GRASS: semi-automated NMR-based structure elucidation of saccharides

Kapaev, Roman R.; Toukach, Filip V.

doi:10.1093/bioinformatics/btx696

Cited by 32 publications

(11 citation statements)

References 24 publications

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“…The 13 C NMR chemical shifts were analyzed and compared to published values by GODDESS (Kapaev and Toukach, 2016) and GRASS NMR (Kapaev and Toukach, 2018) simulation, and structure elucidation web services were implemented at the platform of the Carbohydrate Structure Database (Toukach and Egorova, 2016).…”

Section: Methodsmentioning

confidence: 99%

Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5

et al. 2019

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In skin, Cutibacterium acnes (former Propionibacterium acnes ) can behave as an opportunistic pathogen, depending on the strain and environmental conditions. Acneic strains of C. acnes form biofilms inside skin–gland hollows, inducing inflammation and skin disorders. The essential exogenous products of C. acnes accumulate in the extracellular matrix of the biofilm, conferring essential bacterial functions to this structure. However, little is known about the actual composition of the biofilm matrix of C. acnes . Here, we developed a new technique for the extraction of the biofilm matrix of Gram-positive bacteria without the use of chemical or enzymatic digestion, known to be a source of artifacts. Our method is based on the physical separation of the cells and matrix of sonicated biofilms by ultracentrifugation through a CsCl gradient. Biofilms were grown on the surface of cellulose acetate filters, and the biomass was collected without contamination by the growth medium. The biofilm matrix of the acneic C. acnes RT5 strain appears to consist mainly of polysaccharides. The following is the ratio of the main matrix components: 62.6% polysaccharides, 9.6% proteins, 4.0% DNA, and 23.8% other compounds (porphyrins precursors and other). The chemical structure of the major polysaccharide was determined using a nuclear magnetic resonance technique, the formula being →6)-α- D -Gal p -(1→4)-β- D -Man p NAc3NAcA-(1→6)-α- D -Glc p -(1→4)-β- D -Man p NAc3NAcA-(1→3)-β-Gal p NAc-(1→. We detected 447 proteins in the matrix, of which the most abundant were the chaperonin GroL, the elongation factors EF-Tu and EF-G, several enzymes of glycolysis, and proteins of unknown function. The matrix also contained more than 20 hydrolases of various substrata, pathogenicity factors, and many intracellular proteins and enzymes. We also performed surface-enhanced Raman spectroscopy analysis of the C. acnes RT5 matrix for the first time, providing the surface-enhanced Raman scattering (SERS) profiles of the C. acnes RT5 biofilm matrix and biofilm biomass. The difference between the matrix and biofilm biomass spectra showed successful matrix extraction rather than simply the presence of cell debris after sonication. These data show the complexity of the biofilm matrix composition and should be essential for the development of new anti- C. acnes biofilms and potential antibiofilm drugs.

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Section: Methodsmentioning

confidence: 99%

Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5

et al. 2019

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“…The 13 C NMR spectrum of the native polysaccharide ( Fig 7 ) contained six major signals accounting for a regular glycopolymer, including one anomeric carbon at δ 105.45, two CH 2 OH groups, three sugar ring carbon signals typical for a furanose cycle, and minor signals (<10%). The preliminary interpretation of 13 C NMR chemical shifts by GRASS (Generation, Ranking and Assignment of Saccharide Structures) [ 66 ] hosted at the Carbohydrate Structure Database [ 67 ] yielded only one match, namely polymeric 2,6-linked β-D-fructofuranose (levan), with linear correlation (LC) between the simulation and the experiment of 1.000, and root-mean-square deviation (RMS) of 0.49 ppm. The next-ranked structural hypothesis had a much worse fit to the experiment (LC 0.994, RMS 1.18 ppm).…”

Section: Resultsmentioning

confidence: 99%

Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020

et al. 2021

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Paenibacillus spp. exopolysaccharides (EPSs) have become a growing interest recently as a source of biomaterials. In this study, we characterized Paenibacillus polymyxa 2020 strain, which produces a large quantity of EPS (up to 68 g/L),and was isolated from wasp honeycombs. Here we report its complete genome sequence and full methylome analysis detected by Pacific Biosciences SMRT sequencing. Moreover, bioinformatic analysis identified a putative levan synthetic operon. SacC and sacB genes have been cloned and their products identified as glycoside hydrolase and levansucrase respectively. The Fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectra demonstrated that the EPS is a linear β-(2→6)-linked fructan (levan). The structure and properties of levan polymer produced from sucrose and molasses were analyzed by FT-IR, NMR, scanning electron microscopy (SEM), high performance size exclusion chromatography (HPSEC), thermogravimetric analysis (TGA), cytotoxicity tests and showed low toxicity and high biocompatibility. Thus, P. polymyxa 2020 could be an exceptional cost-effective source for the industrial production of levan-type EPSs and to obtain functional biomaterials based on it for a broad range of applications, including bioengineering.

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“…The SEM analysis investigated the morphological nature of EPS from B. amyloliquefaciens ( Figure 8 ). The dense, porous and irregular design of EPS is discovered by the SEM study, used as a textured, thickening and stabilising agent to enhance water power and viscosity by the formulation of the matrix consistent with a hydrated polymer [ 79 , 80 ]. The porous nature of EPS has also been reported in the surface morphology and the elemental composition of EPS made from S. thermophiles [ 81 ].…”

Section: Resultsmentioning

confidence: 99%

Structural Characterisation and Assessment of the Novel Bacillus amyloliquefaciens RK3 Exopolysaccharide on the Improvement of Cognitive Function in Alzheimer’s Disease Mice

et al. 2021

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In this study Bacillus amyloliquefaciens RK3 was isolated from a sugar mill effluent-contaminated soil and utilised to generate a potential polysaccharide with anti-Alzheimer’s activity. Traditional and molecular methods were used to validate the strain. The polysaccharide produced by B. amyloliquefaciens RK3 was purified, and the yield was estimated to be 10.35 gL−1. Following purification, the polysaccharide was structurally and chemically analysed. The structural analysis revealed the polysaccharide consists of α-d-mannopyranose (α-d-Manp) and β-d-galactopyranose (β-d-Galp) monosaccharide units connected through glycosidic linkages (i.e, β-d-Galp(1→6)β-d-Galp (1→6)β-d-Galp(1→2)β-d-Galp(1→2)[β-d-Galp(1→6)]β-d-Galp(1→2)α-d-Manp(1→6)α-d-Manp (1→6)α-d-Manp(1→6)α-d-Manp(1→6)α-d-Manp). The scanning electron microscopy and energy-dispersive X-ray spectroscopy imaging of polysaccharides emphasise their compactness and branching in the usual tubular heteropolysaccharide structure. The purified exopolysaccharide significantly impacted the plaques formed by the amyloid proteins during Alzheimer’s disease. Further, the results also highlighted the potential applicability of exopolysaccharide in various industrial and pharmaceutical applications.

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GRASS: semi-automated NMR-based structure elucidation of saccharides

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 32 publications

References 24 publications

Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5

Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5

Production and сharacterization of the exopolysaccharide from strain Paenibacillus polymyxa 2020

Structural Characterisation and Assessment of the Novel Bacillus amyloliquefaciens RK3 Exopolysaccharide on the Improvement of Cognitive Function in Alzheimer’s Disease Mice

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