A Multidimensional Mass Spectrometry-Based Workflow for De Novo Structural Elucidation of Oligosaccharides from Polysaccharides.

Carbohydrates play essential roles in a variety of biological processes that are dictated by their structures. However, characterization of carbohydrate structures remains extremely difficult and generally unsolved. In this work, a de novo mass spectrometry-based workflow was developed to isolate and structurally elucidate oligosaccharides to provide sequence, monosaccharide compositions, and glycosidic linkage positions. The approach employs liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods in a 3-dimensional concept: one high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS) analysis for oligosaccharide sequencing and two ultra high performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-QqQ MS) analyses on fractionated oligosaccharides to determine their monosaccharides and linkages compositions. The workflow was validated by applying the procedure to maltooligosaccharide standards. The approach was then used to determine the structures of oligosaccharides derived from polysaccharide standards and whole food products. The integrated LC-MS workflow will reveal the in-depth structures of oligosaccharides.

Saccharide analysis of onion outer epidermal walls.

BACKGROUND: Epidermal cell walls have special structural and biological roles in the life of the plant. Typically they are multi-ply structures encrusted with waxes and cutin which protect the plant from dehydration and pathogen attack. These characteristics may also reduce chemical and enzymatic deconstruction of the wall for sugar analysis and conversion to biofuels. We have assessed the saccharide composition of the outer epidermal wall of onion scales with different analytical methods. This wall is a particularly useful model for cell wall imaging and mechanics. RESULTS: Epidermal walls were depolymerized by acidic methanolysis combined with 2M trifluoracetic acid hydrolysis and the resultant sugars were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Total sugar yields based on wall dry weight were low (53%). Removal of waxes with chloroform increased the sugar yields to 73% and enzymatic digestion did not improve these yields. Analysis by gas chromatography/mass spectrometry (GC/MS) of per-O-trimethylsilyl (TMS) derivatives of the sugar methyl glycosides produced by acidic methanolysis gave a high yield for galacturonic acid (GalA) but glucose (Glc) was severely reduced. In a complementary fashion, GC/MS analysis of methyl alditols produced by permethylation gave substantial yields for glucose and other neutral sugars, but GalA was severely reduced. Analysis of the walls by 13C solid-state NMR confirmed and extended these results and revealed 15% lipid content after chloroform extraction (potentially cutin and unextractable waxes). CONCLUSIONS: Although exact values vary with the analytical method, our best estimate is that polysaccharide in the outer epidermal wall of onion scales is comprised of homogalacturonan (~ 50%), cellulose (~ 20%), galactan (~ 10%), xyloglucan (~ 10%) and smaller amounts of other polysaccharides. Low yields of specific monosaccharides by some methods may be exaggerated in epidermal walls impregnated with waxes and cutin and call for cautious interpretation of the results.

Genomic, Transcriptomic and Enzymatic Insight into Lignocellulolytic System of a Plant Pathogen Dickeya sp. WS52 to Digest Sweet Pepper and Tomato Stalk.

Abstract:Dickeya sp., a plant pathogen, causing soft rot with strong pectin degradation capacity was taken for the comprehensive analysis of its corresponding biomass degradative system, which has not been analyzed yet. Whole genome sequence analysis of the isolated soft-rotten plant pathogen Dickeya sp. WS52, revealed various coding genes which involved in vegetable stalk degradation-related properties. A total of 122 genes were found to be encoded for putative carbohydrate-active enzymes (CAZy) in Dickeya sp. WS52. The number of pectin degradation-related genes, was higher than that of cellulolytic bacteria as well as other Dickeya spp. strains. The CAZy in Dickeya sp.WS52 contains a complete repertoire of enzymes required for hemicellulose degradation, especially pectinases. In addition, WS52 strain possessed plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Transcriptome analysis revealed that parts of genes encoding lignocellulolytic enzymes were significantly upregulated in the presence of minimal salt medium with vegetable stalks. However, most of the genes were related to lignocellulolytic enzymes, especially pectate lyases and were downregulated due to the slow growth and downregulated secretion systems. The assay of lignocellulolytic enzymes including CMCase and pectinase activities were identified to be more active in vegetable stalk relative to MSM + glucose. However, compared with nutrient LB medium, it needed sufficient nutrient to promote growth and to improve the secretion system. Further identification of enzyme activities of Dickeya sp.WS52 by HPLC confirmed that monosaccharides were produced during degradation of tomato stalk. This identified degradative system is valuable for the application in the lignocellulosic bioenergy industry and animal production.

Phenotyping and cell wall polysaccharide composition dataset of five arabidopsis ecotypes grown at optimal or sub-optimal temperatures.

This article presents experimental data describing the morphology and the cell wall monosaccharide content of rosettes and flower stems of five Arabidopsis thaliana ecotypes grown at two contrasted temperatures. Besides, cell wall polysaccharides are reconstructed from data of monosaccharide quantification. The well-described and sequenced Columbia (Col) ecotype and four newly-described Pyrenees ecotypes (Duruflé et al., 2019) have been grown at two different temperatures (15 °C and 22 °C). For macrophenotyping, we provide dataset regarding (i) rosettes such as measurement of diameter and fresh mass as well as number of leaves just before bolting and (ii) floral stems at the first flower stage such as length, number of cauline leaves, mass and diameter at its base. Regarding cell wall composition, we provide data of quantification of seven monosaccharides and the reconstruction three polysaccharides. All these data are markers to differentiate both growth temperatures and the different ecotypes. They constitute a valuable resource for the community to study the adaptation of A. thaliana ecotypes to sub-optimal temperature growth conditions.

Structural characterisation of new immunoadjuvant saponins from leaves and the first study of saponins from the bark of Quillaja brasiliensis by liquid chromatography electrospray ionisation ion trap mass spectrometry.

INTRODUCTION: Quillaja brasiliensis (St. A. -Hil. & Tul) Mart (Quillajaceae) is a species native to South America, which is rich in saponins. Saponins are used in different industries, so there is a constant demand for this type of compound. Based on the wide range of applications for the saponins found in this species, notably as immunoadjuvants, we conducted a comprehensive study of this tree and its saponins. OBJECTIVE: The purpose of this work is to complete the characterisation of the immunoadjuvant saponin fraction from Q. brasiliensis leaves and further study the saponin fraction obtained from Q. brasiliensis bark. METHODOLOGY: Saponin fractions were studied using mass spectrometry in combination with classical methods of monosaccharide and methylation analysis. We performed direct infusion and liquid chromatography/electrospray ionisation ion trap multiple-stage mass spectrometry (DI-ESI-IT-MSn and LC-ESI-IT-MS2 ). RESULTS: Seventy-five saponins, 21 from leaves and 54 from bark, were tentatively identified according to their molecular mass, fragmentation pattern and chromatographic behaviour. This work represents the first investigation of saponins from the bark of Q. brasiliensis and some of them presented new structural motifs not previously reported in the genus Quillaja. CONCLUSION: The efficiency and selectivity of the data dependent LC-MS2 method allowed the rapid profiling of saponins from Q. brasiliensis. The results of the monosaccharide and methylation analysis performed in saponins from Q. brasiliensis fractions and Q. saponaria Molina (Quillajaceae) fraction gives further support to the structures proposed according to the mass spectral data, validating the strategy used in the present work.

Structural Analysis of Exopolysaccharides from Lactic Acid Bacteria.

Production of exopolysaccharides by lactic acid bacteria is a common phenomenon. Structural information of these widely diverse biopolymers is rendered by the monosaccharide composition, the anomeric configurations, the type of glycosidic linkages, the presence of repeating units and noncarbohydrate substituents, and finally the presentation of a chemical molecular structure or composite model. The detailed structural analysis of polysaccharides is a time-consuming pursuit, including the use of different techniques, such as chemical degradation methods (e.g., hydrolysis), separation methods (e.g., SEC-chromatography and HPLC/HPAEC), and identification methods (e.g., GLC-EIMS and 1H/13C NMR spectroscopy). In this chapter, some analytical methods are described and demonstrated for two different exopolysaccharides from lactic acid bacteria.

Structural elucidation of fucoidan from Cladosiphon okamuranus (Okinawa mozuku).

Fucoidan is a sulphated polysaccharide, made up mainly of l-fucose, which is found in brown seaweeds. Its chemical structure is diverse and depends on maturity, species and geographical location. The objective of this study was to elucidate the chemical structure of fucoidan from Cladosiphon okamuranus harvested in Japan. The fucoidan was subject to purification prior to monosaccharide profiling, sulphate content determination, and linkage analysis. Our results showed that Japanese Cladosiphon okamuranus fucoidan contained 70.13 ±â€¯0.22 wt% fucose and 15.16 ±â€¯1.17 wt% sulphate. Other minor monosaccharides found were d-xylose, d-galactose, d-mannose, d-glucose, d-arabinose, d-rhamnose and d-glucuronic acid. Linkage analysis revealed that fucopyranoside units along the backbone are linked, through α-1,3-glycosidic bonds, with fucose branching at C-2, and one sulphate group at C-4 per every three fucose units, i.e. the structure of fucoidan from Japanese Cladosiphon okamuranus is [→3)-α-fuc(1→]0.52[→3)-α-fuc-4-OSO3-(1→]0.33[→2)-α-fuc]0.14.

Analysis of Monosaccharides from Arabidopsis Seed Mucilageand Whole Seeds Using HPAEC-PAD.

Arabidopsis seed coat epidermal cells deposit a significant quantity of mucilage, composed of the cell wall components pectin, hemicellulose, and cellulose, into the apoplast during development. When mature seeds are hydrated, mucilage extrudes to form a gelatinous capsule around the seed. Determining the monosaccharide composition of both extruded mucilage and whole seeds is an essential technique for characterizing seed coat developmental processes and mutants with altered mucilage composition. This protocol covers growth of plants to produce seeds suitable for analysis, extraction of extruded mucilage using water and sodium carbonate (used for mutants with impaired mucilage release), and extraction of alcohol insoluble residue (AIR) from whole seeds. The prepared polysaccharides are then hydrolyzed using sulfuric acid, which hydrolyses all polysaccharides including cellulose. Sensitive and reproducible quantification of the resulting monosaccharides is achieved using high-performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD).

Analysis of Cell Wall Teichoic Acids in Staphylococcus aureus.

Most bacterial cells are surrounded by a surface composed mainly of peptidoglycan (PGN), a glycopolymer responsible for ensuring the bacterial shape and a telltale molecule that betrays the presence of bacteria to the host immune system. In Staphylococcus aureus, as in most gram-positive bacteria, peptidoglycan is concealed by covalently linked molecules of wall teichoic acids (WTA)-phosphate rich molecules made of glycerol and ribitol phosphates which may be tailored by different amino acids and sugars.In order to analyze and compare the composition of WTA produced by different S. aureus strains, we describe methods to: (1) quantify the total amount of WTA present at the bacterial cell surface, through the determination of the inorganic phosphate present in phosphodiester linkages of WTA; (2) identify which sugar constituents are present in the assembled WTA molecules, by detecting the monosaccharides, released by acid hydrolysis, through an high-performance anion exchange chromatography analysis coupled with pulsed amperometric detection (HPAEC-PAD) and (3) compare the polymerization degree of WTA found at the cell surface of different S. aureus strains, through their different migration in a polyacrylamide gel electrophoresis (PAGE).

Strategy to identify and quantify polysaccharide gums in gelled food concentrates.

A strategy for the unambiguous identification and selective quantification of xanthan gum and locust bean gum (LBG) in gelled food concentrates is presented. DNA detection by polymerase chain reaction (PCR) showed to be a fast, sensitive, and selective method that can be used as a first screening tool in intact gelled food concentrates. An efficient isolation procedure is described removing components that may interfere with subsequent analyses. NMR spectroscopy enabled the direct identification of xanthan gum and the discrimination between different galactomannans in the isolated polysaccharide fraction. An enzymatic fingerprinting method using endo-ß-mannanase, in addition to being used to differentiate between galactomannans, was developed into a selective, quantitative method for LBG, whereas monosaccharide analysis was used to quantify xanthan gum. Recoveries for xanthan gum and LBG were 87% and 70%, respectively, with in-between day relative standard deviations below 20% for xanthan gum and below 10% for LBG.

Purification, characterisation and protective effects of polysaccharides from alfalfa on hepatocytes.

The objective of this study was to determine the preliminary characteristics and protective effects of alfalfa polysaccharides (APS) on hepatocytes in vitro. The crude APS was purified by DEAE-cellulose and Sephadex G-100 chromatography, resulting in the four purified fractions: APS-1, APS-2, APS-3 and APS-4. The results indicated that APS-3 had higher carbohydrate and uronic acid contents and that APS-4 had a more complicated monosaccharide composition compared to the other purified fractions. The average molecular weights of APS-1, APS-2, APS-3 and APS-4 were 48,536, 6,221, 66,559 and 13,076 Da, respectively. Furthermore, APS (crude and its purified fractions) restored the activities of antioxidant enzymes and increased the total antioxidant capacity of hepatocytes subjected to H2O2-induced oxidative stress. Furthermore, APS treatment counteracted the increases in lactic dehydrogenase and malonaldehyde in the culture supernatant. These results clearly demonstrate that APS possesses a protective effect against oxidative injury in hepatocytes.

A novel condition for capillary electrophoretic analysis of reductively aminated saccharides without removal of excess reagents.

We have identified novel CE conditions for the separation of 7-amino-4-methylcoumarin-labeled monosaccharides and oligosaccharides from glycoproteins. Using a neutrally coated capillary and alkaline borate buffer containing hydroxypropylcellulose and ACN, saccharide derivatives form anionic borate complexes, which move from the cathode to the anode in an electric field and are detected near the anodic end. Excess labeling reagents and other fluorescent products remain at the cathodic end. Fluorimetric detection using an LED as a light source enables determination of monosaccharide derivatives with good linearity between at least 0.4 and 400 µM, may correspond to 140 amol to 140 fmol. The lower LOD (S/N = 5) is only 80 nM in the sample solution (ca. 28 amol). The results were comparable to reported values using fluorometric detection LC. The method was also applied to the analysis of oligosaccharides that were enzymatically released from glycoproteins. Fine resolution enables profiling of glycans in glycoproteins. The applicability of the method was examined by applying it to other derivatives labeled with nonacidic tags such as ethyl p-aminobenzoate- and 2-aminoacridone-labeled saccharides.

Two-mode Analysis by High-performance Liquid Chromatography of ρ-Aminobenzoic Ethyl Ester-derivatized Monosaccharides.

ρ-Aminobenzoic ethyl ester (ABEE)-derivatized monosaccharides were separated by HPLC with a trifluoroacetic acid (TFA) solution or borate buffer as the eluent. In the case of the TFA solution, ABEE-derivatized monosaccharides of the neutral and amino sugars found in animal glycoproteins were separated in a simultaneous analysis. In the case of the borate buffer, ABEE-derivatized monosaccharides of identical molecular weights such as ABEE-Gal, -Glc, and -Man were separated as stereoisomers. Glucuronic acid and galacturonic acid were detected and separated within 8 min. The relationship between the peak areas and the amounts of ABEE-derivatized monosaccharides was linear in the range of 1 to 1000 pmol.