Molecular genetics of nucleotide sugar interconversion pathways in plants

Identification and characterization of pectin related gene NbGAE6 through virus-induced gene silencing in Nicotiana benthamiana

Virus-induced gene silencing (VIGS) is a transient based reverse genetic tool used to elucidate the function of novel gene in N. benthamiana. In current study, 14 UDP-D-glucuronate 4-epimerase (GAE) family members were identified and their gene structure, phylogeny and expression pattern were analyzed. VIGS system was optimized for the functional characterization of NbGAE6 homologous genes in N. benthamiana. Whilst the GAE family is well-known for the interconversion of UDP-D-GlcA and UDP-D-GalA during pectin synthesis. Our results revealed that the downregulation of these genes significantly reduced the amount of GalA in the homogalacturunan which is the major component of pectin found in primary cell wall. Biphenyl assay and high performance liquid chromatography analysis (HPLC) depicted that the level of 'GalA' monosaccharide reduced to 40-51% in VIGS plants as compared to the wild type plants. Moreover, qRT-PCR also confirmed the downregulation of the NbGAE6 mRNA in VIGS plants. In all, this is the first comprehensive study of the optimization of VIGS system for the provision of rapid silencing of GAE family members in N. benthamiana, eliminating the need of stable transformants.

Fruit Salad in the Lab: Comparing Botanical Species to Help Deciphering Fruit Primary Metabolism

Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration of fruit development, coordination of ripening changes (climacteric vs. non-climacteric type) and biochemical composition at ripeness is linked to sweetness and acidity. The main constituents of mature fruit result from different strategies of carbon transport and metabolism. Thus, the timing and nature of phloem loading and unloading can largely differ from one species to another. Furthermore, accumulations and transformations of major soluble sugars, organic acids, amino acids, starch and cell walls are very variable among fruit species. Comparing fruit species therefore appears as a valuable way to get a better understanding of metabolism. On the one hand, the comparison of results of studies about species of different botanical families allows pointing the drivers of sugar or organic acid accumulation but this kind of comparison is often hampered by heterogeneous analysis approaches applied in each study and incomplete dataset. On the other hand, cross-species studies remain rare but have brought new insights into key aspects of primary metabolism regulation. In addition, new tools for multi-species comparisons are currently emerging, including meta-analyses or re-use of shared metabolic or genomic data, and comparative metabolic flux or process-based modeling. All these approaches contribute to the identification of the metabolic factors that influence fruit growth and quality, in order to adjust their levels with breeding or cultural practices, with respect to improving fruit traits.

A Possible Role of the Aleurone Expressed Gene HvMAN1 in the Hydrolysis of the Cell Wall Mannans of the Starchy Endosperm in Germinating Hordeum vulgare L. Seeds

The barley endo-β-mannanase (MAN) gene family (HvMAN1-6) has been identified and the expression of its members analyzed throughout different plant organs, and upon grain development and germination. The HvMAN1 gene has been found to be highly expressed in developing and germinating grains. The MAN (EC 3.2.1.78) enzymatic activity gets a maximum in grains at 48 h of germination (post-germination event). Immunolocalization of mannan polymers in grains has revealed the presence of these polysaccharides in the endosperm cell walls (CWs). By mRNA in situ hybridization assays, the HvMAN1 transcripts have been localized to the aleurone layer, but not to the dead starchy endosperm cells. These data suggest that MAN1 is synthesized in the aleurone layer during early grain imbibition and moves potentially through the apoplast to the endosperm where the hydrolysis of the mannan polymers takes place after germination sensu stricto. Hence, mannans in the starchy endosperm CWs, besides their structural function, could be used as reserve compounds upon barley post-germination.

UDP-D-galactose synthesis by UDP-glucose 4-epimerase 4 is required for organization of the trans-Golgi network/early endosome in Arabidopsis thaliana root epidermal cells

Endomembrane organization is essential for cell physiology. We previously identified an Arabidopsis thaliana mutant in which a plasma membrane (PM) marker GFP-NIP5;1 and trans-Golgi network/early endosome (TGN/EE) markers were accumulated in intracellular aggregates in epidermal cells of the root elongation zone. The mutant was identified as an allele of UDP-glucose epimerase 4 (UGE4)/root hair defective 1/root epidermal bulgar 1, which was previously described as a mutant with swollen root epidermal cells and has an altered sugar composition in cell wall polysaccharides. Importantly, these defects including aggregate formation were restored by supplementation of D-galactose in the medium. These results suggested that UDP-D-galactose synthesis by UGE4 is important for endomembrane organization in addition to cell wall structure. Here, we further investigated the nature of the aggregates using various markers of endomembrane compartments and BOR1-GFP, which traffics from PM to vacuole in response to high-B supply. The markers of multi-vesicular bodies/late endosomes (MVB/LEs) and BOR1-GFP were strongly accumulated in the intracellular aggregates, while those of the endoplasmic reticulum (ER), the vacuolar membrane, and the Golgi were only slightly affected in the uge4 mutant. The abnormal localizations of these markers in the uge4 mutant differed from the effects of inhibitors of actin and microtubule polymerization, although they also affected endomembrane organization. Furthermore, electron microscopy analysis revealed accumulation of abnormal high-electron-density vesicles in elongating epidermal cells. The abnormal vesicles were often associated or interconnected with TGN/EEs and contained ADP-ribosylation factor 1, which is usually localized to the Golgi and the TGN/EEs. On the other hand, structures of the ER, Golgi apparatus, and MVB/LEs were apparently normal in uge4 cells. Together, our data indicate the importance of UDP-D-galactose synthesis by UGE4 for the organization and function of endomembranes, especially TGN/EEs, which are a sorting station of the secretory and vacuolar pathways.

Molecular cloning of a {beta}-galactosidase from radish that specifically hydrolyzes {beta}-(1->3)- and {beta}-(1->6)-galactosyl residues of Arabinogalactan protein

A basic beta-galactosidase with high specificity toward beta-(1-->3)- and beta-(1-->6)-galactosyl residues was cloned from radish (Raphanus sativus) plants by reverse transcription-PCR. The gene, designated RsBGAL1, contained an open reading frame consisting of 2,532 bp (851 amino acids). It is expressed in hypocotyls and young leaves. RsBGAL1 was highly similar to beta-galactosidases having exo-beta-(1-->4)-galactanase activity found in higher plants and belongs to family 35 of the glycosyl hydrolases. Recombinant RsBGAL1 was expressed in Pichia pastoris and purified to homogeneity. The recombinant enzyme specifically hydrolyzed beta-(1-->3)- and beta-(1-->6)-galactooligosaccharides, the same substrates as the native enzyme isolated from radish seeds (Sekimata et al., 1989). It split off about 90% of the carbohydrate moieties of an arabinogalactan protein extracted from radish roots in concerted action with microbial alpha-l-arabinofuranosidase and beta-glucuronidase. These results suggest that RsBGAL1 is a new kind of beta-galactosidase with different substrate specificity than other beta-galactosidases that exhibit exo-beta-(1-->4)-galactanase activity. The C-terminal region (9.6 kD) of RsBGAL1 is significantly similar to the Gal lectin-like domain, but this region is not retained in the native enzyme. Assuming posttranslational processing of RsBGAL1 with elimination of the Gal lectin-like domain results in a protein consisting of two subunits with molecular masses of 46 and 34 kD (calculated from the RsBGAL1 gene sequence). This is in good agreement with the SDS-PAGE and matrix-assisted laser desorption/ionization-time-of flight mass spectrometry measurements for subunits of the native enzyme (45 and 34 kD) and may thus partially explain the formation process of the native enzyme.

Characterization and expression patterns of UDP-D-glucuronate decarboxylase genes in barley

UDP-D-glucuronate decarboxylase (EC 4.1.1.35) catalyzes the synthesis of UDP-D-xylose from UDP-D-glucuronate in an essentially irreversible reaction that is believed to commit glycosyl residues to heteroxylan and xyloglucan biosynthesis. Four members of the barley (Hordeum vulgare) UDP-D-glucuronate decarboxylase gene family, designated HvUXS1 to HvUXS4, have been cloned and characterized. Barley HvUXS1 appears to be a cytosolic enzyme, while the others are predicted to be membrane-bound proteins with single transmembrane helices. Heterologous expression of a barley HvUXS1 cDNA in Escherichia coli yields a soluble enzyme that converts UDP-d-glucuronate to UDP-D-xylose, is associated with a single molecule of bound NAD+, and is subject to feedback inhibition by UDP-D-xylose. Quantitative PCR shows that the HvUXS1 mRNA is most abundant among the 4 HvUXS genes, accounting for more than 80% of total HvUXS transcripts in most of the tissues examined. The abundance of HvUXS1 mRNA is 10-fold higher in mature roots and stems than in leaves, developing grains, or floral tissues. Transcriptional activities of HvUXS2 and HvUXS4 genes are relatively high in mature roots, coleoptiles, and stems compared with root tips, leaves, and floral tissues, while HvUXS3 mRNA is low in all tissues. In barley leaf sections, levels of the most abundant mRNA, encoding HvUXS1, reflect the amount of soluble enzymic protein and activity. In selected tissues where HvUXS1 transcript levels are high, cell walls have higher arabinoxylan contents.

The biosynthesis of UDP-galacturonic acid in plants. Functional cloning and characterization of Arabidopsis UDP-D-glucuronic acid 4-epimerase

UDP-GlcA 4-epimerase (UGlcAE) catalyzes the epimerization of UDP-alpha-D-glucuronic acid (UDP-GlcA) to UDP-alpha-D-galacturonic acid (UDP-GalA). UDP-GalA is a precursor for the synthesis of numerous cell-surface polysaccharides in bacteria and plants. Using a biochemical screen, a gene encoding AtUGlcAE1 in Arabidopsis (Arabidopsis thaliana) was identified and the recombinant enzyme biochemically characterized. The gene belongs to a small gene family composed of six isoforms. All members of the UGlcAE gene family encode a putative type-II membrane protein and have two domains: a variable N-terminal region approximately 120 amino acids long composed of a predicted cytosolic, transmembrane, and stem domain, followed by a large conserved C-terminal catalytic region approximately 300 amino acids long composed of a highly conserved catalytic domain found in a large protein family of epimerase/dehydratases. The recombinant epimerase has a predicted molecular mass of approximately 43 kD, although size-exclusion chromatography suggests that it may exist as a dimer (approximately 88 kD). AtUGlcAE1 forms UDP-GalA with an equilibrium constant value of approximately 1.9 and has an apparent K(m) value of 720 microm for UDP-GlcA. The enzyme has maximum activity at pH 7.5 and is active between 20 degrees C and 55 degrees C. Arabidopsis AtUGlcAE1 is not inhibited by UDP-Glc, UDP-Gal, or UMP. However, the enzyme is inhibited by UDP-Xyl and UDP-Ara, suggesting that these nucleotide sugars have a role in regulating the synthesis of pectin. The cloning of the AtUGlcAE1 gene will increase our ability to investigate the molecular factors that regulate pectin biosynthesis in plants. The availability of a functional recombinant UDP-GlcA 4-epimerase will be of considerable value for the facile generation of UDP-d-GalA in the amounts required for detailed studies of pectin biosynthesis.

The biosynthesis of D-Galacturonate in plants. functional cloning and characterization of a membrane-anchored UDP-D-Glucuronate 4-epimerase from Arabidopsis

Pectic cell wall polysaccharides owe their high negative charge to the presence of D-galacturonate, a monosaccharide that appears to be present only in plants and some prokaryotes. UDP-D-galacturonate, the activated form of this sugar, is known to be formed by the 4-epimerization of UDP-D-glucuronate; however, no coding regions for the epimerase catalyzing this reaction have previously been described in plants. To better understand the mechanisms by which precursors for pectin synthesis are produced, we used a bioinformatics approach to identify and functionally express a UDP-D-glucuronate 4-epimerase (GAE1) from Arabidopsis. GAE1 is predicted to be a type II membrane protein that belongs to the family of short-chain dehydrogenases/reductases. The recombinant enzyme expressed in Pichia pastoris established a 1.3:1 equilibrium between UDP-D-galacturonate and UDP-D-glucuronate but did not epimerize UDP-D-Glc or UDP-D-Xyl. Enzyme assays on cell extracts localized total UDP-D-glucuronate 4-epimerase and recombinant GAE1 activity exclusively to the microsomal fractions of Arabidopsis and Pichia, respectively. GAE1 had a pH optimum of 7.6 and an apparent Km of 0.19 mm. The recombinant enzyme was strongly inhibited by UDP-D-Xyl but not by UDP, UDP-D-Glc, or UDP-D-Gal. Analysis of Arabidopsis plants transformed with a GAE1:GUS construct showed expression in all tissues. The Arabidopsis genome contains five GAE1 paralogs, all of which are transcribed and predicted to contain a membrane anchor. This suggests that all of these enzymes are targeted to an endomembrane system such as the Golgi where they may provide UDP-D-galacturonate to glycosyltransferases in pectin synthesis.

RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis

Pectins are major components of primary plant cell walls and the seed mucilage of Arabidopsis. Despite progress in the structural elucidation of pectins, only very few enzymes participating in or regulating their synthesis have been identified. A first candidate gene involved in the synthesis of pectinaceous rhamnogalacturonan I is RHM2, a putative plant ortholog to NDP-rhamnose biosynthetic enzymes in bacteria. Expression studies with a promoter beta-glucuronidase construct and reverse transcription PCR data show that RHM2 is expressed ubiquitously. Rhm2 T-DNA insertion mutant lines were identified using a reverse genetics approach. Analysis of the rhm2 seeds by various staining methods and chemical analysis of the mucilage revealed a strong reduction of rhamnogalacturonan I in the mucilage and a decrease of its molecular weight. In addition, scanning electron microscopy of the seed surface indicated a distorted testa morphology, illustrating not only a structural but also a developmental role for RGI or rhamnose metabolism in proper testa formation.

MUCILAGE-MODIFIED4 encodes a putative pectin biosynthetic enzyme developmentally regulated by APETALA2, TRANSPARENT TESTA GLABRA1, and GLABRA2 in the Arabidopsis seed coat

The Arabidopsis seed coat epidermis undergoes a complex process of differentiation that includes the biosynthesis and secretion of large quantities of pectinaceous mucilage, cytoplasmic rearrangement, and secondary cell wall biosynthesis. Mutations in MUM4 (MUCILAGE-MODIFIED4) lead to a decrease in seed coat mucilage and incomplete cytoplasmic rearrangement. We show that MUM4 encodes a putative NDP-l-rhamnose synthase, an enzyme required for the synthesis of the pectin rhamnogalacturonan I, the major component of Arabidopsis mucilage. This result suggests that the synthesis of monosaccharide substrates is a limiting factor in the biosynthesis of pectinaceous seed coat mucilage. In addition, the reduced cytoplasmic rearrangement observed in the absence of a key enzyme in pectin biosynthesis in mum4 mutants establishes a causal link between mucilage production and cellular morphogenesis. The cellular phenotype seen in mum4 mutants is similar to that of several transcription factors (AP2 [APETALA2], TTG1 [TRANSPARENT TESTA GLABRA1], TTG2 MYB61, and GL2 [GLABRA2]). Expression studies suggest that MUM4 is developmentally regulated in the seed coat by AP2, TTG1, and GL2, whereas TTG2 and MYB61 appear to be regulating mucilage production through alternate pathway(s). Our results provide a framework for the regulation of mucilage production and secretory cell differentiation.

Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development

We have conducted a comprehensive metabolic profiling on tomato (Lycopersicon esculentum) leaf and developing fruit tissue using a recently established gas chromatography-mass spectrometry profiling protocol alongside conventional spectrophotometric and liquid chromatographic methodologies. Applying a combination of these techniques, we were able to identify in excess of 70 small-M(r) metabolites and to catalogue the metabolite composition of developing tomato fruit. In addition to comparing differences in metabolite content between source and sink tissues of the tomato plant and after the change in metabolite pool sizes through fruit development, we have assessed the influence of hexose phosphorylation through fruit development by analyzing transgenic plants constitutively overexpressing Arabidopsis hexokinase AtHXK1. Analysis of the total hexokinase activity in developing fruits revealed that both wild-type and transgenic fruits exhibit decreasing hexokinase activity with development but that the relative activity of the transgenic lines with respect to wild type increases with development. Conversely, both point-by-point and principal component analyses suggest that the metabolic phenotype of these lines becomes less distinct from wild type during development. In summary, the data presented in this paper demonstrate that the influence of hexose phosphorylation diminishes during fruit development and highlights the importance of greater temporal resolution of metabolism.