Chemo-enzymatic synthesis of the carbohydrate antigen N-glycolylneuraminic acid from glucose

N-Glycolylneuraminic acid (Neu5Gc) is a non-human sialic acid, which may play a significant role in human pathologies, such as cancer and vascular disease. Further studies into the role of Neu5Gc in human disease are hindered by limited sources of this carbohydrate. Using a chemo-enzymatic approach, Neu5Gc was accessed in six steps from glucose. The synthesis allows access to gram-scale quantities quickly and economically and produces Neu5Gc in superior quality to commercial sources. Finally, we demonstrate that the synthesized Neu5Gc can be incorporated into the cell glycocalyx of human cells, which do not naturally synthesize this sugar. The synthesis produces Neu5Gc suitable for in vitro or in vivo use.     

Enhancement of disease resistance to Magnaporthe grisea in rice by accumulation of hydroxy linoleic acid

Linoleic acid (18:2) and linolenic acid (18:3) are sources for various oxidized metabolites called oxylipins, some of which inhibit growth of fungal pathogens. In a previous study, we found disease resistance to rice blast fungus Magnaporthe grisea enhanced in 18:2-accumulating transgenic rice (F78Ri) in which the conversion from 18:2 to 18:3 was suppressed. Here, we demonstrate that 18:2-derived hydroperoxides and hydroxides (HPODEs and HODEs, respectively) inhibit growth of M. grisea more strongly than their 18:3-derived counterparts. Furthermore, in F78Ri plants, the endogenous levels of HPODEs and HODEs increased significantly, compared with wild-type plants. These results suggest that the increased accumulation of antifungal oxylipins, such as HPODEs and HODEs, causes the enhancement of disease resistance against M. grisea.     

Microbial production of N-acetylneuraminic acid by genetically engineered Escherichia coli

Previously, we described the production of N-acetylneuraminic acid (NeuAc) from N-acetylglucosamine (GlcNAc) in a system combining recombinant Escherichia coli expressing GlcNAc 2-epimerase (slr1975), E. coli expressing NeuAc synthetase (neuB), and Corynebacterium ammoniagenes. However, this system was unsuitable for large-scale production because of its complexity and low productivity. To overcome these problems, we constructed a recombinant E. coli simultaneously overexpressing slr1975 and neuB. This recombinant E. coli produced 81 mM (25 g/L) NeuAc in 22 h without the addition of C. ammoniagenes cells. For manufacturing on an industrial scale, it is preferable to use unconcentrated culture broth as the source of enzymes, and therefore, a high-density cell culture is required. An acetate-resistant mutant strain of E. coli (HN0074) was selected as the host strain because of its ability to grow to a high cell density. The NeuAc aldolase gene of E. coli HN0074 was disrupted by homologous recombination yielding E. coli N18-14, which cannot degrade NeuAc. After a 22 h reaction with 540 mM (120 g/L) GlcNAc in a 5 L jar fermenter, the culture broth of E. coli N18-14 overexpressing slr1975 and neuB contained 172 mM (53 g/L) NeuAc.     

Development of Full-Length cDNAs from Chinese Cabbage (Brassica rapa Subsp. pekinensis) and Identification of Marker Genes for Defence Response

Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp. pekinensis) started early because of strong interest in this species. Here, we report the development of a library of Chinese cabbage full-length cDNA clones, the RIKEN BRC B. rapa full-length cDNA (BBRAF) resource, to accelerate research on Brassica species. We sequenced 10 000 BBRAF clones and confirmed 5476 independent clones. Most of these cDNAs showed high homology to Arabidopsis genes, but we also obtained more than 200 cDNA clones that lacked any sequence homology to Arabidopsis genes. We also successfully identified several possible candidate marker genes for plant defence responses from our analysis of the expression of the Brassica counterparts of Arabidopsis marker genes in response to salicylic acid and jasmonic acid. We compared gene expression of these markers in several Chinese cabbage cultivars. Our BBRAF cDNA resource will be publicly available from the RIKEN Bioresource Center and will help researchers to transfer Arabidopsis-related knowledge to Brassica crops.     

Application of photoaffinity labeling with [(3)H] all trans- and 9-cis-retinoic acids for characterization of cellular retinoic acid--binding proteins I and II

Cellular retinoic acid-binding proteins (CRABPs) are carrier proteins thought to play a crucial role in the transport and metabolism of all-trans-retinoic acid (atRA) and its derivatives within the cell. This report describes a novel photoaffinity-based binding assay involving competition between potential ligands of CRABP and [(3)H]atRA or [(3)H]-9-cis-RA for binding to the atRA-binding sites of CRABP I and II. Photoaffinity labeling of purified CRABPs with [(3)H]atRA was light- and concentration-dependent, saturable, and protected by several retinoids in a concentration-dependent manner, indicating that binding occurred in the CRABP atRA-binding site. Structure-function relationship studies demonstrated that oxidative changes to the atRA beta-ionone ring did not affect ligand potency. However, derivatives lacking a terminal carboxyl group and some cis isomers did not bind to CRABPs. These studies also identified two novel ligands for CRABPs: 5,6-epoxy-RA and retinoyl-beta-D-glucuronide (RAG). The labeling of both CRABPs with 9-cis-RA occurred with much lower affinity. Experimental evidence excluded nonspecific binding of RAG to CRABPs and UDP-glucuronosyltransferases, the enzymes responsible for RAG synthesis. These results established that RAG is an effective ligand of CRABPs. Therefore, photoaffinity labeling with [(3)H]atRA can be used to identify new ligands for CRABP and retinoid nuclear receptors and also provide information concerning the identity of amino acid(s) localized in the atRA-binding site of these proteins.     

Two triacylated and tetraglucosylated anthocyanins from Ipomoea asarifolia flowers

Two triacylated and tetraglucosylated anthocyanins derived from cyanidin were isolated from the flowers of Ipomoea asarifolia and their structures elucidated using chemical, GC, MS and NMR methods (1H and 13C, TOCSY-1D, DQF-COSY, DIFFNOE and HMBC). These complex pigments were found to consist of cyanidin 3-O-[2-O-(6-O-E-caffeoyl-beta-D-glucopyranosyl)]-[6-O-[4-O-(6-O-E-3,5-dihydroxycinnamoyl-beta-D-glucopyranosyl)-E-caffeoyl]-beta-D-glucopyranosyl]-5-O-beta-D-glucopyranoside and cyanidin 3-O-[2-O-(6-O-E-p-coumaroyl-beta-D-glucopyranosyl)]-[6-O-[4-O-(6-O-E-p-coumaroyl-beta-D-glucopyranosyl)-E-caffeoyl]-beta-D-glucopyranosyl]-5-O-beta-D-glucopyranoside.     

Sialylation using N-glycolylneuraminyl phosphite donors to synthesize Neu5Gc-containing glycans

Efficient sialylations using N-glycolylneuraminic acid (Neu5Gc) phosphite donors having an acetyl or benzyl group on the glycolyl moiety are described in the synthesis of Neu5Gc-containing glycans. Both phosphite donors 1 and 2 were readily coupled with primary and secondary acceptor alcohols in propionitrile at −78 °C to provide the desired glycosides with good α-selectivities.     

Synthesis of the starfish ganglioside LLG-3 tetrasaccharide

The first synthesis of the ganglioside LLG-3 tetrasaccharide, which has attractive biological activities as well as a unique structure, is described. A C8-methoxy decorated sialic acid building block was initially prepared and a glycolic acid moiety was then introduced by sialylation. Amide condensation between the sialyl glycolic acid and an amino group at C5 on the sialyllactoside unit afforded the fully protected LLG-3 tetrasaccharide. Finally, the desired tetrasaccharide part of LLG-3 was obtained after careful global deprotection.     

Determination of the hydroxycinnamate profile of 12 members of the Asteraceae family

The hydroxycinnamates of the leaves of 12 plants of the Astreraceae family, Achillea millefolium, Arnica montana, Artemesia dracunculus, Cichorium intybus, Cnicus benedictus, Cynara scolymus, Echinops humilis, Inula helenium, Lactuca sativa, Petasites hybridus, Solidago virgaurea, and Tanacetum parthenium were investigated qualitatively by LC-MSⁿ. Thirty-nine chlorogenic acids were detected and all characterized to regioisomeric level on the basis of their fragmentation pattern in the tandem MS spectra, most of them for the first time from these sources with two of them previously not reported in nature. Both chlorogenic acids based on trans and cis-cinnamic acid substituents were identified. Assignment to the level of individual regioisomers was possible for seven caffeoylquinic acids (1-7), 11 dicaffeoylquinic acids (17-27), six feruloylquinic acids (9-14), two p-coumaroylquinic acids (15-16), two caffeoyl-feruloylquinic acids (28 and 29), four caffeoyl-p-coumaroylquinic acids (30-33), three dicaffeoyl-succinoylquinic acids (34-36), two dicaffeoyl-methoxyoxaloylquinic acids (37 and 38), and one tricaffeoylquinic acid (39). Furthermore, one caffeoylshikimic acid (40), one caffeoyltartaric acid (41), three dicaffeoyltartaric acids (42-44), and three caffeoyl-feruloyltartaric acids (45-47) were detected and shown to possess characteristic tandem MS spectra and were tentatively assigned on the basis of their retention time and previously developed hierarchical keys.     

Acylated anthocyanins from the violet-blue flowers of Orychophragonus violaceus

Three acylated cyanidin 3-sambubioside-5-glucosides (1-3) were isolated from the violet-blue flowers of Orychophragonus violaceus, and their structures were determined by chemical and spectroscopic methods. Two of those acylated anthocyanins (1 and 3) were cyanidin 3-O-[2-O-(2-O-(4-O-(6-O-(4-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-xylopyranosyl)-6-O-(4-O-(beta-D-glucopyranosyl)-trans-acyl)-beta-D-glucopyranoside]-5-O-(6-O-malonyl-beta-D-glucopyranoside)s, in which the acyl groups were p-coumaric acid for 1, and sinapic acid for 3, respectively. The last anthocyanin 2 was cyanidin 3-O-[2-O-(2-O-(4-O-(6-O-(4-O-(beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-glucopyranosyl)-trans-caffeoyl)-beta-D-xylopyranosyl)-6-O-(4-O-(beta-D-glucopyranosyl)-trans-feruloyl)-beta-D-glucopyranoside]-5-O-beta-D-glucopyranoside. In these flowers, the anthocyanins 2 and 3 were present as dominant pigments, and 1 was obtained in rather small amounts.     

Chemotaxonomic evaluation of Turkish species of Salvia: Fatty acid compositions of seed oils

Fatty acid composition of nine species of Salvia, naturally growing in Turkey was determined: Salvia syriaca, Salvia potentillifolia, Salvia candidissima ssp. occidentalis, Salvia macrochlamys, Salvia poculata, Salvia tomentosa, Salvia recognita, Salvia virgata and Salvia ceratophylla. The main compounds were found to be linoleic acid (18:2; 24.3–69.2%), linolenic acid (18:3; 0.6–40.8%), oleic acid (18:1; 8.3–31.0%), palmitic acid (16:0; 3.8–21.0%) and stearic acid (18:0; 1.8–5.2%). Fatty acid composition of Salvia seed oils could be used as a chemotaxonomical marker.     

Glucuronide triterpene saponins from Bersama engleriana

Five 3-O-glucuronide triterpene saponins (1-5) were isolated from the stem bark of Bersama engleriana Gurke along with two known saponins, polyscias saponin C and aralia saponin 15, and one major C-glycoside xanthone, mangiferin. The structures of the saponins were established mainly by means of spectroscopic methods (one- and two-dimensional NMR spectroscopy as well as FAB-, HRESI-mass spectrometry) as 3-O-[beta-D-glucopyranosyl-(1-->2)-beta-D-glucuronopyranosyl]-28-O-[beta-D-glucopyranosyl]-betulinic acid (1), 3-O-[beta-D-glucopyranosyl-(1-->2)-[beta-D-galactopyranosyl-(1-->3)]-beta-D-glucuronopyranosyl]-oleanolic acid (2), 3-O-[beta-D-glucopyranosyl-(1-->3)-beta-D-glucuronopyranosyl]-28-O-[beta-D-xylopyranosyl-(1-->6)-beta-d-glucopyranosyl]-oleanolic acid (3), 3-O-[beta-D-galactopyranosyl-(1-->3)-beta-D-glucuronopyranosyl]-28-O-[beta-D-glucopyranosyl-(1-->4)-beta-D-glucopyranosyl]-oleanolic acid (4), and 3-O-[beta-d-glucopyranosyl-(1-->3)-beta-D-galactopyranosyl-(1-->3)-beta-D-glucuronopyranosyl]-28-O-[beta-d-xylopyranosyl-(1-->6)-beta-D-glucopyranosyl]-oleanolic acid (5).     

An improved methodology for the quantification of uronic acid units in xylans and other polysaccharides

Uronic acids can be quantified either by a colorimetric determination after treatment with concentrated sulfuric acid and carbazole or by gas chromatography after methanolysis and subsequent acetylation. Both methods suffer from incomplete hydrolysis, an unavoidable degradation of the products to be analysed, and an inability to separate and quantify different types of uronic acids. In the present work, the fundamental chemistry involved in the two methods has been evaluated, and some modifications to increase their accuracy are suggested. By combining the two methods, a complete quantification of all individual types of uronic acids present in a sample can be achieved.     

Effects of chlorogenic and caffeic acids on IAA oxidase preparations from sweet potato roots

IAA oxidase preparations from sweet potato (Ipomoea batatas) roots oxidised IAA in the absence of added phenolics. Activity was optimal around pH 6·8 and a minor pH optimum occurred around pH 4·3. Both chlorogenic and caffeic acids inhibited IAA oxidase activity at high concentrations (0·6–5·7 nmol/ml) but stimulated enzyme activity at low concentrations (0·10-0·55 nmol/ml); these effects were dependent on IAA and enzyme concentration and on pH. The activities of both substances are compared with those of other phenolics known to stimulate and inhibit plant IAA oxidases.     

Biotransformation of betulinic and betulonic acids by fungi

Betulinic acid (1), a triterpenoid found in many plant species, has attracted attention due to its important pharmacological properties, such as anti-cancer and anti-HIV activities. The closely related, betulonic acid (2) also has similar properties. In order to obtain derivatives potentially useful for detailed pharmacological studies, both compounds were submitted to incubations with selected microorganisms. In this work, both were individually metabolized by the fungi Arthrobotrys, Chaetophoma and Dematium, isolated from the bark of Platanus orientalis as well as with Colletotrichum, obtained from corn leaves; such fungal transformations are quite rare in the scientific literature. Biotransformations with Arthrobotrys converted betulonic acid (2) into 3-oxo-7beta-hydroxylup-20(29)-en-28-oic acid (3), 3-oxo-7beta,15alpha-dihydroxylup-20(29)-en-28-oic acid (4) and 3-oxo-7beta,30-dihydroxylup-20(29)-en-28-oic acid (5); Colletotrichum converted betulinic acid (1) into 3-oxo-15alpha-hydroxylup-20(29)-en-28-oic (6) acid whereas betulonic acid (2) was converted into the same product and 3-oxo-7beta,15alpha-dihydroxylup-20(29)-en-28-oic acid (4); Chaetophoma converted betulonic acid (2) into 3-oxo-25-hydroxylup-20(29)-en-28-oic acid (7) and both Chaetophoma and Dematium converted betulinic acid (1) into betulonic acid (2). Those fungi, therefore, are useful for mild, selective oxidations of lupane substrates at positions C-3, C-7, C-15, C-25 and C-30.     

Cloning and characterization of an aromatic amino acid and leucine permease of Penicillium chrysogenum

The gene encoding the amino acid permease ArlP (Aromatic and leucine Permease) was isolated from the filamentous fungus Penicillium chrysogenum after PCR using degenerated oligonucleotides based on conserved regions of fungal amino acid permeases. The cDNA clone was used for expression of the permease in Saccharomyces cerevisiae M4054, which is defective in the general amino acid permease Gap1. Upon overexpression, an increase in the uptake of l-tyrosine, l-phenylalanine, l-tryptophan and l-leucine was observed. Further competition experiments indicate that ArlP recognizes neutral and aromatic amino acids with an unbranched β-carbon atom.     

The molecular basis of aminoacylase 1 deficiency

Aminoacylase 1 is a zinc-binding enzyme which hydrolyzes N-acetyl amino acids into the free amino acid and acetic acid. Deficiency of aminoacylase 1 due to mutations in the aminoacylase 1 (ACY1) gene follows an autosomal-recessive trait of inheritance and is characterized by accumulation of N-acetyl amino acids in the urine. In affected individuals neurological findings such as febrile seizures, delay of psychomotor development and moderate mental retardation have been reported. Except for one missense mutation which has been studied in Escherichia coli, mutations underlying aminoacylase 1 deficiency have not been characterized so far. This has prompted us to approach expression studies of all mutations known to occur in aminoacylase 1 deficient individuals in a human cell line (HEK293), thus providing the authentic human machinery for posttranslational modifications. Mutations were inserted using site directed mutagenesis and aminoacylase 1 enzyme activity was assessed in cells overexpressing aminoacylase 1, using mainly the natural high affinity substrate N-acetyl methionine. Overexpression of the wild type enzyme in HEK293 cells resulted in an approximately 50-fold increase of the aminoacylase 1 activity of homogenized cells. Most mutations resulted in a nearly complete loss of enzyme function. Notably, the two newly discovered mutations p.Arg378Trp, p.Arg378Gln and the mutation p.Arg393His yielded considerable residual activity of the enzyme, which is tentatively explained by their intramolecular localization and molecular characteristics. In contrast to aminoacylase 1 variants which showed no detectable aminoacylase 1 activity, aminoacylase 1 proteins with the mutations p.Arg378Trp, p.Arg378Gln and p.Arg393His were also detected in Western blot analysis. Investigations of the molecular bases of additional cases of aminoacylase 1 deficiency contribute to a better understanding of this inborn error of metabolism whose clinical significance and long-term consequences remain to be elucidated.     

Advances in citric acid fermentation by Aspergillus niger: biochemical aspects, membrane transport and modeling

Citric acid is regarded as a metabolite of energy metabolism, of which the concentration will rise to appreciable amounts only under conditions of substantive metabolic imbalances. Citric acid fermentation conditions were established during the 1930s and 1940s, when the effects of various medium components were evaluated. The biochemical mechanism by which Aspergillus niger accumulates citric acid has continued to attract interest even though its commercial production by fermentation has been established for decades. Although extensive basic biochemical research has been carried out with A. niger, the understanding of the events relevant for citric acid accumulation is not completely understood. This review is focused on citric acid fermentation by A. niger. Emphasis is given to aspects of fermentation biochemistry, membrane transport in A. niger and modeling of the production process.     

Draft genome sequence of Gluconobacter thailandicus NBRC 3257

Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is a strict aerobic rod-shaped Gram-negative bacterium. Here, we report the features of this organism, together with the draft genome sequence and annotation. The draft genome sequence is composed of 107 contigs for 3,446,046 bp with 56.17% G+C content and contains 3,360 protein-coding genes and 54 RNA genes.