Discovery of the archaeal chemical link between glycogen (starch) synthase families using a new mass spectrometry assay

Starch and its analogue glycogen are biosynthesized by enzymes that have been classified by sequence similarities into two families that have no significant sequence overlap: the animal/fungal glycogen synthases and the plant/bacterial glycogen (starch) synthases. Recent gene sequence analysis of putative archaea enzymes implicates them as a third family that links the structural and functional features of the other two classes. Herein, we present the first rapid electrospray ionization mass spectrometry-based assay to quantify any carbohydrate-polymerizing activity, the first cloning and recombinant expression as well as verification of the putative function of a glycogen synthase from the hyperthermophilic archaea Pyrococcus furiosus, and the characterization of a variety of glycogen synthases with the new assay. The new assay allowed the determination of Km and Vmax values for the rabbit, yeast, and P. furiosus glycogen synthases. Most surprisingly, unlike the synthases from rabbit or yeast and in contradiction to what would be expected from structural studies of other nucleotide-sugar binding proteins, the synthase from the archaea source accepts both uridine- and adenine-diphosphate activated glucose competitively and with comparable affinities to form a glucose polymer. This loose substrate specificity implicates this protein as the chemical link between the two branches of glycogen synthases that have evolved to accept primarily one or the other nucleotide as well as a good source enzyme for polymer bioengineering efforts.     

Evolutionary divergence of sedoheptulose 7-phosphate cyclases leads to several distinct cyclic products

Sedoheptulose 7-phosphate cyclases are enzymes that utilize the pentose phosphate pathway intermediate, sedoheptulose 7-phosphate, to generate cyclic precursors of many bioactive natural products, such as the antidiabetic drug acarbose, the crop protectant validamycin, and the natural sunscreens mycosporine-like amino acids. These proteins are phylogenetically related to the dehydroquinate (DHQ) synthases from the shikimate pathway and are part of the more recently recognized superfamily of sugar phosphate cyclases, which includes DHQ synthases, aminoDHQ synthases, and 2-deoxy-scyllo-inosose synthases. Through genome mining and biochemical studies, we identified yet another subset of DHQS-like proteins in the actinomycete Actinosynnema mirum and the myxobacterium Stigmatella aurantiaca DW4/3-1. These enzymes catalyze the conversion of sedoheptulose 7-phosphate to 2-epi-valiolone, which is predicted to be an alternative precursor for aminocyclitol biosynthesis. Comparative bioinformatics and biochemical analyses of these proteins with 2-epi-5-epi-valiolone synthases (EEVS) and desmethyl-4-deoxygadusol synthases (DDGS) provided further insights into their genetic diversity, conserved amino acid sequences, and plausible catalytic mechanisms. The results further highlight the uniquely diverse DHQS-like sugar phosphate cyclases, which may provide new tools for chemoenzymatic, stereospecific synthesis of various cyclic molecules.     

Neue enzymatische Analysenmethoden zur Bestimmung von Maltose,Stärke und Lactat in der Lebensmittelchemie

1. Determination of Maltose. Maltose is hydrolyzed by the enzyme α-glucosidase into glucose, which is determined by the enzymes hexokinase and glucose-6-phosphate-dehydrogenase. α-Glucosidase is specific for oligosaccharides with α-1,4 and α-1,2 bonds.
2. Determination of Starch and Glycogen. Starch and glycogen are splitted to glucose by the enzyme amylo-glucosidase. Starch has to be dissolved before enzymatic cleavage. A comparison of different methods for preparing starch solutions is given.
3. Determination of d- and l-Lactate. It is possible to determine d-lactate and l-lactate with the specific enzymes d-lactate-dehydrogenase and l-lactate-dehydrogenase. By different samples it is shown that no equal quantities of d- and l-lactate were found in the analyzed foods.

     

Isolation, identification and characterisation of starch-interacting proteins by 2-D affinity electrophoresis

A 2-D affinity electrophoretic technique (2-DAE) has been used to isolate proteins that interact with various starch components from total barley endosperm extracts. In the first dimension, proteins are separated by native PAGE. The second-dimensional gel contains polysaccharides such as amylopectin and glycogen. The migration of starch-interacting proteins in this dimension is determined by their affinity towards a particular polysaccharide and these proteins are therefore spatially separated from the bulk of proteins in the crude extract. Four distinct proteins demonstrate significant affinity for amylopectin and have been identified as starch branching enzyme I (SBEI), starch branching enzyme IIa (SBEIIa), SBEIIb and starch phosphorylase using polyclonal antibodies and zymogram activity analysis. In the case of starch phosphorylase, a protein spot was excised from a 2-DAE polyacrylamide gel and analysed using Q-TOF MS/MS, resulting in the alignment of three internal peptide sequences with the known sequence of the wheat plastidic starch phosphorylase isoform. This assignment was confirmed by the determination of the enzyme's function using zymogram analysis. Dissociation constants (Kd) were calculated for the three enzymes at 4 degrees C and values of 0.20, 0.21 and 1.3 g/L were determined for SBEI, SBEIIa and starch phosphorylase, respectively. Starch synthase I could also be resolved from the other proteins in the presence of glycogen and its identity was confirmed using a polyclonal antibody and by activity analysis. The 2-DAE method described here is simple, though powerful, enabling protein separation from crude extracts on the basis of function.     

Effect of Resistant Starch on Hydrolysis and Fermentation of Corn Starch for Ethanol

Starch samples with 0% or 30% amylose were subjected to four different liquefaction enzyme treatments (at various temperature and pH conditions) followed by simultaneous saccharification and fermentation (SSF). Resistant starch (RS) measurements were conducted for the initial starch sample, after liquefaction and after SSF. Initial RS was higher for 30% amylose starch samples (16.53 g/100 g sample) compared with 0% amylose (0.76 g/100 g sample). Higher initial RS resulted in lower conversion of starch into sugars and lower final ethanol yields. The four enzymes hydrolyzed RS, but in varying amounts. Higher temperature liquefaction hydrolyzed a larger portion of RS, resulting in higher ethanol concentrations and lower final residual solids (non-fermentables), whereas lower temperature liquefaction hydrolyzed a smaller portion of RS and resulted in lower ethanol concentrations and higher final residual solids. Decreases in resistant starch after high temperature liquefaction were 55% to 74%, whereas low temperature liquefaction decreases were 11% to 43%. For all enzyme treatments, RS content of starch samples decreased further after SSF.     

Enzymatic Synthesis of α-Glucose-1-phosphate: A Study Employing a New α-1,4 Glucan Phosphorylase from Corynebacterium callunae 1

Abstract

In synthetic pathways to complex carbohydrates such as oligosaccharides or nucleotide sugars the activated sugar 1-phosphates serve as important starting molecules. In this study the enzymatic synthesis of α-glucose-1-phosphate (Glc-1-P) has been investigated using a new bacterial α-glucan phosphorylase from Corynebacterium callunae. The major factors governing the rate of reaction and the attainable degree of substrate conversion have been identified and, accordingly, for optimizing the yield and limiting reaction time for the enzymatic process several points must be considered: (i) the pH-dependent equilibrium of reaction, (ii) product inhibition of the phosphorylase and (iii) enzymatic cleavage of α-1,6 glycosidic linkages present in α-1,4-glucans such as starch or maltodextrins by pullulanases to improve their phosphorolytic conversion. Results obtained in continuous experiments with the phosphorylase retained in an ultrafiltration membrane reactor confirmed the complete operational stability of the enzyme for several days at 30 °C. Since no more than approximately 18 % of the inorganic phosphate can be converted into Glc-1-P an efficient procedure for phosphate and product recovery will be particularly important.     

Bacterial Diterpene Biosynthesis

This Minireview summarises recent developments in the biosynthesis of diterpenes by diterpene synthases in bacteria. It is structured by the class of enzyme involved in the first committed step towards diterpenes, starting with type I diterpene synthases, followed by type II enzymes and the more recently discovered UbiA‐related diterpene synthases. A special emphasis lies on the reaction mechanisms of diterpene synthases that convert simple linear precursors through cationic cascades into structurally complex, usually polycyclic carbon skeletons with multiple stereogenic centres. A further main focus of this Minireview is a discussion of how these mechanisms can be unravelled. Downstream modifications to bioactive molecules are also covered.     

On-line FT-Raman spectroscopic monitoring of starch gelatinisation and enzyme catalysed starch hydrolysis

The hydrolysis of starch by α-amylase and amyloglucosidase and the kinetics of these technically important reactions were investigated by FT-Raman spectroscopy. During the technical starch hydrolysis process, three reactions proceed one after the other but partly in parallel: the gelatinisation, the hydrolysis of starch to dextrin (liquefaction) by α-amylase, and the hydrolysis of dextrin to glucose (saccharification) by glucoamylase. These three reactions were studied separately. Potato starch or dextrin in concentrations of 50 g/l were suspended or dissolved in water, the reaction chamber was placed in a heated water bath, and defined, varied amounts of enzymes in solution were added. The reactions were monitored on-line in a bypass loop. The greatest spectral changes were observed due to the swelling and gelatinisation of starch. The liquefaction of starch to dextrin was started with the addition of α-amylase at a temperature of 80°C and the spectral changes were monitored. In a similar way, a solution/suspension of dextrin was used to investigate the reaction of glucoamylase at 50°C. Both enzymatic reactions were performed at four different enzyme activities. All reactions showed distinctive spectral changes, which can, in principle, be evaluated for the determination of the degree of starch hydrolysis. As a Nd:YAG laser at 1064 nm was used, fluorescence excitation was not observed despite the use of crude, technical-grade enzymes. The findings demonstrate the potential use of Raman spectroscopy in monitoring and control of technical enzyme reactions.     

Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production

Microbial production can be advantageous over the extraction of phytoterpenoids from natural plant sources, but it remains challenging to rationally and rapidly access efficient pathway variants. Previous engineering attempts mainly focused on the mevalonic acid (MVA) or methyl-d-erythritol phosphate (MEP) pathways responsible for the generation of precursors for terpenoids biosynthesis, and potential interactions between diterpenoids synthases were unexplored. Miltiradiene, the product of the stepwise conversion of (E,E,E)-geranylgeranyl diphosphate (GGPP) catalyzed by diterpene synthases SmCPS and SmKSL, has recently been identified as the precursor to tanshionones, a group of abietane-type norditerpenoids rich in the Chinese medicinal herb Salvia miltiorrhiza . Here, we present the modular pathway engineering (MOPE) strategy and its application for rapid assembling synthetic miltiradiene pathways in the yeast Saccharomyces cerevisiae . We predicted and analyzed the molecular interactions between SmCPS and SmKSL, and engineered their active sites into close proximity for enhanced metabolic flux channeling to miltiradiene biosynthesis by constructing protein fusions. We show that the fusion of SmCPS and SmKSL, as well as the fusion of BTS1 (GGPP synthase) and ERG20 (farnesyl diphosphate synthase), led to significantly improved miltiradiene production and reduced byproduct accumulation. The MOPE strategy facilitated a comprehensive evaluation of pathway variants involving multiple genes, and, as a result, our best pathway with the diploid strain YJ2X reached miltiradiene titer of 365 mg/L in a 15-L bioreactor culture. These results suggest that terpenoids synthases and the precursor supplying enzymes should be engineered systematically to enable an efficient microbial production of phytoterpenoids.     

Redesigning enzymes based on adaptive evolution for optimal function in synthetic metabolic pathways

Nature has balanced most metabolic pathways such that no one enzyme in the pathway controls the flux through that pathway. However, unnatural or nonnative, constructed metabolic pathways may have limited product flux due to unfavorable in vivo properties of one or more enzymes in the pathway. One such example is the mevalonate-based isoprenoid biosynthetic pathway that we previously reconstructed in Escherichia coli. We have used a probable mechanism of adaptive evolution to engineer the in vivo properties of two enzymes (3-hydroxy-3-methylglutaryl-CoA reductase [tHMGR] and many terpene synthases) in this pathway and thereby eliminate or minimize the bottleneck created by these inefficient or nonfunctional enzymes. Here, we demonstrate how we significantly improved the productivity (by approximately 1000 fold) of this reconstructed biosynthetic pathway using this strategy. We anticipate that this strategy will find broad applicability in the functional construction (or reconstruction) of biological pathways in heterologous hosts.     

Role of NO and NO synthases in oncogenesis

The review focuses on the role of NO and NO synthases in the signaling pathways responsible for the occurrence and development of leukemias. Some classes of inhibitors of different NO synthase isoforms that exhibit cytotoxic activity against leukemia cells are described.     

Cooperativity and substrate specificity of an alkaline amylase and neopullulanase complex of Micrococcus halobius OR-1

The saccharifying alkaline amylase and neopullulanase complex of Micrococcus halobius OR-1 hydrolyzes both α-(1,4)- and α-(1,6)-glycosidic linkages of different linear and branched polysaccharides. The following observations were made concerning the analysis of the coexpressed amylase and neopullulanase enzymes. Even though the enzymes were subjected to a rigorous purification protocol, the activities could not be separated, because both the enzymes were found to migrate in a single peak. By contrast, two independent bands of amylolytic activity at 70 kDa and pullulanolytic activity at 53 kDa were evident by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), reducing and nonreducing PAGE, and zymographic analysis on different polysaccharides. Preferential chemical modification of the enzyme and concomitant high-performance thin-layer chromatographic analyses of the saccharides liberated showed that amylase is sensitive to 1-(dimethylamino-propyl)-3-ethyl carbodiimide-HCl and cleaved α-(1,4) linkages of starch, amylose, and amylopectin producing predominantly maltotriose. On the other hand, formalin-sensitive neopullulanase acts on both α-(1,4) and α-(1,6) linkages of pullulan and starch with maltotriose and panose as major products. It is understood that neopullulanase exhibits dual activity and acts in synergy with amylase toward the hydrolysis of α-(1,4) linkages, thereby increasing the overall reaction rate; however, such a synergism is not seen in zymograms, in which the enzymes are physically separated during electrophoresis. It is presumed that SDS-protein intercalation dissociated the enzyme complex, without altering the individual active site architecture, with only the synergism lost. The optimum temperature and pH of amylase and neopullulanase were 60°C and 8.0, respectively. The enzymes were found stable in high alkaline pH for 24 h. Therefore, the saccharifying alkaline amylase and neopullulanase of M. halobius OR-1 evolved from tapioca cultivar shows a highly active and unique enzyme complex with several valuable biochemical features.     

Dielectric relaxation analysis of starch oligomers and polymers with respect to their chain length

Starch belongs to the polyglucan group. This type of polysaccharide shows a broad β-relaxation process in dielectric spectra at low temperatures, which has its molecular origin in orientational motions of sugar rings via glucosidic linkages. This chain dynamic was investigated for α(1,4)-linked starch oligomers with well-defined chain lengths of 2, 3, 4, 6, and 7 anhydroglucose units (AGUs) and for α(1,4)-polyglucans with average degrees of polymerization of 5, 10, 56, 70, and so forth (up to 3000; calculated from the mean molecular weight). The activation energy (E_a) of the segmental chain motion was lowest for dimeric maltose (E_a = 49.4 ± 1.3 kJ/mol), and this was followed by passage through a maximum at a degree of polymerization of 6 (E_a = 60.8 ± 1.8 kJ/mol). Subsequently, E_a leveled off at a value of about 52 ± 1.5 kJ/mol for chains containing more than 100 repeating units. The results were compared with the values of cellulose-like oligomers and polymers bearing a β(1,4)-linkage. Interestingly, the shape of the E_a dependency on the chain length of the molecules was qualitatively the same for both systems, whereas quantitatively the starch-like substances generally showed higher E_a values. Additionally, and for comparison, three cyclodextrins were measured by dielectric relaxation spectroscopy. The ringlike molecules, with 6, 7, and 8 α(1,4)-linked AGUs, showed moderately different types of dielectric spectra. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 188–197, 2004     

Bioinformatics Analysis of Oligosaccharide Phosphorylation Effect on the Stabilization of the β-Amylase Ligand Complex

Starch is the most abundant storage carbohydrate produced in plants. The beginning of transitory starch degradation in plants depends mainly on day cycle, posttranslational regulation of enzyme activity, and starch phosphorylation, but the molecular mechanism of these factors' influence is not yet precisely described. The aim of our analysis was to investigate the effect of phosphorylation on the intermolecular energies for stabilization of the complexes between the set of phosphorylated and nonphosphorylated carbohydrate ligands and Solanum tuberosum (L.) β-amylase model. For performing protein-ligand docking procedures and calculating the binding energies, the DOCK6 and Glide 4.5 program suites were applied. We have observed simultaneously the effect of chain elongation, phosphorylation, and chain branching. Results of flexible ligand docking show that phosphorylation as well as chain elongation increase the stabilization of the ligand-protein complex.     

Synthesis of CMS under ultrasonic irradiation

Starch is a granular mixture of nomopolymers of α-D-glucopyranosyl units. These polymer molecules are hydrogen bonded and aligned radially in the granule. Starch is an important ingredient in manufacturing a wide range of industrial products such as food, paper, textiles, and building materials. Today, starch is chemically modified for speciality use. Modification of starch properties by derivatization is an important factor in the continued and increased use of starch to provide thickening, gelling, binding, adhesive, and film forming functionality. Carboxymethylstarch (CMS) is one of important starch derivatives. The study in exploitation and use of CMS has been acitvated since 1980s. At present, it is widely used in medicine, functional food, commodity, dope and so on.     

Biopolymers for biocatalysis: Structure and catalytic mechanism of hydroxynitrile lyases

Hydroxynitrile lyases catalyze the reversible cleavage of α-cyanohydrins to yield hydrocyanic acid and the corresponding aldehyde or ketone. Besides its biological interest, this class of enzymes is also of relevance in industrial biocatalysis for the enantioselective condensation of HCN with a variety of aldehydes and ketones. Several distinctly different types of hydroxynitrile lyases (HNLs) are known, which must have originated through convergent evolution from different ancestral proteins. Three-dimensional structural data are known for three classes of hydroxynitrile lyases. Insights into the reaction mechanisms emerged from a combination of structural, enzyme kinetic, spectroscopic, and molecular modeling data. For all three types of HNLs, mechanisms involving acid–base catalysis were proposed. In members belonging to the α,β-hydrolase type, the amino acid residues of the catalytic triad presumably act as general acid/base, whereas for flavine adenine dinucleotide (FAD)-dependent HNLs a single histidine residue fulfills this function. In the third type of HNL—which is related to carboxypeptidase—acid–base catalysis involves the carboxylate of the C-terminal residue. The catalytic relevance of a positive electrostatic potential in the active site was suggested in some of the mechanistic proposals. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 479–486, 2004     

A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase

In many bacteria tenI is found clustered with genes involved in thiamin thiazole biosynthesis. However, while TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity, and the role of this enzyme in thiamin biosynthesis remains unknown. In this contribution, we identify the function of TenI as a thiazole tautomerase, describe the structure of the enzyme complexed with its reaction product, identify the substrates phosphate and histidine 122 as the acid/base residues involved in catalysis, and propose a mechanism for the reaction. The identification of the function of TenI completes the identification of all of the enzymes needed for thiamin biosynthesis by the major bacterial pathway.     

Molecular size and mass distributions of native starches using complementary separation methods: Asymmetrical Flow Field Flow Fractionation (A4F) and Hydrodynamic and Size Exclusion Chromatography (HDC-SEC)

Starch consists of a mixture of two α-glucans built mainly upon α-(1,4) linkages: amylose, an essentially linear polymer, and amylopectin, a branched polymer containing 5-6% of α-(1,6) linkages. The aim of the present work was to analyze the structural properties of native starches displaying different amylose-to-amylopectin ratios and arising from different botanical sources, using asymmetrical flow field flow fractionation (A4F) and a combination of hydrodynamic and size-exclusion chromatography (HDC-SEC) coupled with multiangle laser light scattering, online quasi-elastic light scattering, and differential refractive index techniques. The procedure, based upon dimethyl sulfoxide pretreatment and then solubilization in water, generates a representative injected sample without altering the initial degree of polymerization. The amylopectin weight-average molar masses and radii of gyration were around 1.0 × 10(8)-4.8 × 10(8) g mol(-1) and 110-267 nm, respectively. For each starch sample, the hydrodynamic radius (R(H)) distributions and the molar mass distributions obtained from the two fractionation systems coupled with light scattering techniques were analyzed. The size determination scales were extended by means of R(H) calibration curves. HDC-SEC and A4F data could be matched. However, A4F enabled a better separation of amylopectins and therefore an enhanced structural characterization of the starches. The two advantages of this experimental approach are (1) it can directly obtain distributions as a function of both molar mass and size, while taking account of sample heterogeneity, and (2) it is possible to compare the results obtained using the different techniques through the direct application of R(H) distributions.     

Gaining insight into the inhibition of glycoside hydrolase family 20 exo-β-N-acetylhexosaminidases using a structural approach

One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray structural analysis of a representative family 20 exo-β-N-acetylhexosaminidase in complex with various known classes of inhibitor of these types of enzymes, which highlights how different inhibitor classes can inhibit the same enzyme. This study will aid in the future development of inhibitors of not only exo-β-N-acetylhexosaminidases but also other types of glycoside hydrolases.     

柘树根多糖的分离纯化及结构表征

以柘树[Cudrania tricuspidata(Carr.) Bur.]的根为材料, 经热水抽提、木瓜蛋白酶-Sevag法除蛋白、乙醇沉淀和DEAE-Sephadex A-50凝胶柱层析分离纯化, 得到一种水溶性的柘树根多糖(CPS-0). 采用HPLC、糖基组成分析、甲基化分析、GC、GC-MS、NMR(1H NMR, 13C NMR及HMQC)、元素分析、UV和IR等技术对CPS-0的纯度、性质、组成和结构进行表征. 结果表明, CPS-0仅含葡萄糖, 分子量为4.6×103, 主链由1,4-连接的α-D-葡萄糖残基组成, 其侧链由末端及1,4-连接的葡萄糖残基构成, 取代于主链分支点葡萄糖的6位, 平均每10个葡萄糖残基组成的重复单元中含有1个分支.