Cloning and characterization of several cDNAs for UDP-glucose pyrophosphorylase from barley (Hordeum vulgare) tissues

Transcriptome Dynamics during Spike Differentiation of Wheat Reveal Amazing Changes in Cell Wall Metabolic Regulators

Coordinated cell proliferation and differentiation result in the complex structure of the inflorescence in wheat. It exhibits unique differentiation patterns and structural changes at different stages, which have attracted the attention of botanists studying the dynamic regulation of its genes. Our research aims to understand the molecular mechanisms underlying the regulation of spike development genes at different growth stages. We conducted RNA-Seq and qRT-PCR evaluations on spikes at three stages. Our findings revealed that genes associated with the cell wall and carbohydrate metabolism showed high expression levels between any two stages throughout the entire process, suggesting their regulatory role in early spike development. Furthermore, through transgenic experiments, we elucidated the role of the cell wall regulator gene in spike development regulation. These research results contribute to identifying essential genes associated with the morphology and development of wheat spike tissue.

Florigen sequestration in cellular membranes modulates temperature-responsive flowering

[Figure: see text].

Low UGP2 Expression Is Associated with Tumour Progression and Predicts Poor Prognosis in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a malignant tumour associated with a high mortality rate and poor prognosis worldwide. Uridine diphosphate-glucose pyrophosphorylase 2 (UGP2), a key enzyme in glycogen biosynthesis, has been reported to be associated with the occurrence and development of various cancer types. However, its diagnostic value and prognostic value in HCC remain unclear. The present study observed that UGP2 expression was significantly downregulated at both the mRNA and protein levels in HCC tissues. Receiver operating characteristic (ROC) curve analysis revealed that UGP2 may be an indicator for the diagnosis of HCC. In addition, Kaplan-Meier and Cox regression multivariate analyses indicated that UGP2 is an independent prognostic factor of overall survival (OS) in patients with HCC. Furthermore, gene set enrichment analysis (GSEA) suggested that gene sets negatively correlated with the survival of HCC patients were enriched in the group with low UGP2 expression levels. More importantly, a significant correlation was identified between low UGP2 expression and fatty acid metabolism. In summary, the present study demonstrates that UGP2 may contribute to the progression of HCC, indicating a potential therapeutic target for HCC patients.

Rice LecRK5 phosphorylates a UGPase to regulate callose biosynthesis during pollen development

The temporary callose layer surrounding the tetrads of microspores is critical for male gametophyte development in flowering plants, as abnormal callose deposition can lead to microspore abortion. A sophisticated signaling network regulates callose biosynthesis but these pathways are poorly understood. In this study, we characterized a rice male-sterile mutant, oslecrk5, which showed defective callose deposition during meiosis. OsLecRK5 encodes a plasma membrane-localized lectin receptor-like kinase, which can form a dimer with itself. Moreover, normal anther development requires the K-phosphorylation site (a conserved residue at the ATP-binding site) of OsLecRK5. In vitro assay showed that OsLecRK5 phosphorylates the callose synthesis enzyme UGP1, enhancing callose biosynthesis during anther development. Together, our results demonstrate that plasma membrane-localized OsLecRK5 phosphorylates UGP1 and promotes its activity in callose biosynthesis in rice. This is the first evidence that a receptor-like kinase positively regulates callose biosynthesis.

Expression of UGP2 and CFL1 expression levels in benign and malignant pancreatic lesions and their clinicopathological significance

BACKGROUND

This study investigated UGP2 (uridine diphosphate-glucose pyrophosphorylase-2) and CFL1 (cofilin-1) expression in pancreatic ductal carcinoma (PDC), paracancerous tissue (PT), benign lesions (BL), and normal tissue (NT) and their clinicopathological significance.

METHODS

Surgical specimens, which were collected from 106 cases of pancreatic ductal carcinoma, 35 cases of paracancerous tissues, 55 cases of benign lesions and 13 cases of normal pancreatic tissues, were fixed with 4% formaldehyde to prepare conventional paraffin-embedded sections. EnVision immunohistochemical was used to stain for UGP2 and CFL1. Kaplan-Meier survival analysis was performed to assess the correlation of expression pattern with survival.

RESULTS

We found that positive UGP2 and CFL1 expression in PDC were significantly higher than those in PT, BL, and NT. In PT and BL with positive UGP2 and CFL1 expression, mild to severe atypical hyperplasia or intraepithelial neoplasia of grades II-III was observed in ductal epithelium. Positive UGP2 and CFL1 expression in cases with high differentiation, no lymph node metastasis, no surrounding invasion, and TNM (tumor-node-metastasis) staging I or/and II were significantly lower than those in cases with poor differentiation, lymph node metastasis, surrounding invasion, and TNM stage III and/or IV. Positive UGP2 expression in male patients was significantly lower than that in female patients. UGP2 and CFL1 expression in PDC were positively correlated. Kaplan-Meier survival analysis showed the degree of differentiation, tumor maximal diameter, TNM stage, lymph node metastasis, and surrounding invasion, and UGP2 and CFL1 expression were closely related to the average survival time of patients with PDC. The survival time of patients with positive UGP2 and CFL1 expression was significantly shorter than that of patients with negative expression. Cox multivariate analysis showed that poor differentiation, tumor maximal diameter ≥ 3 cm, TNM stage III or IV, lymph node metastasis, surrounding invasion, and positive UGP2 and CFL1 expression was negatively correlated with the postoperative survival rate and positively correlated with the mortality of patients with PDC.

CONCLUSION

Positive expression of UGP2 and CFL1 can serve a valuable prognostic factor in pancreatic cancer.

Comparative metabolite and genome analysis of tuber-bearing potato species

The cultivated potato Solanum tuberosum is unrivalled among crop plants for its wild relatives, which potentially represent an important source of genetic diversity to improve the nutritional value of potato varieties and understand metabolism regulation. The main aim of this research was to profile human health-related metabolites in a number of clones from 13 Solanum species. Results from HPLC-DAD and LC-ESI-MS analyses highlighted a high interspecific variability in the level of metabolites analysed. Ascorbic acid was confirmed to be the most abundant antioxidant in potato and chlorogenic acid the primary polyphenol. Generally, metabolite-based hierarchical clustering (HCL) and correlation networks did not group clones of identical species in the same cluster. This might be due to various factors, including the outcrossing nature of potato species, gene expression level and metabolic profiling techniques. Access to the genome sequence of S. tuberosum and S. commersonii allowed comparison of the genes involved in ascorbic acid, aromatic amino acid, phenylpropanoid and glycoalkaloid biosynthesis and helped interpret their respective pathways.

Characterization of a new UDP-sugar pyrophosphorylase from Hordeum vulgare (barley)

The broad substrate spectrum of UDP-sugar pyrophosphorylases from plant salvage pathways is of high interest for the synthesis of expensive nucleotide sugars by straightforward enzyme cascade reactions in combination with monosaccharide kinases. We here present a new UDP-sugar pyrophosphorylase from Hordeum vulgare with favorable biochemical properties like broad pH and temperature tolerances as well as a broad substrate spectrum and high synthesis stability. Enzyme properties were determined and reaction conditions were optimized by high-through-put multiplexed capillary electrophoresis analysis. In combination with a galactokinase UDP-α-d-galactose (UDP-Gal) was efficiently synthesized with a space-time-yield of 17g/L*h for full conversion of 10mM substrate within 20min by 1.2U of each enzyme.

Overexpression of UDP-glucose pyrophosphorylase from Larix gmelinii enhances vegetative growth in transgenic Arabidopsis thaliana

A UDP-glucose pyrophosphorylase gene ( LgUGPase ) was identified from Larix gmelinii, and its function in enhancing vegetative growth and cellulose biosynthesis was confirmed by analyzing transgenic Arabidopsis thaliana overexpressed LgUGPase . UDP-glucose pyrophosphorylase (UGPase), an important regulatory enzyme in carbohydrate metabolism, catalyzes the reversible production of glucose 1-phosphate and the conversion of uridine triphosphate to uridine diphosphate glucose and pyrophosphate. In this study, a larch UGPase (LgUGPase) gene was isolated from Larix gmelinii. The 1,443-bp open reading frame encodes a protein of 480 amino acids with a predicted molecular weight of 53.7 kDa and shows striking sequence similarity to UGPase proteins from Pinus taeda and Picea sitchensis. Semiquantitative reverse transcription-polymerase chain reaction showed that the LgUGPase gene was expressed primarily in the larch stem in addition to its root and leaf. Southern blot analysis indicated that LgUGPase is encoded by two genes in the L. gmelinii genome. Overexpression of LgUGPase enhanced vegetative growth in transgenic Arabidopsis and increased the contents of soluble sugars and cellulose, and thickened parenchyma cell walls. These results revealed that L. gmelinii UGPase participates in sucrose/polysaccharide metabolism and cell wall biosynthesis, suggesting that LgUGPase may be a good candidate gene for improvement of fiber cell development in plants.

A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize

In maize developing seeds, transfer cells are prominently located at the basal endosperm transfer layer (BETL). As the first filial cell layer, BETL is a gateway to sugars, nutrients and water from mother plant; and anchor of numerous functions such as sucrose turnover, auxin and cytokinin biosynthesis/accumulation, energy metabolism, defense response, and signaling between maternal and filial generations. Previous studies showed that basal developing endosperms of miniature1 (mn1) mutant seeds lacking the Mn1-encoded cell wall invertase II, are also deficient for hexose. Given the role of glucose as one of the key sugars in protein glycosylation and proper protein folding; we performed a comparative large scale glycoproteome profiling of total proteins of these two genotypes (mn1 mutant vs. Mn1 wild type) using 2D gel electrophoresis and glycosylation/total protein staining, followed by image analysis. Protein identification was done by LC-MS/MS. A total of 413 spots were detected; from which, 113 spots matched between the two genotypes. Of these, 45 showed >20% decrease/increase in glycosylation level and were selected for protein identification. A large number of identified proteins showed decreased glycosylation levels in mn1 developing endosperms as compared to the Mn1. Functional classification of proteins, showed mainly of post-translational modification, protein turnover, chaperone activities, carbohydrate and amino acid biosynthesis/transport, and cell wall biosynthesis. These proteins and activities were related to endoplasmic reticulum (ER) stress and unfolded protein response (UPR) as a result of the low glycolsylation levels of the mutant proteins. Overall, these results provide for the first time a global glycoproteome profile of maize BETL-enriched basal endosperm to better understand their role in seed development in maize.

Identification of a UDP-glucose pyrophosphorylase from cotton (Gossypium hirsutum L.) involved in cellulose biosynthesis in Arabidopsis thaliana

UDP-glucose pyrophosphorylase is an important regulatory enzyme for the development of plants and a critical enzyme in synthesis of glycogen. Here, we reported the cloning of a full-length UGP cDNA from cotton, named GhUGP. Real-time PCR analysis indicated the GhUGP expression in root, stem, leaf and flower of cotton, with a higher level in flower and root. The transcription level of GhUGP depended on sucrose and light in short time and increased under low temperature, but decreased in O(2) deficiency. Interestingly, the expression of GhUGP was significantly up-regulated after ethylene induction in cotton ovules. The over-expression of the GhUGP in Arabidopsis showed discrepant phenotype: increase in height and growth rate when compared with control lines. What is more, the transgenic Arabidopsis had increased contents of soluble sugars, starch and cellulose, but not in lignin content. Collectively, these results indicate that cotton UGPase participates in sucrose/polysaccharides metabolism and cell wall biosynthesis and provide theoretical deduction supporting GhUGP as a good candidate gene for improving the development of cotton fibers cell.

UDP-glucose pyrophosphorylase is rate limiting in vegetative and reproductive phases in Arabidopsis thaliana

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme in the metabolism of UDP-glucose, a precursor for the synthesis of carbohydrate cell wall components, such as cellulose and callose. The Arabidopsis thaliana genome contains two putative genes encoding UGPase, AtUGP1 and AtUGP2. These genes are expressed in all organs. In order to determine the role of UGPase in vegetative and reproductive organs, we employed a reverse genetic approach using the T-DNA insertion mutants, atugp1 and atugp2. Despite a significant decrease in UGPase activity in both the atugp1 and atugp2 single mutants, no decrease in normal growth and reproduction was observed. In contrast, the atugp1/atugp2 double mutant displayed drastic growth defects and male sterility. At the reproductive phase, in the anthers of atugp1/atugp2, pollen mother cells developed normally, but callose deposition around microspores was absent. Genes coding for enzymes at the subsequent steps in the cellulose and callose synthesis pathway were also down-regulated in the double mutant. Taken together, these results demonstrate that the AtUGP1 and AtUGP2 genes are functionally redundant and UGPase activity is essential for both vegetative and reproductive phases in Arabidopsis. Importantly, male fertility was not restored in the double knockout mutant by an application of external sucrose, whereas vegetative growth was comparable in size with that of the wild type. In contrast, an application of external UDP-glucose recovered male fertility in the double mutant, suggesting that control of UGPase in carbohydrate metabolism is different in the vegetative phase as compared with the reproductive phase in A. thaliana.

Domain-specific determinants of catalysis/substrate binding and the oligomerization status of barley UDP-glucose pyrophosphorylase

UDP-glucose (UDPG) pyrophosphorylase (UGPase) produces UDPG for sucrose and polysaccharide synthesis and glycosylation reactions. In this study, several barley UGPase mutants were produced, either single amino acid mutants or involving deletions of N- and C-terminal domains (Ncut and Ccut mutants, respectively) and of active site region ("NB loop"). The Del-NB mutant yielded no activity, whereas Ncut deletions and most of Ccut mutants, including short deletions at the so called "I-loop" region of C-terminal domain, as well as a single K260A mutant resulted in very low activity. For wt and the mutants, kinetics with UDPG were linear on reciprocal plots, whereas PPi at concentrations above 1 mM exerted strong substrate inhibition. Both K260A and most of the Ccut mutants had very high Km with PPi (up to 33 mM), whereas Ncut deletions had greatly increased Km with UDPG (up to 57 mM). Surprisingly, an 8 amino acid deletion from end of the C-terminus resulted in an enzyme (Ccut-8 mutant) with 44% higher activity when compared to wt, but with similar Km values. Whereas Ccut-8 existed solely as a monomer, other deletion mutants had a more oligomerized status, e.g. Ncut mutants existing primarily as dimers. Overall, the data confirmed the essential role of NB loop in catalysis, but also pointed out to the role of both N- and C-termini for activity, substrate binding and oligomerization. The importance of oligomerization status for enzymatic activity of UGPase is discussed.

Regulation of UDP-glucose pyrophosphorylase isozyme UGP5 associated with cold-sweetening resistance in potatoes

The regulation of UDP-Glc pyrophosphorylase (UGPase) isozyme, UGP5, was investigated in potato tuber. The cDNA for UGP5 was cloned into the bacterial expression vector pET21d and recombinant (RC) enzyme was expressed in E. coli (BL21 star cells). The RC-UGP5 isozyme was purified to near homogeneity using salt precipitation, hydrophobic interaction, and anion-exchange column chromatography. Kinetic analysis revealed that in the synthesis direction, K(m) values for Glc-1-P (0.83 mM) and UTP (0.22 mM) were similar to those observed previously with the mother tuber (MT)-UGP5. In the pyrophosphorolysis direction, the K(m) values for UDP-Glc (0.68 mM) and PPi (0.56 mM) were slightly higher than those observed previously. Maximum reaction velocities (V(max)) for RC-UGP5 were also elevated. Since the molecular mass, charge, and amino acid sequence of the MT- and RC-UGP5 isozymes were identical, it was assumed that altered kinetic constants may be due to an improper folding of RC-UGP5 polypeptide. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and proteomic analysis demonstrated that the UGP5 isozyme was a single polypeptide with a calculated molecular mass of 51.8kDa consisting of 477 amino acids. Native PAGE and kinetic analysis revealed that this polypeptide was monomeric in nature. Immunoblotting with specific antibodies and LC-MS/MS data indicated that UGP5 did not require any post-translational modification (e.g., phosphorylation, O-glycosylation, oligomerization/de-oligomerization, or the presence of the regulatory 14-3-3 proteins) for its regulation. Additionally, the two closely associated isozymes UGP5 and UGP6 in the cv. Snowden are likely the result of allelic differences of UGPase at a single locus.

Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.)

A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T(1) seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T(1) plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.

Survey of differentially expressed proteins and genes in jasmonic acid treated rice seedling shoot and root at the proteomics and transcriptomics levels

Two global approaches were applied to develop an inventory of differentially expressed proteins and genes in rice (cv. Nipponbare) seedling grown on Murashige and Skoog medium with and without jasmonic acid (JA). JA significantly reduced the growth of shoot, root, leaf, and leaf sheath depending on JA concentration (1, 2, 5, 10, 25, and 50 microM) as compared with control. Almost 50% growth inhibition of seedling was observed with 5 microM JA. Shoots and roots of seedlings grown on 5 microM JA for 7 days were then used for proteomics and transcriptomics analyses. Two-dimensional gel electrophoresis revealed 66 and 68 differentially expressed protein spots in shoot and root, respectively, compared to their respective controls. Tandem mass spectrometry analysis of these proteins identified 52 (shoot) and 56 (root) nonredundant proteins, belonging to 10 functional categories. Proteins involved in photosynthesis (44%), cellular respiratory (11%), and protein modification and chaperone (11%) were highly represented in shoot, whereas antioxidant system (18%), cellular respiratory (17%), and defense-related proteins (15%) were highly represented in root. Transcriptomics analysis of shoot and root identified 107 and 325 induced genes and 34 and 213 suppressed genes in shoot and root, respectively. Except of unknown genes with over 57% of the total, most genes encode for proteins involved in secondary metabolism, energy production, protein modification and chaperone, transporters, and cytochrome P450. These identified proteins and genes have been discussed with respect to the JA-induced phenotype providing a new insight into the role of JA in rice seedling growth and development.

KEYWORDS

phytohormone * inhibitory concentration * growth * gel-based approach * mass spectrometry * DNA microarray.

The complex of Sphingomonas elodea ATCC 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members

Gellan gum is a widely used commercial material, available in many different forms. Its economic importance has led to studies into the biosynthesis of exopolysaccharide gellan gum, which is industrially prepared in high yields using Sphingomonas elodea ATCC 31461. Glucose-1-phosphate uridylyltransferase mediates the reversible conversion of glucose-1-phosphate and UTP into UDP-glucose and pyrophosphate, which is a key step in the biosynthetic pathway of gellan gums. Here we present the X-ray crystal structure of the glucose-1-phosphate uridylyltransferase from S. elodea. The S. elodea enzyme shares strong monomeric similarity with glucose-1-phosphate thymidylyltransferase, several structures of which are known, although the quaternary structures of the active enzymes are rather different. A detailed comparison between S. elodea glucose-1-phosphate uridylyltransferase and available thymidylyltransferases is described and shows remarkable structural similarities, despite the low sequence identities between the two divergent groups of proteins.

Rice UDP-glucose pyrophosphorylase1 is essential for pollen callose deposition and its cosuppression results in a new type of thermosensitive genic male sterility

UDP-glucose pyrophosphorylase (UGPase) catalyzes the reversible production of glucose-1-phosphate and UTP to UDP-glucose and pyrophosphate. The rice (Oryza sativa) genome contains two homologous UGPase genes, Ugp1 and Ugp2. We report a functional characterization of rice Ugp1, which is expressed throughout the plant, with highest expression in florets, especially in pollen during anther development. Ugp1 silencing by RNA interference or cosuppression results in male sterility. Expressing a double-stranded RNA interference construct in Ugp1-RI plants resulted in complete suppression of both Ugp1 and Ugp2, together with various pleiotropic developmental abnormalities, suggesting that UGPase plays critical roles in plant growth and development. More importantly, Ugp1-cosuppressing plants contained unprocessed intron-containing primary transcripts derived from transcription of the overexpression construct. These aberrant transcripts undergo temperature-sensitive splicing in florets, leading to a novel thermosensitive genic male sterility. Pollen mother cells (PMCs) of Ugp1-silenced plants appeared normal before meiosis, but during meiosis, normal callose deposition was disrupted. Consequently, the PMCs began to degenerate at the early meiosis stage, eventually resulting in complete pollen collapse. In addition, the degeneration of the tapetum and middle layer was inhibited. These results demonstrate that rice Ugp1 is required for callose deposition during PMC meiosis and bridges the apoplastic unloading pathway and pollen development.

Differential tissue/organ-dependent expression of two sucrose- and cold-responsive genes for UDP-glucose pyrophosphorylase in Populus

Plant UDP-glucose (UDPG) pyrophosphorylase (UGPase) is involved in the production/metabolism of UDPG, a key metabolite for sucrose and cell wall biosynthesis. Two highly similar cDNAs (UGP1 and UGP2) corresponding to UGPase were isolated from cDNA libraries of hybrid aspen (Populus tremula x tremuloides). Expression of both UGPs, as studied by DNA microarrays and EST abundance, was compared to that of three sucrose synthase genes (SUS1-3), also involved in UDPG synthesis. Generally, the UGPs had lower expression than SUS1 and SUS2 genes (especially in tension wood and cambium), with the notable exception of leaves, primary roots and flowers. Based on real-time quantitative PCR, UGP1 in root xylem, leaves and male flowers was by far the predominant transcript, while in other tissues both UGP1 and UGP2 had comparable expression. In leaves, the UGP1 gene, but not UGP2, was upregulated by light and short-term sucrose feeding. Cold treatment led to dramatic organ-specific changes in relative expression of both genes, with UGP2 being upregulated either transiently (leaves), long-term (stems) or not at all (roots), whereas UGP1 was cold-upregulated in all organs. Individual or overall UGP expression patterns only weakly correlated with UGPase activity/protein; however, UGPase activity and protein were correlated in all tissues/conditions. The data suggest that UGPs are differentially expressed at the tissue level and in response to metabolic feedback (sucrose) and cold stress, and point to a tight posttranscriptional/translational control and, possibly, distinct roles for those genes.

Factors affecting oligomerization status of UDP-glucose pyrophosphorylase

UDP-glucose pyrophosphorylase (UGPase) is involved in the production of UDP-glucose, a key precursor to polysaccharide synthesis in all organisms. UGPase activity has recently been proposed to be regulated by oligomerization, with monomer as the active species. In the present study, we investigated factors affecting oligomerization status of the enzyme, using purified recombinant barley UGPase. Incubation of wild-type (wt) UGPase with phosphate or Tris buffers promoted oligomerization, whereas Mops and Hepes completely dissociated the oligomers to monomers (the active form). Similar buffer effects were observed for KK127-128LL and C99S mutants of UGPase; however, the buffers had a relatively small effect on the oligomerization status of the LIV135-137NIN mutant, impaired in deoligomerization ability and showing only 6-9% activity of the wt. Buffer composition had no effect on UGPase activity at UGPase protein concentrations below ca. 20 ng/ml. However, at higher protein concentration the activity in Tris, but not Mops nor Hepes, underestimated the amount of the enzyme. The data suggest that oligomerization status of UGPase can be controlled by subtle changes in an immediate environment (buffers) and by protein dilution. The evidence is discussed in relation to our recent model of UGPase structure/function, and with respect to earlier reports on the oligomeric integrity/activity of UGPases from eukaryotic tissues.

The LPB1 gene is important for acclimation of Chlamydomonas reinhardtii to phosphorus and sulfur deprivation

Organisms exhibit a diverse set of responses when exposed to low-phosphate conditions. Some of these responses are specific for phosphorus limitation, including responses that enable cells to efficiently scavenge phosphate from internal and external stores via the production of high-affinity phosphate transporters and the synthesis of intracellular and extracellular phosphatases. Other responses are general and occur under a number of different environmental stresses, helping coordinate cellular metabolism and cell division with the growth potential of the cell. In this article, we describe the isolation and characterization of a mutant of Chlamydomonas reinhardtii, low-phosphate bleaching (lpb1), which dies more rapidly than wild-type cells during phosphorus limitation. The responses of this mutant to nitrogen limitation appear normal, although the strain is also somewhat more sensitive than wild-type cells to sulfur deprivation. Interestingly, depriving the cells of both nutrients simultaneously allows for sustained survival that is similar to that observed with wild-type cells. Furthermore, upon phosphorus deprivation, the lpb1 mutant, like wild-type cells, exhibits increased levels of mRNA encoding the PHOX alkaline phosphatase, the PTB2 phosphate transporter, and the regulatory element PSR1. The mutant strain is also able to synthesize the extracellular alkaline phosphatase activity upon phosphorus deprivation and the arylsulfatase upon sulfur deprivation, suggesting that the specific responses to phosphorus and sulfur deprivation are normal. The LPB1 gene was tagged by insertion of the ARG7 gene, which facilitated its isolation and characterization. This gene encodes a protein with strong similarity to expressed proteins in Arabidopsis (Arabidopsis thaliana) and predicted proteins in Oryza sativa and Parachlamydia. A domain in the protein contains some similarity to the superfamily of nucleotide-diphospho-sugar transferases, and it is likely to be localized to the chloroplast or mitochondrion based on programs that predict subcellular localization. While the precise catalytic role and physiological function of the putative protein is not known, it may function in some aspect of polysaccharide metabolism and/or influence phosphorus metabolism (either structural or regulatory) in a way that is critical for allowing the cells to acclimate to nutrient limitation conditions.

Toward a blueprint for UDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

Molecular cloning and sequence variation of UDP-glucose pyrophosphorylase cDNAs from potatoes sensitive and resistant to cold sweetening

RT-PCR was used to isolate seven cDNAs encoding uridine diphosphate-glucose pyrophosphorylase (UGPase) from six potato cultivars that differed markedly in their ability to sweeten in cold storage (2-4 degrees C). These sequences were compared to two potato UGPase-cDNAs previously published. All cDNAs were highly conserved (97.6-99.9%) and coded for polypeptides with 477 amino acids. The cDNAs could be placed into two sequence classes depending on whether they contained a BamH1 site at nucleotide positions 1315-1320. The presence of the BamH1 site (substitution of a C for a T at bp position 1320) did not lead to a change of an amino acid in the mature protein. There were 27 nucleotide polymorphisms that co-segregated along with the BamH1 site, five of which led to an amino acid change (i.e., bp positions (5) Thr for Ala; (30) Glu for Asp; (82) Lys for Asn; (445) Lys for Glu; and (450) Val for Ile). All of the encoded polypeptides contained the five highly conserved lysine residues located at positions 263, 329, 367, 409 and 410 that have been demonstrated necessary for catalytic activity of UGPase. All polypeptides had putative glycosylation sites at amino acid positions 168 (NQS) and 307 (NLS). The Ser at position 420 provided a putative site for phosphorylation as well as a binding motif for 14-3-3 proteins.

Characterization of the ugpG gene encoding a UDP-glucose pyrophosphorylase from the gellan gum producer Sphingomonas paucimobilis ATCC 31461

The ugpGgene, which codes for a UDP-glucose pyrophosphorylase (UGP) (or glucose-1-phosphate uridylyltransferase; EC 2.7.7.9) in Sphingomonas paucimobilis ATCC 31461, was cloned and sequenced. This industrial strain produces the exopolysaccharide gellan, a new commercial gelling agent, and the ugpG gene may convert glucose-1-phosphate into UDP-glucose in the gellan biosynthetic pathway. The ugpG gene is capable of restoring the capacity of an Escherichia coli galU mutant to grow on galactose by functional complementation of its deficiency for UDP-glucose pyrophosphorylase activity. As expected, the predicted gene product shows strong homology to UDP-glucose pyrophosphorylases from several bacterial species. The N-terminal region of UgpG exhibits the motif GXGTRXLPXTK, which is highly conserved among bacterial XDP-sugar pyrophosphorylases, and a lysine residue (K(192)) is located within a VEKP motif predicted to be essential for substrate binding or catalysis. UgpG was purified to homogeneity as a heterologous fusion protein from crude cell extracts prepared from IPTG-induced cells of E. coli, using affinity chromatography. Under denaturing conditions, the fusion protein S-UgpG-His(6) migrated with an estimated molecular mass of 36 kDa [corresponding to the predicted molecular mass of native UgpG (31.2 kDa) plus 5 kDa for the S and histidine tags). Kinetic analysis of UgpG in the reverse reaction (pyrophosphorolysis) showed a typical Michaelis-Menten substrate saturation pattern. The apparent K(m) and V(max) values estimated for UDP-glucose were 7.5 microM and 1275 micromol/min/g.

Oligomerization status, with the monomer as active species, defines catalytic efficiency of UDP-glucose pyrophosphorylase

Barley UDP-glucose pyrophosphorylase (UGPase), a key enzyme for the synthesis of sucrose, cellulose and other saccharides, was expressed in Escherichia coli and purified. Using both native electrophoresis and gel filtration, the recombinant and crude leaf UGPase proteins were found to exist as a mixture of monomers, dimers and higher-order polymers. In order to understand the molecular basis for the oligomerization of UGPase, a conserved Cys residue was replaced (C99S mutant) and several amino acids were substituted (LIV to NIN, KK to LL and LLL to NNN) in a conserved hydrophobic domain (amino acids 117-138). The C99S mutant had about half the V (max) of the wild-type and a 12-fold higher K (m) for PP(i), whereas NIN and LL mutations lowered the V (max) by 12- and 2-fold, respectively, with relatively small effects on substrate K (m) values (the NNN mutant was insoluble/inactive). The NIN mutation resulted in a low-activity oligomerized enzyme form, with very little monomer formation. Activity staining on native PAGE gels as well as gel-filtration studies demonstrated that the monomer was the sole enzymically active form. Possible implications of the oligomerization status of UGPase for post-translational regulation of the enzyme are discussed.

A second UDP-glucose pyrophosphorylase is required for differentiation and development in Dictyostelium discoideum

Uridine diphosphoglucose pyrophosphorylase (UDPGP) is a developmentally regulated enzyme in Dictyostelium discoideum, which is involved in trehalose, cellulose, and glycogen synthesis. Two independent UDPGP proteins are believed to be responsible for this activity. To determine the relative contributions of each protein, the genes encoding them were disrupted individually. Cells lacking the udpgp1 gene exhibit normal growth and development and make normal levels of cellulose. In agreement with these phenotypes, udpgp1(-) cells still have UDPGP activity, although at a reduced level. This supports the importance of the second UDPGP gene. This newly identified gene, ugpB, encodes an active UDPGP as determined by complementation in Escherichia coli. When this gene is disrupted, cells undergo aberrant differentiation and development ending with small, gnarled fruiting bodies. These cells also have decreased spore viability and decreased levels of glycogen, whose production requires UDPGP activity. These phenotypes suggest that UgpB constitutes the major UDPGP activity produced during development. Sequence analysis of the two UDPGP genes shows that UgpB has higher homology to other eukaryotic UDPGPs than does UDPGP1. This includes the presence of 5 conserved lysine residues. Udpgp1 only has 1 of these lysines.

Molecular cloning and characterization of a cDNA encoding poplar UDP-glucose dehydrogenase, a key gene of hemicellulose/pectin formation

Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.

Sucrose and light regulation of a cold-inducible UDP-glucose pyrophosphorylase gene via a hexokinase-independent and abscisic acid-insensitive pathway in Arabidopsis

UDP-glucose pyrophosphorylase (UGPase) is a key enzyme producing UDP-glucose, which is involved in an array of metabolic pathways concerned with, among other functions, the synthesis of sucrose and cellulose. An Arabidopsis thaliana UGPase-encoding gene, Ugp, was profoundly up-regulated by feeding sucrose to the excised leaves and by an exposure of plants to low temperature (5 degrees C). The UGPase activity and its protein content also increased under conditions of sucrose feeding and exposure to cold. The sucrose effect on Ugp was apparently specific and was mimicked by exposure of dark-adapted leaves to light. Drought and O2 deficiency had some down-regulating effects on expression of Ugp. The sugar-signalling pathway for Ugp regulation was independent of hexokinase, as was found by using transgenic plants with increased and decreased expression of the corresponding gene. Subjecting mutants deficient in abscisic acid (ABA) to cold stress conditions had no effect on Ugp expression profiles. Okadaic acid was a powerful inhibitor of Ugp expression, whereas it up-regulated the gene encoding sucrose synthase (Sus1), indicating distinct transduction pathways in transmitting the sugar signal for the two genes in A. thaliana. We suggest that Ugp gene expression is mediated via a hexokinase-independent and ABA-insensitive pathway that involves an okadaic acid-responsive protein phosphatase. The data point towards Ugp as a possible regulatory entity that is closely involved in the homoeostatic readjustment of plant responses to environmental signals.

Cellular UDP-glucose deficiency caused by a single point mutation in the UDP-glucose pyrophosphorylase gene

We previously isolated a mutant cell that is the only mammalian cell reported to have a persistently low level of UDP-glucose. In this work we obtained a spontaneous revertant whose UDP-glucose level lies between those found in the wild type and the mutant cell. The activity of UDP-glucose pyrophosphorylase (UDPG:PP), the enzyme that catalyzes the formation of UDP-glucose, was in the mutant 4% and in the revertant 56% of the activity found in the wild type cell. Sequence analysis of UDPG: PP cDNAs from the mutant cell showed one missense mutation, which changes amino acid residue 115 from glycine to aspartic acid. The substituted glycine is located within the largest stretch of strictly conserved residues among eukaryotic UDPG:PPs. The analysis of the cDNAs from the revertant cell indicated the presence of an equimolar mixture of the wild type and the mutated mRNAs, suggesting that the mutation has reverted in only one of the alleles. In summary, we demonstrate that the G115D substitution in the Chinese hamster UDPG:PP dramatically impairs its enzymatic activity, thereby causing cellular UDP-glucose deficiency.

Molecular cloning and expression of the large subunit of ADP-glucose pyrophosphorylase from barley (Hordeum vulgare) leaves

A cDNA clone, blpl14, corresponding to the large subunit of ADP-glucose pyrophosphorylase (AGPase), has been isolated from a cDNA library prepared from leaves of barley (Hordeum vulgare L.). An open reading frame encodes a protein of 503 aa, with a calculated molecular weight of 54815. The derived aa sequence contains a putative transit peptide sequence, required for targeting to plastids, and has a highly conserved positioning of critical Lys residues that are believed to be involved in effector binding. The derived aa sequence shows 97% identity with the corresponding protein from wheat, but only 36% identity with AGPase from E. coli. The blpl14 gene is expressed predominantly in leaves and to a lesser degree in seed endosperm, but not roots, of barley.