Extracellular metabolomics: a metabolic footprinting approach to assess fiber degradation in complex media

This work reports the implementation and optimization of a method for high-throughput analysis of metabolites produced by the breakdown of natural polysaccharides by microorganisms. Our simple protocol enables simultaneous separation and quantification of more than 40 different sugars and sugar derivatives, in addition to several organic acids in complex media, using 50-mul samples and a standard gas chromatography-mass spectrometry platform that was fully optimized for this purpose. As an implementation proof-of-concept, we assayed extracellular metabolite levels of three bacterial strains cultivated on complex medium rich in polysaccharides and under identical growth conditions. We demonstrate that the metabolic footprinting profile data distinguish among sample types such as typical metabolomics data. Moreover, we demonstrate that the differential metabolite-level data provide insight on specific fibrolytic activity of the different microbial strains and lay the groundwork for integrated proteome-metabolome studies of fiber-degrading microorganisms.     

2,3-Diamino-2,3-dideoxyuronic and 5,7-diamino-3,5,7,9-tetradeoxynonulosonic acids: new components of bacterial polysaccharides

Abstract The discovery of the derivatives of 2,3-diamino-2,3-dideoxyuronic acids and 5,7-diamino-3,5,7,9-tetradeoxynonulosonic acids in bacterial polysaccharides enlarges the list of natural monosaccharides. Many of the new sugars carry unusual N -substituents, such as formyl, ( R )-3-hydroxybutyryl, and acetimidoyl groups. They are most characteristics of O-chains of Pseudomonas aeruginosa lipopolysaccharides, composed almost exclusively of amino sugars or amphoteric amino sugars; the latter seem to play an important role as serological determinants. The identification of these sugars and the structural determination of the O-specific polysaccharides provide the chemical basis for the classification of P. aeruginosa strains. Some of the new monosaccharides enter also the polysaccharides from some other bacteria.     

Structure of the core part of the lipopolysaccharides from Proteus penneri strains 7, 8, 14, 15, and 21

The core-lipid A region of the lipopolysaccharides from Proteus penneri strains 7, 8, 14, 15, and 21 was studied using NMR spectroscopy, ESI MS, and chemical analysis after alkaline deacylation, deamination, and mild-acid hydrolysis of the lipopolysaccharides. The following general structure of the major core oligosaccharides is proposed: [abstract: see text] where all sugars are in the pyranose form and have the D configuration unless otherwise stated, Hep and DDHep=L-glycero- and D-glycero-D-manno-heptose, respectively, K=H, and Q=H in strain 8 or alpha-Glc in strains 7, 14, 15, and 21. In addition, several minor structural variants are present, including those lacking Ara4N in strains 7 and 15 and having the alpha-GlcN residue N-acylated to a various degree with glycine in strains 7, 8, 14, and 21. In strain 14, there are also core oligosaccharides with K=amide of beta-D-GalpA with putrescine, spermidine, or 4-azaheptane-1,7-diamine; remarkably, these structural variants lack either the PEtN group or the alpha-Hep-(1-->2)-alpha-DDHep disaccharide fragment at alpha-D-GalpA. While structural features of the inner core part are shared by Proteus strains studied earlier, the outermost Q-(1-->4)-alpha-GalNAc-(1-->2)-alpha-DDHep-(1-->6)-alpha-GlcN oligosaccharide unit has not been hitherto reported.     

Structure of the O-polysaccharide of Proteus mirabilis O38 containing 2-acetamidoethyl phosphate and N-linked D-aspartic acid

The O-antigen of Proteus mirabilis O38 was found to be unique among bacterial polysaccharides and to have the following structure: [carbohydrate structure in text] where D-Qui4N(Ac-D-Asp) is 4-(N-acetyl-D-aspart-4-ylamino)-4,6-dideoxy-D-glucose and AcEtnP is 2-acetamidoethyl phosphate. Neither of these entities have been hitherto found in natural polysaccharides. Structural studies were performed using 1D and 2D NMR spectroscopy, including experiments run in an H2O/D2O mixture to reveal correlations for NH protons. In addition, dephosphorylation, carboxyl reduction and selective cleavages were applied. Solvolysis of the polysaccharide with anhydrous HF gave an alpha-D-GlcNAc-(1-->3)-D-Qui4N(Ac-D-Asp) disaccharide. Solvolysis with trifluoromethanesulfonic (triflic) acid afforded D-GlcNAc6(AcEtnP), thus showing the suitability of this reagent for the preparation of phosphorylated sugar derivatives.     

Determination of saccharide content in pneumococcal polysaccharides and conjugate vaccines by GC-MSD

A simple and sensitive gas chromatographic method was designed for quantitative analysis of Streptococcus pneumoniae capsular polysaccharides, activated polysaccharides, and polysaccharide conjugates. Pneumococcal serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F polysaccharide or conjugate were subjected to methanolysis in 3N hydrochloric acid in methanol followed by re-N-acetylation and trimethylsilylation. Derivatized samples were chromatographed and detected using gas chromatography with mass selective detector. Gas chromatographic results were compared with colorimetric values with agreement of 92 to 123% over the range of all samples tested. Monosaccharides released during methanolysis included hexoses, uronic acids, 6-deoxy-hexoses, amino sugars, and alditols. Quantitative recovery of monosaccharides was achieved for all serotypes by the use of a single methanolysis, derivatization, and chromatography procedure. Response factors generated from authentic monosaccharide standards were used for quantitation of pneumococcal polysaccharides and conjugates with confirmation of peak assignments by retention time and mass spectral analysis. This method allows saccharide quantitation in multivalent pneumococcal vaccine intermediates and final drug products with low-level detection (10 pg) and peak purity.     

Structural investigation of the O-specific polysaccharides of Morganella morganii consisting of two higher sugars

The lipopolysaccharide of the bacterium Morganella morganii (strain KF 1676, RK 4222) yielded two polysaccharides, PS1 and PS2, when subjected to mild acid degradation followed by GPC. The polysaccharides were studied by 1H and 13C NMR spectroscopy, including two-dimensional COSY, TOCSY, NOESY, 1H,(13)C HMQC, and HMBC experiments. Each polysaccharide was found to contain a disaccharide repeating unit consisting of two higher sugars, 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxy-L-glycero-D-galacto-non-2-ulosonic acid (a derivative of 8-epilegionaminic acid, 8eLeg5Am7Ac) and 2-acetamido-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-2,6-dideoxy-D-galactose (shewanellose, She). The two polysaccharides differ only in the ring size of shewanellose and have the following structures:Shewanellose has been previously identified in a phenol-soluble polysaccharide from Shewanella putrefaciens A6, which shows a close structural similarity to PS2.     

Evidence for cross-linking in tomato cutin using HR-MAS NMR spectroscopy

Cutin is a polyester biopolymer component of plant leaf and fruit cuticles, most often associated with waxes and cuticular polysaccharides, and sometimes with another aliphatic biopolymer called cutan. Insolubility of these cuticular biopolymers has made it difficult to apply traditional analytical techniques for structure determination, because most techniques providing molecular level details require solubility. By using the relatively new technique of one and two-dimensional high-resolution magic angle spinning (HR-MAS) NMR spectroscopy, with added information from solid-state 13C NMR spectroscopy, detailed through-bond connectivities and assignments are made for cutin from Lycopersicon esculentum (tomato) fruit. Based on the data obtained, tomato cutin is found to be predominantly an aliphatic polyester with some olefinic and aromatic moieties, consistent with previous studies that employed various degradative approaches. Aside from esters, there are free primary and secondary alcohol groups, as well as free fatty acids. A significant finding is the presence of alpha-branched fatty acids/esters. Mid-chain hydroxyls appear to be generally unesterified, but esters of mid-chain hydroxyls have been identified. The alpha-branched fatty acids/esters and esters of mid-chain hydroxyls could point towards cross-linking.     

Structure of a major glycolipid from Thermus oshimai NTU-063

The structure of a major glycolipid isolated from the thermophilic bacteria Thermus oshimai NTU-063 was elucidated. The sugar and fatty acid compositions were determined by GC-MS and HPLC analysis on their methanolysis and methylation derivatives, respectively. After removal of both O- and N-acyl groups by alkaline treatment, the glycolipid was converted to a fully acetylated tetraglycosyl glycerol derivative, the structure of which was then determined by NMR spectroscopy (TOCSY, HSQC, HMBC). Thus, the complete structure of the major glycolipid from T. oshimai NTU-063 was established as beta-Glcp-(1-->6)-beta-Glcp-(1-->6)-beta-GlcpNAcyl-(1-->2)-alpha-Glcp-(1-->1)-glycerol diester. The N-acyl groups on the 2-amino-2-deoxy-glucopyranose residue are C15:0 and C17:0 fatty acids, whereas the fatty acids of glycerol diester are more heterogeneous including both straight and branched fatty acids from C15:0 to C18:0.     

Biochemical Changes in Root Exudate and Xylem Sap of Tomato Plants Infected with Meloidogyne incognita

Under two monoxenic culture techniques of growing plants (filter paper and silica sand cultures), sugar in root exudate from Meloidogyne incognita-infected tomato increased 133 to 836% over controls. In contrast, amino acids were moderately reduced 52 to 56%. Chromatographic analysis showed that galled root exudate contained three sugars, twelve amino acids, and three organic acids, whereas healthy root exudate contained four sugars, fifteen amino acids, and four organic acids. Polysaccharide was responsible for the large increase of sugars in galled root exudates. The concn and the absolute amount of total sugars in the infected plant xylem sap were greater than in healthy plant xylem sap up to 6 wk after inoculation, whereas amino acids were moderately lower than in controls throughout the test period. Chromatographic analysis showed that xylem sap from both healthy and infected plants at 4 wk after inoculation contained four sugars and five organic acids. We identified 18 and 17 amino acids in the healthy and infected plant xylem sap, respectively. The concn of sugar increased as the nematode inoculum increased at 2, 4 and 6 wk after inoculation. The amino acids in all samples from the infected plant moderately decreased with an increase of nematode inoculum. We suggest that changes in total sugars and amino acids, of infected plant xylem sap and root exudate are a probable mechanism by which tomato plants are predisposed to Fusarium wilt.     

Extracellular polysaccharides of Erwinia futululu,a bacterium associated with a fungal canker disease of Eucalyptus spp

Extracellular polysaccharides (EPSs) produced by an Erwinia spp. associated with a fungal canker disease of Eucalyptus were fractionated into two polysaccharides, one that was identified with that produced by Erwinia stewartii. The other has a similar structure, but with one terminal Glc residue replaced by pyruvic acid to give 4,6-O-[(R)-1-carboxyethylidene)-Galp. Their structures were determined using a combination of chemical and physical techniques including methylation analysis, periodate oxidation, low-pressure gel filtration and anion-exchange chromatographies, high-pH anion-exchange chromatography, mass spectrometry and 1D and 2D 1H NMR spectroscopy. The new polysaccharides, identified as EPS Futululu FF-1 and FF-2, have the following structures:The molecular weights of the polysaccharides range from 1.3-2.1x10(6) and their hydrodynamic properties are those of polydisperse, polyanionic biopolymers with pseudoplastic, non-thixotropic flow characteristics in aqueous solutions.     

Degradation of carbohydrate moieties of arabinogalactan-proteins by glycoside hydrolases from Neurospora crassa

Arabinogalactan-proteins (AGPs) are a family of plant proteoglycans having large carbohydrate moieties attached to core-proteins. The carbohydrate moieties of AGPs commonly have β-(1→3)(1→6)-galactan as the backbone, to which other auxiliary sugars such as l-Ara and GlcA are attached. For the present study, an α-l-arabinofuranosidase belonging to glycoside hydrolase family (GHF) 54, NcAraf1, and an endo-β-(1→6)-galactanase of GHF 5, Nc6GAL, were identified in Neurospora crassa. Recombinant NcAraf1 (rNcAraf1) expressed in Pichia pastoris hydrolyzed radish AGPs as well as arabinan and arabinoxylan, showing relatively broad substrate specificity toward polysaccharides containing α-l-arabinofuranosyl residues. Recombinant Nc6GAL (rNc6GAL) expressed in P. pastoris specifically acted on β-(1→6)-galactosyl residues. Whereas AGP from radish roots was hardly hydrolyzed by rNc6GAL alone, β-(1→6)-galactan side chains were reduced to one or two galactan residues by a combination of rNcAraf1 and rNc6GAL. These results suggest that the carbohydrate moieties of AGPs are degraded by the concerted action of NcAraf1 and Nc6GAL secreted from N. crassa.     

The extraction process optimization and physicochemical properties of polysaccharides from the roots of Euphorbia fischeriana

Response surface methodology (RSM) was used to determine the optimum extraction conditions for polysaccharides (EFP) from the roots of Euphorbia fischeriana. A Box-Behnken design (BBD) with four independent variables was investigated, such as extraction temperature (°C), water/solid ratio, extraction number (n), and extraction time (h). The results indicated optimum extraction conditions were extraction temperature of 97 °C, water/solid ratio of 9:1, extraction number of 2 and extraction time of 2.4 h, respectively. Under these conditions, the experimental value was 24.6 ± 0.62, which was well in close agreement with value predicted by the model. The preliminary chemical analysis of EFP revealed the EFP contained 25.43% polysaccharides, 20.42% uronic acids, 2.54% sulfate radical and 23.41% proteins. And the neutral polysaccharides were mainly composed of glucose, arabinose, rhamnose, galactose, xylose, mannose in the ratio of 21:8:5:3:1:1.     

Structural elucidation of fungal polysaccharides isolated from the cell wall of Plectosphaerella cucumerina and Verticillium spp

The structure of acidic fungal polysaccharides isolated from the cell wall of Plectosphaerella cucumerina, Verticillium dahliae, and V. albo-atrum has been investigated by chemical analysis, methylation analysis, and 1D and 2D 1H and 13C NMR spectroscopy. The polysaccharides have an idealized repeating block of the type: [carbohydrates: see text] linked to a small mannan core (<15%), where n=13, m=13, p=5, and q=8 for P. cucumerina, and n=16, m=16, p=6, and q <1 for both Verticillium species.     

Amide-esters from Aglaia tenuicaulis--first representatives of a class of compounds structurally related to bisamides and flavaglines

Six amide-esters and two sulphur-containing bisamides were isolated from the leaves, stem and root bark of Aglaia tenuicaulis together with two bisamides from the leaves of A. spectabilis. Their structures were elucidated by spectroscopic methods. The co-occurrence of amide-esters and bisamides suggests close biosynthetic connections replacing only one nitrogen atom of putrescine with oxygen. Putrescine appears to be the common building block linked to various acids from which the cinnamoyl moiety represents the prerequisite for an incorporation of bisamides into flavaglines. Corresponding amide-esters are apparently not incorporated, but closely related amide-alcohol derivatives were found as part of benzopyran and benzofuran flavaglines. The structure of a amide-alcohol is described, representing an artifact due to hydrolysis of an amide-ester during TLC purification. A hypothetical amide-amine building block is suggested to form the characteristic pyrimidinone structures only found in benzofuran flavaglines. Structural and biosynthetic connections between amide-esters, bisamides and flavaglines are discussed and the chemotaxonomic significance of accumulating specific derivatives within the genus Aglaia is highlighted.     

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.     

Preparation and antimicrobial activity of hydroxypropyl chitosan

Water-soluble hydroxypropyl chitosan (HPCS) derivatives with different degrees of substitution (DS) and weight-average molecular weight (Mw) were synthesized from chitosan and propylene epoxide under basic conditions. Their structure was characterized by IR spectroscopy, NMR spectroscopy, and elemental analysis, which showed that both the OH groups at C-6 and C-3 and the NH2 group of chitosan were alkylated. The DS value of HPCS ranged from 1.5 to 3.1 and the Mw was between 2.1x10(4) and 9.2x10(4). In vitro antimicrobial activities of the HPCS derivatives were evaluated by the Kirby-Bauer disc diffusion method and the macrotube dilution broth method. The HPCS derivatives exhibited no inhibitory effect on two bacterial strains (Escherichia coli and Staphylococcus aureus); however, some inhibitory effect was found against four of the six pathogenic fruit fungi investigated. Some derivatives (HPCS1, HPCS2, HPCS3, HPCS3-1, and HPCS4) were effective against C. diplodiella and F. oxysporum. HPCS3-1 is the most effective one with MIC values of 5.0, 0.31, 0.31, and 0.16mg/mL against A. mali, C. diplodiella, F. oxysporum, and P. piricola, respectively. Antifungal effects were also observed for HPCS2 and HPCS3-1 against A. mali, as well as HPCS3 and HPCS3-1 against P. piricola. The results suggest that relatively lower DS and higher Mw value enhances the antifungal activity of HPCS derivatives.     

Structure elucidation and sulfated derivatives preparation of two alpha-D-glucans from Gastrodia elata Bl. and their anti-dengue virus bioactivities

The structures of two glucans, WGEW and AGEW, isolated from Gastrodia elata Bl. were elucidated using monosaccharide composition analysis by gas chromatography (GC), methylation analysis by gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy. Their structures were deduced as an alpha-D-(1-->4)-glucan with an alpha-(1-->4) linked branch attached to O-6 branch points with different branch degrees. Their sulfate derivatives with distinct degrees of substitution (DS) were prepared. The substitution position was assigned to O-6 according to the (13)C NMR spectra. All sulfated derivatives showed strong anti-dengue virus bioactivities. The structure-activity relationships (SAR) between the polysaccharides and their sulfated derivatives were also investigated. Results showed that the higher the DS is, the more potent the impact on the dengue virus infection would be.     

S-Substituted cysteine derivatives and thiosulfinate formation in Petiveria alliacea-part II

Three cysteine derivatives, (R)-S-(2-hydroxyethyl)cysteine, together with (R(S)R(C))- and (S(S)R(C))-S-(2-hydroxyethyl)cysteine sulfoxides, have been isolated from the roots of Petiveria alliacea. Furthermore, three additional amino acids, S-methyl-, S-ethyl-, and S-propylcysteine derivatives, were detected. They were present only in trace amounts (<3 microg g(-1) fr. wt), precluding determination of their absolute configurations and oxidation states. In addition, four thiosulfinates, S-(2-hydroxyethyl) (2-hydroxyethane)-, S-(2-hydroxyethyl) phenylmethane-, S-benzyl (2-hydroxyethane)- and S-benzyl phenylmethanethiosulfinates, have been found in a homogenate of the roots. The formation pathways of various benzyl/phenyl-containing compounds previously found in the plant were also discussed.     

Glucans of lichenized fungi: significance for taxonomy of the genera Parmotrema and Rimelia

The glucans of lichenized fungi are an important class of polysaccharides with structural and chemotaxonomic roles. The water-insoluble glucans of the genus Parmotrema (P. austrosinense, P. delicatulum, P. mantiqueirense, P. schindleri, and P. tinctorum) and those of Rimelia (R. cetrata and R. reticulata), were investigated in order to evaluate the significance in chemotyping, with nigeran [(1-->3),(1-->4)-alpha-glucan] and lichenan [(1-->3),(1-->4)-beta-glucan] characterized using (1)H and (13)C NMR, methylation analysis, and controlled Smith degradations. Results from all species were similar, suggesting that glucan chemistry does not support separation of Rimelia from Parmotrema.     

Structural characterisation of novel lichen heteroglycans by NMR spectroscopy and methylation analysis

Two galactofuranomannans, Ths-4 and Ths-5, were isolated from the lichen, Thamnolia vermicularis var. subuliformis, using ethanol fractionation and anion-exchange and size-exclusion chromatography. The average molecular weights of Ths-4 and Ths-5 were estimated to be 19 and 200 kDa, respectively. Structural characterisation of Ths-4, Ths-5 and their partially hydrolysed derivatives was performed by methanolysis and methylation analysis. The intact and partially hydrolysed Ths-4 was further analysed using NMR spectroscopy (1D, COSY, NOESY, TOCSY, HSQC and HMBC). According to the data obtained, the heteroglycans Ths-4 and Ths-5 have similar structures, but have large differences in molecular weight. The structure is composed of 3-O-linked and 5-O-linked galactofuranosyl chains linked to a mannan core. The mannan core consists of a main chain of alpha-(1-->6)-linked mannopyranosyl residues, substituted at O-2 with either a single alpha-mannopyranosyl unit or an alpha-Manp-(1-->2)-alpha-Manp-(1-->2)-alpha-Manp group in the ratio of approximately 1:3, respectively. The polysaccharides have idealised repeating blocks as is shown.