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Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.

The integration of metabolomics and transcriptomics can provide precise information on gene-to-metabolite networks for identifying the function of unknown genes unless there has been a post-transcriptional modification. Here, we report a comprehensive analysis of the metabolome and transcriptome of Arabidopsis thaliana over-expressing the PAP1 gene encoding an MYB transcription factor, for the identification of novel gene functions involved in flavonoid biosynthesis. For metabolome analysis, we performed flavonoid-targeted analysis by high-performance liquid chromatography-mass spectrometry and non-targeted analysis by Fourier-transform ion-cyclotron mass spectrometry with an ultrahigh-resolution capacity. This combined analysis revealed the specific accumulation of cyanidin and quercetin derivatives, and identified eight novel anthocyanins from an array of putative 1800 metabolites in PAP1 over-expressing plants. The transcriptome analysis of 22,810 genes on a DNA microarray revealed the induction of 38 genes by ectopic PAP1 over-expression. In addition to well-known genes involved in anthocyanin production, several genes with unidentified functions or annotated with putative functions, encoding putative glycosyltransferase, acyltransferase, glutathione S-transferase, sugar transporters and transcription factors, were induced by PAP1. Two putative glycosyltransferase genes (At5g17050 and At4g14090) induced by PAP1 expression were confirmed to encode flavonoid 3-O-glucosyltransferase and anthocyanin 5-O-glucosyltransferase, respectively, from the enzymatic activity of their recombinant proteins in vitro and results of the analysis of anthocyanins in the respective T-DNA-inserted mutants. The functional genomics approach through the integration of metabolomics and transcriptomics presented here provides an innovative means of identifying novel gene functions involved in plant metabolism.

Arabidopsis↗

Developmental regulation of glycosyltransferases involved in biosynthesis of asparagine-linked glycoproteins in mouse mammary gland.

Three glycosyltransferases, namely N-acetylglucosaminyl-1-phosphotransferase, mannosyltransferase and glucosyltransferase, involved in the biosynthesis of asparagine-linked glycoproteins in the mouse mammary gland, were identified by characterization of the products formed by these enzymes. The tissue capacities of the glycosyltransferases, measured as pmol product formed g tissue-1 min-1, increase during developmental cycle of the gland until, at late lactational stage, they reach more than 34, 14 and 60 times, respectively, the basal level found in the tissue of virgin animals. Among the three enzymes at late lactational stage the specific activities of glucosyltransferase and N-acetylglucosaminyl-1-phosphotransferase increase 7-fold and 4-fold respectively, whereas mannosyltransferase shows a mere 1.4-fold increase during tissue development. All of the enzymes, both in terms of tissue capacity and specific activity, return to the basal levels of the virgin gland one month after the end of lactation. The activities of the three enzymes in the lactating gland decrease precipitously following treatment of mice with bromocriptine, a drug that interferes with the release of prolactin from the pituitary gland and thereby inhibits milk synthesis and secretion. These results indicate that the three glycosyltransferases are developmentally regulated during the growth and differentiation of the mouse mammary gland.

Animals↗

A method for the isolation of RNA from Streptococcus salivarius and its application to the transcriptional analysis of the gtfJK locus.

The glucosyltransferases from oral streptococci cleave sucrose and polymerize the glucose moieties. In Streptococcus salivarius ATCC 25975, two glucosyltransferase-encoding genes, gtfJ and gtfK, are closely linked and transcribed in the same direction. A procedure for the isolation of intact RNA from this organism was devised. The procedure incorporated a high-temperature mutanolysin treatment and selective precipitation by LiCl. The RNA was subject to Northern hybridization and RNase protection assays and it was concluded that the two genes are transcribed separately. A potential factor-independent transcription terminator was located in the intergenic region.

Base Sequence↗

Streptococcus mutans glucan-binding protein-A affects Streptococcus gordonii biofilm architecture.

The glucan-binding protein-A (GbpA) of Streptococcus mutans has been shown to contribute to the architecture of glucan-dependent biofilms formed by this species and influence virulence in a rat model. As S. mutans synthesizes multiple glucosyltransferases and nonglucosyltransferase glucan-binding proteins (GBPs), it is possible that there is functional redundancy that overshadows the full extent of GbpA contributions to S. mutans biology. Glucan-associated properties such as adhesion, aggregation, and biofilm formation were examined independently of other S. mutans GBPs by cloning the gbpA gene into a heterologous host, Streptococcus gordonii, and derivatives with altered or diminished glucosyltransferase activity. The presence of GbpA did not alter dextran-dependent aggregation nor the initial sucrose-dependent adhesion of S. gordonii. However, expression of GbpA altered the biofilm formed by wild-type S. gordonii as well as the biofilm formed by strain CH107 that produced primarily alpha-1,6-linked glucan. Expression of gbpA did not alter the biofilm formed by strain DS512, which produced significantly lower quantities of parental glucan. These data are consistent with a role for GbpA in facilitating the development of biofilms that harbor taller microcolonies via binding to alpha-1,6-linkages within glucan. The magnitude of the GbpA effect appears to be dependent on the quantity and linkage of available glucan.

Bacterial Adhesion↗

Enzymatic Mechanisms Involved in Phenanthrene Degradation by the White Rot Fungus Pleurotus ostreatus.

The enzymatic mechanisms involved in the degradation of phenanthrene by the white rot fungus Pleurotus ostreatus were examined. Phase I metabolism (cytochrome P-450 monooxygenase and epoxide hydrolase) and phase II conjugation (glutathione S-transferase, aryl sulfotransferase, UDP-glucuronosyltransferase, and UDP-glucosyltransferase) enzyme activities were determined for mycelial extracts of P. ostreatus. Cytochrome P-450 was detected in both cytosolic and microsomal fractions at 0.16 and 0.38 nmol min(sup-1) mg of protein(sup1), respectively. Both fractions oxidized [9,10-(sup14)C]phenanthrene to phenanthrene trans-9,10-dihydrodiol. The cytochrome P-450 inhibitors 1-aminobenzotriazole (0.1 mM), SKF-525A (proadifen, 0.1 mM), and carbon monoxide inhibited the cytosolic and microsomal P-450s differently. Cytosolic and microsomal epoxide hydrolase activities, with phenanthrene 9,10-oxide as the substrate, were similar, with specific activities of 0.50 and 0.41 nmol min(sup-1) mg of protein(sup-1), respectively. The epoxide hydrolase inhibitor cyclohexene oxide (5 mM) significantly inhibited the formation of phenanthrene trans-9,10-dihydrodiol in both fractions. The phase II enzyme 1-chloro-2,4-dinitrobenzene glutathione S-transferase was detected in the cytosolic fraction (4.16 nmol min(sup-1) mg of protein(sup-1)), whereas aryl adenosine-3(prm1)-phosphate-5(prm1)-phosphosulfate sulfotransferase (aryl PAPS sulfotransferase) UDP-glucuronosyltransferase, and UDP-glucosyltransferase had microsomal activities of 2.14, 4.25, and 4.21 nmol min(sup-1) mg of protein(sup-1), respectively, with low activity in the cytosolic fraction. However, when P. ostreatus culture broth incubated with phenanthrene was screened for phase II metabolites, no sulfate, glutathione, glucoside, or glucuronide conjugates of phenanthrene metabolites were detected. These experiments indicate the involvement of cytochrome P-450 monooxygenase and epoxide hydrolase in the initial phase I oxidation of phenanthrene to form phenanthrene trans-9,10-dihydrodiol. Laccase and manganese-independent peroxidase were not involved in the initial oxidation of phenanthrene. Although P. ostreatus had phase II xenobiotic metabolizing enzymes, conjugation reactions were not important for the elimination of hydroxylated phenanthrene.

Journal Article↗

Binding of lectins to Streptococcus mutans cells and type-specific polysaccharides, and effect on adherence.

The lectin concanavalin A (Con A) agglutinated the cells of 13 of 15 strains of the seven serotypes of Streptococcus mutans in an 18-h incubation period. Strains of types a, d, f, and g agglutinated within 2 h. Strains of a, d, and f were also agglutinated in 2 h by the castor bean lectin RCA. S. sanguis, S. salivarius, S. bovis, Actinomyces viscosus, A. naeslundii, and Lactobacillus plantarum were agglutinated within 2 h. The S. mutans type f polysaccharide was precipitated by Con A. The a, b, c, d, and e polysaccharides were not precipitated. Glucan from d and e strains of S. mutans and dextran T2000 were also precipitated by Con A. D-glucose inhibited the agglutination of type f cells by Con A and the agglutination of type d cells by D-galactose. The quantity of [acetyl-3H]Con A bound was not proportional to the degree of agglutination. Cells grown in sucrose medium bound more Con A than those grown in glucose medium. After treatment with dextranase, the sucrose-grown cells bound two- to fourfold more Con A. The binding of Con A to the type-specific polysaccharide or to teichoic acid could not be determined by the use of specific antibody due to the binding of Con A to the antibody globulin on the cell surface. Con A bound to S. mutans cells did not inhibit the activity of cell-bound glucosyltransferase, glucan synthesis, and in vitro adherence. Bound Con A also did not inhibit the ability of heat-treated cells to bind glucosyltransferase, synthesize glucan, and produce in vitro adherence.

Agglutination↗

Protective secretory immunoglobulin A antibodies in humans following oral immunization with Streptococcus mutans.

Ingestion of a vaccine containing killed Streptococcus mutans, originally isolated from each volunteer, daily for 10 consecutive days induced increased levels of specific secretory immunoglobulin A (sIgA) antibodies to S. mutans cells and two cell surface proteins, glucosyltransferase and surface antigen I/II, in parotid saliva and tears of four healthy males and in parotid saliva, tears, colostrum, and milk of a pregnant woman. In addition, these antibodies inhibited glucosyltransferase activity. Both IgA1 and IgA2 antibodies were induced. The levels of IgA antibodies in all secretions remained significantly above preimmunization levels for more than 50 days after oral administration of antigen. A second series of immunizations for 7 consecutive days resulted in even higher levels of sIgA antibodies, which peaked earlier and persisted longer than those observed after the primary immunizations. No increase in levels of antibodies in serum were detected in any subject. Antibodies reactive with human heart and kidney antigens could not be detected in saliva, tears, colostrum, milk, or serum samples collected at any time during the immunization regimen. The numbers of viable S. mutans organisms in dental plaque and whole saliva decreased after each series of immunizations, which correlated with increased levels of IgA antibodies in saliva, suggesting that IgA antibodies in saliva were responsible for the reduced adherence of this bacterium. These results indicate that ingested S. mutans antigen induces secretion of specific IgA1 and IgA2 antibodies in saliva, tears, colostrum, and milk, providing further evidence for the existence of a common mucosal immune system.

Administration, Oral↗

Characterization by affinity electrophoresis of an alpha-1,6-glucan-binding protein from Streptococcus sobrinus.

Glucan-binding protein 1 (GBP1), the most abundant glucan-binding protein isolated from culture supernatants of Streptococcus sobrinus 6715-49, has been purified by affinity chromatography on Sephadex G-50 followed by gel permeation chromatography with Bio-Gel P-10. The specificity and affinity of GBP1 for glucans were assessed by affinity electrophoresis. GBP1 did not detectably bind to glucans lacking linear arrays of alpha-1,6 linkages. The association constant for the linear alpha-1,6-glucan Dextran T2000 was 3 x 10(7) M-1. Providing small isomaltosaccharide ligands to compete with this dextran indicated that the binding site maximally accommodated isomaltosaccharides with a degree of polymerization of 8. When glucans produced by purified S. sobrinus glucosyltransferases were tested, GBP1 displayed the highest affinity for the glucan from the soluble-product, primer-independent glucosyltransferase.

Bacterial Proteins↗

Biosynthetic elongation of isolated teichuronic acid polymers via glucosyl- and N-acetylmannosaminuronosyltransferases from solubilized cytoplasmic membrane fragments of Micrococcus luteus.

Cytoplasmic membrane fragments of Micrococcus luteus catalyze in vitro biosynthesis of teichuronic acid from uridine diphosphate D-glucose (UDP-glucose), uridine diphosphate N-acetyl-D-mannosaminuronic acid (UDP-ManNAcA), and uridine diphosphate N-acetyl-D-glucosamine. Membrane fragments solubilized with Thesit (dodecyl alcohol polyoxyethylene ether) can utilize UDP-glucose and UDP-ManNAcA to effect elongation of teichuronic acid isolated from native cell walls. When UDP-glucose is the only substrate supplied, the detergent-solubilized glucosyltransferase incorporates a single glucosyl residue onto each teichuronic acid acceptor. When both UDP-glucose and UDP-ManNAcA are supplied, the glucosyltransferase and the N-acetylmannosaminuronosyltransferase act cooperatively to elongate the teichuronic acid acceptor by multiple additions of the disaccharide repeat unit. As shown by polyacrylamide gel electrophoresis, low-molecular-weight fractions of teichuronic acid are converted to higher-molecular-weight polymers by the addition of as many as 17 disaccharide repeat units.

Cell Fractionation↗

Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae.

Beta1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, beta1,3-glucan, and chitin. It has been postulated that the synthesis of beta1,6-glucan begins in the endoplasmic reticulum with the formation of protein-bound primer structures and that these primer structures are extended in the Golgi complex by two putative glucosyltransferases that are functionally redundant, Kre6 and Skn1. This is followed by maturation steps at the cell surface and by coupling to other cell wall macromolecules. We have reinvestigated the role of Kre6 and Skn1 in the biogenesis of beta1,6-glucan. Using hydrophobic cluster analysis, we found that Kre6 and Skn1 show significant similarities to family 16 glycoside hydrolases but not to nucleotide diphospho-sugar glycosyltransferases, indicating that they are glucosyl hydrolases or transglucosylases instead of genuine glucosyltransferases. Next, using immunogold labeling, we tried to visualize intracellular beta1,6-glucan in cryofixed sec1-1 cells which had accumulated secretory vesicles at the restrictive temperature. No intracellular labeling was observed, but the cell surface was heavily labeled. Consistent with this, we could detect substantial amounts of beta1,6-glucan in isolated plasma membrane-derived microsomes but not in post-Golgi secretory vesicles. Taken together, our data indicate that the synthesis of beta1, 6-glucan takes place largely at the cell surface. An alternative function for Kre6 and Skn1 is discussed.

Amino Acid Sequence↗

Enzymes of collagen synthesis and type III procollagen aminopropeptide in the evaluation of D-penicillamine and medroxyprogesterone treatments of primary biliary cirrhosis.

Changes in serum immunoreactive prolyl hydroxylase protein (IRPH), galactosylhydroxylysyl glucosyltransferase activity (GGT) and the aminoterminal propeptide of type III procollagen [Pro(III)-N-P] were studied in 21 patients with primary biliary cirrhosis during a follow-up period of up to three years. The patients received either D-penicillamine (600 mg/day), medroxyprogesterone acetate (5 mg/day), or a placebo, or no treatment after the D-penicillamine or medroxyprogesterone medication, each period lasting from nine to 15 months. The individual serum IRPH, GGT, and Pro(III)-N-P concentrations exceeded the upper normal limit in most patients. No significant changes were found in any of these three serum markers during any of the five different periods, nor was there any evidence for a decrease in the raised prolyl 4-hydroxylase activity in the hepatic biopsy specimens in response to any of the treatments. Galactosylhydroxylysyl glucosyltransferase activity decreased significantly in these specimens during medroxyprogesterone therapy, but the interpretation of this, the only positive change, remains unclear. The data suggest that D-penicillamine or medroxyprogesterone therapy may have no favourable effect on the increased hepatic collagen formation involved in primary biliary cirrhosis.

Adult↗

The effects of anabolic steroids on collagen synthesis in rat skeletal muscle and tendon. A preliminary report.

We measured the activities of prolyl 4-hydroxylase and galactosylhydroxylysyl glucosyltransferase (both enzymes of collagen biosynthesis) and the concentration of hydroxyproline in male rat soleus muscle and Achilles tendon during anabolic steroid treatment at 1 and 3 weeks. The rats were treated using a therapeutic dosage or a dosage that was five times the therapeutic level. After 1 week, the activity of prolyl 4-hydroxylase decreased significantly (P less than 0.01) in both treated groups in the soleus muscle, but the activity of galactosylhydroxylsyl glucosyltransferase decreased significantly (P less than 0.05) only in the group given a therapeutic dose. After 3 weeks, the activities were at the control level. In the Achilles tendon, the activity of prolyl 4-hydroxylase and the hydroxyproline concentration decreased significantly (P less than 0.05) in the group given high doses at 3 weeks. Anabolic steroid treatment seems to have at least a transitory effect on collagen biosynthesis in male rat muscle and tendon; in tendon this effect is seen only with high doses.

Achilles Tendon↗

Modification of enzyme activities concerned with collagen metabolism in the heart of spontaneously hypertensive and aortic-constricted rats.

The activities of three enzymes concerned with collagen metabolism 4-prolyl hydroxylase, UDP-glucose: collagen glucosyltransferase and glucosyl-galactosyl-hydroxylysine glucohydrolase and 4-hydroxyproline content have been studied in the cardiac ventricles of spontaneously hypertensive rats (SHR) during prehypertensive, hypertensive and sustained hypertensive stages (respectively 4.5, 12 and 19 weeks of age). They were compared with values observed in age-matched normotensive Wistar Kyoto rats (WKY). The same studies have been performed in parallel on aortic-constricted rats (ACR) 8 days after suprarenal constriction of the abdominal aorta. The most striking finding was a significant increase in cardiac prolyl hydroxylase specific activity in the ACR but not in the SHR. No variation in 4-hydroxyproline concentration was found in the hearts of ACR. In contrast, a decrease in 4-hydroxyproline concentration was found in the hearts of SHR at 19 weeks. Cardiac glucosyltransferase specific activity was significantly elevated only in the SHR at 12 weeks. No variation in glucohydrolase specific activity was detected in the hearts of either SHR or ACR. The cardiac enzyme activities all decreased with age. These data show that the alterations in cardiac collagen metabolism are different in SHR and ACR. The patterns of the alterations found in the heart mirror those observed in the aorta in both models under the same experimental conditions.

Age Factors↗

Serological properties of cellular and extracellular glycerol teichoic acid antigens of Streptococcus mutans.

Cell-free supernatant of Streptococcus mutans cultures was concentrated by 50% ammonium sulphate precipitation to 1/50 of the original culture volume. Most extracellular glucosyltransferase activity was detected in the supernatant. Furthermore, the supernatant reacted with serotype specific antiserum, showing immunological identities with the serotype specific polysaccharide antigen obtained from whole cells by hot saline or NaOH extraction in double diffusion tests. Immunoelectrophoretic analysis also revealed that the supernatant antigen possessed significant quantities of lipid-bound and free glycerol teichoic acid antigens. The lipoteichoic acid (LTA) was obtained from whole cells by phenol-water extraction. The lipid-teichoic acid linkage was easily split by mild acid or alkaline hydrolysis. The supernatant and phenol antigens spontaneously sensitized sheep red blood cells. These antigens were adsorbed to hydroxyapatite powder. The extracellular LTA and glucosyltransferase were found to be closely associated and difficult to separate chromatographically. In vivo significance of these properties of LTA and GTase is discussed in terms of the ecology of S. mutans and other oral streptococci.

Antigens, Bacterial↗

[Anti-caries vaccines].

Even though the reduction of caries-incidence in developed countries, its increasing has been observed nowadays. The use of a vaccine was object of many researches, going under modifications and evaluations during years. Wallace and McCollum showed the chance to induce experimental cavities, while Clarke and McIntosh were the first underlining the roll of S. mutans and Lactobacilli as efforts of the pathology. Williams was the first working with humans and Zinner and Fitzgerald continued. So since Bowen the research tried to build a vaccine made of single bacterial molecules with antigenic power. We can count about a large number of targets, like: the Ag I/II, the glucosyltransferase enzyme (GTF), the glucan-binding-protein (GBP), the destranase, the fruttosyltransferase and the glucans. Among the substances used to obtain a vaccine cacao revealed its capacity against bacteria able to develop cavities, thanks to its cariostatic and anti-glucosyltransferase activity due to polyphenols, that we can find in green tea too. It's also interesting a technique that gives passive antibodies like cow's milk, but in particular the one of a monoclonal antibody made with biotechnology of plants: the Guy's 13. It does not show substantial differences in comparison with the human Ig and it's able to prevent the installation of micro-organism and to reduce cavities in adult patients already infected. For the setting-up of a vaccine, however, only studies, comparison and research will be able to show precise instruments of defence.

Antibodies, Monoclonal↗

Characterization of a mutant of serotype g Streptococcus mutans strain 6715 lacking dextran-induced agglutination.

A spontaneous mutant of Streptococcus mutans 6715 (serotype g) defective in dextran-induced agglutination ability was isolated. The wild type strain and its mutant were termed as 6715-DP and 6715-DN, respectively. Both strains possessed serotype g antigen, and exerted similar sugar fermentation patterns. Strain 6715-DP was rapidly and strongly agglutinated upon addition of high molecular weight dextran, whereas the mutant strain 6715-DN was not. [14C]Dextran prepared from Leuconostoc mesenteroides dextransucrase and [14C]sucrose bound to fresh or lyophilized 6715-DP cells, but not to the mutant 6715-DN cells. However, both strains adhered to a glass surface in the presence of sucrose. Furthermore, heat-treated (100 degrees C, 10 min) cells of both strains bound cell-free glucosyltransferase, although dextran agglutination ability of strain 6715-DP was destroyed by this treatment, indicating that receptors for dextran and glucosyltransferase were different entities. Furthermore, serotype c, e, and f strains S. mutans did not agglutinate upon addition of dextran, nor did they bind [14C]dextran. However, all these strains and both 6715-DP and 6715-DN strains induced marked dental caries in SPF rats. It is concluded that dextran-induced agglutination ability is not a necessary condition for S. mutans to induce dental caries.

Agglutination↗

CARBOHYDRATE METABOLISM IN LIVER FROM FOETAL AND NEONATAL SHEEP.

1. During development of the sheep, the activities of UDP-glucose-alpha-glucan glucosyltransferase and UDP-glucose pyrophosphorylase and the glycogen content are highest in the liver of lambs 2 weeks old and considerably lower in liver from adult sheep. 2. The activity of hexokinase and the rate of incorporation of [(14)C]-glucose into glycogen are much lower in liver from postnatal sheep than in rat liver. 3. The activities of hexose diphosphatase and glucose 6-phosphatase and the rates of incorporation of [(14)C]pyruvate and [(14)C]propionate into glycogen increase from low levels in the liver of foetal sheep to maxima a few weeks after birth. The activities in the liver of adult sheep are slightly lower. 4. The incorporation rate of [(14)C]pyruvate into glucose has been measured in liver slices from rats, sheep and chick embryos at several ages of these animals. This pathway is active in liver from foetal sheep, embryonic chicks and postnatal rats or sheep, but is absent from the liver from foetal rats. 5. Fructose metabolism, as measured by the rates of incorporation of [(14)C]fructose into glycogen and glucose in liver slices and by assays of liver ketohexokinase, is barely detectable in the liver of foetal sheep and appears soon after birth. 6. During development of the sheep, the incorporation rate of [(14)C]galactose into glycogen in liver slices is highest in foetal sheep and decreases with increasing age of the animal. 7. These findings are discussed with reference to the changing pattern of carbohydrate metabolism during neonatal development of liver in the sheep.

Animals↗

SOME BIOCHEMICAL CHANGES IN THE GUINEA PIG DURING INFECTION WITH COXIELLA BURNETII.

Paretsky, D. (University of Kansas, Lawrence), C. M. Downs, and C. W. Salmon. Some biochemical changes in the guinea pig during infection with Coxiella burnetii. J. Bacteriol. 88:137-142. 1964.-Guinea pigs infected with Coxiella burnetii, the rickettsial agent of Q fever, were studied for 11 days postinfection. Maximal changes in liver lipids, liver phosphorylase, and uridine diphosphate glucose (UDPG)-glycogen glucosyl-transferase activities occurred 3 to 4 days post-infection. In this period, total liver lipids increased from 1.26 to 5.46 mg/mg of N, with the largest increment in the glyceride fraction. Liver glycogen virtually disappeared by the second day, with no chemically detectable restoration until the eleventh day. A pattern of altered phosphorylase and UDPG-glycogen transglucosylase activities was observed, with maximal phosphorylase and minimal glucosyltransferase activities at the third and fourth days. Histochemical observations confirmed chemical analyses for lipids and glycogen.

Animals↗