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Ruda A, Aytenfisu AH, Angles d’Ortoli T, MacKerell AD, Widmalm G. Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields. Phys Chem Chem Phys 2023; 25:3042-3060. [PMID: 36607620 PMCID: PMC9890503 DOI: 10.1039/d2cp05203b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D 1H,1H-NOESY and 1D 1H,1H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly 13C-isotope labeled α-D-[1,2-13C2]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on 13C,13C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.
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Affiliation(s)
- Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Asaminew H. Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
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2
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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Xu Z, Li X, Tian X, Yang S, Li Y, Li Z, Guo T, Kong J. Characterization of the antioxidant activities of the exopolysaccharides produced by Streptococcus thermophilus CGMCC 7.179. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Li Q, Geng X, Zhu L, Zheng F, Chen E, Wang G, Li X. Structural characterization and antioxidant properties of a novel polysaccharide isolated from Jiuzao in vitro and in vivo. Food Res Int 2022; 162:111940. [DOI: 10.1016/j.foodres.2022.111940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022]
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5
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Zeng F, Zhou H, Lin X, Li Y, Liang Y, Xie Q, Atakpa EO, Shen C, Zhang C. Enhanced remediation of fracturing flowback fluids by the combined application of a bioflocculant/biosurfactant-producing Bacillus sp. SS15 and its metabolites. CHEMOSPHERE 2022; 302:134870. [PMID: 35537625 DOI: 10.1016/j.chemosphere.2022.134870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
Fracturing flowback fluids (FFFs), which is generated from the process of oil and gas exploitation, is one of the major environmental concerns. In this study, a bacterial strain, Bacillus sp. SS15, capable of producing both bioflocculant (BF) and biosurfactant (BS), was isolated from oil-contaminated mudflat sediment. The BS produced by SS15 was identified as lipopeptide, which could reduce the surface tension of water from 74.2 mN/m to 36.6 mN/m with a critical micelle concentration of 44.4 mg/L. It also exhibited strong tolerance against a wide range of pH (2-12), temperature (4-60 °C), and salinity (0-100 g/L). Meanwhile, the BF produced by SS15 exhibited high flocculating activity (84.9%) for kaolin suspension, and was confirmed to be thermostable, salt-tolerant, and alkaliphilic. The combined treatment of bioremediation (introducing SS15 and BS) followed by flocculation (introducing BF) greatly promoted the removal of chroma (85.7% reduction), suspended solids (94.4% reduction), chemical oxygen demand (84.9% reduction), n-alkanes (50.0% reduction), and polycyclic aromatic hydrocarbons (66.5% reduction), respectively. The genome analysis showed that strain SS15 possessed abundant genes related to the synthesis of carbohydrate, protein, and lipid, which might play an important role in BF and BS synthesis. The findings in this study demonstrated that Bacillus sp. SS15 has promising prospect in the remediation of FFFs.
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Affiliation(s)
- Feng Zeng
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China; Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Hanghai Zhou
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Xiaoyun Lin
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Yanhong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China.
| | - Yanpeng Liang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Qinglin Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | | | - Chaofeng Shen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chunfang Zhang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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Zhao X, Chen G, Wang F, Zhao H, Wei Y, Liu L, Zhang H. Extraction, characterization, antioxidant activity and rheological behavior of a polysaccharide produced by the extremely salt tolerant Bacillus subtilis LR-1. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Riu F, Ruda A, Engström O, Muheim C, Mobarak H, Ståhle J, Kosma P, Carta A, Daley DO, Widmalm G. A Lead-Based Fragment Library Screening of the Glycosyltransferase WaaG from Escherichia coli. Pharmaceuticals (Basel) 2022; 15:ph15020209. [PMID: 35215321 PMCID: PMC8877264 DOI: 10.3390/ph15020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
Glucosyl transferase I (WaaG) in E. coli catalyzes the transfer of an α-d-glucosyl group to the inner core of the lipopolysaccharide (LPS) and plays an important role in the biogenesis of the outer membrane. If its activity could be inhibited, the integrity of the outer membrane would be compromised and the bacterium would be susceptible to antibiotics that are normally prevented from entering the cell. Herein, three libraries of molecules (A, B and C) were docked in the binding pocket of WaaG, utilizing the docking binding affinity as a filter to select fragment-based compounds for further investigations. From the results of the docking procedure, a selection of compounds was investigated by molecular dynamics (MD) simulations to obtain binding free energy (BFE) and KD values for ligands as an evaluation for the binding to WaaG. Derivatives of 1,3-thiazoles (A7 and A4) from library A and 1,3,4-thiadiazole (B33) from library B displayed a promising profile of BFE, with KD < mM, viz., 0.11, 0.62 and 0.04 mM, respectively. Further root-mean-square-deviation (RMSD), electrostatic/van der Waals contribution to the binding and H-bond interactions displayed a favorable profile for ligands A4 and B33. Mannose and/or heptose-containing disaccharides C1–C4, representing sub-structures of the inner core of the LPS, were also investigated by MD simulations, and compound C42− showed a calculated KD = 0.4 µM. In the presence of UDP-Glc2−, the best-docked pose of disaccharide C42− is proximate to the glucose-binding site of WaaG. A study of the variation in angle and distance was performed on the different portions of WaaG (N-, the C- domains and the hinge region). The Spearman correlation coefficient between the two variables was close to unity, where both variables increase in the same way, suggesting a conformational rearrangement of the protein during the MD simulation, revealing molecular motions of the enzyme that may be part of the catalytic cycle. Selected compounds were also analyzed by Saturation Transfer Difference (STD) NMR experiments. STD effects were notable for the 1,3-thiazole derivatives A4, A8 and A15 with the apo form of the protein as well as in the presence of UDP for A4.
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Affiliation(s)
- Federico Riu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (F.R.); (A.C.)
| | - Alessandro Ruda
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (O.E.); (H.M.); (J.S.)
| | - Olof Engström
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (O.E.); (H.M.); (J.S.)
| | - Claudio Muheim
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden; (C.M.); (D.O.D.)
| | - Hani Mobarak
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (O.E.); (H.M.); (J.S.)
| | - Jonas Ståhle
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (O.E.); (H.M.); (J.S.)
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences—Vienna, 1190 Vienna, Austria;
| | - Antonio Carta
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy; (F.R.); (A.C.)
| | - Daniel O. Daley
- Arrhenius Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden; (C.M.); (D.O.D.)
| | - Göran Widmalm
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (O.E.); (H.M.); (J.S.)
- Correspondence:
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8
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Furevi A, Ruda A, Angles d’Ortoli T, Mobarak H, Ståhle J, Hamark C, Fontana C, Engström O, Apostolica P, Widmalm G. Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER. Carbohydr Res 2022; 513:108528. [DOI: 10.1016/j.carres.2022.108528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/02/2023]
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Inagaki M, Iwakuma R, Kawakami S, Otsuka H, Rakotondraibe HL. Detecting and Differentiating Monosaccharide Enantiomers by 1H NMR Spectroscopy. JOURNAL OF NATURAL PRODUCTS 2021; 84:1863-1869. [PMID: 34191514 PMCID: PMC8319160 DOI: 10.1021/acs.jnatprod.0c01120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Monosaccharides play important roles in living organisms. They are present in essential glycoproteins, nucleic acids, and glycolipids as well as cell walls and bioactive natural product glycosides and polysaccharides. Monosaccharides are optically active, and as a routine, scientists make sure that their absolute configurations are determined when new natural glycosides are isolated. Many determination methods for the absolute configuration of monosaccharides have been reported, and thus far, taking advantage of their optical rotation differences is the most used and efficient method to distinguish enantiomers. This method, however, is not very convenient, because it requires a milligram amount of each pure sample and the availability of a polarimeter. Identification methods dealing with comparison of the retention times of the d- and l-diastereomeric monosaccharide derivatives by GC, TLC Rf values, HPLC, or UPLC have been also reported. Although effective, these methods still require sample preparation and a few milligrams of the test compounds. A new method with simple sample preparation to distinguish enantiomers of monosaccharides by analyzing the 1H NMR spectra of their diastereomeric derivatives has been developed. The monosaccharide components of a commercially available saponin-rich Panax ginseng and monoglycosides have been successfully identified using this procedure.
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Affiliation(s)
- Masanori Inagaki
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
- Yasuda Women’s University, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Hiroshima, Japan
| | - Risa Iwakuma
- Yasuda Women’s University, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Hiroshima, Japan
| | - Susumu Kawakami
- Yasuda Women’s University, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Hiroshima, Japan
| | - Hideaki Otsuka
- Yasuda Women’s University, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Hiroshima, Japan
| | - Harinantenaina L. Rakotondraibe
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
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Exopolysaccharides produced by Pediococcus acidilactici MT41-11 isolated from camel milk: Structural characteristics and bioactive properties. Int J Biol Macromol 2021; 185:1036-1049. [PMID: 34175337 DOI: 10.1016/j.ijbiomac.2021.06.152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
In this study, the chemical structure and bioactive properties of the EPS of Pediococcus acidilactici MT41-11 isolated from camel milk were investigated. Two polysaccharide fractions (EPS-1, EPS-2) with molecular weights about 69.0 kDa were obtained, which were purified using DEAE-Sepharose and Sephadex G-100 chromatography. Based on monosaccharide composition, FT-IR, and 1D, 2D NMR spectra, concluded that EPS-1 had a backbone composed of →2)-α-d-Manp-(1→, →3)-α-d-Manp-(1→ and with branches containing α-d-Manp-(1→, EPS-2 had a backbone composed of →6)-β-d-Glcp-(1→, and with branches containing →2)-α-l-Fucp-(1→, →3)-α-d-Glcp-(1→, →2)-α-d-Glcp-(1→, β-d-Glcp-(1→, and α-d-Glcp-(1→. Remarkably, in vitro assays showed that EPS possessed multiple bioactive properties, including stimulating Lactobacillus growth and a high DPPH free radical scavenging activity. Also, it has a good ability to anti-biofilms. Overall, the analysis of all data showed EPS from P. acidilactici MT41-11 can be used as anti-oxidant, anti-biofilm agent, and also as a potential candidate prebiotic for health food or medicine industry.
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11
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Duran Garzon C, Habrylo O, Lemaire A, Guillaume A, Carré Y, Millet C, Fourtot-Brun C, Trezel P, Le Blond P, Perrin A, Georgé S, Wagner M, Coutel Y, Levavasseur L, Pau-Roblot C, Pelloux J. Characterization of a novel strain of Aspergillus aculeatinus: From rhamnogalacturonan type I pectin degradation to improvement of fruit juice filtration. Carbohydr Polym 2021; 262:117943. [PMID: 33838820 DOI: 10.1016/j.carbpol.2021.117943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Aspergillus spp. are well-known producers of pectinases commonly used in the industry. Aspergillus aculeatinus is a recently identified species but poorly characterized. This study aimed at giving a comprehensive characterization of the enzymatic potential of the O822 strain to produce Rhamnogalacturonan type I (RGI)-degrading enzymes. Proteomic analysis identified cell wall degrading enzymes (cellulases, hemicellulases, and pectinases) that accounted for 92 % of total secreted proteins. Twelve out of fifty proteins were identified as RGI-degrading enzymes. NMR and enzymatic assays revealed high levels of arabinofuranosidase, arabinanase, galactanase, rhamnogalacturonan hydrolases and rhamnogalacturonan acetylesterase activities in aqueous extracts. Viscosity assays carried out with RGI-rich camelina mucilage confirmed the efficiency of enzymes secreted by O822 to hydrolyze RGI, by decreasing viscosity by 70 %. Apple juice trials carried out at laboratory and pilot scale showed an increase in filtration flow rate and yield, paving the way for an industrial use of enzymes derived from A. aculeatinus.
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Affiliation(s)
- Catalina Duran Garzon
- UMR Transfrontalière INRAe BioEcoAgro 1158 - BIOPI, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Olivier Habrylo
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Adrien Lemaire
- UMR Transfrontalière INRAe BioEcoAgro 1158 - BIOPI, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Anaïs Guillaume
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Yoann Carré
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Clémence Millet
- Centre Technique de la Conservation des Produits Agricoles, 41 avenue Paul Claudel, 80480 Dury-Amiens, France
| | - Catherine Fourtot-Brun
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Pauline Trezel
- UMR Transfrontalière INRAe BioEcoAgro 1158 - BIOPI, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Pascal Le Blond
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Aurore Perrin
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Stéphane Georgé
- Centre Technique de la Conservation des Produits Agricoles, 41 avenue Paul Claudel, 80480 Dury-Amiens, France
| | - Magali Wagner
- Centre Technique de la Conservation des Produits Agricoles, 41 avenue Paul Claudel, 80480 Dury-Amiens, France
| | - Yves Coutel
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Loïc Levavasseur
- Centre de Recherche et Innovation Soufflet, 1 rue de la Poterne à Sel, 10400 Nogent sur Seine, France
| | - Corinne Pau-Roblot
- UMR Transfrontalière INRAe BioEcoAgro 1158 - BIOPI, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Jérôme Pelloux
- UMR Transfrontalière INRAe BioEcoAgro 1158 - BIOPI, SFR Condorcet FR CNRS 3417, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France.
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de Carvalho SS, Ribeiro LDP, Forim MR, da Silva MFDGF, Bicalho KU, Fernandes JB, Vendramim JD. Avocado kernels, an industrial residue: a source of compounds with insecticidal activity against silverleaf whitefly. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2260-2268. [PMID: 32875452 DOI: 10.1007/s11356-020-10675-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Fruit processing waste, such as kernels (endocarp + seed) of avocado [Persea americana Mill. (Lauraceae)], could be used as raw material in the preparation of botanical insecticides. In light of this potential, this study assessed the insecticidal action of extracts and fractions from kernels of two avocado cultivars (Breda and Margarida) on Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) biotype B, an important pest species in tropical conditions. Ethanolic and aqueous extracts prepared from kernels of P. americana, regardless of the plant cultivar used, caused promising insecticidal activity to whitefly nymphs. Based on yield in crude extracts [10.32 and 9.85% (w/w), respectively, for cultivars Breda and Margarida], on the bioassay results with crude extracts and on the chemical profiles, the ethanolic extract of kernels of P. americana cv. Breda was chose for the continuation of the study. Thus, the ethanolic extract of kernels of cv. Breda (LC50 = 197.84 ppm and LC90 = 567.19 ppm) was selected and subjected to fractionation by the liquid-liquid partition technique. The hexane and dichloromethane fractions of this extract caused significant mortality of nymphs. The analysis using the ultraviolet (UV) and hydrogen nuclear magnetic resonance (1H NMR) showed the presence of long-chain aliphatic compounds (alkanols or acetogenins of Lauraceae), alkylfurans (or avocadofurans), and unsaturated fatty acids in these fractions, which are possibly related to bioactivity observed in B. tabaci, besides saccharides. The results show that kernels of P. americana are promising sources of compounds with insecticidal action for the control of B. tabaci biotype B, a great opportunity to transform environmental problems into eco-friendly solutions to agriculture.
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Affiliation(s)
- Sheila Salles de Carvalho
- Department of Entomology and Acarology, "Luiz de Queiroz" College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, 13418-900, Brazil
| | - Leandro do Prado Ribeiro
- Research Center for Family Agriculture, Agricultural Research and Rural Extension Company of Santa Catarina (CEPAF/EPAGRI), Rua Servidão Ferdinando Ricieri Tusset S/N - Bairro São Cristóvão, Chapecó, Santa Catarina, CEP 89803-904, Brazil.
| | - Moacir Rossi Forim
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | | | - Keylla Utherdyany Bicalho
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | - João Batista Fernandes
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | - José Djair Vendramim
- Department of Entomology and Acarology, "Luiz de Queiroz" College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, 13418-900, Brazil
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Buffa R, Hermannová M, Sojka M, Svozil V, Šulc P, Halamková P, Pospíšilová M, Krejčí H, Velebný V. Hyaluronic acid chloramide-Synthesis, chemical structure, stability and analysis of antimicrobials. Carbohydr Polym 2020; 250:116928. [PMID: 33049842 DOI: 10.1016/j.carbpol.2020.116928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Electron-deficient chlorine covalently immobilised on an amido group of hyaluronic acid (HA) can be potentially exceptional for applications requiring biodegradable and biocompatible polymers with enhanced antibacterial or antiviral activity. This expectation is supported by the assumption that a small amount of HA chloramide (HACl) is formed in the extracellular matrix under inflammatory conditions by a reaction of endogenous HA with hypochlorous acid (HClO) generated by a myeloperoxidase/H2O2/Cl- system. HACl synthesis optimisation showed significant limitations of HClO as an oxidative agent where only lower degrees of substitution (DS) was achieved. Commercially available oxidative agents based on chlorinated isocyanuric acid were successfully tested, producing the HA chain with almost entirely chlorinated amidic groups. The structure of the final HACl was thoroughly studied using advanced 2-dimensional NMR methodologies and LC/MS. Stability of HACl at different temperatures was monitored over 12 months. Preliminary antimicrobial and antiviral tests demonstrated the potential of HACl for applications in biomedicine.
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Affiliation(s)
- Radovan Buffa
- Contipro Ltd., Dolní Dobrouč 401, 56102, Czech Republic.
| | | | - Martin Sojka
- Regional Public Health Authority, Komárno, Slovakia
| | - Vít Svozil
- Contipro Ltd., Dolní Dobrouč 401, 56102, Czech Republic
| | - Petr Šulc
- Contipro Ltd., Dolní Dobrouč 401, 56102, Czech Republic
| | | | | | - Helena Krejčí
- Contipro Ltd., Dolní Dobrouč 401, 56102, Czech Republic
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14
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Liu X, Ren Z, Yu R, Chen S, Zhang J, Xu Y, Meng Z, Luo Y, Zhang W, Huang Y, Qin T. Structural characterization of enzymatic modification of Hericium erinaceus polysaccharide and its immune-enhancement activity. Int J Biol Macromol 2020; 166:1396-1408. [PMID: 33166554 DOI: 10.1016/j.ijbiomac.2020.11.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/02/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022]
Abstract
In this study, the enzyme degradation of Hericium erinaceus polysaccharide (HEP) was successfully modified with endo-rhamnosidase to obtain the enzymatic hydrolysis of Hericium erinaceus polysaccharide product (EHEP). The gas chromatography-mass spectrometry (GC-MS), high performance gel permeation chromatography (HPGPC), Fourier transformed infrared spectrometry (FT-IR), scanning electron microscopy (SEM), atomic particle microscopy (AFM), nuclear magnetic resonance (NMR) and particle size distribution were used to characterize polysaccharides. In vitro, EHEP significantly enhanced the phagocytosis, NO, CD40 and CD86 by macrophage than HEP. In vivo, female Balb/c mice were injected respectively with EHEP and HEP after administrated with cyclophosphamide, once a day for 7 days. On days 11, the morphology and structure of jejunal sections, immunofluorescence of spleen and peritoneal macrophages were determined. These results indicated that the enzymatic hydrolysis product could enhance the activation of peritoneal macrophages, and enhance the immunomodulation function of HEP. This study demonstrated that enzymatic modification was an effective method to improve the activities of HEP, and could be developed as a potential technology for use in pharmaceutical and cosmeceutical industry.
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Affiliation(s)
- Xiaopan Liu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Zhe Ren
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Ruihong Yu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Shixiong Chen
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Junwen Zhang
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yongde Xu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Zhen Meng
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yang Luo
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Weini Zhang
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yifan Huang
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Tao Qin
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
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15
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Structural analysis of the O-antigen polysaccharide from Escherichia coli O188. Carbohydr Res 2020; 498:108051. [PMID: 33075674 DOI: 10.1016/j.carres.2020.108051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional 1H and 13C NMR spectroscopy experiments, where inter-residue correlations were identified by 1H,13C-heteronuclear multiple-bond correlation and 1H,1H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 Å, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.
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16
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Qin T, Liu X, Luo Y, Yu R, Chen S, Zhang J, Xu Y, Meng Z, Huang Y, Ren Z. Characterization of polysaccharides isolated from Hericium erinaceus and their protective effects on the DON-induced oxidative stress. Int J Biol Macromol 2019; 152:1265-1273. [PMID: 31759000 DOI: 10.1016/j.ijbiomac.2019.10.223] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023]
Abstract
In this study, the structure characteristic of the Hericium erinaceus polysaccharide (HEP) was investigated using Fourier transformed infrared spectrometry (FT-IR), gas chromatography-mass spectrometry (GC-MS), gel permeation chromatography (GPC), methylation and nuclear magnetic resonance (NMR). The results showed that HEP, with a molecular weight of 43 KDa, was mainly composed of glucose and rhamnose. The linkages of the sugar residues of HEP were → 6) β-d-Glcp-(1 → and → 2) -α-l-Rhap-(1 → residue at the end of the branches. The Fusarium toxin deoxynivalenol (DON)-induced cellular injury model for IPEC-J2 cells was established and used to investigate the protective effects of HEP against the oxidative stress. The results suggest that HEP could significantly protect IPEC-J2 cells from DON-induced oxidative stress, inhibit DON-induced apoptosis and reduce the production of reactive oxygen species (ROS). Overall, this study suggested that HEP could be explored as potential antioxidant agents for DON-induced intestinal mucosa injury.
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Affiliation(s)
- Tao Qin
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xiaopan Liu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yang Luo
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Ruihong Yu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Shixiong Chen
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Junwen Zhang
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yongde Xu
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Zhen Meng
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yifan Huang
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
| | - Zhe Ren
- Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health in Fujian province, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
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17
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Isolation, structural characterizations and bioactivities of exopolysaccharides produced by Bacillus licheniformis. Int J Biol Macromol 2019; 141:298-306. [PMID: 31465808 DOI: 10.1016/j.ijbiomac.2019.08.217] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/16/2019] [Accepted: 08/25/2019] [Indexed: 12/29/2022]
Abstract
Extraction polysaccharide from microorganism is a research hotspot. In this work, a new type of water-soluble exopolysaccharides (EPS) was isolated from Bacillus licheniformis. Firstly, response surface methodology (RSM), based on a three-level, three-factor, was used to determine optimum conditions for EPS extraction. And RSM analysis indicated optimum condition was at the temperature of 8 °C for 10.44 h with ethanol at a concentration of 79.22% (v/v), the maximum yield of EPS was 3.07 g/mL. Secondly, EPS were seperated using DEAE-Sepharose Fast Flow column chromatography and acquired two polysaccharide fractions, BL-P1 and BL-P2. BL-P1 had larger molecular weight than BL-P2 from structural analyses, because of higher content of mannose, ribose, glucuronic acid, galactose, arabinose and fructose in BL-P2. Moreover, the characterization of BL-P1 and BL-P2 was investigated with Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR) spectroscopy, the results indicated that EPS was mainly composed of→3)-α-d-Galp-(1→, →3,5)-α-l-Araf-(1→, →3)-β-d-Glcp-(1→, β-d-Glcp-(1 → and→4)-β-l-Fucp-(1 → 4)-β-d-Xylp-(1 → 4)-α-l-Rhap (1 → 3) -β-d-Manp-(4 → residues. In vitro antioxidant activity assay, EPS exhibited potent quenching capacities on hydroxyl and 1, 1-diphenyl-2-picrylhydrazyl (DPPH) radicals in a dose-dependent manner. Furthermore, BL-P2 had higher activity than BL-P1 in inhibiting α-amylase and α-glucosidase, which would have potential to be applied in nutraceutical and pharmaceutical industries.
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18
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NMR solution geometry of saccharides containing the 6-O-(α-D-glucopyranosyl)-α/β-D-glucopyranose (isomaltose) or 6-O-(α-D-galactopyranosyl)-α/β-D-glucopyranose (melibiose) core. Carbohydr Res 2019; 473:18-35. [DOI: 10.1016/j.carres.2018.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022]
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19
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El-Deeb NM, Yassin AM, Al-Madboly LA, El-Hawiet A. A novel purified Lactobacillus acidophilus 20079 exopolysaccharide, LA-EPS-20079, molecularly regulates both apoptotic and NF-κB inflammatory pathways in human colon cancer. Microb Cell Fact 2018; 17:29. [PMID: 29466981 PMCID: PMC5820793 DOI: 10.1186/s12934-018-0877-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The direct link between inflammatory bowel diseases and colorectal cancer is well documented. Previous studies have reported that some lactic acid bacterial strains could inhibit colon cancer progression however; the exact molecules involved have not yet been identified. So, in the current study, we illustrated the tumor suppressive effects of the newly identified Lactobacillus acidophilus DSMZ 20079 cell-free pentasaccharide against colon cancer cells. The chemical structure of the purified pentasaccharide was investigated by MALDI-TOF mass spectrum, 1D and 2D Nuclear Magnetic Resonance (NMR). The anticancer potentiality of the purified pentasaccharide against both Human colon cancer (CaCo-2) and Human breast cancer (MCF7) cell lines with its safety usage pattern were evaluated using cytotoxicity, annexin V quantification and BrdU incorporation assays. Also, the immunomodulatory effects of the identified compound were quantified on both LPS-induced PBMC cell model and cancer cells with monitoring the immunophenotyping of T and dendritic cell surface marker. At molecular level, the alteration in gene expression of both inflammatory and apoptotic pathways were quantified upon pentasaccharide-cellular treatment by RTqPCR. RESULTS The obtained data of the spectroscopic analysis, confirmed the structure of the newly extracted pentasaccharide; (LA-EPS-20079) to be: α-D-Glc (1→2)][α-L-Fuc(1→4)] α-D-GlcA(1→2) α-D-GlcA(1→2) α-D-GlcA. This pentasaccharide, recorded safe dose on normal mammalian cells ranged from 2 to 5 mg/ml with cancer cells selectivity index, ranged of 1.96-51.3. Upon CaCo-2 cell treatment with the non-toxic dose of LA-EPS-20079, the inhibition percentage in CaCo-2 cellular viability, reached 80.65 with an increase in the ratio of the apoptotic cells in sub-G0/G1 cell cycle phase. Also, this pentasaccharide showed potentialities to up-regulate the expression of IKbα, P53 and TGF genes. CONCLUSION The anticancer potentialities of LA-EPS-20079 oligosaccharides against human colon cancer represented through its regulatory effects on both apoptotic and NF-κB inflammatory pathways.
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Affiliation(s)
- Nehal M El-Deeb
- Biopharmacetical Product Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications, New Borg El-Arab City, 21934, Alexandria, Egypt.
| | - Abdelrahman M Yassin
- Biopharmacetical Product Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications, New Borg El-Arab City, 21934, Alexandria, Egypt
| | - Lamiaa A Al-Madboly
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt.
| | - Amr El-Hawiet
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
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20
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Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM. O 2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J Biol Chem 2017; 292:18897-18915. [PMID: 28928219 PMCID: PMC5704474 DOI: 10.1074/jbc.m117.809160] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a conserved protein linking cullin-1 to F-box proteins in SCF (Skp1/Cullin-1/F-box protein) E3 ubiquitin ligases, which modify protein substrates with polyubiquitin chains that typically target them for 26S proteasome-mediated degradation. In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. Previous studies have shown that the glycan promotes organization of the F-box-binding region in Skp1 and aids in Skp1's association with F-box proteins. Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. Molecular dynamics trajectories of glycosylated Skp1 whose calculated monosaccharide relaxation kinetics and rotational correlation times agreed with the NMR data indicated that the glycan interacts with the loop connecting two α-helices of the F-box-combining site. In these trajectories, the helices separated from one another to create a more accessible and dynamic F-box interface. These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. The increased sampling of an open Skp1 conformation can explain how glycosylation enhances interactions with F-box proteins in cells.
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Affiliation(s)
- M Osman Sheikh
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | - Gordon Chalmers
- the Complex Carbohydrate Research Center, and
- the Department of Computer Science, University of Georgia, Athens, Georgia 30602
| | - Christopher M Schafer
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | | | - Robert J Woods
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | | | - Brad Bendiak
- the Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James H Prestegard
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology,
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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21
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Rahman K, Mandalasi M, Zhao P, Sheikh MO, Taujale R, Kim HW, van der Wel H, Matta K, Kannan N, Glushka JN, Wells L, West CM. Characterization of a cytoplasmic glucosyltransferase that extends the core trisaccharide of the Toxoplasma Skp1 E3 ubiquitin ligase subunit. J Biol Chem 2017; 292:18644-18659. [PMID: 28928220 DOI: 10.1074/jbc.m117.809301] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/12/2017] [Indexed: 01/06/2023] Open
Abstract
Skp1 is a subunit of the SCF (Skp1/Cullin 1/F-box protein) class of E3 ubiquitin ligases that are important for eukaryotic protein degradation. Unlike its animal counterparts, Skp1 from Toxoplasma gondii is hydroxylated by an O2-dependent prolyl-4-hydroxylase (PhyA), and the resulting hydroxyproline can subsequently be modified by a five-sugar chain. A similar modification is found in the social amoeba Dictyostelium, where it regulates SCF assembly and O2-dependent development. Homologous glycosyltransferases assemble a similar core trisaccharide in both organisms, and a bifunctional α-galactosyltransferase from CAZy family GT77 mediates the addition of the final two sugars in Dictyostelium, generating Galα1, 3Galα1,3Fucα1,2Galβ1,3GlcNAcα1-. Here, we found that Toxoplasma utilizes a cytoplasmic glycosyltransferase from an ancient clade of CAZy family GT32 to catalyze transfer of the fourth sugar. Catalytically active Glt1 was required for the addition of the terminal disaccharide in cells, and cytosolic extracts catalyzed transfer of [3H]glucose from UDP-[3H]glucose to the trisaccharide form of Skp1 in a glt1-dependent fashion. Recombinant Glt1 catalyzed the same reaction, confirming that it directly mediates Skp1 glucosylation, and NMR demonstrated formation of a Glcα1,3Fuc linkage. Recombinant Glt1 strongly preferred the full core trisaccharide attached to Skp1 and labeled only Skp1 in glt1Δ extracts, suggesting specificity for Skp1. glt1-knock-out parasites exhibited a growth defect not rescued by catalytically inactive Glt1, indicating that the glycan acts in concert with the first enzyme in the pathway, PhyA, in cells. A genomic bioinformatics survey suggested that Glt1 belongs to the ancestral Skp1 glycosylation pathway in protists and evolved separately from related Golgi-resident GT32 glycosyltransferases.
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Affiliation(s)
- Kazi Rahman
- From the Department of Biochemistry and Molecular Biology.,the Departments of Microbiology and Immunology and
| | - Msano Mandalasi
- From the Department of Biochemistry and Molecular Biology.,Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | - Peng Zhao
- the Complex Carbohydrate Research Center, and
| | | | - Rahil Taujale
- the Complex Carbohydrate Research Center, and.,the Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Hyun W Kim
- From the Department of Biochemistry and Molecular Biology
| | | | - Khushi Matta
- the Department of Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260
| | - Natarajan Kannan
- From the Department of Biochemistry and Molecular Biology.,the Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Lance Wells
- From the Department of Biochemistry and Molecular Biology.,the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology, .,Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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22
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Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG. Databases and Associated Tools for Glycomics and Glycoproteomics. Methods Mol Biol 2017; 1503:235-264. [PMID: 27743371 DOI: 10.1007/978-1-4939-6493-2_18] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).
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Affiliation(s)
- Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Jodie L Abrahams
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Barbara Adamczyk
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
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23
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Hamark C, Berntsson RPA, Masuyer G, Henriksson LM, Gustafsson R, Stenmark P, Widmalm G. Glycans Confer Specificity to the Recognition of Ganglioside Receptors by Botulinum Neurotoxin A. J Am Chem Soc 2016; 139:218-230. [PMID: 27958736 DOI: 10.1021/jacs.6b09534] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly poisonous botulinum neurotoxins, produced by the bacterium Clostridium botulinum, act on their hosts by a high-affinity association to two receptors on neuronal cell surfaces as the first step of invasion. The glycan motifs of gangliosides serve as initial coreceptors for these protein complexes, whereby a membrane protein receptor is bound. Herein we set out to characterize the carbohydrate minimal binding epitope of the botulinum neurotoxin serotype A. By means of ligand-based NMR spectroscopy, X-ray crystallography, computer simulations, and isothermal titration calorimetry, a screening of ganglioside analogues together with a detailed characterization of various carbohydrate ligand complexes with the toxin were accomplished. We show that the representation of the glycan epitope to the protein affects the details of binding. Notably, both branches of the oligosaccharide GD1a can associate to botulinum neurotoxin serotype A when expressed as individual trisaccharides. It is, however, the terminal branch of GD1a as well as this trisaccharide motif alone, corresponding to the sialyl-Thomsen-Friedenreich antigen, that represents the active ligand epitope, and these compounds bind to the neurotoxin with a high degree of predisposition but with low affinities. This finding does not correlate with the oligosaccharide moieties having a strong contribution to the total affinity, which was expected to be the case. We here propose that the glycan part of the ganglioside receptors mainly provides abundance and specificity, whereas the interaction with the membrane itself and protein receptor brings about the strong total binding of the toxin to the neuronal membrane.
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Affiliation(s)
- Christoffer Hamark
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Ronnie P-A Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Linda M Henriksson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Robert Gustafsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
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24
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Shashkov AS, Zhang W, Perepelov AV, Weintraub A, Liu B, Widmalm G, Knirel YA. Structure of the O-polysaccharide of Escherichia coli O132. Carbohydr Res 2016; 427:44-7. [PMID: 27101383 DOI: 10.1016/j.carres.2016.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/20/2016] [Indexed: 11/19/2022]
Abstract
Mild acid degradation of the lipopolysaccharide of Escherichia coli O132 released its O-polysaccharide. Analysis by 1D and 2D (1)H and (13)C NMR spectroscopy prior and subsequent to O-deacetylation, in conjunction with sugar analysis, revealed a linear pentasaccharide repeating unit of the O-polysaccharide having the following structure: →2)-α-d-Galf-(1→3)-α-l-Rhap2Ac-(1→4)-α-d-Glcp-(1→2)-α-l-Rhap-(1→3)-β-d-GlcpNAc-(1→ Putative functions of genes in the O-antigen gene cluster of E. coli O132 are consistent with the O-polysaccharide structure.
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Affiliation(s)
- Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Wenwen Zhang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
| | - Andrej Weintraub
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Karolinska University Hospital, S-141 86 Stockholm, Sweden
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, 300457 Tianjin, China
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
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Angles d'Ortoli T, Widmalm G. Synthesis of the tetrasaccharide glycoside moiety of Solaradixine and rapid NMR-based structure verification using the program CASPER. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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26
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Kapla J, Engström O, Stevensson B, Wohlert J, Widmalm G, Maliniak A. Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems. Phys Chem Chem Phys 2015; 17:22438-47. [PMID: 26252429 DOI: 10.1039/c5cp02472b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.
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Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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27
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Structural studies of the exopolysaccharide from Lactobacillus plantarum C88 using NMR spectroscopy and the program CASPER. Carbohydr Res 2015; 402:87-94. [DOI: 10.1016/j.carres.2014.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/03/2023]
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28
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Ravenscroft N, Cescutti P, Gavini M, Stefanetti G, MacLennan CA, Martin LB, Micoli F. Structural analysis of the O-acetylated O-polysaccharide isolated from Salmonella paratyphi A and used for vaccine preparation. Carbohydr Res 2014; 404:108-16. [PMID: 25665787 DOI: 10.1016/j.carres.2014.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/10/2014] [Accepted: 12/13/2014] [Indexed: 01/08/2023]
Abstract
Salmonella paratyphi A is increasingly recognized as a common cause of enteric fever cases and there are no licensed vaccines against this infection. Antibodies directed against the O-polysaccharide of the lipopolysaccharide of Salmonella are protective and conjugation of the O-polysaccharide to a carrier protein represents a promising strategy for vaccine development. O-Acetylation of S. paratyphi A O-polysaccharide is considered important for the immunogenicity of S. paratyphi A conjugate vaccines. Here, as part of a programme to produce a bivalent conjugate vaccine against both S. typhi and S. paratyphi A diseases, we have fully elucidated the O-polysaccharide structure of S. paratyphi A by use of HPLC-SEC, HPAEC-PAD/CD, GLC, GLC-MS, 1D and 2D-NMR spectroscopy. In particular, chemical and NMR studies identified the presence of O-acetyl groups on C-2 and C-3 of rhamnose in the lipopolysaccharide repeating unit, at variance with previous reports of O-acetylation at a single position. Moreover HR-MAS NMR analysis performed directly on bacterial pellets from several strains of S. paratyphi A also showed O-acetylation on C-2 and C-3 of rhamnose, thus this pattern is common and not an artefact from O-polysaccharide purification. Conjugation of the O-polysaccharide to the carrier protein had little impact on O-acetylation and therefore should not adversely affect the immunogenicity of the vaccine.
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Affiliation(s)
- N Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - P Cescutti
- Department of Life Sciences, Blg. C11, Università di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - M Gavini
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - G Stefanetti
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - C A MacLennan
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - L B Martin
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - F Micoli
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy.
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29
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Fontana C, Weintraub A, Widmalm G. Structural Elucidation of the O-Antigen Polysaccharide from Escherichia coli O181. ChemistryOpen 2014; 4:47-55. [PMID: 25861570 PMCID: PMC4380953 DOI: 10.1002/open.201402068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 12/02/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) is an important pathogen associated to food-borne infection in humans; strains of E. coli O181, isolated from human cases of diarrhea, have been classified as belonging to this pathotype. Herein, the structure of the O-antigen polysaccharide (PS) from E. coli O181 has been investigated. The sugar analysis showed quinovosamine (QuiN), glucosamine (GlcN), galactosamine (GalN), and glucose (Glc) as major components. Analysis of the high-resolution mass spectrum of the oligosaccharide (OS), obtained by dephosphorylation of the O-deacetylated PS with aqueous 48 % hydrofluoric acid, revealed a pentasaccharide composed of two QuiNAc, one GlcNAc, one GalNAc, and one Glc residue. The 1H and 13C NMR chemical shift assignments of the OS were carried out using 1 D and 2 D NMR experiments, and the OS was sequenced using a combination of tandem mass spectrometry (MS/MS) data and NMR 13C NMR glycosylation shifts. The structure of the native PS was determined using NMR spectroscopy, and it consists of branched pentasaccharide repeating units joined by phosphodiester linkages: →4)[α-l-QuipNAc-(1→3)]-α-d-GalpNAc6Ac-(1→6)-α-d-Glcp-(1→P-4)-α-l-QuipNAc-(1→3)-β-d-GlcpNAc-(1→; the O-acetyl groups represent 0.4 equivalents per repeating unit. Both the OS and PSs exhibit rare conformational behavior since two of the five anomeric proton resonances could only be observed at an elevated temperature.
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Affiliation(s)
- Carolina Fontana
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University S-106 91 Stockholm (Sweden)
| | - Andrej Weintraub
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institute, Karolinska University Hospital S-141 86 Stockholm (Sweden)
| | - Göran Widmalm
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University S-106 91 Stockholm (Sweden)
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30
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Jakhetia R, Marri A, Ståhle J, Widmalm G, Verma NK. Serotype-conversion in Shigella flexneri: identification of a novel bacteriophage, Sf101, from a serotype 7a strain. BMC Genomics 2014; 15:742. [PMID: 25174528 PMCID: PMC4159516 DOI: 10.1186/1471-2164-15-742] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shigella flexneri is the major cause of bacillary dysentery in the developing countries. The lipopolysaccharide (LPS) O-antigen of S. flexneri plays an important role in its pathogenesis and also divides S. flexneri into 19 serotypes. All the serotypes with an exception for serotype 6 share a common O-antigen backbone comprising of N-acetylglucosamine and three rhamnose residues. Different serotypes result from modification of the basic backbone conferred by phage-encoded glucosyltransferase and/or acetyltransferase genes, or plasmid-encoded phosphoethanolamine transferase. Recently, a new site for O-acetylation at positions 3 and 4 of RhaIII, in serotypes 1a, 1b, 2a, 5a and Y was shown to be mediated by the oacB gene. Additionally, this gene was shown to be carried by a transposon-like structure inserted upstream of the adrA region on the chromosome. RESULTS In this study, a novel bacteriophage Sf101, encoding the oacB gene was isolated and characterised from a serotype 7a strain. The complete sequence of its 38,742 bp genome encoding 66 open reading frames (orfs) was determined. Comparative analysis revealed that phage Sf101 has a mosaic genome, and most of its proteins were >90% identical to the proteins from 12 previously characterised lambdoid phages. In addition, the organisation of Sf101 genes was found to be highly similar to bacteriophage Sf6. Analysis of the Sf101 OacB identified two amino acid substitutions in the protein; however, results obtained by NMR spectroscopy confirmed that Sf101-OacB was functional. Inspection of the chromosomal integration site of Sf101 phage revealed that this phage integrates in the sbcB locus, thus unveiling a new site for integration of serotype-converting phages of S. flexneri, and determining an alternative location of oacB gene in the chromosome. Furthermore, this study identified oacB gene in several serotype 7a isolates from various regions providing evidence of O-acetyl modification in serotype 7a. CONCLUSIONS This is the first report on the isolation of bacteriophage Sf101 which contains the S. flexneri O-antigen modification gene oacB. Sf101 has a highly mosaic genome and was found to integrate in the sbcB locus. These findings contribute an advance in our current knowledge of serotype converting phages of S. flexneri.
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Affiliation(s)
| | | | | | | | - Naresh K Verma
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Bldg, 134 Linnaeus Way, Canberra ACT 0200, Australia.
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31
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Pauli GF, Chen SN, Lankin DC, Bisson J, Case RJ, Chadwick LR, Gödecke T, Inui T, Krunic A, Jaki B, McAlpine JB, Mo S, Napolitano JG, Orjala J, Lehtivarjo J, Korhonen SP, Niemitz M. Essential parameters for structural analysis and dereplication by (1)H NMR spectroscopy. JOURNAL OF NATURAL PRODUCTS 2014; 77:1473-87. [PMID: 24895010 PMCID: PMC4076039 DOI: 10.1021/np5002384] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 05/12/2023]
Abstract
The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain (1)H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1-1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen ((1)H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms.
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Affiliation(s)
- Guido F. Pauli
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jonathan Bisson
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Ryan J. Case
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Lucas R. Chadwick
- Bells Brewery, 8938 Krum Avenue, Kalamazoo, Michigan 49009, United States
| | - Tanja Gödecke
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Taichi Inui
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Aleksej Krunic
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Birgit
U. Jaki
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Shunyan Mo
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - José G. Napolitano
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jimmy Orjala
- Department
of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Juuso Lehtivarjo
- School of Pharmacy, University of Eastern Finland, P.O.
Box 1627, 70211 Kuopio, Finland
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Turska-Szewczuk A, Pietras H, Duda KA, Kozińska A, Pękala A, Holst O. Structure of the O-specific polysaccharide from the lipopolysaccharide of Aeromonas sobria strain Pt312. Carbohydr Res 2014; 403:142-8. [PMID: 25037826 DOI: 10.1016/j.carres.2014.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/30/2014] [Accepted: 06/11/2014] [Indexed: 11/30/2022]
Abstract
The O-specific polysaccharide (OPS) obtained by mild-acid degradation of the lipopolysaccharide from Aeromonas sobria strain Pt312 was studied by sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, NOESY, 1H-detected 1H,13C HSQC, and HMBC experiments. The sequence of the sugar residues was determined using 1H,1H NOESY and 1H,13C HMBC experiments. It was found that the OPS was built up of disaccharide repeating units composed of GlcpNAc and non-stoichiometrically O-acetylated Rhap residues, and had the structure.
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Affiliation(s)
- Anna Turska-Szewczuk
- Department of Genetics and Microbiology, M. Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Hubert Pietras
- Department of Genetics and Microbiology, M. Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Katarzyna A Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 4a/c, D-23845 Borstel, Germany
| | - Alicja Kozińska
- Department of Fish Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland
| | - Agnieszka Pękala
- Department of Fish Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 4a/c, D-23845 Borstel, Germany
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Structural studies and biosynthetic aspects of the O-antigen polysaccharide from Escherichia coli O42. Carbohydr Res 2014; 403:174-81. [PMID: 24909379 DOI: 10.1016/j.carres.2014.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/06/2014] [Accepted: 05/10/2014] [Indexed: 01/31/2023]
Abstract
The structure of the O-antigen polysaccharide (PS) from Escherichia coli O42 has been investigated by NMR spectroscopy as the main method, which was complemented with sugar analysis, mass spectrometry, and analysis of biosynthetic information. The O-specific chain of the O-deacylated lipopolysaccharide (LPS-OH) consists of branched tetrasaccharide-glycerol repeating units joined by phosphodiester linkages. The lipid-free polysaccharide contains 0.8equiv of O-acetyl groups per repeating unit and has the following teichoic acid-like structure: Based on biosynthetic aspects, this should also be the biological repeating unit. This O-antigen structure is remarkably similar to that of E. coli O28ac, differing only in the presence or absence, respectively, of a glucose residue at the branching point. The structural similarity explains the serological cross-reactivity observed between strains of these two serogroups, and also their almost identical O-antigen gene cluster sequences.
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Côté GL, Cormier RS, Vermillion KE. Glucansucrase acceptor reactions with d-mannose. Carbohydr Res 2014; 387:1-3. [PMID: 24513699 DOI: 10.1016/j.carres.2014.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
The main acceptor product of glucansucrases with d-mannose has not previously been identified. We used glucansucrases that form water-insoluble α-d-glucans to produce increased yields of acceptor products from d-mannose, and identified the major product as 6-O-α-d-glucopyranosyl-d-mannose. Glucansucrases that synthesize insoluble α-d-glucans produced higher yields of the disaccharide compared to typical dextransucrases.
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Affiliation(s)
- Gregory L Côté
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 N. University St., Peoria, IL 61604, USA.
| | - Ryan S Cormier
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 N. University St., Peoria, IL 61604, USA
| | - Karl E Vermillion
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 N. University St., Peoria, IL 61604, USA
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35
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Patel DS, Pendrill R, Mallajosyula SS, Widmalm G, MacKerell AD. Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments. J Phys Chem B 2014; 118:2851-71. [PMID: 24552401 PMCID: PMC3979472 DOI: 10.1021/jp412051v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored.
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Affiliation(s)
- Dhilon S Patel
- Department of Pharmaceutical Sciences, University of Maryland , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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Fontana C, Lundborg M, Weintraub A, Widmalm G. Rapid structural elucidation of polysaccharides employing predicted functions of glycosyltransferases and NMR data: application to the O-antigen of Escherichia coli O59. Glycobiology 2014; 24:450-7. [PMID: 24558268 DOI: 10.1093/glycob/cwu011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A computerized method that uses predicted functions of glycosyltransferases (GTs) in conjunction with unassigned NMR data has been developed for the structural elucidation of bacterial polysaccharides (PSs). In this approach, information about the action of GTs (consisting of possible sugar residues used as donors and/or acceptors, as well as the anomeric configuration and/or substitution position in the respective glycosidic linkages) is extracted from the Escherichia coli O-antigen database and is submitted, together with the unassigned NMR data, to the CASPER program. This time saving methodology, which alleviates the need for chemical analysis, was successfully implemented in the structural elucidation of the O-antigen PS of E. coli O59. The repeating unit of the O-specific chain was determined using the O-deacylated PS and has a branched structure, namely, →6)[α-d-GalpA3Ac/4Ac-(1 → 3)]-α-d-Manp-(1 → 3)-α-d-Manp-(1 → 3)-β-d-Manp-(1 → 3)-α-d-GlcpNAc-(1→. The identification of the O-acetylation positions was efficiently performed by comparison of the (1)H,(13)C HSQC NMR spectra of the O-deacylated lipopolysaccharide and the lipid-free PS in conjunction with chemical shift predictions made by the CASPER program. The side-chain d-GalpA residue carries one equivalent of O-acetyl groups at the O-3 and O-4 positions distributed in the LPS in a 3:7 ratio, respectively. The presence of O-acetyl groups in the repeating unit of the E. coli O59 PS is consistent with the previously proposed acetyltransferase WclD in the O-antigen gene cluster.
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Affiliation(s)
- Carolina Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Moreno FJ, Montilla A, Villamiel M, Corzo N, Olano A. Analysis, structural characterization, and bioactivity of oligosaccharides derived from lactose. Electrophoresis 2014; 35:1519-34. [PMID: 24446419 DOI: 10.1002/elps.201300567] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 12/18/2022]
Abstract
The increasing interest for prebiotic carbohydrates as functional food ingredients has promoted the synthesis of galactooligosaccharides and new lactose derivatives. This review provides a comprehensive overview on the chromatographic analysis, structural characterization, and bioactivity studies of lactose-derived oligosaccharides. The most common chromatographic techniques used for the separation and structural characterization of this type of oligosaccharides, including GC and HPLC in different operational modes, coupled to various detectors are discussed. Insights on oligosaccharide MS fragmentation patterns, using different ionization sources and mass analyzers, as well as data on structural analysis by NMR spectroscopy are also described. Finally, this article deals with the bioactive effects of galacto oligosaccharides and oligosaccharides derived from lactulose on the gastrointestinal and immune systems, which support their consumption to provide significant health benefits.
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Affiliation(s)
- F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación (CIAL) (CSIC-UAM), CEI (UAM+CSIC), Campus de la Universidad Autónoma de Madrid, Madrid, Spain
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38
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Micoli F, Ravenscroft N, Cescutti P, Stefanetti G, Londero S, Rondini S, Maclennan CA. Structural analysis of O-polysaccharide chains extracted from different Salmonella Typhimurium strains. Carbohydr Res 2013; 385:1-8. [PMID: 24384528 DOI: 10.1016/j.carres.2013.12.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Salmonella Typhimurium is the major cause of invasive nontyphoidal Salmonella disease in Africa, with high mortality among children and HIV-infected individuals. Currently, no vaccine is available for use in humans. Antibodies directed against the O-polysaccharide of the lipopolysaccharide molecule of Salmonella mediate bacterial killing and are protective, and conjugation of the O-polysaccharide to a carrier protein represents a possible strategy for vaccine development. Here we have purified the O-polysaccharide from six different strains of S. Typhimurium and fully characterized them using analytical methods including HPLC-SEC, HPAEC-PAD, GC, GC-MS, 1D and 2D NMR spectroscopy. All the O-polysaccharide samples showed a similar bimodal molecular mass distribution, but differed with respect to the amount and position of O-acetylation and glucosylation. For some strains, O-acetyl groups were found not only on C-2 of abequose (factor 5 specificity), but also on C-2 and C-3 of rhamnose; glucose was found to be linked 1→4 or 1→6 to galactose in different amounts according to the strain of origin. This structural variability could have an impact on the immunogenicity of corresponding glycoconjugate vaccines and different strains need to be evaluated in order to identify the appropriate source of O-polysaccharide to use for the development of a candidate conjugate vaccine with broad coverage against S. Typhimurium.
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Affiliation(s)
- Francesca Micoli
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy.
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Paola Cescutti
- Dipartimento di Scienze della Vita, Ed. C11, Università di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - Giuseppe Stefanetti
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - Silvia Londero
- Dipartimento di Scienze della Vita, Ed. C11, Università di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - Simona Rondini
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy
| | - Calman A Maclennan
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, I-53100 Siena, Italy; Medical Research Council Centre for Immune Regulation, Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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