ATP-driven reactions are required for the assembly of large stress granules

Stress granules (SGs) are functional messenger ribonucleoprotein aggregates, and their assembly is an important cellular process required for remodeling the signaling network to cope with extensive environmental stresses. SG formation is a stepwise process that involves the formation of a stable core followed by a less stable outer shell, and this process is often hampered by faulty regulation of protein phosphorylation. It remains unclear, however, which kinase activity is essential for SG formation. Here, we screened small molecule library of kinase inhibitors using a well-validated fluorogenic SG probe. Our screen, time-lapse microscopy, and biochemical analyses identified an ATP-mimetic SG inhibitor that selectively interferes with the fusion and growth, rather than the initial assembly, of SG core structures into the large assemblies. Thus, SGs utilize ATP-dependent chemical reactions to achieve their functional architectures.     

Marginal product pricing in the ecosystem.

Surface membrane biosynthesis and turnover is reviewed focusing mainly on the fate of cell surface constituents after they terminated their sojourn as part of a functional cell structure. The different experimental approaches to study this problem are described and original data are presented on the turnover of surface membrane constituents of chicken embryo cells in culture. It is proposed that as a consequence of surface membrane turnover, certain surface macromolecules are continuously shed from cells. The size and charge of these molecules was found to be identical to molecules released from cells by mild trypsin treatment. The term shedding is proposed for this process which is assumed to occur both in vitro and in vivo. Many systems in which shedding of cell surface constituents is clearly demonstrated or can be tentatively suggested are described. The biological significance of cell surface carbohydrate containing macromolecules and the possible role of these shed cellular entities is discussed.     

Fluorogenic ‘click-on’ dendrimer reporter for rapid profiling of cell proliferation

The application of small molecule fluorescent reporters to monitor biological systems is limited by their poor water solubility and background fluorescence of these reporters. Herein, we describe the synthesis and testing of a fluorogenic ‘click’ dendrimer reporter to monitor cellular processes. The reporter system consists of a polyamidoamine (PAMAM) dendrimer conjugated with 3-azido-7-hydroxy coumarin. After the copper(I)-catalyzed azide–alkyne cycloaddition reaction (‘click’ reaction) with alkyne-derivatized target molecules, the natively non-fluorescent construct has a strong enhancement in fluorescence. This fluorogenic dendrimer reporter can be used to efficiently monitor biological processes and the specificity afforded by the ‘click’ reaction greatly reduces background noise and enhances assay flexibility. We used this fluorogenic dendrimer reporter to monitor incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into newly synthesized DNA, as a surrogate marker of cellular proliferation. We anticipate that this new class of fluorogenic reporter can be used to monitor a wide array of molecules and lends itself to high-throughput profiling of biological systems.     

Chloride secretion,anoctamin 1 and Ca2+ signaling

Channels and transporters play essential biological roles primarily through the transportation of ions and small molecules that are required to maintain cellular activities across the biomembrane. Secondary to transportation, channels and transporters also integrate and coordinate biological functions at different levels, ranging from the subcellular (nm) to multicellular (μm) scales. This is underpinned by efficient functional coupling within molecular assemblies of channels, transporters, proteins, small molecules, and lipids.     

Cardiac Myosin Filaments are Maintained by Stochastic Protein Replacement

Myosin and myosin-binding protein C are exquisitely organized into giant filamentous macromolecular complexes within cardiac muscle sarcomeres, yet these proteins must be continually replaced to maintain contractile fidelity. The overall hypothesis that myosin filament structure is dynamic and allows for the stochastic replacement of individual components was tested in vivo, using a combination of mass spectrometry– and fluorescence-based proteomic techniques. Adult mice were fed a diet that marked all newly synthesized proteins with a stable isotope-labeled amino acid. The abundance of unlabeled and labeled proteins was quantified by high-resolution mass spectrometry over an 8-week period. The rates of change in the abundance of these proteins were well described by analytical models in which protein synthesis defined stoichiometry and protein degradation was governed by the stochastic selection of individual molecules. To test whether the whole myosin filaments or the individual components were selected for replacement, cardiac muscle was chemically skinned to remove the cellular membrane and myosin filaments were solubilized with ionic solutions. The composition of the filamentous and soluble fractions was quantified by mass spectrometry, and filament depolymerization was visualized by real-time fluorescence microscopy. Myosin molecules were preferentially extracted from ends of the filaments in the presence of the ionic solutions, and there was only a slight bias in the abundance of unlabeled molecules toward the innermost region on the myosin filaments. These data demonstrate for the first time that the newly synthesized myosin and myosin-binding protein C molecules are randomly mixed into preexisting thick filaments in vivo and the rate of mixing may not be equivalent along the length of the thick filament. These data collectively support a new model of cardiac myosin filament structure, with the filaments being dynamic macromolecular assemblies that allow for replacement of their components, rather than rigid bodies.     

Chaotic dynamics and fractal space in biochemistry: simplicity underlies complexity

In this work we attempt to analyze the coupling between the dynamics of biochemical reactions (especially chaotic dynamics), and the geometry of cytoarchitecture (especially fractal ultrastructure), because of its importance and consequences for the ultradian dynamic behaviour of cells. Fractal geometry in intracellular macromolecular assemblies suggests that chaotic dynamics occur during their organization. Non-linear interactions in and between spatial and temporal domains and over wide ranges of scales underlie the emergent properties of complex biological systems.     

ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems

MOTIVATION: Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrated systems involved in the exchange of the bacterial cell with its environment. RESULTS: ISYMOD is a knowledge warehouse that consistently integrates in the same environment the data and the methods used for their acquisition. This is achieved through the construction of (1) a domain knowledge base (DKB) devoted to the storage of the knowledge about the systems, their functional specificities, their partners and how they are related and (2) a methodological knowledge base (MKB) which depicts the task layout used to identify and reconstruct functional integrated systems. Instantiation of the DKB is obtained by solving the tasks of the MKB, whereas some tasks need instances of the DKB to be solved. AROM, an object-based knowledge representation system, has been used to design the DKB, and its task manager, AROMTasks, for developing the MKB. In this study two integrated systems, ABC transporters and two component systems, both involved in adaptation processes of a bacterial cell to its biotope, have been used to evaluate the feasibility of the approach.     

Turnover of myelin lipids in aging brain

Turnover rates of myelin membrane components in mouse brains were determined by a method using stable isotope-labeling and mass spectrometry. The half-replacement times based on incorporation rates of newly synthesized molecules for young adult mice were 359 days for cholesterol, 20 days for phosphatidylcholine, 25 days for phosphatidylethanolamine, 94 days for cerebroside and 102 days for ganglioside GM1. The turnover rates of half-lives of myelin components were calculated from the decay curves of initially labeled molecules, and they were about the same as the half-replacement times. Individual components were thus revealed to be metabolized at different rates, and their turnover rates were differently affected by aging. As was observed with phospholipids, myelin pools appeared to be compartmentalized into rapidly and slowly exchanging pools. The turnover rates of cerebroside and GM1 decreased between the young and adult periods and slightly increased in senescence. The latter phenomenon may indicate an enhanced myelin turnover in senescence. The present study reveals the dynamic aspects of myelin membrane turnover during the life span of mouse.     

Turnover of newly synthesized cytochromes P-450scc and P-45011 beta and adrenodoxin in bovine adrenocortical cells in monolayer culture: effect of adrenocorticotropin

The turnover of newly synthesized cytochromes P-450scc and P-45011 beta, and adrenodoxin was investigated in bovine adrenocortical cells in primary monolayer cultures. Cells were pulse-radiolabeled with [35S]methionine, and specific newly synthesized enzymes were immunoisolated at various times following labeling and quantitated. Adrenocorticotropin (ACTH) treatment did not alter the average turnover rate of total cellular proteins or that of total mitochondrial proteins. The half-life of total cellular proteins of control and ACTH-treated cells was determined to be 20.5 and 23 h, respectively. The half-life of mitochondrial proteins of control and ACTH-treated cells was determined to be 42.5 and 44 h, respectively. The turnover rate of newly synthesized cytochrome P-450scc was approximately the same as total mitochondrial protein (t1/2 = 38 h), and was unchanged by ACTH treatment (t1/2 = 42 h). ACTH treatment did not greatly alter the turnover rate of adrenodoxin. The half-life of adrenodoxin from control and ACTH-treated cells was determined to be 20 and 17 h, respectively. However, ACTH treatment appeared to increase the half-life of cytochrome P-45011 beta from 16 h in control cells to 24 h in treated cells. The differential rate of turnover of mitochondrial proteins studied here supports the contention that mitochondria are subject to heterogeneous degradation. It appears that chronic treatment of bovine adrenocortical cells in culture with ACTH leads to increased steroidogenic capacity, primarily as a result of increased synthesis of steroidogenic enzymes, although, as shown for cytochrome P-45011 beta, ACTH action might also increase steroidogenic capacity by increasing the half-life of this steroid hydroxylase.     

Degradation of proteins within the endoplasmic reticulum.

Certain newly synthesized proteins within the endoplasmic reticulum undergo rapid turnover by a non-lysosomal proteolytic pathway. Biochemical and morphological evidence has suggested that these proteins never leave the endoplasmic reticulum before they are degraded. The mechanism(s) for the selective targeting of proteins for degradation within the endoplasmic reticulum is still not understood, but appears to rely on specific structural determinants on the protein substrates. Important cellular functions are likely to be served by this endoplasmic reticulum degradative system, including disposal of abnormal proteins and the selective turnover of metabolically regulated proteins.     

Synthesis of surface H-2 alloantigens in murine splenocytes.

The synthesis and turnover of cell surface H-2 alloantigens were studied in murine splenocytes by the anti-H-2-bind method to separate precursor-labeled surface from intracellular molecules. Results indicate that newly synthesized H-2 antigen, labeled in either its peptide or carbohydrate portion enters a relatively small pool of intracellular H-2 antigen and then is rapidly transported to the plasma membrane which represents a larger compartment. The simplest interpretation of these findings is that H-2 antigen is synthesized and transported along a conventional secretory pathway. Pulse-chase experiments indicate that H-2 antigens are not readily chased from the plasma membrane and are not shed or internalized during short-term culture. The aforementioned observations are discussed in terms of a cellular heterogeneity.     

Intracellular transport of the major glycoprotein of zymogen granule membranes in the rat pancreas. Demonstration of high turnover at the plasma membrane

The intracellular transport and destination of the major glycoprotein associated with zymogen granule membranes in the pancreas (GP-2) was established. In suspensions of isolated acinar cells from rat pancreas, pulse-chase experiments were performed. The incorporation of the first newly synthesized GP-2 molecules into zymogen granule membranes occurred at about 60 min after beginning of the pulse. We demonstrated by using two different methods that newly made GP-2 reaches the cell surface within the same time span. After 6-8 h chase considerable more newly synthesized GP-2 has reached the cell surface than would be expected on account of secreted newly synthesized zymogens. These observations strongly suggest that at least part of the GP-2 molecules bypass the mature zymogen granule compartment on their way to the plasma membrane. GP-2 is the only protein that appears in discernable quantity in the plasma membrane during 1-4 h after a pulse label. Nevertheless GP-2 comprises only a small percentage of externally 125I-iodinated plasma membrane proteins. We conclude that GP-2 has a high turnover rate at the plasma membrane level. Treatment of the acinar cells with the N-glycosylation inhibitor tunicamycin does not block the intracellular transport of GP-2.     

The nature of oxidants and antioxidant systems in the inhibition of mutation and cancer

We briefly review current concepts with regard to the nature of oxygen-derived oxidants in biological systems. Of these substances, hydroxyl radicals derived from hydrogen peroxide seem most likely to be involved in the various stages of carcinogenesis. Hydrogen peroxide detoxification, primarily through glutathione activity, is essential in preventing hydroxyl-radical formation. Transition metals such as iron play a central role in this latter process. Alterations in cellular macromolecules are most likely to take place if hydroxyl-radical formation is directed toward specific intramolecular sites by appropriately sequestered metals. For this reason, repair and turnover events are apt to be more important protective devices than are the actions of molecules which scavenge hydroxyl radicals. Although many cellular constituents are potential targets in free-radical and oxidant attacks leading to carcinogenesis, nucleic acids have been most extensively studied in this connection. On the basis of these investigations, it is a facile conclusion that oxidants might be involved in the early events of carcinogenesis as well as in transformation or promotion. The literature on antioxidants in chemoprevention in animals is supportive of such a role. However, other biochemical effects of antioxidants should raise a note of caution in the interpretation of animal experiments.     

Functionalized carbon nanotubes as emerging nanovectors for the delivery of therapeutics

Functionalized carbon nanotubes (f-CNT) are emerging as a new family of nanovectors for the delivery of different types of therapeutic molecules. The application of CNT in the field of carrier-mediated delivery has become possible after the recent discovery of their capacity to penetrate into the cells. CNT can be loaded with active molecules by forming stable covalent bonds or supramolecular assemblies based on noncovalent interactions. Once the cargos are carried into various cells, tissues and organs they are able to express their biological function. In this review, we will describe the potential of f-CNT to deliver different types of therapeutic molecules.     

Relation between cell wall turnover and cell growth in Bacillus subtilis.

The kinetics of cell wall turnover in Bacillus subtilis have been examined in detail. After pulse labeling of the peptidoglycan with N-acetylglucosamine, the newly formed peptidoglycan is stable for approximately three-quarters of a generation and is then degraded by a process that follows first-order kinetics. Deprivation of an auxotroph of amino acids required for protein synthesis results in a cessation of turnover. If a period of amino acid starvation occurs during the lag phase of turnover, then the initiation of turnover is delayed for a period of time equivalent to the starvation period. During amino acid starvation, new cell wall peptidoglycan is synthesized and added to preexisting cell wall. This peptidoglycan after resumption of growth is also subject to degradation (turnover). It is suggested that cell wall turnover is dependent on cell growth and elongation. Several possible control mechanisms for cell wall autolytic enzymes are discussed in light of these observations.     

Functional studies of newly synthesized benzoic acid derivatives: identification of highly potent retinoid-like activity

Three newly synthesized benzoic acid derivatives (terephthalic acid anilides, chalcone carboxylic acid, and azobenzene carboxylic acid), with a certain structural similarity to retinoic acid, were examined for their retinoid-like bioactivity and their capacity to bind to cellular retinoid binding proteins. Two in vitro systems were used to evaluate their retinoid-like bioactivity: inhibition of adipose conversion of ST 13 murine preadipose cells and growth promotion of murine sarcoma virus (MSV)-transformed 3T3 cells in serum-free culture. All three compounds tested inhibited ST 13 adipose conversion at nanomolar concentrations in a manner similar to classical retinoids such as retinoic acid. The growth-stimulating activity of these compounds on MSV-transformed 3T3 cells was one to two orders of magnitude greater than that of retinoic acid. Simultaneous treatment with these compounds and retinoic acid produced only a barely detectable additive effect, suggesting a common mechanism of action, whereas unrelated mitogens, thrombin, and insulin worked synergistically in combination with retinoic acid. None of the compounds competed with retinol for binding to cellular retinol binding protein. However, two of the three competed with retinoic acid for binding to cellular retinoic acid binding protein. This study provides evidence that the newly synthesized compounds should be included among the retinoids and that their strong biological activity will undoubtedly contribute to the biological and medical application of retinoids.     

Regulation of Bacterial Cell Walls: Turnover of Cell Wall in Staphylococcus aureus

The cell wall of Staphylococcus aureus was shown to undergo turnover during exponential growth. The rate of turnover, about 15% per generation, was identical for both cell wall polymers, peptidoglycan and teichoic acid. Both the old and newly synthesized wall material appeared to undergo turnover at similar rates. The rate of turnover followed first-order kinetics until more than 90% of the original wall was lost. Cell wall turnover was completely blocked under conditions of unbalanced synthesis known to inhibit cellular autolysis, e.g., addition of chloramphenicol. Cell wall turnover was shown to occur in a number of different strains of S. aureus and appears to be widely distributed in this species.     

Mechanisms of biosynthesis of mammalian copper/zinc superoxide dismutase

Copper/zinc superoxide dismutase (SOD1) is an abundant intracellular enzyme with an essential role in antioxidant defense. The activity of SOD1 is dependent upon the presence of a bound copper ion incorporated by the copper chaperone for superoxide dismutase, CCS. To elucidate the cell biological mechanisms of this process, SOD1 synthesis and turnover were examined following 64Cu metabolic labeling of fibroblasts derived from CCS+/+ and CCS-/- embryos. The data indicate that copper is rapidly incorporated into both newly synthesized SOD1 and preformed SOD1 apoprotein, that each process is dependent upon CCS and that once incorporated, copper is unavailable for cellular exchange. The abundance of apoSOD1 is inversely proportional to the intracellular copper content and immunoblot and gel filtration analysis indicate that this apoprotein exists as a homodimer that is distinguishable from SOD1. Despite these distinct differences, the abundance and half-life of SOD1 is equivalent in CCS+/+ and CCS-/- fibroblasts, indicating that neither CCS nor copper incorporation has any essential role in the stability or turnover of SOD1 in vivo. Taken together, these data provide a cell biological model of SOD1 biosynthesis that is consistent with the concept of limited intracellular copper availability and indicate that the metallochaperone CCS is a critical determinant of SOD1 activity in mammalian cells. These kinetic and biochemical findings also provide an important framework for understanding the role of mutant SOD1 in the pathogenesis of familial amyotrophic lateral sclerosis.     

Deposition diseases and 3D domain swapping

Protein aggregation is a feature of both normal cellular assemblies and pathological protein depositions. Although the limited order of aggregates has often impeded their structural characterization, 3D domain swapping has been implicated in the formation of several protein aggregates. Here, we review known structures displaying 3D domain swapping in the context of amyloid and related fibrils, prion proteins, and macroscopic aggregates, and we discuss the possible involvement of domain swapping in protein deposition diseases.