Labeling and chemistry of grapefruit pectic substances

The labeling of a number of polysaccharides found in grapefruit (Citrus paradisi) was achieved by feeding labeled myo-inositol to ripening grapefruit through their cut fruit stem, and allowing 4 days for the metabolism of label. The pectic polysaccharides were isolated by successive extraction of the labeled grapefruit with 80% ethanol, chloroform-methanol (1:1) and finally with 0.2 M Na₂ EDTA to solubilize pectic polysaccharides. The incorporation of label from myo-inositol into galacturonosyl, arabinosyl, xylosyl and galactosyl residues of pectic polysaccharides via myo-inositol oxidation pathway was demonstrated. Ion exchange chromatography of these labeled pectic polysaccharides using DE-52 cellulose resulted in the elution of eight totally or partially resolved polysaccharides with increasing salt concentration. The results suggest that, like other plant tissues, the myo-inositol oxidation pathway is also operative in ripening grapefruit and this metabolic pathway could be successfully utilized to achieve labeling of a number of pectic polysaccharides.     

The use of the 2-aminobenzoic acid tag for oligosaccharide gel electrophoresis

Gel electrophoresis of fluorophore labeled saccharides provides a rapid and reliable method to screen enzymatic and/or chemical treatments of polysaccharides and glycoconjugates, as well as a sensitive and efficient microscale method to separate and purify oligosaccharides for further analysis. A simple and inexpensive method of derivatization and analysis using 2-aminobenzoic acid (anthranilic acid, AA) is described and applied to the extracellular polysaccharide released by the desiccation tolerant cyanobacterium Nostoc commune DRH-1. The results of these analyses suggest a possible protective functionality of two pendent groups, as well as a potential relationship between these groups and the desiccation tolerance of the organism.     

Functional differences between Arctic seawater and sedimentary microbial communities: contrasts in microbial hydrolysis of complex substrates

The activities and structural specificities of extracellular enzymes that initiate microbial remineralization of high-molecular-weight (MW) organic matter were investigated in surface waters and sediments of an Arctic fjord of Svalbard. Hydrolysis rates of a suite of fluorescently labeled macromolecular substrates, including seven commercially available polysaccharides and three high-carbohydrate-content plankton extracts ranged from rapid to not detectable, and differed markedly between seawater and sediments. Order (fastest to slowest) of hydrolysis in surface water was laminarin, Spirulina extract, xylan>chondroitin, alginic acid, Wakame extract>arabinogalactan, fucoidan>Isochrysis extract>pullulan, while in sediments the order was pullulan, laminarin, alginic acid, Wakame extract>chondroitin, xylan>arabinogalactan, Isochrysis extract>Spirulina extract>fucoidan. These differences cannot be explained by simple scaling factors such as differences in microbial cell numbers between seawater and sediments. Other investigations have shown that microbial community composition of Svalbard sediments and of polar bacterioplankton samples differ markedly. These results demonstrate that sedimentary and seawater microbial communities also differ fundamentally in their abilities to access specific high-MW substrates. Substrate bioavailability depends on the capabilities of a microbial community, as well as the chemical and structural features of the substrate itself.     

Fluorescence anisotropy as a means to determine extracellular polysaccharide hydrolase activity in environmental samples

Current approaches to measure the activities of microbial extracellular enzymes in aquatic environments are hampered by slow throughput or by differences between the structure of simple substrate proxies and macromolecules. Here we show that measurements of fluorescence anisotropy can be used to determine the hydrolysis rate of two fluorescently labeled polysaccharides, laminarin and xylan, in environmental samples. A simple analysis shows that the anisotropy of these fluorescently labeled polysaccharides can be approximated using a modification of the Perrin equation.     

Fluorescence probes specific for the plasma membrane of intact human erythrocytes and lymphocytes

Human erythrocytes and lymphocytes were isolated from venous blood and subjected to one of two protocols. In one protocol the suspended cells were labeled with fluorophore (fluorescamine or 12(9)AS). This procedure was followed sequentially by cellular lysis, cellular fractionation, and fluorescence and absorption readings. In the other protocol the suspended cells were lysed, and then the cellular homogenate labeled with fluorophore followed by cellular fractionation and spectroscopy readings. The lymphocytes were fractionated into plasma membrane, cytosol, and nuclear-mitochondrial fractions and the erythrocytes into plasma membrane and cytosol fractions. The results demonstrate that under the given labeling conditions, both fluorescamine and 12(9)AS are highly localized to the plasma membrane of intact human erythrocytes and lymphocytes. Furthermore, by P-31 NMR analysis, fluorophore labeling did not alter cellular high energy phosphate metabolism or cellular permeability to Mn²⁺. Therefore, these fluorophores are potentially powerful probes of human erythrocyte and lymphocyte plasma membrane dynamics in inherited and acquired disease states.     

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane proteins including ion channels², ion pumps³, and transporters⁴. Recent developments have combined site-specific fluorophore labeling alongside TEVC to concurrently examine the conformational dynamics at specific residues and function of these proteins on the surface of single cells.We will describe a method to study the conformational dynamics of membrane proteins by simultaneously monitoring fluorescence and current changes using voltage-clamp fluorometry. This approach can be used to examine the molecular motion of membrane proteins site-specifically following cysteine replacement and site-directed fluorophore labeling^5,6. Furthermore, this method provides an approach to determine distance constraints between specific residues^7,8. This is achieved by selectively attaching donor and acceptor fluorophores to two mutated cysteine residues of interest.In brief, these experiments are performed following functional expression of the desired protein on the surface of Xenopus leavis oocytes. The large surface area of these oocytes enables facile functional measurements and a robust fluorescence signal⁵. It is also possible to readily change the extracellular conditions such as pH, ligand or cations/anions, which can provide further information on the mechanism of membrane proteins⁴. Finally, recent developments have also enabled the manipulation of select internal ions following co-expression with a second protein⁹.Our protocol is described in multiple parts. First, cysteine scanning mutagenesis proceeded by fluorophore labeling is completed at residues located at the interface of the transmembrane and extracellular domains. Subsequent experiments are designed to identify residues which demonstrate large changes in fluorescence intensity (<5%)³ upon a conformational change of the protein. Second, these changes in fluorescence intensity are compared to the kinetic parameters of the membrane protein in order to correlate the conformational dynamics to the function of the protein¹⁰. This enables a rigorous biophysical analysis of the molecular motion of the target protein. Lastly, two residues of the holoenzyme can be labeled with a donor and acceptor fluorophore in order to determine distance constraints using donor photodestruction methods. It is also possible to monitor the relative movement of protein subunits following labeling with a donor and acceptor fluorophore.     

The Efficiency of DNA Labeling with Near-Infrared Fluorescent Dyes

The efficiency of DNA labeling was assessed for 2'-deoxyuridine 5'-triphosphate (dUTP) derivatives containing the Cy7 cyanine dye as a fluorophore. Two fluorescent Cy7-labeled dUTP analogs differed in the chemical structure of the linker between the fluorophore and nucleotide moieties. The efficiency of the polymerase chain reaction (PCR) and inhibition with modified nucleotides were estimated by real-time PCR. The efficiency of labeled nucleotide incorporation in PCR products was measured by quantitative electrophoresis. The efficiency of target DNA labeling was evaluated by binding the fluorescently labeled PCR products to a microarray of oligonucleotide probes immobilized in hydrogel drops (a biochip). The near-infrared hybridization signal was detected by digital luminescence microscopy. An increase in linker length was found to provide more efficient incorporation of the labeled nucleotide. Both of the compounds provided high sensitivity and high specificity of DNA testing via allele-specific hybridization on a biochip.

     

磷酸化底物肽的硫代磷酸化及荧光标记

以蛋白激酶Ａ的一磷酸化底物肽ＬＲＲＡＳＬＧ为模型肽,研究了硫代磷酸化及荧光标记反应条件。荧光标记试剂５－｛「（（２－碘代乙酰）氨）乙基」氨基｝萘－１－磺酸（１,５－ＩＡＥＤＡＮＳ）适宜浓度为１．６ｍｍｏｌ／Ｌ,标记反应缓冲液的适宜ｐＨ为７至８。实验了标记肽分别在Ｎ－端序列分析、电喷雾质谱和０．１％三氟乙酸存在下的稳定性。比较了标记肽和标记肽的紫外吸收光谱的差异特征。初步显示高效液相色谱蛋白酶解肽谱     

Wound debridement potential of glycosidases of the wound-healing maggot, Lucilia sericata

The wound-healing maggot, Lucilia sericata Meigen (Diptera: Calliphoridae), degrades extracellular matrix components by releasing enzymes. The purpose of this study was to investigate the glycosylation profiles of wound slough/eschar from chronic venous leg ulcers and the complementary presence of glycosidase activities in first-instar excretions/secretions (ES1) and to define their specificities. The predominant carbohydrate moieties present in wound slough/eschar were determined by probing one-dimensional Western blots with conjugated lectins of known specificities. The presence of specific glycosidase activities in ES1 was determined using chromogenic and fluorogenic substrates. The removal of carbohydrate moieties from slough/eschar proteins by glycosidases in ES1 was determined by two-dimensional electrophoresis and Emerald 300 glycoprotein staining. α-d-glucosyl, α-d-mannosyl and N-acetlyglucosamine residues were detected on slough/eschar-derived proteins. Furthermore, it was demonstrated that the treatment of slough/eschar with ES1 significantly reduced uptake of the carbohydrate-specific stain. Subsequently, α-d-glucosidase, α-d-mannosidase and N-acetylglucosaminidase activities were identified in ES1. Specific chromogenic and fluorogenic substrates and gel filtration chromatography showed that these activities result from distinct enzymes. These activities were mirrored in the removal of α-d-glucosyl, α-d-mannosyl and N-acetylglucosamine residues from proteins of slough/eschar from maggot-treated wounds. These data suggest that maggot glycosidases remove sugars from slough/eschar proteins. This may contribute to debridement, which is ultimately accomplished by a suite of biochemically distinct enzymes present in ES1.     

Polysaccharide hydrolysis in aggregates and free enzyme activity in aggregate-free seawater from the north-eastern Gulf of Mexico

Marine snow aggregates represent hotspots of carbon remineralization in the ocean. Various aspects of bacterial dynamics have been investigated on marine snow. To date, extracellular enzymatic activities in aggregates have been measured using small substrate proxies that do not adequately reflect the complexity of biomacromolecules such as polysaccharides, proteins and lipids. To address this issue, we used six structurally distinct, fluorescently labelled polysaccharides to measure enzymatic hydrolysis on aggregates formed with a roller table and in aggregate-free (ambient) seawater from two near-coast sites, north-eastern Gulf of Mexico. A single polysaccharide was incubated in aggregates and ambient seawater. Changes in polysaccharide molecular weight were monitored over time to measure the course of enzymatic hydrolysis. All six polysaccharides were hydrolysed in aggregates, indicating a broad range of enzyme activities in aggregate-associated bacteria. Four substrates were also hydrolysed in ambient waters. Epifluorescence microscopy revealed that nearly all of the bacteria present in original waters were incorporated into aggregates. Therefore hydrolytic activities in ambient waters were presumably due to enzymes spatially disconnected from cells and aggregates. Our results show substantial enzymatic activity in cell/aggregate-free seawater, suggesting a significant role of free enzymes in hydrolytic activity in waters from the north-eastern Gulf of Mexico.     

Characterization and heterologous expression of an age-dependent fungal/bacterial type chitinase of Aspergillus nidulans

Under carbon starvation, Aspergillus nidulans produced a fungal/bacterial type chitinase, ChiB. The chiB gene was cloned and subcloned into pJC40 expression vector containing a 10XHis fusion tag, and the ChiB protein was expressed heterologously in Escherichia coli. Recombinant and native ChiB enzymes shared the same optimal pH ranges and showed similar substrate specificities with endo-acting cleavage patterns.     

Chemical probes shed light on protein function

Site-specific protein labeling with synthetic dyes is an emerging technique for live cell imaging. A protein or peptide tag fused to the protein of interest provides the means for attachment of a fluorophore or other small molecule probe, to allow non-invasive imaging of the dynamics of protein localization. The past two years have seen significant advances in such methods, the publication of a number of new tags for labeling, and the imaginative application of established techniques to tackle previously intractable biological questions.     

Induction of cellulose in Schizophyllum commune: thiocellobiose as a new inducer.

Several mono-, di, tetra-, and polysaccharides were screened for their ability to induced cellulase production by the tetrapolar hymenomycete Schizophyllum commune. Out of 21 carbohydrates screened, 4 (thiocellobiose, carboxymethylcellulose, cellobiose, and xylan) induced all three enzymes tested (carboxymethylcellulase, beta-glucosidase, and xylanase). The inducing effect increased with rising concentrations of the inducers up to a certain value, beyond which there was either a leveling off or a decrease of the enzymatic activities. The most powerful inducer, thiocellobiose, showed the highest activity at 0.5 mM. Cellobiose, carboxymethylcellulose, and xylan showed their highest activities at 1 mM and 1%, respectively. Surprisingly, sophorose did not enhance enzyme production. The enzymatic activities were monitored over a period of 24 h. Thiocelloboise elicited a response immediately after incubation, but with all other inducers there was a latency period before their effect could be measured. High-performance liquid chromatography showed no hydrolysis of thiocellobiose when incubated in the presence of S. commune extracellular enzymes.     

Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution

Dihydrouridine (DHU) positions within tRNAs have long been used as sites to covalently attach fluorophores, by virtue of their unique chemical reactivity toward reduction by NaBH(4), their abundance within prokaryotic and eukaryotic tRNAs, and the biochemical functionality of the labeled tRNAs so produced. Interpretation of experiments employing labeled tRNAs can depend on knowing the distribution of dye among the DHU positions present in a labeled tRNA. Here we combine matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) analysis of oligonucleotide fragments and thin layer chromatography to resolve and quantify sites of DHU labeling by the fluorophores Cy3, Cy5, and proflavin in Escherichia coli tRNA(Phe) and E. coli tRNA(Arg). The MALDI-MS results led us to re-examine the precise chemistry of the reactions that result in fluorophore introduction into tRNA. We demonstrate that, in contrast to an earlier suggestion that has long been unchallenged in the literature, such introduction proceeds via a substitution reaction on tetrahydrouridine, the product of NaBH(4) reduction of DHU, resulting in formation of substituted tetrahydrocytidines within tRNA.     

Purification and characterization of the highly thermostable proteases from Bacillus stearothermophilus TLS33

Three thermostable proteases, designated S, N, and B, are extracellular enzymes produced by Bacillus stearothermophilus strain TLS33. They were purified by lysine affinity chromatography, strong anion exchange Q HyperD chromatography, and Ultrogel AcA44 gel filtration. The molecular masses of the enzymes determined by SDS-PAGE and zymography were approximately 36, 53, and 71 kDa, respectively. Thermostable protease S bound strongly to the lysine affinity column and could be purified by this single step. The optimum pH values of proteases S, N, and B were shown to be 8.5, 7.5, and 7.0, respectively. The maximum activities for the enzymes were at 70, 85, and 90 degrees C, respectively. Proteases S, N, and B at pH 7.0 in the presence of 5 mM CaCl(2) retained half their activities after 30 min at 72, 78, and 90 degrees C, respectively. All three thermostable proteases were strongly inhibited by the metal chelators EDTA and 1,10-phenanthroline, and the proteolytic activities were restored by addition of ZnCl(2). They can thus be classified as Zn(2+) metalloproteases. The cleavage specificities of proteases S, N, and B on a 30-residue synthetic peptide from pro-BPN' subtilisin were Tyr-Ile, Phe-Lys, and Gly-Phe, respectively.     

Hydration dependence of active core fluctuations in bacteriorhodopsin

We used neutron scattering and specific hydrogen-deuterium labeling to investigate the thermal dynamics of isotope-labeled amino acids and retinal, predominantly in the active core and extracellular moiety of bacteriorhodopsin (BR) in the purple membrane and the dynamical response to hydration. Measurements on two neutron spectrometers allowed two populations of motions to be characterized. The lower amplitude motions were found to be the same for both the labeled amino acids and retinal of BR and the global membrane. The larger amplitude dynamics of the labeled part, however, were found to be more resilient than the average membrane, suggesting their functional importance. The response to hydration was characterized, showing that the labeled part of BR is not shielded from hydration effects. The results suggest that the inhibition of high-amplitude motions by lowering hydration may play a key role in the slowing down of the photocycle and the proton pumping activity of BR.     

Legume alpha-Galactosidases Which Have Hemagglutinin Properties

Four legume species (four genera) were examined and found to contain hemagglutinins with properties similar to those which we have previously described for the enzymic hemagglutinin in Vigna radiata. Examination of extracts by gel filtration and ion exchange chromatography showed that an alpha-galactosidase activity exactly co-purified with a hemagglutinin activity in each of the four species. The alpha-galactosidase activities in the four species were virtually identical to each other with respect to substrate and inhibitor specificity as well as kinetic behavior. Additionally the hemagglutinin activities in all four species displayed very similar carbohydrate specificities. The inhibitor specificities displayed by the enzymes and the hemagglutinins were qualitatively and quantitatively very nearly identical to each other. The remarkable similarities of these proteins, both to each other and to the previously described Vigna enzymic hemagglutinin, suggest that each of these plants may contain a homologue from a specific class of enzymic hemagglutinin.     

Preparation and properties of fluorescent polysaccharides

A new method for preparing fluorescein derivatives of polysaccharides is described. These derivatives are prepared by activation of the polysaccharide with cyanogen bromide and subsequent reaction with fluoresceinamine. The optimum conditions for coupling have been established in this report. Using this procedure, we have prepared fluorescein derivatives of a wide variety of polysaccharides. Degrees of substitution in the range of 3.0 X 10(-3) to 2.4 X 10(-2) mol of fluorescein per mole of monosaccharide equivalent were obtained. The fluorescent derivatives are stable: no free fluorescein was detected after incubation at 22 degrees C for 48 h or at -10 degrees C for 4 months. The fluorescein-derivatized polysaccharides were found to have the same potency in inhibiting lectin-mediated hemagglutination as the underivatized polysaccharide. In addition, these fluorescent polysaccharides can be radioiodinated to specific activities exceeding 10(6) dpm/micrograms due to incorporation of 125I into fluorescein. The cell binding properties of 125I-fucoidin and 125I-heparin are indistinguishable from the corresponding underivatized polysaccharides. This general approach for preparing fluorescent polysaccharides should produce useful reagents for localizing and quantifying cell surface carbohydrate-binding proteins (lectins).     

The anti-biofouling effect of polyphenols against Streptococcus mutans

Biofouling is a process of surface colonization by microorganisms through cell adhesion and production of extracellular polymers (polysaccharides and proteins). It often causes serious problems in the chemical, medical and pharmaceutical industries. Recently, it was demonstrated that some natural phenolic compounds found in plants and vegetables have an antibiofouling effect, reducing formation of biofilm by Gram-negative bacteria. In this study, Streptococcus mutans, a Gram-positive bacterium was investigated for the antibiofouling effect of polyphenols. It was hypothesized that the two enzymes, glucosyltransferase and fructosyltransferase, produced by S. mutans, would be inhibited by the natural phenolic compounds. When these two enzymes were inhibited, less (or no) biofilms were formed. Enzymes were separated from a S. mutans culture medium, and their activities were measured with five different polyphenols using microtiter-plates and high-performance liquid chromatography. The results of minimum inhibitory concentration (MIC) were used to determine the enzyme inhibition effect of polyphenols on biofilm formation without killing the cells. Most of the polyphenols used showed considerable reduction of biofilm formation. Gallic acid and tannic acid showed significant enzyme inhibition effects below their MICs.