1
|
Bånkestad M, Dorst KM, Widmalm G, Rönnols J. Carbohydrate NMR chemical shift prediction by GeqShift employing E(3) equivariant graph neural networks. RSC Adv 2024; 14:26585-26595. [PMID: 39175672 PMCID: PMC11340439 DOI: 10.1039/d4ra03428g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/02/2024] [Indexed: 08/24/2024] Open
Abstract
Carbohydrates, vital components of biological systems, are well-known for their structural diversity. Nuclear Magnetic Resonance (NMR) spectroscopy plays a crucial role in understanding their intricate molecular arrangements and is essential in assessing and verifying the molecular structure of organic molecules. An important part of this process is to predict the NMR chemical shift from the molecular structure. This work introduces a novel approach that leverages E(3) equivariant graph neural networks to predict carbohydrate NMR spectral data. Notably, our model achieves a substantial reduction in mean absolute error, up to threefold, compared to traditional models that rely solely on two-dimensional molecular structure. Even with limited data, the model excels, highlighting its robustness and generalization capabilities. The model is dubbed GeqShift (geometric equivariant shift) and uses equivariant graph self-attention layers to learn about NMR chemical shifts, in particular since stereochemical arrangements in carbohydrate molecules are characteristics of their structures.
Collapse
Affiliation(s)
- Maria Bånkestad
- Department of Information Technology, Uppsala University Sweden
- RISE Research Institutes of Sweden Stockholm Sweden
| | - Kevin M Dorst
- Department of Organic Chemistry, Stockholm University Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University Sweden
| | - Jerk Rönnols
- RISE Research Institutes of Sweden Stockholm Sweden
| |
Collapse
|
2
|
Xu X, Ding Z, Pu C, Kong C, Chen S, Lu W, Zhang J. The structural characterization and UV-protective properties of an exopolysaccharide from a Paenibacillus isolate. Front Pharmacol 2024; 15:1434136. [PMID: 39185320 PMCID: PMC11341463 DOI: 10.3389/fphar.2024.1434136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
Introduction Overexposure to ultraviolet (UV) light is known to cause damage to the skin, leading to sunburn and photo-aging. Chemical sunscreen products may give rise to health risks including phototoxicity, photosensitivity, and photosensitivity. Natural polysaccharides have attracted considerable interests due to diverse biological activities. Methods A novel polysaccharide isolated was purified and structurally characterized using chemical methods followed by HPLC, GLC-MS, as well as 1D and 2D NMR spectroscopy. The photoprotective effect of the EPS on UVB-induced damage was assessed in vitro using cultured keratinocytes and in vivo using C57BL/6 mouse models. Results The average molecular weight of the EPS was 5.48 × 106 Da, composed of glucose, mannose and galactose residues at a ratio of 2:2:1. The repeating units of the EPS were →3)-β-D-Glcp (1→3) [β-D-Galp (1→2)-α-D-Glcp (1→2)]-α-D-Manp (1→3)-α-D-Manp (1→. In cultured keratinocytes, the EPS reduced cytotoxicity and excessive ROS production induced by UVB irradiation. The EPS also exhibits an inhibitory effect on oxidative stress, inflammation, and collagen degradation found in the photodamage in mice. 1H NMR-based metabolomics analysis for skin suggested that the EPS partly reversed the shifts of metabolic profiles of the skin in UVB-exposed mice. Conclusion The EPS exhibits skin photoprotective effects through regulating oxidative stress both in vivo and in vitro. Our findings highlight that the EPS is a potential candidate in sunscreen formulations for an efficient solution to UVB radiation.
Collapse
Affiliation(s)
- Xiaodong Xu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Zhao Ding
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Chunlin Pu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Changchang Kong
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Shijunyin Chen
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Weiling Lu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing, China
| |
Collapse
|
3
|
Čuljak N, Bellich B, Pedroni A, Butorac K, Pavunc AL, Novak J, Banić M, Šušković J, Cescutti P, Kos B. Limosilactobacillus fermentum strains MC1 and D12: Functional properties and exopolysaccharides characterization. Int J Biol Macromol 2024; 273:133215. [PMID: 38897515 DOI: 10.1016/j.ijbiomac.2024.133215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/17/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Lactic acid bacteria (LAB) produce a broad spectrum of exopolysaccharides (EPSs), commonly used as texturizers in food products. Due to their potential contribution to LAB probiotic properties, like adhesion to human epithelial cells and competitive exclusion of pathogens from human intestinal epithelial cells, this study was focussed on the structural and functional characterization of the EPSs produced by two Limosilactobacillus fermentum strains - MC1, originating from mother's milk, and D12, autochthonous from Croatian smoked fresh cheese. Whole-genome sequencing and functional annotation of both L. fermentum strains by RAST server revealed the genes involved in EPS production and transport, with some differences in functionally related genes. EPSs were extracted from the cell surface of both bacterial strains and purified by size-exclusion chromatography. Structural characterization of the EPSs, achieved by chemical analyses and 1D and 2D NMR spectroscopy, showed that both strains produce an identical mixture of three different EPSs containing galactofuranose and glucopyranose residues. However, a comparison of the functional properties showed that the MC1 strain adhered better to the Caco-2 cell line and exhibited stronger antimicrobial effect against Salmonella enterica serovar Typhimurium FP1 than the D12 strain, which may be attributed to the potential bacteriocin activity of the MC1 strain.
Collapse
Affiliation(s)
- Nina Čuljak
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Barbara Bellich
- Department of Advanced Translational Diagnostics, Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Via dell'Istria 65, 34137 Trieste, Italy
| | - Alice Pedroni
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, Bdg. C11, 34127 Trieste, Italy
| | - Katarina Butorac
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Andreja Leboš Pavunc
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jasna Novak
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Martina Banić
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jagoda Šušković
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, Bdg. C11, 34127 Trieste, Italy.
| | - Blaženka Kos
- Laboratory for Antibiotic, Enzyme, Probiotic and Starter Cultures Technology, Department of Biochemical Engineering, University of Zagreb Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia
| |
Collapse
|
4
|
Toukach P. Carbohydrate Structure Database: current state and recent developments. Anal Bioanal Chem 2024:10.1007/s00216-024-05383-w. [PMID: 38914734 DOI: 10.1007/s00216-024-05383-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/18/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024]
Abstract
Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.
Collapse
Affiliation(s)
- Philip Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Faculty of Chemistry, National Research University Higher School of Economics, Moscow, Russia.
| |
Collapse
|
5
|
Chen JQ, Miao W, Liu Y, Zhou J, Han J, Zhang L, Bian XQ, Zhong T, Wu JL, Li N. Structural characterization, molecular dynamic simulation, and conformational visualization of a water-soluble glucan with high molecular weight from Gastrodia elata Blume. Int J Biol Macromol 2024; 263:130207. [PMID: 38365156 DOI: 10.1016/j.ijbiomac.2024.130207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Polysaccharides have been widely used in the development of natural drugs and health food. However, polysaccharide characterization lags due to inherently complicated features and the limitations of existing detection approaches. We aimed to provide new insight into the fine structure and conformational visualization of polysaccharides from Gastrodia elata Blume, a medicinal and edible plant. A water-soluble polysaccharide (GEP2-6) with the high molecular weight of 2.7 × 106 Da was first obtained, and its purity reached 99.2 %. Chemical and spectroscopic analyses jointly revealed that GEP2-6 was a glucan linked by α-(1 → 4) and α-(1 → 6) glycosidic bonds. After enzymolysis, the local structure of GEP2-6 included α-1,4-Glcp, α-1,6-Glcp, α-1,4,6-Glcp, and α-1-Glcp at a molar ratio of 31.27∶1.32∶1.08∶0.93. The glycosidic linkage pattern of repeating units was further simulated by a glycan database and spatial examination software. The good dissolution performance was interpreted by dynamics simulation and practical molecular characteristics. Spherical flexible chains and the porous stable conformation were corroborated using atomic force microscopy. In addition, GEP2-6 could effectively scavenge DPPH and hydroxyl radicals as a promising natural antioxidant. These efforts will contribute to the expansion of clinical applications of this G. elata polysaccharide and the structural elucidation for macromolecular polysaccharides combined with traditional and modern analysis techniques.
Collapse
Affiliation(s)
- Jia-Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Wen Miao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Ying Liu
- School of Basic Medicinal Sciences and Nursing, Chengdu University, Chengdu 610106, PR China
| | - Jie Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Jie Han
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Li Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Xi-Qing Bian
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao.
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao.
| |
Collapse
|
6
|
Kong C, Chen S, Wang X, Hu C, Li B, Fu R, Zhang J. Hemoadhican, a Tissue Adhesion Hemostatic Material Independent of Blood Coagulation. Adv Healthc Mater 2023; 12:e2300705. [PMID: 37029455 DOI: 10.1002/adhm.202300705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/29/2023] [Indexed: 04/09/2023]
Abstract
Uncontrolled hemorrhage is a leading cause of death, emphasizing the need for novel hemostatic agents. Here, a novel hemostatic polysaccharide hemoadhican (HD) is screened out by analyzing the rheological properties of screened material mixed blood sludges, which is prepared by mixing polysaccharide granules and whole blood to mimic the coagulation in vitro. HD is produced by a bacterial isolate Paenibacillus sp.1229, and the repeating units of HD are →)-α-L-Rhap-(1→3)-β-D-Glcp-(1→4)[4,6-ethylidene-α-D-Galp-(1→4)-α-D-Glcp-(1→3)]-α-D-Manp-(1→. Compared to chitosan and celox, HD achieves more effective hemostasis in animal models with mouse and rat femoral arteries, rat carotid arteries, and rabbit femoral arteries. Especially, HD maintains an excellent hemostatic capability in animals with heparin-induced hemorrhage diathesis. In vitro experiments show HD granules can quickly absorb a small amount of blood component to create a hemophobic blood sludge resistant to high pressure. The blood sludge firmly adheres to damaged tissue and efficiently repels blood. In vitro experiments show that HD does not actively trigger blood coagulation cascade and is independent of blood conditions including heparin treatment. In addition, HD moisturizes wounds and accelerates wound healing, exhibiting excellent biodegradability, and hemocompatibility. The results indicate that HD is a promising hemostatic material for treating traumatic hemorrhages and uncontrollable surgical bleeding.
Collapse
Affiliation(s)
- Changchang Kong
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Beijing, 210094, China
| | - Shijunyin Chen
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Beijing, 210094, China
| | - Xianjin Wang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Beijing, 210094, China
| | - Chengtao Hu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Beijing, 210094, China
| | - Bing Li
- Nanjing Southern Element Biotechnology Co., Ltd, Nanjing, 211899, China
| | - Renjie Fu
- Nanjing Southern Element Biotechnology Co., Ltd, Nanjing, 211899, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, 210094, China
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Beijing, 210094, China
| |
Collapse
|
7
|
Toukach PV, Shirkovskaya AI. Carbohydrate Structure Database and Other Glycan Databases as an Important Element of Glycoinformatics. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022030190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Toukach PV, Egorova KS. Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans. Sci Data 2022; 9:131. [PMID: 35354826 PMCID: PMC8968703 DOI: 10.1038/s41597-022-01186-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
The Carbohydrate Structure Database (CSDB, http://csdb.glycoscience.ru/ ) is a free curated repository storing various data on glycans of bacterial, fungal and plant origins. Currently, it maintains a close-to-full coverage on bacterial and fungal carbohydrates up to the year 2020. The CSDB web-interface provides free access to the database content and dedicated tools. Still, the number of these tools and the types of the corresponding analyses is limited, whereas the database itself contains data that can be used in a broader scope of analytical studies. In this paper, we present CSDB source data files and a self-contained SQL dump, and exemplify their possible application in glycan-related studies. By using CSDB in an SQL format, the user can gain access to the chain length distribution or charge distribution (as an example) in a given set of glycans defined according to specific structural, taxonomic, or other parameters, whereas the source text dump files can be imported to any dedicated database with a specific internal architecture differing from that of CSDB.
Collapse
Affiliation(s)
- Philip V Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow, 119991, Russia.
| | - Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, Moscow, 119991, Russia.
| |
Collapse
|
9
|
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]
|
10
|
Structure and gene cluster of the O-antigen of Enterobacter cloacae G3422. Carbohydr Res 2021; 510:108440. [PMID: 34619615 DOI: 10.1016/j.carres.2021.108440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022]
Abstract
The O-polysaccharide (OPS) was isolated by mild acid degradation of the lipopolysaccharide of Enterobacter cloacae G3422 and studied by chemical methods, including sugar analyses, Smith degradation, and solvolysis with anhydrous trifluoroacetic acid, along with 1H and 13C NMR spectroscopy. The following structure of the branched tetrasaccharide repeating unit was established: The O-antigen gene cluster of Enterobacter cloacae G3422 was sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in a good agreement with the O-antigen structure.
Collapse
|
11
|
Filatov AV, Perepelov AV, Shashkov AS, Burygin GL, Gogoleva NE, Khlopko YA, Grinev VS. Structure and genetics of the O-antigen of Enterobacter cloacae K7 containing di-N-acetylpseudaminic acid. Carbohydr Res 2021; 508:108392. [PMID: 34274818 DOI: 10.1016/j.carres.2021.108392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
The O-antigen (O-polysaccharide) is an essential component of lipopolysaccharide on the surface of Gram-negative bacteria and plays an important role in interaction with host organisms. In this study, we investigated the chemical structure and characterized the gene cluster of Enterobacter cloacae K7 O-antigen. As judged by sugar analyses along with NMR spectroscopy data, E. cloacae K7 antigen has a tetrasaccharide O-unit with the following structure: →8)-β-Psep5Ac7Ac-(2 → 2)-β-l-Rhap-(1 → 4)-α-l-Rhap-(1 → 3)-α-d-Galp-(1→ The O-antigen gene cluster of E. cloacae K7 between conserved genes galF and gnd was sequenced. Most genes necessary for the O-antigen synthesis were found in the cluster and their functions were tentatively assigned by comparison with sequences in the available databases.
Collapse
Affiliation(s)
- Andrei V Filatov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation.
| | - Andrei V Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Gennady L Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049, Saratov, Russian Federation; Vavilov Saratov State Agrarian University, 410012, Saratov, Russian Federation
| | - Natalia E Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, 420111, Kazan, Russian Federation; Kazan Federal University, 420111, Kazan, Russian Federation
| | - Yuriy A Khlopko
- Institute for Cellular and Intracellular Symbiosis, Urals Branch, Russian Academy of Sciences, 460000, Orenburg, Russian Federation
| | - Vyacheslav S Grinev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049, Saratov, Russian Federation
| |
Collapse
|
12
|
Zdorovenko EL, Gannesen AV, Dmitrenok AS, Zhurina MV, Mart'yanov SV, Shashkov AS. Structure of cell-wall glycopolymers of Micrococcus luteus C01. Carbohydr Res 2021; 506:108356. [PMID: 34087653 DOI: 10.1016/j.carres.2021.108356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/19/2022]
Abstract
Glycopolymers of two types were isolated from the cell wall of Micrococcus luteus C01 by stepwise extraction with cold and hot 10% aq CCl3CO2H. The following structures of the glycopolymers were established by compositional analysis and 1D and 2D NMR spectroscopy: where L-Glu indicates glutamic acid.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Andrey V Gannesen
- Federal Research Center "Fundamentals of Biotechnology" of Russian Academy of Sciences, Moscow, Russia
| | - Andrey S Dmitrenok
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Zhurina
- Federal Research Center "Fundamentals of Biotechnology" of Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Mart'yanov
- Federal Research Center "Fundamentals of Biotechnology" of Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
13
|
Zdorovenko EL, Dmitrenok AS, Masi M, Castaldi S, Muzio FM, Isticato R, Valverde C, Knirel YA, Evidente A. Structural studies on the O-specific polysaccharide of the lipopolysaccharide from Pseudomonas donghuensis strain SVBP6, with antifungal activity against the phytopathogenic fungus Macrophomina phaseolina. Int J Biol Macromol 2021; 182:2019-2023. [PMID: 34081955 DOI: 10.1016/j.ijbiomac.2021.05.187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/30/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022]
Abstract
An O-specific polysaccharide (OPS) was isolated from the lipopolysaccharide (LPS) of Pseudomonas donghuensis SVBP6, a bacterium with a broad-spectrum antifungal activity in vitro, particularly that against Macrophomina phaseolina. This latter is one of the most virulent and dangerous pathogens of plants, including soybean which is an economically important crop in Argentina today. The OPS was studied by sugar analysis and spectroscopy (1D and 2D 1H and 13C NMR) showing the following trisaccharide repeating unit: →6)-ɑ-D-ManpNAc-(1 → 3)-β-l-Rhap-(1 → 4)-β-D-Glcp-(1→. The crude LPS, the purified LPS and the O-chain were assayed for their antifungal activity against M. phaseolina at 25, 50, 100, and 200 μg plug-1. The results showed that the crude LPS best inhibition was at 200 μg plug-1, able to inhibit the fungus growth by about 45%, while purified LPS and the corresponding OPS, in the same condition, reduced fungus growth by 65%, and 75%, respectively. Furthermore, the purified LPS and OPS significantly reduced the growth of M. phaseolina already at 100 μg plug-1 compared to the crude LPS. The structure of the O-chain is unique among the bacterial LPS and this is the first time that both the antifungal activity of a bacterial LPS and its corresponding O-chain were described.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991 Moscow, Russia
| | - Andrey S Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991 Moscow, Russia
| | - Marco Masi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Stefany Castaldi
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Federico M Muzio
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas-Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Rachele Isticato
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas-Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991 Moscow, Russia
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy.
| |
Collapse
|
14
|
Zdorovenko EL, Kadykova AA, Shashkov AS, Kiseleva EP, Savich VV, Novik GI. The O-specific polysaccharides structures of Pseudomonas strains isolated from the Ficus elastica. Carbohydr Res 2021; 499:108235. [PMID: 33461053 DOI: 10.1016/j.carres.2021.108235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/28/2022]
Abstract
Two Pseudomonas strains were isolated from the Ficus elastica leaves. The O-antigens were obtained using phenol-water method and mild acid degradation. The following structures of the O-polysaccharides were established by sugar analysis and 2D NMR spectroscopy: OPS of Pseudomonas psychrotolerans BIM B-1171 G -2)[aDGlcp(1-3)]bDRhap(1-3)aDManp(1-3)aDRhap(1- OPS of Pseudomonas sp. BIM B-1172 G -2)bDRhap(1-3)aDRhap(1-3)[aDGlcp(1-2)]aDRhap(1-.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Alexandra A Kadykova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Elena P Kiseleva
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141, Minsk, Belarus
| | - Victoria V Savich
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141, Minsk, Belarus
| | - Galina I Novik
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141, Minsk, Belarus
| |
Collapse
|
15
|
Bellich B, Jou IA, Buriola C, Ravenscroft N, Brady JW, Fazli M, Tolker-Nielsen T, Rizzo R, Cescutti P. The biofilm of Burkholderia cenocepacia H111 contains an exopolysaccharide composed of l-rhamnose and l-mannose: Structural characterization and molecular modelling. Carbohydr Res 2020; 499:108231. [PMID: 33440288 DOI: 10.1016/j.carres.2020.108231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Burkholderia cenocepacia belongs to the Burkholderia Cepacia Complex, a group of 22 closely related species both of clinical and environmental origin, infecting cystic fibrosis patients. B. cenocepacia accounts for the majority of the clinical isolates, comprising the most virulent and transmissible strains. The capacity to form biofilms is among the many virulence determinants of B. cenocepacia, a characteristic that confers enhanced tolerance to some antibiotics, desiccation, oxidizing agents, and host defenses. Exopolysaccharides are a major component of biofilm matrices, particularly providing mechanical stability to biofilms. Recently, a water-insoluble exopolysaccharide produced by B. cenocepacia H111 in biofilm was characterized. In the present study, a water-soluble exopolysaccharide was extracted from B. cenocepacia H111 biofilm, and its structure was determined by GLC-MS, NMR and ESI-MS. The repeating unit is a linear rhamno-tetrasaccharide with 50% replacement of a 3-α-L-Rha with a α-3-L-Man. [2)-α-L-Rhap-(1→3)-α-L-[Rhap or Manp]-(1→3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→]n Molecular modelling was used to obtain information about local structural motifs which could give information about the polysaccharide conformation.
Collapse
Affiliation(s)
- Barbara Bellich
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, Bdg. C11, 34127, Trieste, Italy
| | - Ining A Jou
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Claudia Buriola
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, Bdg. C11, 34127, Trieste, Italy
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mustafa Fazli
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Roberto Rizzo
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, Bdg. C11, 34127, Trieste, Italy
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 1, Bdg. C11, 34127, Trieste, Italy.
| |
Collapse
|
16
|
Zdorovenko EL, Kadykova AA, Shashkov AS, Varbanets LD, Bulyhina TV, Knirel YA. Lipopolysaccharide of Pantoea agglomerans 7460: O-specific polysaccharide and lipid A structures and biological activity. Carbohydr Res 2020; 496:108132. [PMID: 32861900 DOI: 10.1016/j.carres.2020.108132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/04/2020] [Accepted: 08/10/2020] [Indexed: 11/27/2022]
Abstract
Lipopolysaccharide (LPS) was isolated from Pantoea agglomerans 7460 cells by phenol-water extraction. Mild acid degradation allowed to separate OPS and lipid A. Lipid A was analyzed by negative-ion mode ESI MS and found to consist mainly of hexaacylated derivative containing biphosphorylated GlcN disaccharide, four 14:0 (3-OH), 18:0 and 12:0 fatty acids. The structure of the O-specific polysaccharide was established by chemical, NMR and computational methods: The LPS of Р. agglomerans 7460 showed low level of toxicity and pyrogenicity to compare with LPS of E. coli O55:B5 and pyrogenal, respectively. The ability of the modified (succinylated) LPS, which have lost its toxicity, to block the toxic effects of native LPS has been shown.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Alexandra A Kadykova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Liudmyla D Varbanets
- D.K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences, 154 Zabolotnoho Str., 03143, Kiev, Ukraine
| | - Tetiana V Bulyhina
- D.K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences, 154 Zabolotnoho Str., 03143, Kiev, Ukraine
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| |
Collapse
|
17
|
Structural studies of the pectic polysaccharide from fruits of Punica granatum. Carbohydr Polym 2020; 235:115978. [DOI: 10.1016/j.carbpol.2020.115978] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 11/23/2022]
|
18
|
Zdorovenko EL, Kadykova AA, Shashkov AS, Kiseleva EP, Savich VV, Novik GI. O-specific polysaccharides structures of Pseudomonas strains isolated from the strawberry leaves. Carbohydr Res 2020; 489:107932. [PMID: 32035290 DOI: 10.1016/j.carres.2020.107932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/16/2020] [Accepted: 01/31/2020] [Indexed: 11/19/2022]
Abstract
Two Pseudomonas strains were isolated from the strawberry leaves. The O-antigens were obtained using phenol-water method and mild acid degradation. The following structures of the O-polysaccharides were established by sugar analysis and 2D NMR spectroscopy: OPS of Pseudomonas koreensis BIM B-970G →3)-α-D-FucNAcp-(1 → 2)-β-D-Quip3NAc-(1 → 3)-α-L-6dTalp4OAc-(1→ OPS of Pseudomonas oryzihabitans BIM B-1072G →4)-α-L-FucpNAm3OAc-(1 → 3)-α-D-QuipNAc-(1 → 4)-β-D-GlcpNAc3NAcA-(1→ Where Am - acetimidoyl.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Alexandra A Kadykova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia; Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Elena P Kiseleva
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141, Minsk, Republic of Belarus
| | - Victoria V Savich
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141, Minsk, Republic of Belarus
| | - Galina I Novik
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141, Minsk, Republic of Belarus
| |
Collapse
|
19
|
Toukach PV, Egorova KS. New Features of Carbohydrate Structure Database Notation (CSDB Linear), As Compared to Other Carbohydrate Notations. J Chem Inf Model 2019; 60:1276-1289. [DOI: 10.1021/acs.jcim.9b00744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosect 47, Moscow, Russia 119991
- National Research University Higher School of Economics, Myasnitskaya 20, Moscow, Russia 101000
| | - Ksenia S. Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosect 47, Moscow, Russia 119991
| |
Collapse
|
20
|
Li X, Perepelov AV, Filatov AV, Shashkov AS, Liu B. Structure elucidation and gene cluster characterization of the O-antigen of Vibrio cholerae O68 containing (2S,4R)-2,4-dihydroxypentanoic acid. Carbohydr Res 2019; 484:107766. [DOI: 10.1016/j.carres.2019.107766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/28/2019] [Accepted: 08/02/2019] [Indexed: 12/01/2022]
|
21
|
Gray CJ, Migas LG, Barran PE, Pagel K, Seeberger PH, Eyers CE, Boons GJ, Pohl NLB, Compagnon I, Widmalm G, Flitsch SL. Advancing Solutions to the Carbohydrate Sequencing Challenge. J Am Chem Soc 2019; 141:14463-14479. [PMID: 31403778 DOI: 10.1021/jacs.9b06406] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.
Collapse
Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Lukasz G Migas
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Perdita E Barran
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Kevin Pagel
- Institute for Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Peter H Seeberger
- Biomolecular Systems Department , Max Planck Institute for Colloids and Interfaces , Am Muehlenberg 1 , 14476 Potsdam , Germany
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Crown Street , Liverpool L69 7ZB , U.K
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Nicola L B Pohl
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Isabelle Compagnon
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS , Université de Lyon , 69622 Villeurbanne Cedex , France.,Institut Universitaire de France IUF , 103 Blvd St Michel , 75005 Paris , France
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , S-106 91 Stockholm , Sweden
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| |
Collapse
|
22
|
Zdorovenko EL, Kadykova AA, Shashkov AS, Varbanets LD, Bulyhina TV. Pantoea agglomerans P1a lipopolysaccharide: Structure of the O-specific polysaccharide and lipid A and biological activity. Carbohydr Res 2019; 484:107767. [PMID: 31400668 DOI: 10.1016/j.carres.2019.107767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/23/2019] [Accepted: 08/03/2019] [Indexed: 12/14/2022]
Abstract
O-specific polysaccharide and lipid A were obtained from the lipopolysaccharide from new strain of Рantoea agglomerans P1a by mild acid hydrolysis. It was found that the major form of lipid A presented by tetraacylated derivative containing biphosphorylated GlcN disaccharide, three 14:0 (3-OH) and 12:0 residues. The structure of the O-specific polysaccharide was established by chemical, NMR and computational methods: →3)-α-D-Manp-(1 → 4)-β-D-Fucp-(1 → 4)-ɑ-D-Fucp-(1→The LPS of Р. agglomerans P1a showed low level of toxicity and pyrogenicity to compare with LPS of E. coli O55:B5 and pyrogenal (respectively).
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Alexandra A Kadykova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Ludmila D Varbanets
- D.K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences, 154 Zabolotnogo Str, 03143, Kiev, Ukraine
| | - Tetiana V Bulyhina
- D.K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences, 154 Zabolotnogo Str, 03143, Kiev, Ukraine
| |
Collapse
|
23
|
Sizova OV, Shashkov AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Dentovskaya SV. Structure elucidation and gene cluster characterization of the O-antigen of Yersinia kristensenii С-134. Carbohydr Res 2019; 481:9-15. [PMID: 31220629 DOI: 10.1016/j.carres.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/24/2019] [Accepted: 06/01/2019] [Indexed: 11/26/2022]
Abstract
Mild acid degradation of the lipopolysaccharide of Yersinia kristensenii C-134 afforded a glycerol teichoic acid-like O-polysaccharide, which was studied by sugar analysis, O-deacetylation and dephosphorylation along with 1D and 2D NMR spectroscopy. The following structure of the O-polysaccharide was established: This structure is related to those of other Y. kristensenii O-polysaccharides studied earlier. The O-antigen gene cluster of Y. kristensenii С-134 was analyzed and found to be consistent with the O-polysaccharide structure established.
Collapse
Affiliation(s)
- Olga V Sizova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Philip V Toukach
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russian Federation
| | - Rima Z Shaikhutdinova
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Sergei A Ivanov
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Angelina A Kislichkina
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation
| | - Svetlana V Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russian Federation.
| |
Collapse
|
24
|
Gannesen AV, Zdorovenko EL, Botchkova EA, Hardouin J, Massier S, Kopitsyn DS, Gorbachevskii MV, Kadykova AA, Shashkov AS, Zhurina MV, Netrusov AI, Knirel YA, Plakunov VK, Feuilloley MGJ. Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5. Front Microbiol 2019; 10:1284. [PMID: 31293526 PMCID: PMC6598116 DOI: 10.3389/fmicb.2019.01284] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/23/2019] [Indexed: 12/11/2022] Open
Abstract
In skin, Cutibacterium acnes (former Propionibacterium acnes) can behave as an opportunistic pathogen, depending on the strain and environmental conditions. Acneic strains of C. acnes form biofilms inside skin-gland hollows, inducing inflammation and skin disorders. The essential exogenous products of C. acnes accumulate in the extracellular matrix of the biofilm, conferring essential bacterial functions to this structure. However, little is known about the actual composition of the biofilm matrix of C. acnes. Here, we developed a new technique for the extraction of the biofilm matrix of Gram-positive bacteria without the use of chemical or enzymatic digestion, known to be a source of artifacts. Our method is based on the physical separation of the cells and matrix of sonicated biofilms by ultracentrifugation through a CsCl gradient. Biofilms were grown on the surface of cellulose acetate filters, and the biomass was collected without contamination by the growth medium. The biofilm matrix of the acneic C. acnes RT5 strain appears to consist mainly of polysaccharides. The following is the ratio of the main matrix components: 62.6% polysaccharides, 9.6% proteins, 4.0% DNA, and 23.8% other compounds (porphyrins precursors and other). The chemical structure of the major polysaccharide was determined using a nuclear magnetic resonance technique, the formula being →6)-α-D-Galp-(1→4)-β-D-ManpNAc3NAcA-(1→6)-α-D-Glcp-(1→4)-β-D-ManpNAc3NAcA-(1→3)-β-GalpNAc-(1→. We detected 447 proteins in the matrix, of which the most abundant were the chaperonin GroL, the elongation factors EF-Tu and EF-G, several enzymes of glycolysis, and proteins of unknown function. The matrix also contained more than 20 hydrolases of various substrata, pathogenicity factors, and many intracellular proteins and enzymes. We also performed surface-enhanced Raman spectroscopy analysis of the C. acnes RT5 matrix for the first time, providing the surface-enhanced Raman scattering (SERS) profiles of the C. acnes RT5 biofilm matrix and biofilm biomass. The difference between the matrix and biofilm biomass spectra showed successful matrix extraction rather than simply the presence of cell debris after sonication. These data show the complexity of the biofilm matrix composition and should be essential for the development of new anti-C. acnes biofilms and potential antibiofilm drugs.
Collapse
Affiliation(s)
- Andrei V. Gannesen
- Winogradsky Institute of Microbiology, Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, Russia
| | - Evelina L. Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Botchkova
- Winogradsky Institute of Microbiology, Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, Russia
- Department of Physical and Colloid Chemistry, Gubkin University, Moscow, Russia
| | - Julie Hardouin
- Laboratory of Polymers, Biopolymers, Surfaces UMR 6270 PBS, Rouen University, Rouen, France
| | - Sebastien Massier
- Laboratory of Polymers, Biopolymers, Surfaces UMR 6270 PBS, Rouen University, Rouen, France
| | - Dmitry S. Kopitsyn
- Department of Physical and Colloid Chemistry, Gubkin University, Moscow, Russia
| | | | - Alexandra A. Kadykova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Higher Chemical College of the Russian Academy of Sciences, Mendeleyev University of Chemical Technology of Russia, Moscow, Russia
| | - Alexander S. Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Marina V. Zhurina
- Winogradsky Institute of Microbiology, Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, Russia
| | | | - Yuriy A. Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir K. Plakunov
- Winogradsky Institute of Microbiology, Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, Russia
| | - Marc G. J. Feuilloley
- EA4312 Laboratory of Microbiology Signals and Microenvironment, Rouen University, Evreux, France
| |
Collapse
|
25
|
Sizova OV, Shashkov AS, Dmitrenok AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Bogun AG, Dentovskaya SV. Structure and gene cluster of the O-polysaccharide of Yersinia rohdei H274-36/78. Int J Biol Macromol 2019; 122:555-561. [PMID: 30385338 DOI: 10.1016/j.ijbiomac.2018.10.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 10/28/2022]
Abstract
A branched O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Yersinia rohdei H274-36/78 and found to contain d-rhamnose, d-mannose, and 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-d-xylo-hexose called yersiniose A (Yer). Partial acid hydrolysis of the O-polysaccharide eliminated Yer residues to give a modified linear polysaccharide. Studies by sugar analysis and 1H and 13C NMR spectroscopy, including computational NMR analysis, enabled structure elucidation of a hexasaccharide repeating unit of the O-polysaccharide having two Yer residues attached as monosaccharide side chains. The O-antigen gene cluster of Y. rohdei H274-36/78 located between JUMPStart and galF genes contained putative genes for synthesis of precursors of two O-antigen constituents, GDP-d-Man and GDP-d-Rha, whereas genes responsible for synthesis of CDP-Yer were within the chromosome outside the O-antigen gene cluster. Glycosyltransferase genes and ABC 2 transporter genes were present in the O-antigen gene cluster, and hence the structure established is consistent with the polysaccharide synthesis gene content of the genome.
Collapse
Affiliation(s)
- O V Sizova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - A S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - A S Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Ph V Toukach
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation.
| | - Y A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - R Z Shaikhutdinova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
| | - S A Ivanov
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
| | - A A Kislichkina
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
| | - A G Bogun
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
| | - S V Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
| |
Collapse
|
26
|
Zdorovenko EL, Kadykova AA, Shashkov AS, Plotnikova DT, Kiseleva EP, Novik GI, Knirel YA. Structures of cell-wall glycopolymers of Lactobacillus rhamnosus BIM B-1039. Carbohydr Res 2019; 472:138-143. [PMID: 30597450 DOI: 10.1016/j.carres.2018.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 12/08/2018] [Indexed: 11/26/2022]
Abstract
Glycopolymers of two types were isolated from the cell wall of Lactobacillus rhamnosus BIM B-1039 by stepwise extraction with cold and hot 10% aq CCl3CO2H followed by anion-exchange gel chromatography. The following structures of the glycopolymers were established by sugar analysis, Smith degradation and 1D and 2D NMR spectroscopy.
Collapse
Affiliation(s)
- Evelina L Zdorovenko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Alexandra A Kadykova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia; Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Danuta T Plotnikova
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Elena P Kiseleva
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Galina I Novik
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
27
|
Klukowski P, Schubert M. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics. Bioinformatics 2018; 35:293-300. [DOI: 10.1093/bioinformatics/bty465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Piotr Klukowski
- Department of Computer Science, Faculty of Computer Science and Management, Wrocław University of Science and Technology, 50-370 Wrocław, Poland
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Kapaev RR, Toukach PV. Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software. J Chem Inf Model 2016; 56:1100-4. [DOI: 10.1021/acs.jcim.6b00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roman R. Kapaev
- Higher Chemical College of the Russian Academy of Sciences, Miusskaya sq. 9, Moscow 125047, Russia
| | - Philip V. Toukach
- N.D.
Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow 119991, Russia
| |
Collapse
|
30
|
|
31
|
Toukach PV, Egorova KS. Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts. Nucleic Acids Res 2015; 44:D1229-36. [PMID: 26286194 PMCID: PMC4702937 DOI: 10.1093/nar/gkv840] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/07/2015] [Indexed: 12/31/2022] Open
Abstract
The Carbohydrate Structure Databases (CSDBs, http://csdb.glycoscience.ru) store structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in 2005 for bacterial saccharides (as BCSDB). Currently, it includes two parts, the Bacterial CSDB and the Plant&Fungal CSDB. In March 2015, these databases were merged to the single CSDB. The combined CSDB includes information on bacterial and archaeal glycans and derivatives (the coverage is close to complete), as well as on plant and fungal glycans and glycoconjugates (almost all structures published up to 1998). CSDB is regularly updated via manual expert annotation of original publications. Both newly annotated data and data imported from other databases are manually curated. The CSDB data are exportable in a number of modern formats, such as GlycoRDF. CSDB provides additional services for simulation of (1)H, (13)C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycan-based taxon clustering and other.
Collapse
Affiliation(s)
- Philip V Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ksenia S Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| |
Collapse
|