Antibacterial agents that inhibit histidine protein kinase YycG of Bacillus subtilis.

We demonstrated in vitro that YycG-YycF of Bacillus subtilis constitutes a two-component system and shows a specificity of the sensor protein for the cognate phosphorylation partner. Based on inhibition of such an autophosphorylation of YycG, we searched imidazole and zerumbone derivatives to identify the antibacterial agents such as NH125, NH126, NH127, and NH0891.     

Characteristics of 5'-guanylyl imidodiphosphate-activated adenylate cyclase.

Characteristics of adenylate cyclase stimulation by the GTP analog 5'-guanyl imidodiphosphate Gpp(NH)p have been examined in intact frog erythrocytes, frog erythrocyte membranes, and solubilized canine myocardial preparations. Gpp(NH)p caused marked enzyme activation in the erythrocyte membranes and in solubilized myocardial preparations, but had much lesser effects in intact cells. Enzyme activation by Gpp(NH)p exhibited a definite lag period, requiring 10 to 15 min for complete activation at 37 degrees. Activation was essentially irreversible after a 5-hour dialysis sufficient to reduce the Gpp(NH)p levels below threshold for stimulation. Gpp(NH)p-"activated" enzyme differed from native enzyme in several respects, such as its greater temperature stability, and its insensitivity to further stimulation by other activators, such as catecholamine or fluoride. These differences suggest that the enzyme, once fully activated by Gpp(NH)p, may have undergone some modification that is not subject ot facile reversal.     

Characterization of monochloramine toxicity on PC12 cells and protective effect of tocopherol via antioxidative function

Monochloramine (NH(2)Cl) is a physiological oxidant produced by activated neutrophils. In the present work, we studied the underlying mechanism of cytotoxic effects of NH(2)Cl on an undifferentiated rat pheochromocytoma PC12 cell line and the protective effects of antioxidants. The cells treated with 100 microM NH(2)Cl exhibited signs of apoptotic cell death such as phosphatidylserine exposure and caspase activation. To understand the mechanism of NH(2)Cl cytotoxicity, we examined the effect of various kinds of antioxidants including alpha-tocopherol (alpha-Toc) and beta-tocopherol (beta-Toc). These antioxidants exerted a protective effect against NH(2)Cl-induced cell death, and alpha-Toc exhibited the most potent inhibitory effect among the antioxidants used. A loss of cellular glutathione was observed in the cells treated with 100 microM NH(2)Cl. The formation of reactive oxygen species (ROS) was also measured using the fluorescent probe dichlorofluorescin diacetate. The fluorescence intensity increased prior to cell death and an antioxidant, such as alpha-Toc, suppressed the increase in ROS. Interestingly, beta-Toc also exerted similar inhibitory effects on cytotoxicity and caspase activation. These results suggest that free radical mediated process is involved in NH(2)Cl-induced PC12 cell death and that tocopherols inhibit this cell death via antioxidative function.     

The regulation of ammonium translocation in plants

Much controversy exists about whether or not NH(+)(4) is translocated in the xylem from roots to shoots. In this paper it is shown that such translocation can indeed take place, but that interference from other metabolites such as amino acids and amines may give rise to large uncertainties about the magnitude of xylem NH(+)(4) concentrations. Elimination of interference requires sample stabilization by, for instance, formic acid or methanol. Subsequent quantification of NH(+)(4) should be done by the OPA-fluorometric method at neutral pH with 2-mercaptoethanol as the reducing agent since this method is sensitive and reliable. Colorimetric methods based on the Berthelot reaction should never be used, as they are prone to give erroneous results. Significant concentrations of NH(+)(4), exceeding 1 mM, were measured in both xylem sap and leaf apoplastic solution of oilseed rape and tomato plants growing with NO(-)(3) as the sole N source. When NO(-)(3) was replaced by NH(+)(4), xylem sap NH(+)(4) concentrations increased with increasing external concentrations and with time of exposure to NH(+)(4). Up to 11% of the translocated N was constituted by NH(+)(4). Glutamine synthetase (GS) incorporates NH(+)(4) into glutamine, but root GS activity and expression were repressed when high levels of NH(+)(4) were supplied. Ammonium concentrations measured in xylem sap sampled just above the stem base were highly correlated with NH(+)(4) concentrations in apoplastic solution from the leaves. Young leaves tended to have higher apoplastic NH(+)(4) concentrations than older non-senescing leaves. The flux of NH(+)(4) (concentration multiplied by transpirational water flow) increased with temperature despite a decline in xylem NH(+)(4) concentration. Retrieval of leaf apoplastic NH(+)(4) involves both high and low affinity transporters in the plasma membrane of mesophyll cells. Current knowledge about these transporters and their regulation is discussed.     

The environment of amide groups in protein–ligand complexes: H-bonds and beyond

A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein-ligand complexes has been performed based on 3,275 published crystal structures (resolution < or =2.5 A). Most of the amide C=O and NH groups at the protein-ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. [Figure: see text].     

A novel 15N-labeling method to selectively observe 15NH2 resonances of proteins in 1H-detected heteronuclear correlation spectroscopy.

An experimental method to selectively label side-chain NH2 groups of glutamine and asparagine in proteins with 15N is proposed. This selective labeling method enables to observe only 15NH2 resonances and thus, to discriminate between 15NH and 15NH2 resonances in a 1H-detected heteronuclear correlation spectrum. This method gives results with approximately two times higher sensitivity than those obtained by elaborate pulse sequences such as DEPT-HSQC and will be useful for studying the molecular interaction involving the side chains of Asn and Gln residues.     

Specificity of binding of NH2-terminal residue of proteins to ubiquitin-protein ligase. Use of amino acid derivatives to characterize specific binding sites

Previous studies have indicated that at least part of the selection of proteins for degradation takes place at a binding site on ubiquitin-protein ligase, to which the protein substrate is bound prior to ligation to ubiquitin. It was also shown that proteins with free NH2-terminal alpha-NH2 groups bind better to this site than proteins with blocked NH2 termini (Hershko, A., Heller, H., Eytan, E., and Reiss, Y. (1986) J. Biol. Chem. 261, 11992-11999). In the present study, we used simple derivatives of amino acids, such as methyl esters, hydroxamates, or dipeptides, to examine the question of whether the protein binding site of the ligase is able to distinguish between different NH2-terminal residues of proteins. Based on specific patterns of inhibition of the binding to ligase by these derivatives, three types of protein substrates could be distinguished. Type I substrates are proteins that have a basic NH2-terminal residue (such as ribonuclease and lysozyme); these are specifically inhibited by derivatives of the 3 basic amino acids (His, Arg, and Lys) with respect to degradation, ligation to ubiquitin, and binding to ligase. Type II substrates (such as beta-lactoglobulin or pepsinogen, that have a Leu residue at the NH2 terminus) are not affected by the above compounds, but are specifically inhibited by derivatives of bulky hydrophobic amino acids (Leu, Trp, Phe, and Tyr). In these cases, the amino acid derivatives apparently act as specific inhibitors of the binding of the NH2-terminal residue of proteins, as indicated by the following observations: (a) derivatives in which the alpha-NH2 group is blocked were inactive and (b) in dipeptides, the inhibitory amino acid residue had to be at the NH2-terminal position. An additional class (Type III) of substrates comprises proteins that have neither basic nor bulky hydrophobic NH2-terminal amino acid residues; the binding of these proteins is not inhibited by homologous amino acid derivatives that have NH2-terminal residues similar to that of the protein. It is concluded that Type I and Type II proteins bind to distinct and separate subsites of the ligase, specific for basic or bulky hydrophobic NH2-terminal residues, respectively. On the other hand, Type III proteins apparently predominantly interact with the ligase at regions of the protein molecule other than the NH2-terminal residue.     

Short-term ammonium inhibition of nitrogen fixation in Azotobacter

Addition of NH4Cl at low concentrations to Azotobacter chroococcum cells caused an immediate cessation of nitrogenase activity, which was recovered once the added NH+4 was exhausted from the medium. In the presence of inhibitors of ammonium assimilation, such as L-methionine-DL-sulfoximine, L-methionine sulfone or 6-diazo-5-oxo-L-norleucine, externally added NH+4 had no effect on nitrogenase activity and the newly-fixed nitrogen was excreted into the medium as NH+4. It is concluded that, in A. chroococcum, NH+4 must be assimilated to exert its short-term inhibitory effect on nitrogen fixation.     

The beta-adrenoceptor is precoupled to Gs in chicken erythrocyte membranes

In this study we seek to elucidate the mechanism of hormone-independent adenylate cyclase stimulation by Gpp(NH)p in chicken erythrocyte membranes, and the inhibition of this stimulation by propranolol. Membrane treatment with isoprenaline + GMP increased Gpp(NH)p stimulation to near maximal levels [obtainable with isoprenaline + Gpp(NH)p], but reduced stimulation by NaF. The stimulation by Gpp(NH)p was stereoselectively inhibited by propranolol, but not by equal concentrations of the local anaesthetic lignocaine. Propranolol's inhibitory action was abolished following membrane treatment with isoprenaline/GMP. In contrast to its inhibition of Gpp(NH)p stimulation, propranolol did not alter Gpp(NH)p-mediated 3H-GDP release from membranes. The polyene antibiotic filipin, which uncouples receptor (R) from Gs, also abolished Gpp(NH)p stimulation and this effect was partly overcome by membrane treatment. These results are consistent with a model in which free R exists in equilibrium with precoupled R.Gs complexes in the absence of hormone. These complexes are activated by Gpp(NH)p and dissociated by antagonists. The existence of such complexes is a prerequisite for Gpp(NH)p stimulatory action.     

Monochloramine inhibits the expression of E-selectin and intercellular adhesion molecule-1 induced by TNF-alpha through the suppression of NF-kappaB activation in human endothelial cells

Reactive oxygen species have various effects on the expression of cell adhesion molecules induced by proinflammatory cytokines, such as tumor necrosis factor a (T-NF-alpha). We studied the effects of monochloramine (NH2Cl), a physiological oxidant derived from activated neutrophils, on the TNF-alpha-induced expression of E-selectin and intercellular adhesion molecule-1 (ICAM-1) in human umbilical vein endothelial cells (HUVEC). HUVEC were pretreated with or without NH2Cl (20-90 microM for 20 min), then stimulated with TNF-alpha (10 ng/ml), and the expression of E-selectin and ICAM-1 was measured. Without NH2Cl, TNF-alpha induced marked expression of e-selectin and ICAM-1. Pretreatment with NH2Cl resulted in a significant, but transient inhibition of the expression of adhesion molecules. Higher dose of NH2Cl showed more pronounced inhibition, and the inhibitory effect lasted for 8h when 70 microM of NH2Cl was added. TNF-alpha stimulation also induced marked activation of nuclear factor KB (NF-kappaB). Notably, NH2Cl also inhibited this NF-kappaB activation in a dose- and time-dependent manner, which was similar to the inhibition of E-selectin and ICAM-1 expression. In addition, IkappaB-alpha phosphorylation and degradation were also inhibited by NH2Cl pretreatment. These observations indicated that NH2Cl inhibited TNF-alpha-induced expression of E-selectin and ICAM-1 through the inhibition of NF-kappaB activation. We speculate that neutrophil-derived chloramines may have a regulatory role in the recruitment of leukocytes.     

Ammonium is toxic for aging yeast cells, inducing death and shortening of the chronological lifespan

Here we show that in aging Saccharomyces cerevisiae (budding yeast) cells, NH(4) (+) induces cell death associated with shortening of chronological life span. This effect is positively correlated with the concentration of NH(4) (+) added to the culture medium and is particularly evident when cells are starved for auxotrophy-complementing amino acids. NH(4) (+)-induced cell death is accompanied by an initial small increase of apoptotic cells followed by extensive necrosis. Autophagy is inhibited by NH(4) (+), but this does not cause a decrease in cell viability. We propose that the toxic effects of NH(4) (+) are mediated by activation of PKA and TOR and inhibition of Sch9p. Our data show that NH(4) (+) induces cell death in aging cultures through the regulation of evolutionary conserved pathways. They may also provide new insights into longevity regulation in multicellular organisms and increase our understanding of human disorders such as hyperammonemia as well as effects of amino acid deprivation employed as a therapeutic strategy.     

Intracellular digestion of reovirus particles requires a low pH and is an essential step in the viral infectious cycle.

Lysosomotropic drugs such as NH4Cl have been useful for studying the role of low pH in early events in virus infection. NH4Cl blocks the production of infectious progeny virus in mammalian reovirus-infected cells. The inhibitory effect of NH4Cl is mediated by an inhibition of intracellular digestion of reovirus outer capsid proteins. In vitro digestion of viral outer capsid proteins produces infectious partially uncoated particles, called intermediate subviral particles, which are no longer inhibited by the presence of NH4Cl. These results indicate that proteolytic processing of reovirus outer capsid proteins takes place in a low pH compartment of the cell and is an essential step in the viral infectious cycle.     

Kinetics of virus inactivation by ammonia

Ammonia has been shown to be virucidal in sludge and NH(4)Cl solutions, although the rates at which viruses are inactivated have not been thoroughly studied. In the present studies, the kinetics of the poliovirus type 1 (strain CHAT) and bacteriophage f2 inactivation were examined in such a way that the effects of OH(-) and NH(4) (+) could be separated from those of NH(3). Purified virus stocks were placed into solutions of NH(4)Cl and control solutions containing an equivalent concentration of NaCl and incubated at 20 degrees C. The percentage of virus surviving was calculated, and the kinetics were evaluated by constructing semilogarithmic plots of data. At all pH values and NH(3) concentrations studied, the kinetics of the inactivation of both viruses were pseudo-first order. OH(-) had no measurable effect on the viruses, whereas the effects of NH(4) (+) and Na(+) were similar. A dose-response relationship between NH(3) and the viruses was also found. Bacteriophage f2 was approximately 4.5 times more resistant to the effects of NH(3) than was poliovirus.     

Ammonium chloride affects receptor number and lateral mobility of the vasopressin V2-type receptor in the plasma membrane of LLC-PK1 renal epithelial cells: role of the cytoskeleton

The acidotropic agent ammonium chloride (NH4Cl) not only affects receptor metabolism by inhibiting lysosomal acidification, but can also affect the targeting of proteins to specific membranes in polarized cells, possibly through effects mediated by the cytoskeleton. The present study examines the effects of NH4Cl and perturbers of cytoskeleton structure on vasopressin V2 receptor expression in LLC-PK1 renal epithelial cells. Surprisingly, long-term pretreatment of cells with NH4Cl or short-term treatment with the actin perturber cytochalasin B resulted in an up to 70% increase in specific Arg-8-vasopressin binding compared to control cells, which was independent of the presence of NH4Cl in the binding test, and apparently the result of increased V2 receptor expression. Perturbers of microtubules such as colchicine and vinblastine had no such effect. A rhodamine-labeled analog of vasopressin was used to fluorescently label the V2 receptor of LLC-PK1 cells, and microscopic measurements of membrane-localized fluorescence confirmed the increased V2 receptor expression in the basal plasma membrane subsequent to NH4Cl pretreatment. Lateral mobility of the V2 receptor was measured in living cells using the technique of microphotolysis (photobleaching). The fraction of mobile receptors was 0.2 in cells pretreated with NH4Cl, markedly reduced compared to that of 0.9 in untreated cells. The apparent lateral diffusion coefficient D was about 3 x 10(-10) cm2/s in both pretreated and untreated cells. Results for fluorescence labeling of the actin cytoskeleton indicate that NH4Cl pretreatment of LLC-PK1 cells results in perturbation of microfilament structure. All results imply that the cytoskeleton plays a central role in V2 receptor expression and lateral mobility.     

Characterization of Brucella abortus and Brucella melitensis native haptens as outer membrane O-type polysaccharides independent from the smooth lipopolysaccharide.

Brucella native haptens (NHs) extracted with hot water from smooth (S)-type B. abortus and B. melitensis were purified to high levels of serological activity and compared with the polysaccharide obtained by acid hydrolysis (PS) of the S lipopolysaccharide (S-LPS). By 13C nuclear magnetic resonance analysis, NHs showed the spectrum of a homopolymer of alpha-1,2- or alpha-1,2- plus alpha-1,3-linked 4-formamido-4,6-dideoxy-D-mannose (N-formylperosamine) previously reported for the LPS O chain. However, while PS contained up to 0.6% 3-deoxy-D-manno-2-octulosonate, this LPS-core marker was absent from NH. High performance liquid chromatography and thin-layer chromatography showed heterogeneity in NH purified from whole cells but not in PS. By immunoprecipitation, polysaccharides indistinguishable from NH were demonstrated in extracts obtained with phenol-water, saline at 60 degrees C, and ether-water treatments, and none of these treatments caused S-LPS hydrolysis detectable with antibodies to the O chain and lipid A. Two lines of evidence showed that NH was in the cell surface. First, NH became biotinylated when B. abortus live cells were labelled with biotin-hydrazide, and the examination of cell fractions and electron microscopy sections with streptavidin-peroxidase and streptavidin-coloidal gold, respectively, showed that labelling was extrinsic. Moreover, whereas only traces of NH were found in cytosols, the amount of NH was enriched in cell envelopes and in the outer membrane blebs spontaneously released by brucellae during growth. Interactions between NH and S-LPS were observed in crude cell extracts, and such interactions could be reconstituted by using purified NH and LPS. The results demonstrate that NH is not a hydrolytic product of S-LPS and suggest a model in which LPS-independent O-type polysaccharides (NH) are intertwined with the O chain in the outer membrane of S-type brucellae.     

NH2-terminal processing of Drosophila melanogaster actin. Sequential removal of two amino acids

Class II actins, such as Drosophila and mammalian skeletal muscle actins, have genes that code for a Met-X-Asp NH2 terminus where X is usually cysteine. These actins have an Ac-Asp NH2 terminus so two amino acids must be removed. To determine the nature of this processing, we labeled Drosophila Schneider L-2 cells with [35S]methionine or cysteine, isolated the actin, and analyzed the NH2-terminal actin tryptic peptides and their thermolysin digestion products. After a 4-h labeling period, we detected completed actin polypeptide chains with either an unblocked Asp or an Ac-Asp NH2 terminus. No intermediate with an NH2-terminal Cys or Met could be demonstrated. If, however, Drosophila mRNA was translated in a mRNA-dependent rabbit reticulocyte lysate system, an additional 43-kDa actin intermediate was observed. On the basis of thermolysin digestion studies and experiments using mild acid hydrolysis of a labeled actin NH2-terminal tryptic peptide fragment, we identified this intermediate as having an Ac-Cys-Asp NH2 terminus. In a time-dependent fashion, Ac-Cys was removed generating actin with an exposed NH2-terminal Asp which was subsequently acetylated to produce the mature form of actin. The removal of Met and the acetylation of Cys may occur early in translation while the nascent polypeptide chain is still attached to the ribosome. Subsequent processing occurs following completion of the synthesis of the actin polypeptide. The removal of Ac-Cys from Drosophila actin is thus similar to removal of Ac-Met from the NH2 terminus of class I actins although in the case of the class II actins, it is the second amino acid that is removed as an acetylated species.     

Complemental Effect of Osmotic Stabilizers and Their Roles in Degradation Cell Walls of Blue-Green Algae

The compound osmotic stabilizers consisted of several salt solutions exerted a greater effect on the isolation of blue-green algae spheroplasts than a single salt solution. However, the effect of compound osmotic stabilizers on the spheroplast stability could be multiphasic. Some osmotic stabilizers, such as the solution of (NH4) 2C4H406, (NH4) 2SO4 and MgSO4, exerted degradation on cell walls of the blue-green alga; among which the (NH4) 2C4H406 solution (0.15 mol/L) had the greatest degradation resulting in formation of spheroplasts. The spheroplasts were sensitive to hypotonic condition but were less transparent.     

Polyamine-DNA interactions. Condensation of chromatin and naked DNA

We have used flow linear dichroism (LD) and light scattering at 90 degrees to study the condensation of both DNA and calf thymus chromatin by polyamines, such as spermine, spermidine and its analogs designated by formula NH3+(CH2)iNH2+(CH2)jNH3+, where i = 2,3 and j = 2,3, putrescine, cadaverine and MgCl2. It has been found that the different polyamines affect DNA and chromatin in a similar way. The level of compaction of the chromatin fibers induced by spermine, spermidine and the triamines NH3+(CH2)3NH2+(CH2)3NH3+ and NH3+(CH2)3NH2+(CH2)2NH3+ and MgCl2 is found to be identical. The triamine NH3+(CH2)3NH2+(CH2)2NH3+ and the diamines studied condense neither chromatin nor DNA. This drastic difference in the action of the triamines indicates that not only the charge, but also the structure of the polycations might play essential roles in their interactions with DNA and chromatin. It is shown that a mixture of mono- and multivalent cations affect DNA and chromatin condensation competitively, but not synergistically, as claimed in a recent report by Sen and Crothers (Biochemistry 25, 1495-1503, 1986). We have also estimated the extent of negative charge neutralization produced by some of the polyamines on their binding to chromatin fibers. The stoichiometry of polyamine binding at which condensation of chromatin is completed is found to be two polyamine molecules per DNA turn. The extent of neutralization of the DNA phosphates by the histones in these compact fibers is estimated to be about 55%. The model of polyamine interaction with chromatin is discussed.     

Rat clusterin isolated from primary Sertoli cell-enriched culture medium is sulfated glycoprotein-2 (SGP-2)

Clusterin, a glycoprotein originally isolated from ram rete testis fluid, is a dimer composed of monomers with non-identical NH2-terminal amino acid sequences. In view of its possible role in cell-cell interactions in the seminiferous epithelium, we sought to identify such a protein in the rat. Using the bioassay developed for the ovine protein, rat clusterin was purified to apparent homogeneity by HPLC from primary Sertoli cell-enriched culture media. This protein is also a heterodimer consisting of monomers of Mr 43,000 (alpha) and Mr 35,000 (beta). NH2-Terminal amino acid sequence analysis indicated that the alpha subunit has a sequence of NH2-SLMPLSHYGPLSFHNMFQPFFDMIHQAQQA and the beta subunit, NH2-EQEFSDNELQELSTQGSRYVNKEIQNAVQG. These two subunits show marked similarity with the corresponding subunits of ram clusterin isolated from rete testis fluid. Using an antibody against the alpha subunit of rat clusterin, a cDNA clone was isolated from a rat testicular lambda gt11 cDNA library. Analyses of the amino acid sequence derived from the isolated rat clusterin cDNA and of the NH2-terminal amino acid sequences indicate that rat clusterin is identical to a Sertoli cell glycoprotein previously designated sulfated glycoprotein-2.