A Glycan Array‐Based Assay for the Identification and Characterization of Plant Glycosyltransferases

Growing plants with modified cell wall compositions is a promising strategy to improve resistance to pathogens, increase biomass digestibility, and tune other important properties. In order to alter biomass architecture, a detailed knowledge of cell wall structure and biosynthesis is a prerequisite. We report here a glycan array‐based assay for the high‐throughput identification and characterization of plant cell wall biosynthetic glycosyltransferases (GTs). We demonstrate that different heterologously expressed galactosyl‐, fucosyl‐, and xylosyltransferases can transfer azido‐functionalized sugar nucleotide donors to selected synthetic plant cell wall oligosaccharides on the array and that the transferred monosaccharides can be visualized “on chip” by a 1,3‐dipolar cycloaddition reaction with an alkynyl‐modified dye. The opportunity to simultaneously screen thousands of combinations of putative GTs, nucleotide sugar donors, and oligosaccharide acceptors will dramatically accelerate plant cell wall biosynthesis research.     

Two sequence elements of glycosyltransferases involved in urdamycin biosynthesis are responsible for substrate specificity and enzymatic activity.

BACKGROUND: Two deoxysugar glycosyltransferases (GTs), UrdGT1b and UrdGT1c, involved in urdamycin biosynthesis share 91% identical amino acids. However, the two GTs show different specificities for both nucleotide sugar and acceptor substrate. Generally, it is proposed that GTs are two-domain proteins with a nucleotide binding domain and an acceptor substrate site with the catalytic center in an interface cleft between these domains. Our work aimed at finding out the region responsible for determination of substrate specificities of these two urdamycin GTs. RESULTS: A series of 10 chimeric GT genes were constructed consisting of differently sized and positioned portions of urdGT1b and urdGT1c. Gene expression experiments in host strains Streptomyces fradiae Ax and XTC show that nine of 10 chimeric GTs are still functional, with either UrdGT1b- or UrdGT1c-like activity. A 31 amino acid region (aa 52-82) located close to the N-terminus of these enzymes, which differs in 18 residues, was identified to control both sugar donor and acceptor substrate specificity. Only one chimeric gene product of the 10 was not functional. Targeted stepwise alterations of glycine 226 (G226R, G226S, G226SR) were made to reintroduce residues conserved among streptomycete GTs. Alterations G226S and G226R restored a weak activity, whereas G226SR showed an activity comparable with other functional chimeras. CONCLUSIONS: A nucleotide sugar binding motif is present in the C-terminal moiety of UrdGT1b and UrdGT1c from S. fradiae. We could demonstrate that it is an N-terminal section that determines specificity for the nucleotide sugar and also the acceptor substrate. This finding directs the way towards engineering this class of streptomycete enzymes for antibiotic derivatization applications. Amino acids 226 and 227, located outside the putative substrate binding site, might be part of a larger protein structure, perhaps a solvent channel to the catalytic center. Therefore, they could play a role in substrate accessibility to it.     

Utility of Bioluminescent Homogeneous Nucleotide Detection Assays in Measuring Activities of Nucleotide-Sugar Dependent Glycosyltransferases and Studying Their Inhibitors

Traditional glycosyltransferase (GT) activity assays are not easily configured for rapid detection nor for high throughput screening because they rely on radioactive product isolation, the use of heterogeneous immunoassays or mass spectrometry. In a typical glycosyltransferase biochemical reaction, two products are generated, a glycosylated product and a nucleotide released from the sugar donor substrate. Therefore, an assay that detects the nucleotide could be universal to monitor the activity of diverse glycosyltransferases in vitro. Here we describe three homogeneous and bioluminescent glycosyltransferase activity assays based on UDP, GDP, CMP, and UMP detection. Each of these assays are performed in a one-step detection that relies on converting the nucleotide product to ATP, then to bioluminescence using firefly luciferase. These assays are highly sensitive, robust and resistant to chemical interference. Various applications of these assays are presented, including studies on the specificity of sugar transfer by diverse GTs and the characterization of acceptor substrate-dependent and independent nucleotide-sugar hydrolysis. Furthermore, their utility in screening for specific GT inhibitors and the study of their mode of action are described. We believe that the broad utility of these nucleotide assays will enable the investigation of a large number of GTs and may have a significant impact on diverse areas of Glycobiology research.     

Glycomimetics Targeting Glycosyltransferases: Synthetic,Computational and Structural Studies of Less‐Polar Conjugates

The Leloir donors are nucleotide sugars essential for a variety of glycosyltransferases (GTs) involved in the transfer of a carbohydrate to an acceptor substrate, typically a protein or an oligosaccharide. A series of less‐polar nucleotide sugar analogues derived from uridine have been prepared by replacing one phosphate unit with an alkyl chain. The methodology is based on the radical hydrophosphonylation of alkenes, which allows coupling of allyl glycosyl compounds with a phosphate unit suitable for conjugation to uridine. Two of these compounds, the GalNAc and galactose derivatives, were further tested on a model GT, such as GalNAc‐T2 (an important GT widely distributed in human tissues), to probe that both compounds bound in the medium–high micromolar range. The crystal structure of GalNAc‐T2 with the galactose derivative traps the enzyme in an inactive form; this suggests that compounds only containing the β‐phosphate could be efficient ligands for the enzyme. Computational studies with GalNAc‐T2 corroborate these findings and provide further insights into the mechanism of the catalytic cycle of this family of enzymes.     

基质辅助激光解吸电离飞行时间质谱法区分大肠杆菌糖基转移酶基因

采用高能碰撞诱导解离(CID)-负离子模式基质辅助激光解吸离子化-飞行时间质谱技术(MALDI TOF MS)区别efgD(大肠杆菌O152中O抗原基因簇内)编码的β-1,3-葡萄糖转移酶和wfgD(大肠杆菌O77中O抗原基因簇内)编码的α-1,3-甘露糖转移酶酶促反应产物-两个脂寡糖非对应异构体.结果表明:由高能CI...     

Fluorosugar chain termination agents as probes of the sequence specificity of a carbohydrate polymerase

Naturally occurring carbohydrate polymers are ubiquitous. They are assembled by polymerizing glycosyltransferases, which can generate polysaccharide products with repeating sequence patterns. The fidelity of enzymes of this class is unknown. We report a method for testing the fidelity of carbohydrate polymerase pattern deposition: we synthesized fluorosugar donors and used them as chain termination agents. The requisite nucleotide fluorosugars could be produced from a single intermediate using the Jacobsen catalyst in a kinetically controlled separation of diastereomers. The resulting fluorosugar donors were used by the galactofuranosyltransferase GlfT2 from Mycobacterium tuberculosis, and the data indicate that this enzyme mediates the cell wall galactan production through a sequence-specific polymerization.     

Pretreatment of Corn Stover with Twin-Screw Extrusion Followed by Enzymatic Saccharification

Pretreatment of biomass before subjecting it to enzyme saccharification is crucial with regards to facilitating access of enzyme to biomass. Extrusion, as a continuous and cost-effective pretreatment method, combines heating with high shear and mixing opening cell walls at the microscopic scale, thus largely increasing the specific surface area (SSA) of biomass for enzyme adsorption. The objective of this study was to examine the effect of extrusion as a pretreatment method and the underlying factors ruling the improvement of sugar yields. The optimum glucose, xylose, and combined sugar recoveries were 48.79%, 24.98%, and 40.07%, respectively, at 27.5% moisture content and 80 rpm screw speed. These yields were 2.2, 6.6, and 2.6 times higher than those for untreated corn stover. X-ray diffraction analysis showed that the crystallinity index was not a good indicator of sugar yield. However, scanning electron microscopy showed that the cellulose network was exposed due to the destruction of the lignin sheath. The Langmuir adsorption model was shown to be an effective tool for the estimation of the SSA of corn stover. The SSA of pretreated samples was significantly amplified over the control, revealing that extrusion can open the cell wall at the microscopic scale, which was especially favorable on sugar yields.     

A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase

Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host–pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl‐3‐phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP‐Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum‐mechanics/molecular‐mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front–side substrate‐assisted S_Ni‐type reaction.     

Structural Snapshots of α‐1,3‐Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases

Glycosyltransferases (GTs) are a key family of enzymes that catalyze the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric configuration. To date, the catalytic mechanism of retaining GTs is a topic of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which the occurrence of a double‐displacement mechanism has been suggested. We report native ternary complexes of the retaining glycosyltransferase α‐1,3‐galactosyltransferase (α3GalT) from Bos taurus , which contains such a nucleophile in the active site, in a productive mode for catalysis in the presence of its sugar donor UDP‐Gal, the acceptor substrate lactose, and the divalent cation cofactor. This new experimental evidence supports the occurrence of a front‐side substrate‐assisted S_Ni‐type reaction for α3GalT, and suggests a conserved common catalytic mechanism among retaining GTs.     

An Aminated GDP-Fucose Analog Useful in the Fucosyltransferase Catalyzed Addition of Biological Probes onto Oligosaccharide Chains1

Abstract

An analog (1) of GDP-fucose, where C-6 is derivatized with an eight-atom spacer terminating in a primary amino group, was chemically synthesized. This amino group in sugar nucleotide 1 can be acylated using an N-hydroxysuccinimide ester of biotin and it can be coupled to another molecule that also contains an amino group using squaric acid diethyl ester as the coupling reagent. In this way, biotin and a blood group A-active trisaccharide were linked to C-6 of fucose in GDP-fucose. Both complex sugar nucleotides thus prepared were active as donors for a human milk fucosyltransferase, which transferred the derivatized α-linked fucose residue to a glycoside of N-acetyllactosamine, thus labeling this sequence with either biotin or the blood-group A trisaccharide. Compound 1 is proposed as a general and versatile reagent which should permit the addition of biological probes to the sugar chains of cell surface glycoproteins or glycolipids.     

The accumulation of phytoalexin in cucumber plant after stress

During the course of pathogens penetrating the plant cell, besides of chemical secretion, the pathogens may cause mechanical signal by the physical pressure on the plant cell. In the current study, we use the pressure as the stress signal to study the induction in plant resistance and the effect of accumulation of phytoalexin. We found that stress can induce the resistance in cucumber seeding significantly. Peptides contained RGD motif can specific block the adhesion between plant cell wall and plasma membrane. When breaking the plant cell wall and plasma membrane by using RGD peptides, the stress induction effect is almost absolutely eliminated. The results of assay with TLC and HPLC showed that stress stimulation could increase the accumulation of cucumber seeding phytoalexin. So, we can conclude that the accumulation of phytoalexin is one possible reason of improve the stress induced resistance. When block the adhesion between plant cell wall and plasma membrane by RGD, there are only part of accumulation of phytoalexin. The results suggest that stress induced resistance and accumulation of phytoalexin of plant is required for the adhesion of plant cell wall–plasma membrane.     

Improvement of saccharification process for bioethanol production from Undaria sp. by gamma irradiation

Recently, many research works have reported on improvements to the saccharification process that increase bioethanol production from cellulosic materials. Gamma irradiation has been studied as an effective method for the depolymerization of complex polysaccharides. In this study, the effect of gamma irradiation on saccharification of Undaria biomass for bioethanol production was investigated. The Undaria biomass was irradiated at doses of 0, 10, 50, 100, 200 and 500 kGy and then hydrolyzed using sulfuric acid. The effects of gamma irradiation were measured through microscopic analysis to determine morphological changes and concentration of the reducing sugar of hydrolysates. Microscopic images show that gamma irradiation causes structure breakage of the Undaria cell wall. The concentration of reducing sugar of hydrolysates significantly increased as a result of gamma irradiation, with or without acid hydrolysis. These results indicate that the combined method of gamma irradiation with acid hydrolysis can significantly improve the saccharification process for bioethanol production from marine algae materials.     

(13)C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall

The ability to accurately and rapidly measure plant cell wall composition, relative monolignol content and lignin-hemicellulose inter-unit linkage distributions has become essential to efforts centered on reducing the recalcitrance of biomass by genetic engineering. Growing (13)C enriched transgenic plants is a viable route to achieve the high-throughput, detailed chemical analysis of whole plant cell wall before and after pretreatment and microbial or enzymatic utilization by (13)C nuclear magnetic resonance (NMR) in a perdeuterated ionic liquid solvent system not requiring component isolation. 1D (13)C whole cell wall ionic liquid NMR of natural abundant and (13)C enriched corn stover stem samples suggest that a high level of uniform labeling (>97%) can significantly reduce the total NMR experiment times up to ～220 times. Similarly, significant reduction in total NMR experiment time (～39 times) of the (13)C enriched corn stover stem samples for 2D (13)C-(1)H heteronuclear single quantum coherence NMR was found.     

超微电极实时监测植物细胞壁参与调控的单细胞活性氧爆发

植物细胞活性氧爆发在植物的抗病以及信号转导中起着非常重要的作用,植物内活性氧产生及代谢受到复杂而精确的机制调控,从而维持正常的活性氧水平以发挥其生理功能. 然而,在单细胞水平开展活性氧爆发实时监测及其调控机制研究一直受到很大的挑战. 本文以碳纤维微盘电极（CFMDE）为基底电极,利用Nafion的模板效应,采用电化学沉积法制得纳米铂颗粒修饰电极（NPt/Nafion/ CFMDE）;同时采用基于聚二甲基硅氧烷（PDMS）的软光刻技术,制备了一种高效固定植物悬浮细胞的琼脂糖阵列微孔芯片. 使用NPt/Nafion/CFMDE实时监测了单个拟南芥原生质体活性氧爆发,并证明电化学监测活性氧的主要成分为过氧化氢. 在此基础上,采用浅层培养法培养原生质体再生植物细胞壁. 电化学监测结果表明,与单个原生质体相比,植物细胞在受到刺激时释放的过氧化氢量显著降低;然而当采用过氧化物酶抑制剂抑制植物细胞壁上过氧化物酶活性后,植物细胞释放过氧化氢量显著回升. 研究结果表明细胞壁在活性氧爆发过程具有很好的调控功能,可望促进植物细胞活性氧爆发及其调控机制的研究.     

Cell surface glycosyltransferases--do they exist?

The presence of glycosyltransferases on surfaces of mammalian cells has been reported by many investigators and a biological role for these enzymes in cell adhesion and cell recognition has been postulated. Critical analysis, however, showed 2 major complications regarding the assay for cell surface glycosyltransferases: 1) hydrolysis of the nucleotide sugar by cell surface enzymes and subsequent intracellular use of the free sugar and 2) loss of cell integrity if trypsinized or EDTA-treated cells were used in suspension assays. We have assayed intact, viable cells in monolayer for cell surface glycosyltransferases using conditions under which intracellular utilization of free sugars generated by hydrolysis of the nucleotide sugar was prevented. Our data demonstrate that the presence of galactosyltransferases on the surface of a variety of cells, including established (normal and virally transformed) as well as nonestablished cells, is unlikely. No evidence for the existence of cell surface fucosyl- and sialytransferases could be obtained, but our data do not exclude the possibility that low levels of these enzymes are present.     

Discovery of new biocatalysts for the glycosylation of terpenoid scaffolds

The synthesis of terpenoid glycosides typically uses a chemical strategy since few biocatalysts have been identified that recognise these scaffolds. In this study, a platform of 107 recombinant glycosyltransferases (GTs), comprising the multigene family of small molecule GTs of Arabidopsis thaliana have been screened against a range of model terpenoid acceptors to identify those enzymes with high activity. Twenty-seven GTs are shown to glycosylate a diversity of mono-, sesqui- and diterpenes, such as geraniol, perillyl alcohol, artemisinic acid and retinoic acid. Certain enzymes showing substantial sequence similarity recognise terpenoids containing a primary alcohol, irrespective of the linear or cyclical structure of the scaffold; other GTs glycosylate scaffolds containing secondary and tertiary alcohols; the carboxyl group of other terpenoids also represents a feature that is recognized by GTs previously known to form glucose esters with many different compounds. These data underpin the rapid prediction of potential biocatalysts from GT sequence information. To explore the potential of GTs as biocatalysts, their use for the production of terpenoid glycosides was investigated by using a microbial-based whole-cell biotransformation system capable of regenerating the cofactor, UDP-glucose. A high cell density fermentation system was shown to produce several hundred milligrams of a model terpenoid, geranyl-glucoside. The activities of the GTs are discussed in relation to their substrate recognition and their utility in biotransformations as a complement or alternative to chemical synthesis.     

Sequestration and transport of lignin monomeric precursors

Lignin is the second most abundant terrestrial biopolymer after cellulose. It is essential for the viability of vascular plants. Lignin precursors, the monolignols, are synthesized within the cytosol of the cell. Thereafter, these monomeric precursors are exported into the cell wall, where they are polymerized and integrated into the wall matrix. Accordingly, transport of monolignols across cell membranes is a critical step affecting deposition of lignin in the secondarily thickened cell wall. While the biosynthesis of monolignols is relatively well understood, our knowledge of sequestration and transport of these monomers is sketchy. In this article, we review different hypotheses on monolignol transport and summarize the recent progresses toward the understanding of the molecular mechanisms underlying monolignol sequestration and transport across membranes. Deciphering molecular mechanisms for lignin precursor transport will support a better biotechnological solution to manipulate plant lignification for more efficient agricultural and industrial applications of cell wall biomass.     

Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state

Glycosyltransferases (GTs) catalyze the highly specific biosynthesis of glycosidic bonds and, as such, are important both as drug targets and for biotechnological purposes. Despite their broad interest, fundamental questions about their reaction mechanism remain to be answered, especially for those GTs that transfer the sugar with net retention of the configuration at the anomeric carbon (retaining glycosyltransferases, ret-GTs). In the present work, we focus on the reaction catalyzed by lipopolysaccharyl-α-1,4-galactosyltransferase C (LgtC) from Neisseria meningitides. We study and compare the different proposed mechanisms (S(N)i, S(N)i-like, and double displacement mechanism via a covalent glycosyl-enzyme intermediate, CGE) by using density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations on the full enzyme. We characterize a dissociative single-displacement (S(N)i) mechanism consistent with the experimental data, in which the acceptor substrate attacks on the side of the UDP leaving group that acts as a catalytic base. We identify several key interactions that help this front-side attack by stabilizing the transition state. Among them, Gln189, the putative nucleophile in a double displacement mechanism, is shown to favor the charge development at the anomeric center by about 2 kcal/mol, compatible with experimental mutagenesis data. We predict that using 3-deoxylactose as acceptor would result in a reduction of k(cat) to 0.6-3% of that for the unmodified substrates. The reactions of the Q189A and Q189E mutants have also been investigated. For Q189E, there is a change in mechanism since a CGE can be formed which, however, is not able to evolve to products. The current findings are discussed in the light of the available experimental data and compared with those for other ret-GTs.     

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.     

Synthesis of modified peptidoglycan precursor analogues for the inhibition of glycosyltransferase

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial target. Their enzymatic cavity is composed of a donor site for the growing glycan chain (where the inhibitor moenomycin binds) and an acceptor site for lipid II substrate. In order to find lead inhibitors able to fill this large active site, we have synthesized a series of substrate analogues of lipid I and lipid II with variations in the lipid, the pyrophosphate, and the peptide moieties and evaluated their biological effect on the GT activity of E. coli PBP1b and their antibacterial potential. We found several compounds able to inhibit the GT activity in vitro and cause growth defect in Bacillus subtilis . The more active was C16-phosphoglycerate-MurNAc-(L-Ala-D-Glu)-GlcNAc, which also showed antibacterial activity. These molecules are promising leads for the design of new antibacterial GT inhibitors.