Flavocytochrome b2: reactivity of its flavin with molecular oxygen

Flavocytochrome b2, a flavohemoprotein, catalyzes the oxidation of lactate at the expense of the physiological acceptor cytochrome c in the yeast mitochondrial intermembrane space. The mechanism of electron transfer from the substrate to monoelectronic acceptors via FMN and heme b2 has been intensively studied over the years. Each prosthetic group is bound to a separate domain, N-terminal for the heme, C-terminal for the flavin. Each domain belongs to a distinct evolutionary family. In particular, the flavodehydrogenase domain is homologous to a number of well-characterized l-2-hydroxy acid-oxidizing enzymes. Among these, some are oxidases for which the oxidative half-reaction produces hydrogen peroxide at the expense of oxygen. For bacterial mandelate dehydrogenase and flavocytochrome b2, in contrast, the oxidative half-reaction requires monoelectronic acceptors. Several crystal structures indicate an identical fold and a highly conserved active site among family members. All these enzymes form anionic semiquinones and bind sulfite, properties generally associated with oxidases, whereas electron transferases are expected to form neutral semiquinones and to yield superoxide anion. Thus, flavocytochrome b2 is a highly unusual dehydrogenase-electron transferase, and one may wonder how its flavin reacts with oxygen. In this work, we show that the separately engineered flavodehydrogenase domain produces superoxide anion in its slow reaction with oxygen. This reaction apparently also takes place in the holoenzyme when oxygen is the sole electron acceptor, because the heme domain autoxidation is also slow; this is not unexpected, in view of the heme domain mobility relative to the tetrameric flavodehydrogenase core (Xia, Z. X., and Mathews, F. S. (1990) J. Mol. Biol. 212, 837-863). Nevertheless, this reaction is so slow that it cannot compete with the normal electron flow in the presence of monoelectronic acceptors, such as ferricyanide and cytochrome c. An inspection of the available structures of family members does not provide a rationale for the difference between the oxidases and the electron transferases.     

Flavocytochrome b2: simulation studies of the electron-transfer reactions among the prosthetic groups.

Simulation studies by digital computer were undertaken in order to test and clarify the interpretations deduced from experimental data concerning the electron transfer mechanism from L-lactate to flavocytochrome b2, which were presented in a preceding paper in this journal. The reaction scheme proposed as the "best" one is composed of 7 steps. It allows the best fitting of the time courses established for the oxidized flavin (Flox), the flavin semiquinone (Flsq), the fully reduced flavin (Flred), and the reduced haem (Hred); it can be extended to 1 s. This scheme also allows a good simulation of the general shape of preequilibrium titration curves obtained at a 200-ms reaction time for Hred and Flsq, and a valuable simulation of the reduction electron paramagnetic resonance time course established for Hred and Flsq at low lactate concentration. The agreement between experimental and simulated curves led to an estimation of some rate constants experimentally unknown, relative (in particular) to the electron exchange between flavin and haem and between couples of flavins. Another interest of these stimulation studies was to point out the obligatory involvement of a slow final step to perform the flavocytochrome b2 full reduction; this step could be controlled by some conformational change of the protein.     

A New Method of the Visualization of the Double-Stranded Mitochondrial and Nuclear DNA

The study describes the method of a sensitive detection of double-stranded DNA molecules in situ. It is based on the oxidative attack on the deoxyribose moiety by copper(I) in the presence of oxygen. We have shown previously that the oxidative attack leads to the formation of frequent gaps in DNA. Here we have demonstrated that the gaps can be utilized as the origins for an efficient synthesis of complementary labeled strands by DNA polymerase I and that such enzymatic detection of the double-stranded DNA is a sensitive approach enabling in-situ detection of both the nuclear and mitochondrial genomes in formaldehyde-fixed human cells.     

改善啤酒酿造过程酶活力方法的研究

以国外大麦Gairdner为原料,分剐用麦芽厂所用的空白水、pH值4．0盐酸溶液、pH值4．0硫酸溶液、100mg／L钙离子溶液、1μg／L赤霉素溶液使大麦浸渍、发芽来达到降低绿麦芽内部pH值的目的,实验结果表明．虽然硫酸、盐酸2种强酸物质具备降低大麦发芽内部pH值的能力,但其食品安全性差、对设备腐蚀大,而用钙离子和赤霉素溶液培养大麦发芽,虽然在大麦发芽过程中对pH值的变化影响不是很稳定,但均能使大麦发芽结束点即绿麦芽的pH值降低,所以对于后期啤酒的酿造均能够使淀粉酶、蛋白酶等活力近于最适pH值状态,为在啤酒酿造过程中减少外源添加酸的使用量,或为温和型弱酸或酸性中草药等物质的添加提供条件。     

Enzymatic Activity in the M Band

Experiments which combined histochemistry and electron microscopy were performed in studying the sites of enzymatic hydrolysis of thiolacetic acid in the presence of lead ions in diaphragmatic and cardiac muscle. It was found that in these striated muscles the electron opaque, final product of the histochemical reaction (PbS) was discretely deposited on the swelling of the thick elemental filaments that occurs at the M band. Additional sites of enzymatic activity occurred in mitrochondria and in round sarcoplasmic bodies. A reaction, probably non-enzymatic, also occurred in contraction bands in the area of the Z bands and in the sarcoplasmic reticulum. To ascertain the enzymatic nature of the reaction and to define the enzyme involved, control experiments were carried out and the effect of various esterase inhibitors was assayed. It is suggested that the M band enzyme is a cholinesterase, but the enzymes in the mitochondria and the sarcoplasmic bodies that hydrolyze the substrate appear to be different. A possible role of the M band enzyme is discussed.     

重组人骨形态发生蛋白-2生物学活性测定新方法的建立

目的:采用小鼠异位成骨技术及甲基麝香草酚蓝比色法检测重组人骨形态发生蛋白-2(rhBMP-2)的生物学活性。方法:将rhBMP-2埋入小鼠肌间隙内,14d后取出新生组织,采用血清钙试剂盒检测其钙含量。结果:随着给药组剂量递增,相应地钙含量也增加,二者具有较强的量效关系。结论:此方法为本实验室独创,较传统的血清碱性磷酸酶方法更为方便、快捷,是一种能够定量检测rhBMP-2活性的新方法。     

Histone H2A Ubiquitination Inhibits the Enzymatic Activity of H3 Lysine 36 Methyltransferases

Histone H3 lysine 27 (H3K27) methylation and H2A monoubiquitination (ubH2A) are two closely related histone modifications that regulate Polycomb silencing. Previous studies reported that H3K27 trimethylation (H3K27me3) rarely coexists with H3K36 di- or tri-methylation (H3K36me2/3) on the same histone H3 tails, which is partially controlled by the direct inhibition of the enzymatic activity of H3K27-specific methyltransferase PRC2. By contrast, H3K27 methylation does not affect the catalytic activity of H3K36-specific methyltransferases, suggesting other Polycomb mechanism(s) may negatively regulate the H3K36-specific methyltransferase(s). In this study, we established a simple protocol to purify milligram quantities of ubH2A from mammalian cells, which were used to reconstitute nucleosome substrates with fully ubiquitinated H2A. A number of histone methyltransferases were then tested on these nucleosome substrates. Notably, all of the H3K36-specific methyltransferases, including ASH1L, HYPB, NSD1, and NSD2 were inhibited by ubH2A, whereas the other histone methyltransferases, including PRC2, G9a, and Pr-Set7 were not affected by ubH2A. Together with previous reports, these findings collectively explain the mutual repulsion of H3K36me2/3 and Polycomb modifications.     

用质粒作底物测定核糖体失活蛋白酶活性的新方法

植物核糖体失活蛋白(ribosome-inactivating protein,RIP)是一类能作用于核糖体最大RNA的独特蛋白质.它是研究蛋白质生物合成中核糖体RNA结构与功能的有力工具.利用RIP能在DNA中脱去一些腺嘌呤碱基使超螺旋DNA解旋的特点,分别以常用的质粒PUC18、PUC19和PBR322 DNA为底物,建立了测定RIP酶活性的一种新方法,其灵敏度是50ng(天花粉蛋白)和5ng(还原型的辛纳毒蛋白),酶催化反应的时间是60min.这个新方法具有方便、快捷、灵敏的特点,避免了常用方法中制备核糖体、提取RNA的仪器和技术条件的限制,检测的时间由原来的几天缩短到约120min,大大地降低了检测的费用,为广泛和深入地研究RIP提供了有利的条件.     

Visualization of the turkey erythrocyte β-adrenergic receptor

We have recently described the affinity chromatography purification of the turkey erythrocyte β-adrenergic receptor. The minute amounts obtained initially precluded extensive biochemical characterization. To improve the yield of the receptor, the erythrocyte membranes have been prepared by a new method. This procedure resulted in a 10-fold higher receptor density in comparison with the membrane preparation used previously. The new membranes also contained a catecholamine-sensitive guanine triphosphatase and an adenylate cyclase sensitive to Gpp(NH)p and l-epinephrine. Solubilization by a double digitonin extraction resulted in a preparation containing 4–6 pmoles of ³H-dihydroalprenolol binding sites per mg of membrane protein. A single step of affinity chromatography on alprenolol-sepharose of the soluble digitonin extract resulted in an additional 1,000-fold purification of the receptor. The overall purification factor was 20,000 relative to the binding activity of the crude membrane preparations. Electrophoresis in SDS-polacrylamide of iodinated purified β-receptors revealed, after autoradiography, the presence of four major components. Three of these, corresponding to molecular weights of 170,000, 33,000, and 30,000, respectively, were not affected by reduction with β-mercaptoethanol and were not observed when the digitonin extracts were loaded on the affinity gel in the presence of an excess of l-propranolol. A fourth 52,000-dalton component (60,000 daltons after reduction with β-mercaptoethanol) remained apparent even when affinity purification was prevented by addition of l-propranolol. Our results suggest that the β-adrenergic receptor is composed of at least three subunits that interact by noncovalent bonds.     

A New Chelation Method for Determining ATPase Activity in Skeletal Muscle

Traditional methods for visualizing ATPase in sections use heavy metals that generate visible metal salfide products. These methods use unpleasant and toxic reagents. We report a safer method using a novel ferric ion chelating agent to produce highly specific, low background, and permanent staining of muscle fiber enzymes.     

A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase

Despite decades of research and the availability of the full genomic sequence of the baker’s yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an explosion of high-quality genomic and structural data from multiple organisms, ranging from bacteria to mammals. New computational methods now allow us to integrate these data and extract meaningful insights into the functional identity of uncharacterized proteins in yeast. Here, we created a database of sensitive sequence similarity predictions for all yeast proteins. We use this information to identify candidate enzymes for known biochemical reactions whose enzymes are unidentified, and show how this provides a powerful basis for experimental validation. Using one pathway as a test case we pair a new function for the previously uncharacterized enzyme Yhr202w, as an extra-cellular AMP hydrolase in the NAD degradation pathway. Yhr202w, which we now term Smn1 for Scavenger MonoNucleotidase 1, is a highly conserved protein that is similar to the human protein E5NT/CD73, which is associated with multiple cancers. Hence, our new methodology provides a paradigm, that can be adopted to other organisms, for uncovering new enzymatic functions of uncharacterized proteins.     

Requirement for Phospholipase C-γ1 Enzymatic Activity in Growth Factor-Induced Mitogenesis

The cytoplasmic regions of the receptors for epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) bind and activate phospholipase C-γ1 (PLC-γ1) and other signaling proteins in response to ligand binding outside the cell. Receptor binding by PLC-γ1 is a function of its SH2 domains and is required for growth factor-induced cell cycle progression into the S phase. Microinjection into MDCK epithelial cells and NIH 3T3 fibroblasts of a polypeptide corresponding to the noncatalytic SH2-SH2-SH3 domains of PLC-γ1 (PLC-γ1 SH2-SH2-SH3) blocked growth factor-induced S-phase entry. Treatment of cells with diacylglycerol (DAG) or DAG and microinjected inositol-1,4,5-triphosphate (IP₃), the products of activated PLC-γ1, did not stimulate cellular DNA synthesis by themselves but did suppress the inhibitory effects of the PLC-γ1 SH2-SH2-SH3 polypeptide but not the cell cycle block imposed by inhibition of the adapter protein Grb2 or p21 Ras. Two c-fos serum response element (SRE)-chloramphenicol acetyltransferase (CAT) reporter plasmids, a wild-type version, wtSRE-CAT, and a mutant, pm18, were used to investigate the function of PLC-γ1 in EGF- and PDGF-induced mitogenesis. wtSRE-CAT responds to both protein kinase C (PKC)-dependent and -independent signals, while the mutant, pm18, responds only to PKC-independent signals. Microinjection of the dominant-negative PLC-γ1 SH2-SH2-SH3 polypeptide greatly reduced the responses of wtSRE-CAT to EGF stimulation in MDCK cells and to PDGF stimulation in NIH 3T3 cells but had no effect on the responses of mutant pm18. These results indicate that in addition to Grb2-mediated activation of Ras, PLC-γ1-mediated DAG production is required for EGF- and PDGF-induced S-phase entry and gene expression, possibly through activation of PKC.     

New Method for Visualization of Vascular Networks in Nonperfused Fixed Tissues

A new method of visualizing the angioarchitecture of tissues has been developed that uses blood components in nonperfused materials. Tissue blocks are fixed in 4% paraformaldehyde and cut with a vibratome into 50-60 μm sections. Endogenous peroxidase in red blood cells is then reduced in the presence of hydrogen peroxide with the resultant oxidation of the chromogen 3,3'-diaminobenzidine (DAB). This generates a dark, highly insoluble reaction product throughout the vascular system. The visualization of vascular components can be further enhanced by exposing the sections to peroxidase-conjugated IgG to increase the background staining of the blood plasma. The technique minimizes preparation artifact and permits the application of morphometric analytical methods, thus allowing parameters such as the volume density of the vascular bed to be quantified.     

A Real-Time Fluorogenic Assay for the Visualization of Glycoside Hydrolase Activity in Planta

There currently exists a diverse array of molecular probes for the in situ localization of polysaccharides, nucleic acids, and proteins in plant cells, including reporter enzyme strategies (e.g. protein-glucuronidase fusions). In contrast, however, there is a paucity of methods for the direct analysis of endogenous glycoside hydrolases and transglycosidases responsible for cell wall remodeling. To exemplify the potential of fluorogenic resorufin glycosides to address this issue, a resorufin β-glycoside of a xylogluco-oligosaccharide (XXXG-β-Res) was synthesized as a specific substrate for in planta analysis of XEH activity. The resorufin aglycone is particularly distinguished for high sensitivity in muro assays due to a low pK_a (5.8) and large extinction coefficient (ε 62,000 m⁻¹cm⁻¹), long-wavelength fluorescence (excitation 571 nm/emission 585 nm), and high quantum yield (0.74) of the corresponding anion. In vitro analyses demonstrated that XXXG-β-Res is hydrolyzed by the archetypal plant XEH, nasturtium (Tropaeolum majus) NXG1, with classical Michaelis-Menten substrate saturation kinetics and a linear dependence on both enzyme concentration and incubation time. Further, XEH activity could be visualized in real time by observing the localized increase in fluorescence in germinating nasturtium seeds and Arabidopsis (Arabidopsis thaliana) inflorescent stems by confocal microscopy. Importantly, this new in situ XEH assay provides an essential complement to the in situ xyloglucan endotransglycosylase assay, thus allowing delineation of the disparate activities encoded by xyloglucan endotransglycosylase/hydrolase genes directly in plant tissues. The observation that XXXG-β-Res is also hydrolyzed by diverse microbial XEHs indicates that this substrate, and resorufin glycosides in general, may find broad applicability for the analysis of wall restructuring by polysaccharide hydrolases during morphogenesis and plant-microbe interactions.The development and application of molecular probes for the localization of biomolecules in planta continues to have a profound impact on the field of plant physiology. A number of elegant techniques have been devised for the detection of nucleic acids, polypeptides, and polysaccharides in situ, including DNA/RNA hybridization (Jin and Lloyd, 1997), reporter protein fusions (Jefferson et al., 1987; Ehrhardt, 2003; Chapman et al., 2005; Stewart, 2005; Berg and Beachy, 2008; Nelson et al., 2008), immunohistochemical methods (Walker et al., 2001; Chapman et al., 2005), applications of natural carbohydrate-binding proteins (Knox, 2008), and direct spectroscopy (Vicente et al., 2007). While there now exists a considerable toolbox to identify the location to which biomolecules are directed in the cell, elucidation of specific biochemical function at the site of localization often remains challenging.Presently, there is a growing interest in the roles of glycoside hydrolases (GHs) and transglycosylases in plant cell wall biogenesis, remodeling, and degradation (Minic and Jouanin, 2006; Vicente et al., 2007; Gilbert et al., 2008; Lopez-Casado et al., 2008). A technical limitation of many studies, however, is that enzyme activities can only be measured for crude whole-tissue extracts, or purified or recombinant enzymes, and thus cannot be directly correlated with the high-resolution in situ localization of other biomacromolecules. As such, the in situ analysis of GH activities responsible for the degradation of plant cell wall polysaccharides has received comparatively little attention, primarily due to a paucity of convenient assay methods (Vicente et al., 2007). Some notable exceptions include the use of commercially available X (5-bromo-4-chloro-3-indolyl glycoside) substrates for the detection of exoglycosidase activity (Monroe et al., 1999; Chantarangsee et al., 2007; Macquet et al., 2007; Wen et al., 2008). Likewise, transglycosylase activity has been visualized in higher plant and yeast cell walls using sulforhodamine-oligosaccharide acceptor substrates (Vissenberg et al., 2000; Bourquin et al., 2002; Nishikubo et al., 2007; Cabib et al., 2008). Both types are examples of end point, or stopped, assays, in which precipitated indigoid dyes or incorporated fluorescent oligosaccharide conjugate, respectively, are observed after a terminal incubation time.In this study, we have developed the use of resorufin glycosides as substrates for the real-time, continuous observation of GH activity in situ (Fig. 1). Enzymatic hydrolysis of such substrates releases the resorufin aglycone, which is distinguished by a low pK_a value (5.8) and a large extinction coefficient (ε 62,000 m⁻¹cm⁻¹), long-wavelength fluorescence (excitation/emission maxima, 571 nm/585 nm), and high quantum yield (0.74) of the resorufinyl anion (Bueno et al., 2002). The pK_a value and spectral properties make resorufin glycosides particularly suitable for high sensitivity in muro enzyme activity assays due to significant ionization of resorufin at typical apoplastic pH values (Felle, 2005). To highlight the potential of this class of substrates in cell wall morphological studies, we have chemically synthesized a xylogluco-oligosaccharide (XGO) resorufin β-glycoside (XXXG-β-Res; Fig. 1 [1]; XGO nomenclature according to Fry et al., 1993) and demonstrated its use for the real-time imaging of xyloglucan endohydrolase (XEH) activity in plant tissues from nasturtium (Tropaeolum majus) and Arabidopsis (Arabidopsis thaliana) by confocal fluorescence microscopy.Open in a separate windowFigure 1.Use of resorufin glycosides as fluorogenic substrates for glycosidases. R = saccharide or hydrogen; [1] and [2], substrates for determination of (xylo)glucanase activity. Oligosaccharide nomenclature is according to Fry et al. (1993). [See online article for color version of this figure.]     

Enzymatic reduction of the α, β-unsaturated carbon bond in citral

Bacteria, yeasts and filamentous fungi were screened for enantio-specific reduction of the α, β-unsaturated carbon bond in citral to produce citronellal. While a traditional aqueous screening system revealed only Zymomonas mobilis as positive, citronellal was produced in an aqueous/organic two liquid phase system by 11 of the 46 tested strains, which demonstrates the relevance of applying two-phase systems to screening strategies. Z. mobilis and Citrobacter freundii formed 1 mM citronellal in 3 h in the presence of a NADPH regenerating system and 20% (v/v) toluene. In comparison to these bacteria, the eukaryotic strains showed at least five-fold lower citral reductase activities. The bacterial strains produced preferentially the (S)-enantiomer of citronellal with e.e. values of >99% for Z. mobilis and 75% for Citrobacter freundii. In contrast the yeasts produced preferentially (R)-citronellal, i.e. Candida rugosa with an enantiomeric excess value of more than 98%. Many strains formed alcoholic by-products, viz. geraniol, nerol and citronellol. For Z. mobilis the production of these alcohols was suppressed in the presence of various organic solvents, e.g. toluene, and further decreased after EDTA addition.     

Enzymatic Activity in Mitochondria from Orobanche

Mitochondria from Orobanche were analysed for the activities of aconitate hydratase, isocitrate dehydrogenase, succinate dehydro-genase, fumarate hydratase, malate dehydrogenase, NADH oxidase, substrate-cytochrome c oxidoreductases, glutamate dehydrogenase, aminotransferases, ATPase and “malic” enzyme. The specific activities of isocitrate dehydrogenase, NADH oxidase, substrate-cytochrome c oxidoreductases and glutamate dehydrogenase in the mitochondria) fraction from parasite tissue compared favourably with those reported for most of the mitochondria from growing and storage tissues. Succinate dehydrogenase, fumarate hydratase and aspartate aminotransferase were of intermediate activity, while aconitate hydratase and malate dehydrogenase had rather low activity, and “malic” enzyme had very low activity in comparison with other preparations. The relevance of these findings in relation to mitochondrial metabolism in the parasite is discussed. No evidence was obtained to suggest any basic abnormality in the biochemical properties of the mitochondria from Orobanche centua which may be correlated with its obligatorily parasitic existence.     

A Highly Sensitive Method for Quantitative Determination of L-Amino Acid Oxidase Activity Based on the Visualization of Ferric-Xylenol Orange Formation

L-amino acid oxidase (LAAO) has important biological roles in many organisms, thus attracting great attention from researchers to establish its detection methods. In this study, a new quantitative in-gel determination of LAAO activity based on ferric-xylenol orange (Fe^IIIXO) formation was established. This method showed that due to the conversion of Fe^II to Fe^III by H₂O₂ and subsequent formation of Fe^IIIXO complex halo in agar medium, the logarithm of H₂O₂ concentration from 5 to 160 µM was linearly correlated to the diameter of purplish red Fe^IIIXO halo. By extracting the LAAO-generated H₂O₂ concentration, the LAAO activity can be quantitatively determined. This Fe^IIIXO agar assay is highly sensitive to detect H₂O₂ down to micromolar range. More importantly, it is easy to handle, cheap, reproducible, convenient and accurate. Coupled with SDS-PAGE, it can directly be used to determine the number and approximate molecular weight of LAAO in one assay. All these features make this in-gel Fe^IIIXO assay useful and convenient as a general procedure for following enzyme purification, assaying fractions from a column, or observing changes in activity resulting from enzyme modifications, hence endowing this method with broad applications.     

A New Method for Purifing Cyt b6f Protein Complex

A new protocol which is much simpler than current procedures, has been developed for purification of the Cyt b6f protein complex. The protocol contained only two steps dialysis-cen- trifugation and stepwise precipitation with ammonium sulfate. Moreover, this method is suitable for larger scale preparation. The purified complex from spinach ( Spinacia oleracea L. ) contained 9.8 nmol Cyt f per milligram protein. 2 Cyt b6(b-hemes) and 1 Chl a per Cyt f. SDS-PAGE showed four main bands and one weak band with low molecular weight. Its activity(PQ2H2→Cyt c)was around 80 μmol Cyt c·nmol Cyt f-1·h-l