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PubMed2005

Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization.

We have exploited emulsion-based in vitro compartmentalization (IVC) to devise a method for the selection of zinc finger proteins (ZFPs) on the basis of their DNA-binding specificity. A library of ZFPs fused to a C-terminal peptide tag is encoded by a set of DNA cassettes that are prepared wholly in vitro. In addition to the ZFP gene, each DNA cassette also carries a given DNA target binding site sequence for which one wishes to isolate ZFP binders. An aliquot of the library is added to bacterial S30 extract and emulsified in mineral oil so that most of the aqueous droplets contain, on average, no more than one gene. If an intra-compartmentally expressed ZFP binds specifically to its encoding DNA via the target binding site, the complex can be purified by affinity capture via the peptide tag after breaking the emulsion, thus rescuing the gene. We present proof-of-principle for this IVC selection method by selecting a specific high-affinity ZFP gene from a high background of a related gene. We also propose that high-affinity ZFPs can be used as genotype-phenotype linkages to enable selection of other proteins using IVC.

Binding Sites↗
PubMed2004

Compartmentalization of the splicing machinery in plant cell nuclei.

The cell nucleus is a membrane-surrounded organelle that contains numerous compartments in addition to chromatin. Compartmentalization of the nucleus is now accepted as an important feature for the organization of nuclear processes and for gene expression. Recent studies on nuclear organization of splicing factors in plant cells provide insights into the compartmentalization of the plant cell nuclei and conservation of nuclear compartments between plants and metazoans.

Alternative Splicing↗
PubMed2000

Intracellular compartmentation of organelles and gradients of low molecular weight species.

Intracellular compartmentation of metabolites without intervening membranes is an important concept that has emerged from consideration of the metabolic inhomogeneities associated with a highly organized and structured cytoplasm within mammalian cells. This recognition is primarily due to the development of experimental approaches to measure metabolite or ion concentrations at specific subcellular sites, thereby providing a means to study concentration gradients within the aqueous cytoplasm in intact cells. The presence of mitochondrial clusters has been shown to create gradients of low molecular weight species, such as O2, ATP, and pH, with important implications for substrate supply for function and regulation of cellular processes. Moreover, the existence of kinetically distinct precursor pools has been shown to result in functional compartmentation of biochemical pathways, such as DNA replication and carbohydrate metabolism. The creation of these specialized microzones of metabolism in accordance with their association with cellular organelles or membranal structures may be integral to normal function and regulation of adult mammalian cells.

Adenosine Triphosphate↗
PubMed1998

Compartmentalization of bacterial antigens: differential effects on priming of CD8 T cells and protective immunity.

Bacterial pathogens synthesize numerous proteins that are either secreted or localized within bacterial cells. To address the impact of antigen compartmentalization on T cell immunity, we constructed recombinant Listeria monocytogenes that express a model CD8T cell epitope as a secreted or nonsecreted fusion protein. Both forms of the antigen, either secreted into the host cell cytoplasm or retained within bacterial cells, efficiently prime CD8 T cell responses. However, epitope-specific CD8 T cells confer protection only against bacteria secreting the antigen but not against the bacteria expressing the nonsecreted form of the same antigen. This dichotomy as a result of antigen compartmentalization suggests that bacterial antigens are presented by multiple MHC class I pathways to prime CD8 T cells, but only the endogenous pathway provides target antigens for CD8 T cell-mediated protective immunity.

Antigens, Bacterial↗
PubMed1996

Quantification of intraluminal free [Ca] in the agonist-sensitive internal calcium store using compartmentalized fluorescent indicators: some considerations.

Many fluorescent Ca indicators, particularly those loaded as acetoxymethyl (AM)-ester derivatives, are known to become compartmentalized into organelles. This property can be exploited to measure changes in free [Ca] in subcellular compartments, including the inositol (1,4,5)-trisphosphate-sensitive store. However, quantitative measurement of free [Ca] within a particular compartment is complicated by the fact that dye may accumulate in a variety of organelles and, in many cases, by the Mg sensitivity of the indicator. Here the issue of the quantification of free [Ca] within the thapsigargin-sensitive store in BHK-21 fibroblasts using the low affinity Ca indicator, Mag-Fura-2, has been re-examined. At least 88 +/- 1.3% (SEM) of the compartmentalized dye was determined to be confined to the thapsigargin-sensitive store, with the remaining fraction accounted for by other compartments where [Ca] was below the detection limit for the dye (< 5 microM). In situ calibrations with ionophores indicated that the apparent free resting intraluminal [Ca] was 260 +/- 43 microM (SEM). Our analysis shows, however, that dye reporting from regions of low [Ca] contributes disproportionately to the Mag-Fura-2 ratio measured over the whole cell, potentially resulting in large underestimations of intraluminal [Ca] in agonist-sensitive stores. Free [Ca] in the agonist-sensitive store was calculated to be as high as 539 +/- 92 microM, assuming 12% of the Mag-Fura-2 to be in compartments where [Ca] was below 5 microM. In comparison, perturbations arising from the presence of Mg in stores are predicted to be relatively minor.

Animals↗
PubMedDate not supplied

Compartmentalization of regulatory proteins in the cell nucleus.

The cell nucleus is increasingly recognized as a spatially organized structure. In this review, the nature and controversies associated with nuclear compartmentalization are discussed. The relationship between nuclear structure and organization of proteins involved in the regulation of RNA polymerase II-transcribed genes is then discussed. Finally, very recent data on the mobility of these proteins within the cell nucleus is considered and their implications for regulation through compartmentalization of proteins and genomic DNA are discussed.

Acetylation↗
PubMedDate not supplied

Neurochemical compartmentation of monkey and human visual cortex: similarities and variations in calbindin immunoreactivity across species.

The compartmental organization of visual cortical neurons was examined across species of primates by directly comparing the pattern of immunoreactivity for the 28-kD vitamin D-dependent calcium-binding protein (calbindin) in area 17 of squirrel monkeys, macaques, and neurologically normal adult humans. Area 17 of macaques and squirrel monkeys was similar in that somata and processes intensely immunoreactive for calbindin were present in the same layers (II-III, IVB, and V) and in both species formed a well-stained matrix that surrounded the CO-rich puffs in layer III. These intensely calbindin-immunoreactive neurons were identified as subpopulations of GABA-immunoreactive neurons. Among the most obvious differences in the two monkey species was the distribution of calbindin-positive elements outside of layer III: a dense immunostained matrix surrounded the puffs in layers II, IVB, V, and VI of squirrel monkeys but the immunostained neurons adopted no regular pattern outside layer III in macaques. In addition, although somata lightly immunoreactive for calbindin were present in both species, they were much more abundant in squirrel monkeys than macaques. The pattern of calbindin immunostaining in human area 17 resembled that of macaques in forming an intense matrix that surrounded puffs only in layer III, yet also resembled that of squirrel monkeys by including large numbers of light immunoreactive somata. These lightly immunostained somata included a very dense population forming a prominent band in layer IVA of human visual cortex. We conclude that for layer III of primary visual cortex, a similar pattern of neuronal chemistry exists across species of primates which is related to this layer's compartmental organization. Yet for other layers, the expression of calbindin immunoreactivity varies from one species to the next, perhaps reflecting variations in other neuronal properties.

Aged↗
PubMedDate not supplied

A self-compartmentalizing protease in Rhodococcus: the 20S proteasome.

The 26S proteasome represents a major, energy-dependent and self-compartmentalizing protease system in eukaryotes. The proteolytic core of this complex, the 20S proteasome, is also ubiquitous in archaea. Although absent from most eubacteria, this multi-subunit protease was recently discovered in Rhodococcus and appears to be confined to actinomycetes. The eubacterial 20S proteasome represents an attractive complementary system to study proteasome assembly, quaternary structure, and catalytic mechanism. In addition, it is likely to contribute substantially to our understanding of the role of various self-compartmentalizing proteases in bacterial cells.

Adenosine Triphosphatases↗
PubMedDate not supplied

Compartmentalization and transport in beta-lactam antibiotic biosynthesis by filamentous fungi.

A proper description of the biosynthesis of fungal beta-lactam antibiotics requires detailed knowledge of the cell biology of the producing organisms. This involves a delineation of the compartmentalization of the biosynthetic pathways, and of the consequential transport steps across the cell-boundary plasma membrane and across organellar membranes. Of the enzymes of the penicillin biosynthetic pathway in Penicillium chrysogenum and Aspergillus nidulans, delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) and isopenicillin N synthase (IPNS) probably have a cytosolic location. Acyl-coenzyme A:isopenicillin N acyltransferase (IAT) is located in microbodies. Of the two enzymes that may be involved in activation of the side chain, acetyl-coenzyme A synthetase (ACS) is located in the cytosol, and phenylacetyl-coenzyme A ligase (PCL) is probably located in the microbody. All enzymes of the cephalosporin biosynthesis pathway in Cephalosporium acremonium probably have a cytosolic location. The vacuole may play an ancillary role in the supply of precursor amino acids, and in the storage of intermediates. The distribution of precursors, intermediates, end- and side-products, the transport of nutrients. precursor, intermediates and products across the plasma membrane, and the transport of small solutes across organellar membranes, is discussed. The relevance of compartmentalization is considered against the background of recent biotechnological innovations of fungal beta-lactam biosynthesis pathways.

Anti-Bacterial Agents↗
PubMed1998

On the use of Bayesian methods for evaluating compartmental neural models.

Computational modeling is being used increasingly in neuroscience. In deriving such models, inference issues such as model selection, model complexity, and model comparison must be addressed constantly. In this article we present briefly the Bayesian approach to inference. Under a simple set of commonsense axioms, there exists essentially a unique way of reasoning under uncertainty by assigning a degree of confidence to any hypothesis or model, given the available data and prior information. Such degrees of confidence must obey all the rules governing probabilities and can be updated accordingly as more data becomes available. While the Bayesian methodology can be applied to any type of model, as an example we outline its use for an important, and increasingly standard, class of models in computational neuroscience--compartmental models of single neurons. Inference issues are particularly relevant for these models: their parameter spaces are typically very large, neurophysiological and neuroanatomical data are still sparse, and probabilistic aspects are often ignored. As a tutorial, we demonstrate the Bayesian approach on a class of one-compartment models with varying numbers of conductances. We then apply Bayesian methods on a compartmental model of a real neuron to determine the optimal amount of noise to add to the model to give it a level of spike time variability comparable to that found in the real cell.

Action Potentials↗
PubMedDate not supplied

On the origin of intracellular compartmentation and organized metabolic systems.

The history of the development of the ideas and research of organized metabolic systems during last three decades is shortly reviewed. The cell cytoplasm is crowded with solutes, soluble macromolecules such as enzymes, nucleic acids, structural proteins and membranes. The high protein density within the large compartments of the cells predominantly determines the major characteristics of cellular environment such as viscosity, diffusion and inhomogeneity. The fact that the solvent viscosity of cytoplasm is not substantially different from the water is explained by intracellular structural heterogeneity: the intrinsic macromolecular density is relatively low within the interstitial voids in the cell because many soluble enzymes are apparently integral parts of the insoluble cytomatrix and are not distributed homogeneously. The molecular crowding and sieving restrict the mobility of very large solutes, binding severely restrict the mobility of smaller solutes. One of consequence of molecular crowding and hindered diffusion is the need to compartmentalize metabolic pathway to overcome diffusive barriers. Although the movement of small molecules is slowed down in the cytoplasm, the metabolism can successfully proceed and even be facilitated by metabolite channeling which directly transfers the intermediate from one enzyme to an adjacent enzyme without the need of free aqueous-phase diffusion. The enhanced probability for intermediates to be transferred from one active site to the other by sequential enzymes requires stable or transient interactions of the relevant enzymes, which associate physically in non-dissociable, static multienzyme complexes--metabolones, particles containing enzymes of a part or whole metabolic systems. Therefore, within the living cell the metabolism depends on the structural organization of enzymes forming microcompartments. Since cells contain many compartments and microenvironments, the measurement of the concentration of metabolites in whole cells or tissues gives an average cellular concentration and not that which is actually sensed by the active site of a specific enzyme. Thus, the microcompartmentation could provide a mechanism which can control metabolic pathways. Independently and in parallel to the developments described above, the ideas of compartmentation came into existence from the necessity to explain important physiological phenomena, in particular in heart research and in cardiac electrophysiology. These phenomena demonstrated the physiological importance of the biophysical and biochemical mechanisms described in this review.

Cell Compartmentation↗
PubMed1978

Phosphorus nuclear-magnetic-resonance studies of compartmentation in muscle.

1. Phosphorus nuclear-magnetic-resonance measurements were made on rat vastus lateralis muscle. 2. In the absence of oxygenation, the resonance from P1 broadens, as the 'energy pool' of the muscle gradually runs down. This, together with measurements of transverse relaxation times (T2) indicate that the intracellular pH is not uniform within the muscle volume. 3. Incubation of the muscle with acetate buffer at low pH (5.2) results in splitting of the P1 resonance into two components; one corresponds to phosphate in a low-pH environment and the other to phosphate in its original environment. These observations indicate that P1 is distributed among different compartments in the muscle cell. 4. Compartmentation of sugar phosphate (mainly glucose 6-phosphate) is also indicated by this method, but no evidence has been obtained for this type of compartmentation of ATP and phosphocreatine.

Acetates↗
PubMed1980

Free pyrimidine nucleotide pool of Ehrlich ascites-tumour cells. Compartmentation with respect to the synthesis of heterogeneous nuclear RNA and precursors to ribosomal RNA.

The incorporation of [14C]orotate and [14C]uridine into UMP residues of hnRNA (heterogeneous nuclear RNA) and pre-rRNA (precursors to rRNA) of Eharlich ascites-tumour cells was compared: orotate was incorporated at a markedly higher rate into hnRNA. On the other hand, the rate of incorporation of uridine into pre-rRTNA was even somewhat higher than into hnRNA. The ratio of specific radioactivities of CMP to UMP residues in pre-rRNA and hnRNA was studied. At all times of labelling this ratio was similar for both RNA species independently of the precursor used. On addition of excess unlabelled uridine, the CMP/UMP labelling ratio in both pre-rRNA and hnRNA rose. However, this increase was much more pronounced with hnRNA. It is concluded that nuclear pyrimidine nucleotide pool for RNA synthesis is compartmentalized. The synthesis of hnRNa is supplied preferentially by the large and the small compartment, respectively. A detailed model for the cellular compartmentation of uridine nucleotide precursors to RNA is proposed.U

Animals↗
PubMed2005

Compartmentalization of transport and phosphorylation of glucose in a hepatoma cell line.

The first steps of glucose metabolism are carried out by members of the families of GLUTs (glucose transporters) and HKs (hexokinases). Previous experiments using the inhibitor of glucose transport, CB (cytochalasin B), revealed that compartmentalization of GLUTs and HKs is a major factor in the control of glucose uptake in L6 myotubes [Whitesell, Ardehali, Printz, Beechem, Knobel, Piston, Granner, Van Der Meer, Perriott and May (2003) Biochem. J. 370, 47-56]. In the present paper, we evaluate compartmentalization of GLUTs and HKs in a hepatoma cell line, H4IIE, which is characterized by excess GLUT activity, HKI in a particulate and a cytosolic fraction, and insignificant G6Pase (glucose-6-phosphatase) activity. The measured activity of glucose transport exceeded the rate of phosphorylation approx. 30-fold. Treatment with 25 microM CB (K(i) approximately 3 microM in H4IIE cells) paradoxically increased the excess of GLUTs over phosphorylation (GLUTs are inhibited 80%, while phosphorylation is inhibited 98%). The global relationships of the data could be reconciled most simply by a two-compartment model. In this model, phosphorylation of glucose is carried out by a subset of HK molecules supplied by a subset of GLUTs that are more sensitive to CB than the other GLUTs. The agent, DCC (dicyclohexylcarbodi-imide) caused HKI to translocate from the particulate compartment to the cytosolic compartment and potently inhibited glucose phosphorylation. The particulate compartment may represent the mitochondria, to which the more CB-sensitive GLUTs may control the transport of glucose.

3-O-Methylglucose↗
PubMed2005

Compartmental oxidation of thiol-disulphide redox couples during epidermal growth factor signalling.

Exogenously added ROS (reactive oxygen species) cause generalized oxidation of cellular components, whereas endogenously generated ROS induced by physiological stimuli activate discrete signal transduction pathways. Compartmentation is an important aspect of such pathways, but little is known about its role in redox signalling. We measured the redox states of cytosolic and nuclear Trx1 (thioredoxin-1) and mitochondrial Trx2 (thioredoxin-2) using redox Western blot methodologies during endogenous ROS production induced by EGF (epidermal growth factor) signalling. The glutathione redox state was measured by HPLC. Results showed that only cytosolic Trx1 undergoes significant oxidation. Thus EGF signalling involves subcellular compartmental oxidation of Trx1 in the absence of a generalized cellular oxidation.

Cell Compartmentation↗
PubMed1986

Turnover of phosphomonoester groups and compartmentation of polyphosphoinositides in human erythrocytes.

The turnover of phosphomonoester groups of phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] was investigated in human erythrocytes by short-term labelling with [32P]Pi. The procedure applied ensured a quantitative extraction of erythrocyte polyphosphoinositides as well as their reliable separation for the determinations of pool sizes and specific radioactivities. The pool sizes of phosphatidylinositol (PtdIns), PtdIns4P and PtdIns(4,5)P2 are 25, 11 and 44 nmol/ml of cells respectively. Under steady-state conditions, the phosphorylation fluxes from [gamma-32P]ATP into PtdIns4P and PtdIns(4,5)P2 are in the ranges 14-22 and 46-94 nmol X h-1 X ml of cells-1 respectively. Only 25-60% of total PtdIns4P and 6-10% of total PtdIns(4,5)P2 take part in the rapid tracer exchange, i.e. are compartmentalized. In isolated erythrocyte ghosts, the turnover of PtdIns4P approximately corresponds to that in intact erythrocytes, although any compartmentation can be excluded in this preparation. Under the conditions of incubation employed, the turnover of PtdIns(4,5)P2 is more than one order of magnitude smaller in isolated ghosts than that obtained for intact erythrocytes.

Adenosine Triphosphate↗
PubMed2007

Differential distribution of NCX1 contributes to spine-dendrite compartmentalization in CA1 pyramidal cells.

Compartmentalization of Ca(2+) between dendritic spines and shafts is governed by diffusion barriers and a range of Ca(2+) extrusion mechanisms. The distinct contribution of different Ca(2+) clearance systems to Ca(2+) compartmentalization in dendritic spines versus shafts remains elusive. We applied a combination of ultrastructural and functional imaging methods to assess the subcellular distribution and role of NCX1 in rat CA1 pyramidal cells. Quantitative electron microscopic analysis of preembedding immunogold reactions revealed uniform densities of NCX1 along the shafts of apical and basal dendrites, but densities in dendritic shafts were approximately seven times higher than in dendritic spines. In line with these results, two-photon imaging of synaptically activated Ca(2+) transients during NCX blockade showed preferential action localized to the dendritic shafts for NCXs in regulating spine-dendrite coupling.

Animals↗
PubMed1996

cAMP compartmentation is responsible for a local activation of cardiac Ca2+ channels by beta-adrenergic agonists.

The role of cAMP subcellular compartmentation in the progress of beta-adrenergic stimulation of cardiac L-type calcium current (ICa) was investigated by using a method based on the use of whole-cell patch-clamp recording and a double capillary for extracellular microperfusion. Frog ventricular cells were sealed at both ends to two patch-clamp pipettes and positioned approximately halfway between the mouths of two capillaries that were separated by a 5-micron thin wall. ICa could be inhibited in one half or the other by omitting Ca2+ from one solution or the other. Exposing half of the cell to a saturating concentration of isoprenaline (ISO, 1 microM) produced a nonmaximal increase in ICa (347 +/- 70%; n = 4) since a subsequent application of ISO to the other part induced an additional effect of nearly similar amplitude to reach a 673 +/- 130% increase. However, half-cell exposure to forskolin (FSK, 30 microM) induced a maximal stimulation of ICa (561 +/- 55%; n = 4). This effect was not the result of adenylyl cyclase activation due to FSK diffusion in the nonexposed part of the cell. To determine the distant effects of ISO and FSK on ICa, the drugs were applied in a zero-Ca solution. Adding Ca2+ to the drug-containing solutions allowed us to record the local effect of the drugs. Dose-response curves for the local and distant effects of ISO and FSK on ICa were used as an index of cAMP concentration changes near the sarcolemma. We found that ISO induced a 40-fold, but FSK induced only a 4-fold, higher cAMP concentration close to the Ca2+ channels, in the part of the cell exposed to the drugs, than it did in the rest of the cell. cAMP compartmentation was greatly reduced after inhibition of phosphodiesterase activity with 3-isobutyl-methylxanthine, suggesting the colocalization of enzymes involved in the cAMP cascade. We conclude that beta-adrenergic receptors are functionally coupled to nearby Ca2+ channels via local elevations of cAMP.

Adenylyl Cyclases↗