Molecular genetics of nucleotide sugar interconversion pathways in plants

Nucleotide sugar interconversion pathways represent a series of enzymatic reactions by which plants synthesize activated monosaccharides for the incorporation into cell wall material. Although biochemical aspects of these metabolic pathways are reasonably well understood, the identification and characterization of genes encoding nucleotide sugar interconversion enzymes is still in its infancy. Arabidopsis mutants defective in the activation and interconversion of specific monosaccharides have recently become available, and several genes in these pathways have been cloned and characterized. The sequence determination of the entire Arabidopsis genome offers a unique opportunity to identify candidate genes encoding nucleotide sugar interconversion enzymes via sequence comparisons to bacterial homologues. An evaluation of the Arabidopsis databases suggests that the majority of these enzymes are encoded by small gene families, and that most of these coding regions are transcribed. Although most of the putative proteins are predicted to be soluble, others contain N-terminal extensions encompassing a transmembrane domain. This suggests that some nucleotide sugar interconversion enzymes are targeted to an endomembrane system, such as the Golgi apparatus, where they may co-localize with glycosyltransferases in cell wall synthesis. The functions of the predicted coding regions can most likely be established via reverse genetic approaches and the expression of proteins in heterologous systems. The genetic characterization of nucleotide sugar interconversion enzymes has the potential to understand the regulation of these complex metabolic pathways and to permit the modification of cell wall material by changing the availability of monosaccharide precursors.     

Galactose biosynthesis in Arabidopsis: genetic evidence for substrate channeling from UDP-D-galactose into cell wall polymers

The biosynthesis of plant cell wall polysaccharides requires the concerted action of nucleotide sugar interconversion enzymes, nucleotide sugar transporters, and glycosyl transferases. How cell wall synthesis in planta is regulated, however, remains unclear. The root epidermal bulger 1 (reb1) mutant in Arabidopsis thaliana is partially deficient in cell wall arabinogalactan-protein (AGP), indicating a role for REB1 in AGP biosynthesis. We show that REB1 is allelic to ROOT HAIR DEFICIENT 1 (RHD1), one of five ubiquitously expressed genes that encode isoforms of UDP-D-glucose 4-epimerase (UGE), an enzyme that acts in the formation of UDP-D-galactose (UDP-D-Gal). The RHD1 isoform is specifically required for the galactosylation of xyloglucan (XG) and type II arabinogalactan (AGII) but is not involved either in D-galactose detoxification or in galactolipid biosynthesis. Epidermal cell walls in the root expansion zone lack arabinosylated (1-->6)-beta-D-galactan and galactosylated XG. In cortical cells of rhd1, galactosylated XG is absent, but an arabinosylated (1-->6)-beta-D-galactan is present. We conclude that the flux of galactose from UDP-D-Gal into different downstream products is compartmentalized at the level of cytosolic UGE isoforms. This suggests that substrate channeling plays a role in the regulation of plant cell wall biosynthesis.     

Nucleotide sugars and glycosyltransferases for synthesis of cell wall matrix polysaccharides

The current interest in cell wall biosynthesis is expanding because of the increasing evidence that the properties of the cell wall mediate cellular interactions during growth, development and differentiation. Much effort has been put forward to the identification of glycosyltransferases because of their obvious importance in polysaccharide synthesis. Enzymes involved in nucleotide sugar production and transport are also important because of the potential to manipulate the composition of cell walls through substrate level control. Molecular genetics have begun to uncover genes for important enzymes in polysaccharide biosynthesis including glycosyltransferases and enzymes of nucleotide sugar metabolism; but at this time, much is inferred from comparisons to bacteria, yeast and animal cells. This review examines the production and transport of nucleotide sugars, the protein structure of glycosyltransferases, and implications for the cellular mechanisms of cell wall biosynthesis.     

Biochemical genetics of nucleotide sugar interconversion reactions

During the past few years, substantial progress has been made to understand the enzymology and regulation of nucleotide sugar interconversion reactions that are irreversible in vivo on thermodynamic grounds. Feedback inhibition of enzymes by metabolic end products appears to be a common theme but some experimental results on recombinant enzymes are difficult to interpret. Using a combination of metabolic flux analysis, enzyme assays, and bioinformatics approaches, the significance of several proposed alternate pathways has been clarified. Expression of plant nucleotide sugar interconversion enzymes in yeast has become a promising approach to understand metabolic regulation and produce valuable compounds. In a major advance for the understanding of the synthesis of arabinosylated cell wall polysaccharides, reversibly glycosylated proteins turned out to act as mutases that interconvert the pyranose and furanose forms of UDP-L-arabinose.     

BRITTLE PLANT1 is required for normal cell wall composition and mechanical strength in rice

A series of nucleotide sugar interconversion enzymes (NSEs) generate the activated sugar donors required for biosynthesis of cell wall matrix polysaccharides and glycoproteins. UDP‐glucose 4‐epimerases (UGEs) are NSEs that function in the interconversion of UDP‐glucose (UDP‐Glc) and UDP‐galactose (UDP‐Gal). The roles of UDP‐glucose 4‐epimerases in monocots remain unclear due to redundancy in the pathways. Here, we report a brittle plant (bp1) rice mutant that exhibits brittle leaves and culms at all growth stages. The mutant culms had reduced levels of rhamnogalacturonan I, homogalacturonan, and arabinogalactan proteins. Moreover, the mutant had altered contents of uronic acids, neutral noncellulosic monosaccharides, and cellulose. Map‐based cloning demonstrated that OsBP1 encodes a UDP‐glucose 4‐epimerase (OsUGE2), a cytosolic protein. We also show that BP1 can form homo‐ and hetero‐protein complexes with other UGE family members and with UDP‐galactose transporters 2 (OsUGT2) and 3 (OsUGT3), which may facilitate the channeling of Gal to polysaccharides and proteoglycans. Our results demonstrate that BP1 participates in regulating the sugar composition and structure of rice cell walls.     

Matrix polysaccharide precursors in Arabidopsis cell walls are synthesized by alternate pathways with organ-specific expression patterns

The expression pattern of the single-copy gene UDP-glucose dehydrogenase (Ugd) was analysed in transgenic Arabidopsis plants by promoter:GUS and GFP fusions, Western blots, activity assays and histochemical activity staining. The enzyme oxidizes UDP-glucose to UDP-glucuronic acid and thus directs carbohydrates irreversibly into a cell wall-specific pool of nucleotide sugars. UDP-glucuronic acid is the central intermediate in the interconversion pathway to other nucleotide sugars, including the UDP-derivatives of arabinose, xylose, apiose and galacturonic acid which account for half the biomass of a typical Arabidopsis leaf cell wall. These activated sugars are needed as substrates for the biosynthesis of matrix polysaccharide polymers. In plants up to 5 days old the Ugd gene is strongly expressed in young roots, but very little in hypocotyls. Older plants show a more uniform expression pattern with a preference for the vascular system. A complex expression pattern was observed in flowers with high activity in the stamen, stigma and nectaries. Meristems in the leaf axil of rosette and inflorescence leaves exhibit a high level of activity of the Ugd gene. Although many of the growing tissues show high activity levels of the Ugd gene, others such as the hypocotyl and the cotyledons of young seedlings do not. Instead these tissues efficiently incorporate 3H-inositol into their cell walls. This indicates the biosynthesis of UDP-glucuronic acid through an alternative pathway via the oxidation of inositol to glucuronic acid and subsequent activation to the nucleotide sugar. The data strongly suggest two alternative pathways for matrix polysaccharide precursors with spatial and developmental regulation.     

Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry

Understanding the intricate metabolic processes involved in plant cell wall biosynthesis is limited by difficulties in performing sensitive quantification of many involved compounds. Hydrophilic interaction liquid chromatography is a useful technique for the analysis of hydrophilic metabolites from complex biological extracts and forms the basis of this method to quantify plant cell wall precursors. A zwitterionic silica-based stationary phase has been used to separate hydrophilic nucleotide sugars involved in cell wall biosynthesis from milligram amounts of leaf tissue. A tandem mass spectrometry operating in selected reaction monitoring mode was used to quantify nucleotide sugars. This method was highly repeatable and quantified 12 nucleotide sugars at low femtomole quantities, with linear responses up to four orders of magnitude to several 100 pmol. The method was also successfully applied to the analysis of purified leaf extracts from two model plant species with variations in their cell wall sugar compositions and indicated significant differences in the levels of 6 out of 12 nucleotide sugars. The plant nucleotide sugar extraction procedure was demonstrated to have good recovery rates with minimal matrix effects. The approach results in a significant improvement in sensitivity when applied to plant samples over currently employed techniques.     

Cytokinin biosynthesis and interconversion

To maintain hormone homeostasis, the rate of cytokinin biosynthesis, interconversion, and degradation is regulated by enzymes in plant cells. Cytokinins can be synthesized via direct (de novo) or indirect (tRNA) pathways. In the de novo pathway, a cytokinin nucleotide is synthesized from 5'-AMP and isopentenyl pyrophosphate; a key enzyme which catalyzes this synthesis has been isolated from plant tissues, slime mold, and some microorganisms. Studies on the in vitro synthesis of the isopentenyl side chain of cytokinin in tRNA demonstrated that the isopentenyl group was derived from mevalonate, and turnover of the cytokinin-containing tRNA may serve as a minor source of free cytokinins in plant cells. The interconversion of cytokinin bases, nucleosides and nucleotides is a major feature of cytokinin metabolism; and enzymes that regulate the interconversion have been identified. The N⁶-side chain and purine moiety of cytokinins are often modified and some of the enzymes involved in the modifications have been isolated. Most of the cytokinin metabolites have been characterized but very few enzymes regulating their metabolism have been purified to homogeneity. It remains a significant challenge to isolate plant genes involved in the regulation of cytokinin biosynthesis, interconversion and degradation.     

Growth regulators and the control of nucleotide sugar flux

A small number of plant growth regulators are involved in the control of cell expansion. Despite knowledge of some of their signal transduction cascades, surprisingly little is known of how basic cell expansion-related processes, such as cell wall biosynthesis, are affected during growth. The Arabidopsis (Arabidopsis thaliana) mutant root hair defective1 (rhd1) lacks a functional UDP-glucose 4-epimerase gene, UGE4, which is involved in channeling UDP-D-galactose (UDP-D-Gal) into cell wall polymers. Here, we use rhd1 as a genetic model to analyze the physiological and genetic controls of nucleotide sugar flux. We find that ethylene specifically suppresses all visible aspects of the rhd1 phenotype. The ethylene-triggered suppression of rhd1 is negatively regulated by CONSTITUTIVE TRIPLE RESPONSE1 and requires the function of the wild-type genes ETHYLENE INSENSITIVE2 (EIN2), EIN4, AUXIN-RESISTENT1, and ETHYLENE-INSENSITIVE ROOT1 but does not depend on the activity of wild-type ETHYLENE RECEPTOR1 or EIN3 genes, highlighting the nonlinearity of ethylene signal transduction. Ethylene does not induce the expression of alternative UGE genes but, instead, suppresses the expression of two isoforms, UGE1 and UGE3, in a tissue-specific manner. Ethylene restores the biosynthesis of galactose-containing xyloglucan and arabinosylated galactan cell wall polymers in rhd1 back to wild-type levels. However, the dependence on UGE4 of pectic (1-->4)-beta-D-galactan and glucuronosyl-modified AGP biosynthesis is exacerbated. Our data suggest that ethylene and auxin together participate in the flux control of UDP-D-Gal into cell wall polymers and that the genetic control of this process is qualitatively distinct from previously described responses to ethylene.     

Stimulation of cell wall biosynthesis and structural changes in response to cytokinin- and elicitor-treatments of suspension-cultured Phaseolus vulgaris cells

Qualitative sugar flux into cell wall polysaccharides has been determined for two model systems. The first, treatment of suspension-cultured French bean (Phaseolus vulgaris L.) cells with an increase in the cytokinin/auxin ratio and in the concentration of sucrose, models some aspects of differentiation. Wall changes are characterised by up to a five-fold increase in thickness due to the laying down of extra wall material. Sugar flux following labelling of cells with [¹⁴C]-sucrose was examined during the period of maximum extractable catalytic activities of the enzymes of sugar nucleotide conversion determined previously. Increased secretion was observed in all major groups of polysaccharides, particularly the cellulosic fraction. Analysis of the sugars in the hemicellulosic fraction indicated that the newly synthesised polysaccharide was most probably xylan. It was confirmed by immunolocalisation of xylan in these walls. This treatment thus increases incorporation into the wall of components characteristic of secondary wall. In the second system, which models the defence response, suspension cultures were treated with an elicitor from the walls of Colletotrichum lindemuthianum. Again, sugar flux was determined by labelling cells with [¹⁴C]-sucrose and examined during the period determined previously of maximum extractable catalytic activities of the enzymes of sugar nucleotide conversion. Increased secretion into unextractable polymers was the major change and was consistent with the occurrence of oxidative processes leading to immobilisation of some wall components. Callose, a polysaccharide characteristic of the defence response was immunolocalised in these walls but not in those of control cells.     

Golgi transporters: opening the gate to cell wall polysaccharide biosynthesis

The synthesis of non-cellulosic polysaccharides occurs in the Golgi apparatus and requires a great number of metabolites (substrates and ions). Many enzymes use these substrates to add sugar residues to nascent polysaccharides chains or to introduce methyl and acetyl groups onto these polymers. Most of these metabolites are in the cytosol and their transport to the Golgi lumen is essential for proper polysaccharide biosynthesis. Different transporters activities have been described in Golgi membranes, but many more are thought to be present to provide all the substrates required for polysaccharide biosynthesis and to pump the ions for maintaining ionic homeostasis. Their functional analysis will help us to understand the role these transporters play in cell wall biosynthesis.     

Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae

The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so‐called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide‐rhamnose synthase/epimerase‐reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy‐thymidine diphosphate (dTDP)‐rhamnose, a precursor of L‐rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal–host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)‐rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.     

Tinkering with heparan sulfate sulfation to steer development

Heparan sulfate (HS) proteoglycans, at the cell surface and extracellular matrix, facilitate ligand-receptor interactions crucial to many physiological processes. The distinct sulfation patterns of HS sugar chains presented by their protein core are key to HS proteoglycan activity. Tight regulation of several Golgi complex enzyme families is crucial to produce complex tissue-specific HS sequences. Several in vivo models deficient in HS biosynthesis enzymes demonstrate that developmental abnormalities result from modified HS structure. This review will discuss the plasticity of sulfation requirements on HS for activating protein ligands, which might reflect a flexible HS biosynthetic mechanism. In addition, the latest discovery of HS acting enzymes, the Sulfs, responsible for extracellular tweaking of HS sulfation levels subsequent to biosynthesis will be considered.     

Mechanisms of UDP-Glucose Synthesis in Plants

Substantial progress has been made in studies on enzymes synthesizing UDP-glucose (UDPG) which is essential for sucrose and cell wall biosynthesis, and in an array of other processes, e.g. glycosylation of proteins and lipids. The enzymes include UDPG pyrophosphorylase, UDP-sugar pyrophosphorylase (USPase) and sucrose synthase (SuSy). Genes coding for those proteins are under complex spatial and temporal regulation, and are frequently coexpressed. Recent evidence for regulation of some of the UDPG-synthesizing proteins by posttranslational modifications and oligomerization, together with discoveries of novel isozymes and unexpected locations within a cell (including chloroplasts and mitochondria) have made the studies exciting, but complex. The enzymes differ in specificity for sugar and nucleotide portions of their substrates/products, and may be involved in distinct metabolic pathways, but also in signaling. Homology models for USPase and SuSy structures are presented, based on recent crystallization of structurally related proteins. Future challenges in research on UDPG-producing enzymes are underlined.     

Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

The plant cell cytosol is a dynamic and complex intracellular matrix that, by definition, contains no compartmentalization. Nonetheless, it maintains a wide variety of biochemical networks and often links metabolic pathways across multiple organelles. There have been numerous detailed proteomic studies of organelles in the model plant Arabidopsis thaliana, although no such analysis has been undertaken on the cytosol. The cytosolic protein fraction from cell suspensions of Arabidopsis thaliana was isolated and analyzed using offline strong cation exchange liquid chromatography and LC-MS/MS. This generated a robust set of 1071 cytosolic proteins. Functional annotation of this set revealed major activities in protein synthesis and degradation, RNA metabolism and basic sugar metabolism. This included an array of important cytosol-related functions, specifically the ribosome, the set of tRNA catabolic enzymes, the ubiquitin-proteasome pathway, glycolysis and associated sugar metabolism pathways, phenylpropanoid biosynthesis, vitamin metabolism, nucleotide metabolism, an array of signaling and stress-responsive molecules, and NDP-sugar biosynthesis. This set of cytosolic proteins provides for the first time an extensive analysis of enzymes responsible for the myriad of reactions in the Arabidopsis cytosol and defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding in the cytosol.     

Genetic alteration of UDP‐rhamnose metabolism in Botrytis cinerea leads to the accumulation of UDP‐KDG that adversely affects development and pathogenicity

Botrytis cinerea is a model plant‐pathogenic fungus that causes grey mould and rot diseases in a wide range of agriculturally important crops. A previous study has identified two enzymes and corresponding genes (bcdh, bcer) that are involved in the biochemical transformation of uridine diphosphate (UDP)‐glucose, the major fungal wall nucleotide sugar precursor, to UDP‐rhamnose. We report here that deletion of bcdh, the first biosynthetic gene in the metabolic pathway, or of bcer, the second gene in the pathway, abolishes the production of rhamnose‐containing glycans in these mutant strains. Deletion of bcdh or double deletion of both bcdh and bcer has no apparent effect on fungal development or pathogenicity. Interestingly, deletion of the bcer gene alone adversely affects fungal development, giving rise to altered hyphal growth and morphology, as well as reduced sporulation, sclerotia production and virulence. Treatments with wall stressors suggest the alteration of cell wall integrity. Analysis of nucleotide sugars reveals the accumulation of the UDP‐rhamnose pathway intermediate UDP‐4‐keto‐6‐deoxy‐glucose (UDP‐KDG) in hyphae of the Δbcer strain. UDP‐KDG could not be detected in hyphae of the wild‐type strain, indicating fast conversion to UDP‐rhamnose by the BcEr enzyme. The correlation between high UDP‐KDG and modified cell wall and developmental defects raises the possibility that high levels of UDP‐KDG result in deleterious effects on cell wall composition, and hence on virulence. This is the first report demonstrating that the accumulation of a minor nucleotide sugar intermediate has such a profound and adverse effect on a fungus. The ability to identify molecules that inhibit Er (also known as NRS/ER) enzymes or mimic UDP‐KDG may lead to the development of new antifungal drugs.     

Streptococcal dTDP‐L‐rhamnose biosynthesis enzymes: functional characterization and lead compound identification

Biosynthesis of the nucleotide sugar precursor dTDP‐L‐rhamnose is critical for the viability and virulence of many human pathogenic bacteria, including Streptococcus pyogenes (Group A Streptococcus; GAS), Streptococcus mutans and Mycobacterium tuberculosis. Streptococcal pathogens require dTDP‐L‐rhamnose for the production of structurally similar rhamnose polysaccharides in their cell wall. Via heterologous expression in S. mutans, we confirmed that GAS RmlB and RmlC are critical for dTDP‐L‐rhamnose biosynthesis through their action as dTDP‐glucose‐4,6‐dehydratase and dTDP‐4‐keto‐6‐deoxyglucose‐3,5‐epimerase enzymes respectively. Complementation with GAS RmlB and RmlC containing specific point mutations corroborated the conservation of previous identified catalytic residues. Bio‐layer interferometry was used to identify and confirm inhibitory lead compounds that bind to GAS dTDP‐rhamnose biosynthesis enzymes RmlB, RmlC and GacA. One of the identified compounds, Ri03, inhibited growth of GAS, other rhamnose‐dependent streptococcal pathogens as well as M. tuberculosis with an IC₅₀ of 120–410 µM. Importantly, we confirmed that Ri03 inhibited dTDP‐L‐rhamnose formation in a concentration‐dependent manner through a biochemical assay with recombinant rhamnose biosynthesis enzymes. We therefore conclude that inhibitors of dTDP‐L‐rhamnose biosynthesis, such as Ri03, affect streptococcal and mycobacterial viability and can serve as lead compounds for the development of a new class of antibiotics that targets dTDP‐rhamnose biosynthesis in pathogenic bacteria.     

Wood cell walls: biosynthesis, developmental dynamics and their implications for wood properties

Progress has been made toward understanding the biosynthesis and modifications of the cellulose and the hemicellulose/pectin matrix of woody cell walls (and hence wood properties) by identifying 1600 carbohydrate active enzymes (CAZYmes) in Populus, and pinpointing key candidates involved in various developmental stages of wood formation. Transgenic modifications of primary wall modifying enzymes have demonstrated on the possibility of shaping the dimension of wood cells. Candidates for the biosynthesis of secondary wall matrix have been identified, and the cellulose microfibril angle of wood fibers has been modified. In addition, molecular analysis of the plastic development of wood cell walls has provided further information regarding the mechanisms regulating their structure.