Studies on Microbial Metabolism of Sugar Nucleotides

The fermentative production of uridine diphosphate N-acetylglucosamine (UDPAG) from 5′-UMP and glucosamine by dried cells of baker’s yeast was studied. UDPAG was found to accumulate in a reaction system containing 5′-UMP, glucosamine, fructose, inorganic phosphate and magnesium ions with dried baker’s yeast as an enzyme source. UDPAG was separated from the reaction mixture by means of anion exchange column chromatography and was identified by several biochemical methods.

The reaction conditions for the fermentative production of UDPAG were examined. The yield of UDPAG was about 40~66% based on 5′-UMP added when fermentation conditions were optimized. The concentration of glucosamine and potassium phosphate buffer, and pH as well as the water content of dried cells greatly affected the formation of UDPAG.     

糖核苷酸的生物合成和应用

糖基化是生物体中最重要的反应之一,通过糖基化作用可以形成具有多种生物功能的糖缀合物。糖核苷酸作为Leloir型糖基转移酶催化的转糖基反应的糖基供体,在聚糖和糖缀合物的生物合成中必不可少。然而,糖核苷酸的成本较高、可用性有限等因素阻碍了生物催化级联反应在工业中大规模的应用。因此,人们越来越关注糖核苷酸的合成策略,以实现其在多种领域的广泛应用。目前,糖核苷酸及其衍生物的化学合成方法已经建立起来,但合成反应的产量通常很低,而酶法（化学-酶法）和细胞工厂法在合成糖核苷酸过程中具有显著优势。本文主要围绕哺乳动物中常见的9种糖核苷酸,概述了其类型和结构、酶法（化学-酶法）和细胞工厂法两种制备方法。伴随糖核苷酸的高效合成,其多种功能逐渐被发现和应用。本文进一步概述了糖核苷酸在聚糖及糖缀合物合成、糖基转移酶生化性质表征以及生物正交标记策略等方面的应用,对生物化学、糖生物学的研究以及相关医药产品的研发具有十分重要的意义。     

糖核苷酸类化合物的合成与在生物学研究中的应用

糖基化是指在酶的作用下,蛋白质、脂质或小分子等连上糖类化合物的过程.它在生物体内广泛存在并有十分重要的生物学意艾.它是通过糖基转移酶催化完成的,其中糖核苷酸是糖基化过程中糖的供体.本文简要叙述了糖核苷酸类化合物的有机合成和生化合成的方法以及该类化合物在抗生素糖基化途径研究、糖基转移酶的生物化学研究和化学生物学机理研究中的应用.     

Studies on Synthetic Nucleotides

A direct synthetic method of adenine nucleotides has been described. Treatment of adenine with 2,3-di-O-benzoyl-5-diphenylphosphoryl-d-ribofuranosyl bromide in acetonitrile at 40°C, followed by removal of the protecting groups gave AMP and 3-iso-AMP. The structure and configuration in glycosidic center of the latter was established by UV and NMR spectral studies. Furthermore, treatment of 3-iso-AMP with 5′-nucleotidase gave the nucleoside, which is identical with 3-isoadenosine in its physical properties.     

Sugar Nucleotides from the Fungus Aureobasidium

Peptides showing inhibitory activity against the angiotensin I-converting enzyme (ACE) were investigated from the fibroin fraction of discarded silk fabric. Fibroin, which was hydrolyzed with alcalase after partial hydrolysis with hot aqueous 40% CaCl₂, released two major active peptides showing ACE-inhibitory activity. The two peptides were identified as glycyl-valyl-glycyl-tyrosine (GVGY) and glycyl-valyl-glycyl-alanyl-glycyl-tyrosine (GVGAGY) by analyses with a protein sequencer and LC/MS/MS. GVGY, whose ACE-inhibitory activity has not previously been reported, showed a blood pressure-depressing effect on spontaneously hypertensive rat (SHR).     

Tracing the Early Emergence of Microbial Sulfur Metabolisms

Abstract

Hydrogen sulfide (nH₂S) and sulfur oxide (SO _n ; n?=?1, 2, 3) gases in early Earth’s globally anoxic atmosphere were subjected to gas-phase chemical transformations by UV light. A principal photolysis pathway at that time produced elemental sulfur aerosols with mass-independently fractionated (MIF) isotopic values carrying variable minor isotope (³³S, ³⁶S) compositions. These rained into the sulfate-deficient Archean (ca. 3.85–2.5 Ga) oceans to react with [Fe²⁺]_aq and form sedimentary sulfides. The MIF-bearing sulfides were incorporated into Archean sediments, including banded iron formations (BIF). Such aerosols may also have fueled microbial sulfur metabolisms, and thus are traceable by the MIF sulfur isotopes. Yet, data show that before ～3.5 Ga mass-dependent³⁴S/³²S values in Early Archean sediments tend to fall within a narrow (±0.1%) range even as they carry mass-independent values. By about 3.5 Ga, ³⁴S/³²S values show much greater changes (>1%) in range congruent with microbial metabolic processing. Here, we trace probable pathways of elemental sulfur aerosols into Archean sediments, and couple our study with analysis of the evolutionary relationships of enzymes involved in sulfur metabolism to explain the observed trends. Our model explains why elemental sulfur aerosols were apparently not utilized by the Eoarchean (pre-3.65 Ga) biosphere even though an immediate precursor to the required enzyme may have already been present.

• Highlights

• Evolution of microbial sulfur metabolisms is tracked by multiple sulfur isotopes

• Alkaline hydrothermal vents were an abode for early microbial life

• Sulfite detoxification prompted anaerobic respiration

• Reversal of respiratory electron transport chain (ETC) stimulated photothiotrophy

• Surplus e- acceptors permitted the emergence of elemental sulfur reduction

     

Studies on the Pyruvate and Carbohydrate Metabolisms by Lactic Acid Bacteria

The formation of ketopentoses from aldopentoses was demonstrated by six strains of hetero-fermentative lactic acid bacteria (heterofermenters). The dried bacterial cells harvested on malt extract and their cell-free extracts were found to reveal isomerization of d-xylose or l-arabinose to corresponding ketopentoses in the presence of borate, while any formation of ketopentose was never observed with the enzyme preparations of homofermenters except L. xylosus and Pc. lindneri. The ketopentoses were isolated by a Dowex-l borate column, and identified by paper-chromatography. Results obtained were as follows: xylulose was formed from xylose by six strains of heterofermenters (L. fermentum, Leuc. mesenteroides, L. brevis, L. buchneri, L. gayonii and L. fermenti) and by L. xylosus. Ribulose was obtained from arabinose by L. brevis, L. pento-aceticus, L. gayonii, L. buchneri and Pc. linderi.     

Enzymatic Studies on the Oxidation of Sugar and Sugar Alcohol

During the course of studies on the oxidative metabolism of d-sorbitol by acetic acid bacteria, it was found that d-sorbitol was almost quantitatively converted to 5-keto-d-fructose via l-sorbose by a certain strain of Gluconobacter suboxydans. In addition to 5-keto-d-fructose, three γ-pyrone compounds, kojic acid, 5-oxymaltol, and 3-oxykojic acid, 2-keto-l-gulonate, and several organic acids such as succinic, glycolic, and glyceric acids were confirmed in the culture filtrate of this bacterium.

• The most suitable carbon source for 5-ketofructose fermentation by Gluconobacter suboxydans Strain 1 was confirmed to be d-sorbitol or l-sorbose using growing and resting cells. d-Fructose had little effect on the formation of this dicarbonylhexose.

• The optimal pH for the formation from l-sorbose by intact cells was found to be at 4.2.

• The activity of the pentose phosphate cycle in the resting cells was calculated as 13~17 μatoms/hr/mg of dry cells by the use of the manometric techniques.

• There was no strain tested so far which could accumulate a large amount of 5- keto-d-fructose from d-sorbitol except this bacterium.

• The experimental results shown in this paper makes the prediction that a certain dehydrogenating system of l-sorbose is functional in the organism, and the metabolic pathways of d-sorbitol via l-sorbose and 5-keto-d-fructose is proposed.

     

AMP-activated Protein Kinase Suppresses Biosynthesis of Glucosylceramide by Reducing Intracellular Sugar Nucleotides

The membrane glycolipid glucosylceramide (GlcCer) plays a critical role in cellular homeostasis. Its intracellular levels are thought to be tightly regulated. How cells regulate GlcCer levels remains to be clarified. AMP-activated protein kinase (AMPK), which is a crucial cellular energy sensor, regulates glucose and lipid metabolism to maintain energy homeostasis. Here, we investigated whether AMPK affects GlcCer metabolism. AMPK activators (5-aminoimidazole-4-carboxamide 1-β-d-ribofuranoside and metformin) decreased intracellular GlcCer levels and synthase activity in mouse fibroblasts. AMPK inhibitors or AMPK siRNA reversed these effects, suggesting that GlcCer synthesis is negatively regulated by an AMPK-dependent mechanism. Although AMPK did not affect the phosphorylation or expression of GlcCer synthase, the amount of UDP-glucose, an activated form of glucose required for GlcCer synthesis, decreased under AMPK-activating conditions. Importantly, the UDP-glucose pyrophosphatase Nudt14, which degrades UDP-glucose, generating UMP and glucose 1-phosphate, was phosphorylated and activated by AMPK. On the other hand, suppression of Nudt14 by siRNA had little effect on UDP-glucose levels, indicating that mammalian cells have an alternative UDP-glucose pyrophosphatase that mainly contributes to the reduction of UDP-glucose under AMPK-activating conditions. Because AMPK activators are capable of reducing GlcCer levels in cells from Gaucher disease patients, our findings suggest that reducing GlcCer through AMPK activation may lead to a new strategy for treating diseases caused by abnormal accumulation of GlcCer.     

宁夏甜菜丛根病的研究

发生在宁夏甜菜上的一种病毒病的病株叶丛主要表现为黄化、焦桔和叶脉黄化坏死。从其分离的病毒粒子呈杆状,宽约20nm,长度为65—110nm、270—300nm和390—420nm,能侵染甜菜、菠菜、昆诺阿藜、苋色藜、番杏,与甜菜坏死黄脉病毒(BNYVV)抗血清呈阳性反应。综上所述,认为该病害是由BNYVV引起的。     

Mass Isotopomer Analysis of Metabolically Labeled Nucleotide Sugars and N- and O-Glycans for Tracing Nucleotide Sugar Metabolisms

Nucleotide sugars are the donor substrates of various glycosyltransferases, and an important building block in N- and O-glycan biosynthesis. Their intercellular concentrations are regulated by cellular metabolic states including diseases such as cancer and diabetes. To investigate the fate of UDP-GlcNAc, we developed a tracing method for UDP-GlcNAc synthesis and use, and GlcNAc utilization using ¹³C₆-glucose and ¹³C₂-glucosamine, respectively, followed by the analysis of mass isotopomers using LC-MS.Metabolic labeling of cultured cells with ¹³C₆-glucose and the analysis of isotopomers of UDP-HexNAc (UDP-GlcNAc plus UDP-GalNAc) and CMP-NeuAc revealed the relative contributions of metabolic pathways leading to UDP-GlcNAc synthesis and use. In pancreatic insulinoma cells, the labeling efficiency of a ¹³C₆-glucose motif in CMP-NeuAc was lower compared with that in hepatoma cells.Using ¹³C₂-glucosamine, the diversity of the labeling efficiency was observed in each sugar residue of N- and O-glycans on the basis of isotopomer analysis. In the insulinoma cells, the low labeling efficiencies were found for sialic acids as well as tri- and tetra-sialo N-glycans, whereas asialo N-glycans were found to be abundant. Essentially no significant difference in secreted hyaluronic acids was found among hepatoma and insulinoma cell lines. This indicates that metabolic flows are responsible for the low sialylation in the insulinoma cells. Our strategy should be useful for systematically tracing each stage of cellular GlcNAc metabolism.Protein glycosylation, which is the most abundant post-translational modification, has important roles in many biological processes by modulating conformation and stability, whereas its dysregulation is associated with various diseases such as diabetes and cancer (1, 2). Glycosylation is regulated by various factors including glucose metabolism, the availability and localization of nucleotide sugars, and the expression and localization of glycosyltransferases (3, 4). Thus, ideally all of these components should be considered when detecting changes in a dynamic fashion; namely, it is necessary not only to take a snapshot but also to make movies of the dynamic changes in glycan metabolism.Glucose is used by living cells as an energy source via the glycolytic pathway as well as a carbon source for various metabolites including nucleotide sugars (e.g. UDP-GlcNAc and CMP-NeuAc). These nucleotide sugars are transported into the Golgi apparatus, and added to various glycans on proteins. UDP-GlcNAc is the donor substrate for N-acetylglucosaminyl (GlcNAc)¹ transferases; alternatively, it is used in the cytosol for O-GlcNAc modification (i.e. O-GlcNAcylation) of intracellular proteins (5). The UDP-GlcNAc synthetic pathway is complex as it is a converging point of glucose, nucleotide, fatty acid and amino acid metabolic pathways. Thus, the metabolic flow of glucose modulates the branching patterns of N-glycans via UDP-GlcNAc concentrations because many of the key GlcNAc transferases that determine the branching patterns have widely different K_m values for UDP-GlcNAc ranging from 0.04 mm to 11 mm (6, 7). Indeed, it was demonstrated that the branching formation of N-glycans in T cells is stimulated by the supply from the hexosamine pathway, whereby it regulates autoimmune reactions promoted by T cells (8).UDP-GlcNAc is also used for the synthesis of CMP-NeuAc, the donor substrate for sialyltransferases (9). The CMP-NeuAc concentration is controlled by the feedback inhibition of UDP-GlcNAc epimerase/ManNAc kinase by the final product CMP-NeuAc, and hence a high CMP-NeuAc level reduces metabolic flow in CMP-NeuAc de novo synthesis (10). However, there is still only limited information about how the levels of nucleotide sugars dynamically change in response to the environmental cues, and how such changes are reflected in the glycosylation of proteins.Stable isotope labeling is a promising approach to quantify metabolic changes in response to external cues (11, 12). For example, the use of nuclear magnetic resonance to obtain isotopomer signals of metabolically labeled molecules has been applied to trace the flux in glycolysis and fatty acid metabolism (13). An approach based on the mass isotopomers of labeled metabolites with ¹³C₆-glucose has been developed to monitor the UDP-GlcNAc synthetic pathway (13–15). The method based on the labeling ratio of each metabolite related to UDP-GlcNAc synthesis has clarified the contribution of each metabolic pathway (14). Moseley reported a novel deconvolution method for modeling UDP-GlcNAc mass isotopomers (15).Previous studies into the use of nucleotide sugars in glycosylation have relied on the specific detection of metabolically radiolabeled glycans (16). It is possible not only to deduce the glycan structures but also to trace their relative contributions to glycan synthesis without MS. On the other hand, mass isotopomer analysis of glycans labeled with stable isotope provides the ratios of labeled versus unlabeled molecules from MS spectra and structural details of the glycans. However, there are only a limited number of publications reporting the application of stable isotope labeling of glycans for monitoring the dynamics of glycans (17). To date, there have been no reports describing a systematic method for tracing cellular GlcNAc biosynthesis and use based on mass isotopomer analysis.The aim of this study was to extend our knowledge of the synthesis and metabolism of UDP-GlcNAc as well as its use in the synthesis of CMP-NeuAc, N- and O-glycans. We recently developed a conventional HPLC method for simultaneous determination of nucleotide sugars including unstable CMP-NeuAc (18). We first established an LC-MS method for isotopomer analysis of ¹³C₆-glucose labeled nucleotide sugars for tracing UDP-GlcNAc metabolism from synthesis to use, because previous methods were not suitable for estimating UDP-GlcNAc use in CMP-NeuAc de novo synthesis (15). We also established a method for isotopomer analysis of labeled N- and O-glycan to monitor the metabolic flow of hexosamine into glycans. Using these two methods, we demonstrated the differences in the use of hexosamines between hepatoma and pancreatic insulinoma cell lines. Our approach may be useful for identifying a metabolic “bottleneck” that governs the turnover speed and patterns of cellular glycosylation, which may be relevant for various applications including glycoprotein engineering and discovery of disease biomarkers.     

Compound-Specific Isotopic Fractionation Patterns Suggest Different Carbon Metabolisms among Chloroflexus-Like Bacteria in Hot-Spring Microbial Mats

Stable carbon isotope fractionations between dissolved inorganic carbon and lipid biomarkers suggest photoautotrophy by Chloroflexus-like organisms in sulfidic and nonsulfidic Yellowstone hot springs. Where co-occurring, cyanobacteria appear to cross-feed Chloroflexus-like organisms supporting photoheterotrophy as well, although the relatively small ¹³C fractionation associated with cyanobacterial sugar biosynthesis may sometimes obscure this process.     

Studies on Antioxidative Substances of Microbial Origin

Aminopeptidase T (AP-T) is a metallo-dependent dimeric enzyme of Thermus aquaticus YT-1, an extremely thermophilic bacterium. We cloned the AP-T gene from T. aquaticus YT-1 into Escherichia coli using a synthetic oligonucleotide as a hybridization probe. The nucleotide sequence of the AP-T gene was found to encode 408 amino acid residues with GTG as a start codon. The molecular weight was calculated to be 44,820. The AP-T was overproduced in E. coli (about 5% of total soluble protein) when the start codon of the gene was changed from GTG to ATG, and the gene was downstream from the tac promoter. The AP-T expressed in E. coli was heat stable and easily purified by heat treatment (80°C, 30 min). The N-terminal amino acid sequence of AP-T showed similarity with that of aminopeptidase II from Bacillus stearothermophilus.     

The Discovery of Intramolecular Stereoelectronic Forces That Drive The Sugar Conformation in Nucleosides and Nucleotides

Abstract

This report summarizes our results⁸ on how the determination of the thermodynamics of the two-state North (N, C2′-exo-C3′-endo) ? South (S,C2′-endo-C3′-exo) pseudorotational equilibrium in aqueous solution (pD 0.6 - 12.0) basing on vicinal ³J_HH extracted from ¹H-NMR spectra measured at 500 MHz from 278K to 358K yields an experimental energy inventory of the unique stereoelectronic forces that dictate the conformation of the sugar moiety in β-D-ribonucleosides (rNs), β-D-nucleotides, in the mirror-image β-D- versus β-L-2′-deoxynucleosides (dNs) as well as in α-D- or L- versus β-D- or L-2′-dNs. Our work shows for the first time that the free-energies of the inherent internal flexibilities of β-D- versus β-L-2′-dNs and α-D- versus α-L-2′-dNs are identical, whereas the aglycone promoted tunability of the constituent sugar conformation is grossly affected in the α-nucleosides compared to the β-counterparts.     

京尼平苷的微生物转化研究

本文利用高产β-葡萄糖苷酶菌种制备游离细胞和固定化细胞,在温和条件下可将京尼平苷转化为京尼平,转化率高达98%.通过条件优化,得到了最优转化条件:京尼平添加量1.5%,pH自然,摇瓶装量20%,28 ℃、150 rpm转化24 h.固定化细胞可连续使用4次.这种微生物转化法安全、高效,产品纯度高,是生产京尼平的一种新方法.     

微生物发酵转化牛蒡子的研究

从牛蒡子药材中筛选到一株具有转化牛蒡子苷能力的菌株HB-2,对牛蒡子进行发酵,利用其产生的β-葡萄糖苷酶将牛蒡子苷转化为牛蒡子苷元。研究了该菌株对牛蒡子的发酵动力学,HPLC测得转化率达95%以上。发酵产物经大孔吸附树脂、硅胶柱层析及重结晶等方法制备出牛蒡子苷元纯品,并采用核磁共振(NMR)、红外(IR)、质谱(MS)等方法对产物进行了鉴定。     

Metabolisms of Nucleosides in Bacteria

The mechanism of trans-N-ribosylation in Corynebacterium sepedonicum was investigated. Using the DEAE-cellulose colum chromatography, this enzyme activity was divided into two fractions. One cleaved uridine to uracil and ribose phosphate, and the other decomposed inosine into hypoxanthine and ribose phosphate, in the presence of inorganic phosphate. The ribose phosphate was isolated and crystallized.

Several analytical data indicated that the ribose phosphate was ribose-1-phosphate. These two enzyme fractions catalyzed the formation of nucleosides from ribose-1-phosphate and bases.

Most of bacteria, which had the activity to transfer N-ribosyl group between purine and pyrimidine, could synthesize the nucleoside from base and ribose-1-phosphate.     

微生物混合发酵的研究及应用

由于不同微生物之间的正相互作用,人们发现应用两种或两种以上微生物混合发酵能更好地解决实践中的许多问题。在过去几年中,对微生物的混合发酵的应用以及其中微生物之间的相互作用机理的研究取得了明显进展,主要有以下4个方面:(1)对生物质的降解利用;(2)对环境污染物的降解;(3)生产特定的代谢产物;(4)混合发酵的工艺。综述了微生物混合发酵的应用及相关机理、涉及的微生物和影响因素。