to desiccation stress has been one of the major hurdles in storing cells in the desiccated state. An important strategy to reduce desiccation sensitivity involves use of the disaccharide trehalose. Trehalose is known to improve desiccation tolerance in mammalian cells when present on both sides of the cell membrane. Because trehalose is membrane impermeant the development of desiccation strategies involving this promising sugar is hindered. We explored the potential of using a high-capacity trehalose transporter (TRET1) from the African chironomid Polypedilum vanderplanki[21] to introduce trehalose into the cytoplasm of mammalian cells and thereby increase desiccation tolerance. When Chinese hamster ovary cells (CHO) were stably transfected with TRET1 (CHO–TRET1 cells) and incubated with 0.4M trehalose for 4h at 37°C, a sevenfold increase in trehalose uptake was observed compared to the wild-type CHO cells. Following trehalose loading, desiccation tolerance was investigated by evaporative drying of cells at 14% relative humidity. After desiccation to 2.60g of water per gram dry weight, a 170% increase in viability and a 400% increase in growth (after 7days) was observed for CHO–TRET1 relative to control CHO cells. Our results demonstrate the beneficial effect of intracellular trehalose for imparting tolerance to partial desiccation.

Bromomaleimide-linked bioconjugates are cleavable in mammalian cells.

Bromomaleimide-linked bioconjugates are cleavable in mammalian cells.

Selection for intrabody solubility in mammalian cells using GFP fusions

Single-chain antibody fragments (scFv) expressed in the cytoplasm of mammalian cells, also called intrabodies, have many applications in functional proteomics. These applications are, however, limited by the aggregation-prone behaviour of many intrabodies. We show here that two scFv with highly homologous sequences and comparable soluble expression levels in Escherichia coli cytoplasm have different behaviours in mammalian cells. When over-expressed, one of the scFv aggregates in the cytoplasm whereas the second one is soluble and active. When expressed at low levels, using a retroviral vector, as a fusion with the green fluorescent protein (GFP) the former does not form aggregates and is degraded, resulting in weakly fluorescent cells, whereas the latter is expressed as a soluble protein, resulting in strongly fluorescent cells. These data suggest that the GFP signal can be used to evaluate the soluble expression of intrabodies in mammalian cells. When applied to a subset of an E.coli-optimised intrabody library, we showed that the population of GFP+ cells contains indeed soluble mammalian intrabodies. Altogether, our data demonstrate that the requirements for soluble intrabody expression are different in E.coli and mammalian cells, and that intrabody libraries can be directly optimised in human cells using a simple GFP-based assay.