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Liu X, Gilbert RG. Normal and abnormal glycogen structure - A review. Carbohydr Polym 2024; 338:122195. [PMID: 38763710 DOI: 10.1016/j.carbpol.2024.122195] [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: 02/09/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/21/2024]
Abstract
Glycogen, a complex branched glucose polymer, is found in animals and bacteria, where it serves as an energy storage molecule. It has linear (1 → 4)-α glycosidic bonds between anhydroglucose monomer units, with branch points connected by (1 → 6)-α bonds. Individual glycogen molecules are referred to as β particles. In organs like the liver and heart, these β particles can bind into larger aggregate α particles, which exhibit a rosette-like morphology. The mechanisms and bonding underlying the aggregation process are not fully understood. For example, mammalian liver glycogen has been observed to be molecularly fragile under certain conditions, such as glycogen from diabetic livers fragmenting when exposed to dimethyl sulfoxide (DMSO), while glycogen from healthy livers is much less fragile; this indicates some difference, as yet unknown, in the bonding between β particles in healthy and diabetic glycogen. This fragility may have implications for blood sugar regulation, especially in pathological conditions such as diabetes.
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Affiliation(s)
- Xin Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory, and Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Centre for Nutrition & Food Sciences, Queensland Alliance for Agriculture & Food Innovations (QAAFI), The University of Queensland, QLD 4072, Australia
| | - Robert G Gilbert
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory, and Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Centre for Nutrition & Food Sciences, Queensland Alliance for Agriculture & Food Innovations (QAAFI), The University of Queensland, QLD 4072, Australia.
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2
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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Analysis of Sugars in Honey Samples by Capillary Zone Electrophoresis Using Fluorescence Detection. SEPARATIONS 2023. [DOI: 10.3390/separations10030150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The applicability of capillary electrophoresis (CE) with light-emitting diode-induced fluorescence detection (LEDIF) for the separation of sugars in honey samples was studied. An amount of 25 mM ammonium acetate (pH 4.5) with 0.3% polyethylene oxide (PEO) was found to be optimal for the efficient separation of carbohydrates. 8-aminopyrene-1,3,6-trisulfonic acid (APTS) was used for the labeling of the carbohydrate standards and honey sugars for fluorescence detection. The optimized method was applied in the quantitative analysis of fructose and glucose by direct injection of honey samples. Apart from the labeling reaction, no other sample preparation was performed. The mean values of the fructose/glucose ratio for phacelia honey, acacia honey and honeydew honey were 0.86, 1.61 and 1.42, respectively. The proposed method provides high separation efficiency and sensitive detection within a short analysis time. Apart from the labeling reaction, it enables the injection of honeys without sample pretreatment. This is the first time that fluorescence detection has been applied for the CE analysis of sugars in honeys.
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4
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Garber JM, Fordwour OB, Zandberg WF. A Rapid Protocol for Preparing 8-Aminopyrene-1,3,6-Trisulfonate-Labeled Glycans for Capillary Electrophoresis-Based Enzyme Assays. Methods Mol Biol 2023; 2657:223-239. [PMID: 37149535 DOI: 10.1007/978-1-0716-3151-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Purified glycan standards are required for glycan arrays, characterizing substrate specificities of glycan-active enzymes, and to serve as retention-time or mobility standards for various separation techniques. This chapter describes a method for the rapid separation, and subsequent desalting, of glycans labeled with the highly fluorescent fluorophore 8-aminopyrene-1,3,6-trisulfonate (APTS). By using fluorophore-assisted carbohydrate electrophoresis (FACE) on polyacrylamide gels, a technique amenable to equipment readily available in most molecular biology laboratories, many APTS-labeled glycans can be simultaneously resolved. Excising specific gel bands containing the desired APTS-labeled glycans, followed by glycan elution from the gel by simple diffusion and subsequent solid-phase extraction (SPE)-based desalting, affords a single glycan species free of excess labeling reagents and buffer components. The described protocol also offers a simple, rapid method for the simultaneous removal of excess APTS and unlabeled glycan material from reaction mixtures. This chapter describes a FACE/SPE procedure ideal for preparing glycans for capillary electrophoresis (CE)-based enzyme assays, as well as for the purification of rare, commercially unavailable glycans from tissue culture samples.
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Affiliation(s)
- Jolene M Garber
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Osei B Fordwour
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Wesley F Zandberg
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada.
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Robb M, Hobbs JK, Boraston AB. Separation and Visualization of Glycans by Fluorophore-Assisted Carbohydrate Electrophoresis. Methods Mol Biol 2023; 2657:215-222. [PMID: 37149534 DOI: 10.1007/978-1-0716-3151-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fluorophore-assisted carbohydrate electrophoresis (FACE) is a method in which a fluorophore is covalently attached to the reducing end of carbohydrates, thereby allowing high-resolution separation by electrophoresis and visualization. This method can be used for carbohydrate profiling and sequencing, as well as for determining the specificity of carbohydrate-active enzymes. Here we describe and demonstrate the use of FACE to separate and visualize the glycans released following digestion of oligosaccharides by glycoside hydrolases (GHs) using two examples: (i) the digestion of chitobiose by the streptococcal β-hexosaminidase GH20C and (ii) the digestion of glycogen by the GH13 member SpuA.
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Affiliation(s)
- Mélissa Robb
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
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6
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Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. THE ISME JOURNAL 2022; 16:1818-1830. [PMID: 35414716 PMCID: PMC9213526 DOI: 10.1038/s41396-022-01223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/10/2022] [Accepted: 03/11/2022] [Indexed: 11/08/2022]
Abstract
AbstractMicrobial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α)6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms.
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Guo Z, Wei Y, Zhang Y, Xu Y, Zheng L, Zhu B, Yao Z. Carrageenan oligosaccharides: A comprehensive review of preparation, isolation, purification, structure, biological activities and applications. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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OUP accepted manuscript. Glycobiology 2022; 32:529-539. [DOI: 10.1093/glycob/cwab132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/14/2022] Open
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Hlalukana N, Magengelele M, Malgas S, Pletschke BI. Enzymatic Conversion of Mannan-Rich Plant Waste Biomass into Prebiotic Mannooligosaccharides. Foods 2021; 10:2010. [PMID: 34574120 PMCID: PMC8468410 DOI: 10.3390/foods10092010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 01/16/2023] Open
Abstract
A growing demand in novel food products for well-being and preventative medicine has attracted global attention on nutraceutical prebiotics. Various plant agro-processes produce large amounts of residual biomass considered "wastes", which can potentially be used to produce nutraceutical prebiotics, such as manno-oligosaccharides (MOS). MOS can be produced from the degradation of mannan. Mannan has a main backbone consisting of β-1,4-linked mannose residues (which may be interspersed by glucose residues) with galactose substituents. Endo-β-1,4-mannanases cleave the mannan backbone at cleavage sites determined by the substitution pattern and thus give rise to different MOS products. These MOS products serve as prebiotics to stimulate various types of intestinal bacteria and cause them to produce fermentation products in different parts of the gastrointestinal tract which benefit the host. This article reviews recent advances in understanding the exploitation of plant residual biomass via the enzymatic production and characterization of MOS, and the influence of MOS on beneficial gut microbiota and their biological effects (i.e., immune modulation and lipidemic effects) as observed on human and animal health.
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Affiliation(s)
| | | | - Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, Eastern Cape, South Africa; (N.H.); (M.M.); (B.I.P.)
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10
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Ovalle R, Chen L, Soll CE, Moore CW, Lipke PN. Regioselective degradation of [beta] 1,3 glucan by ferrous ion and hydrogen peroxide (Fenton oxidation). Carbohydr Res 2020; 497:108124. [PMID: 32977214 DOI: 10.1016/j.carres.2020.108124] [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: 12/03/2019] [Revised: 07/22/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
Many species use Fe+2 and H2O2 to oxidize a wide variety of compounds to simpler molecules. Both pathogen killing by leukocytes (neutrophils and lymphocytes) and degradation of cellulose by brown rot fungi rely on excretion of Fe+2 ions and H2O2, the Fenton reagent. To elucidate the mechanism of Fenton oxidation of carbohydrates, β1,3 glucan (laminaran), a major fungal wall polysaccharide, was oxidized using a molar ratio of monomer/Fe+2/H2O2 of 10:1:1 (primarily). We labeled the reaction products and profiled them as fluorescent-labeled molecules in polyacrylamide gels and as hydrophobic-tagged molecules using reverse phase liquid chromatography/mass spectrometry (HPLC/MS). Sub-stoichiometric concentrations of Fe+2 and H2O2 fragmented laminaran into smaller molecules containing carbonyl and carboxylic acid groups visible on fluorescent-labeled carbohydrate polyacrylamide gel electrophoresis. HPLC/MS analysis of glucan fragments showed masses consistent with six classes of molecules: aldoses, dialdoses, uronic acids, hexosuloses, aldonic acids, and hexulosonic acids. The results were consistent with published mechanisms where hydrogen radical (H•) abstraction from a C-H or O-H bond begins a cascade of reactions leading to 1) C-C bond cleavage to produce aldose/dialdose pairs; 2) oxo-group (O = ) addition to produce uronic and aldonic acids; 3) hydroxyl group (HO-) addition to produce gluconolactone and hexosuloses; and 4) hexulosonic acids. Most products resulted from regioselective H• abstractions characteristic of oxidations by ferryl-oxo ion [(FeO)+2] or perferryl-oxo ion [(FeO)+3] in close contact with specific positions in the glycan. Therefore, oxidations initiated by regioselectively-bound Fe ions were the predominant initiators of polysaccharide degradations.
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Affiliation(s)
- Rafael Ovalle
- Biology Department, Brooklyn College of the City University of New York (CUNY), Brooklyn, NY, 11210, USA; Biology PhD Program, Graduate Center of the CUNY, New York, NY, 10016, USA.
| | - Lijie Chen
- Biology Department, Brooklyn College of the City University of New York (CUNY), Brooklyn, NY, 11210, USA; Department of Biology, City College of New York of the CUNY, New York, NY, 10031, USA
| | - Clifford E Soll
- Department of Chemistry, Hunter College of the CUNY, New York, NY, 10065, USA
| | - Carol Wood Moore
- Biology PhD Program, Graduate Center of the CUNY, New York, NY, 10016, USA; CUNY School of Medicine, New York, NY, 10031, USA
| | - Peter N Lipke
- Biology Department, Brooklyn College of the City University of New York (CUNY), Brooklyn, NY, 11210, USA; Biology PhD Program, Graduate Center of the CUNY, New York, NY, 10016, USA.
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Choi YR, Kim KS, Bandu R, Kim H, Lee JE, Shin B, Cho YJ, Park JM, Lee H, Kim KP. Liquid Chromatography/Electrospray Ionization Tandem Mass Spectrometry‐based Structural Analysis of Deacylated Lipooligosaccharides From Escherichia coli. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yu Ri Choi
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient MaterialsKyung Hee University Yongin 17104 Republic of Korea
| | - Kwang Sung Kim
- R&D center, EyeGene Goyang 10551 Republic of Korea
- Department of Integrated Bioscience and BiotechnologySejong University Seoul 05006 Republic of Korea
| | - Raju Bandu
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient MaterialsKyung Hee University Yongin 17104 Republic of Korea
| | - Hyoseon Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient MaterialsKyung Hee University Yongin 17104 Republic of Korea
| | - Jae Eun Lee
- R&D center, EyeGene Goyang 10551 Republic of Korea
| | | | - Yang Je Cho
- R&D center, EyeGene Goyang 10551 Republic of Korea
| | - Jong Moon Park
- College of PharmacyGachon University Incheon 21936 Republic of Korea
| | - Hookeun Lee
- College of PharmacyGachon University Incheon 21936 Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient MaterialsKyung Hee University Yongin 17104 Republic of Korea
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A Multifunctional Polysaccharide Utilization Gene Cluster in Colwellia echini Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan. mSphere 2020; 5:5/1/e00792-19. [PMID: 31915221 PMCID: PMC6952198 DOI: 10.1128/msphere.00792-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on κ-carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of κ-carrageenan and agar, respectively. As the first, we report on the structure/function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated β/κ-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as κ-carrageenases, β-agarases, and β-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 β-galactosidases and show that this new class of enzymes is active only on hybrid β/κ-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize β/κ-, κ-, and ι-carrageenan. Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono- and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium Colwellia echini A3T is a potent enzyme producer since it completely hydrolyzes agar and κ-carrageenan. Here, we report that the genome of C. echini A3T harbors two large gene clusters for the degradation of carrageenan and agar, respectively. Phylogenetical and functional studies combined with transcriptomics and in silico structural modeling revealed that the carrageenolytic cluster encodes furcellaranases, a new class of glycoside hydrolase family 16 (GH16) enzymes that are key enzymes for hydrolysis of furcellaran, a hybrid carrageenan containing both β- and κ-carrageenan motifs. We show that furcellaranases degrade furcellaran into neocarratetraose-43-O-monosulfate [DA-(α1,3)-G4S-(β1,4)-DA-(α1,3)-G], and we propose a molecular model of furcellaranases and compare the active site architectures of furcellaranases, κ-carrageenases, β-agarases, and β-porphyranases. Furthermore, C. echini A3T was shown to encode κ-carrageenases, ι-carrageenases, and members of a new class of enzymes, active only on hybrid β/κ-carrageenan tetrasaccharides. On the basis of our genomic, transcriptomic, and functional analyses of the carrageenolytic enzyme repertoire, we propose a new model for how C. echini A3T degrades complex sulfated marine polysaccharides such as furcellaran, κ-carrageenan, and ι-carrageenan. IMPORTANCE Here, we report that a recently described bacterium, Colwellia echini, harbors a large number of enzymes enabling the bacterium to grow on κ-carrageenan and agar. The genes are organized in two clusters that encode enzymes for the total degradation of κ-carrageenan and agar, respectively. As the first, we report on the structure/function relationship of a new class of enzymes that hydrolyze furcellaran, a partially sulfated β/κ-carrageenan. Using an in silico model, we hypothesize a molecular structure of furcellaranases and compare structural features and active site architectures of furcellaranases with those of other GH16 polysaccharide hydrolases, such as κ-carrageenases, β-agarases, and β-porphyranases. Furthermore, we describe a new class of enzymes distantly related to GH42 and GH160 β-galactosidases and show that this new class of enzymes is active only on hybrid β/κ-carrageenan oligosaccharides. Finally, we propose a new model for how the carrageenolytic enzyme repertoire enables C. echini to metabolize β/κ-, κ-, and ι-carrageenan.
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13
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Naretto A, Fanuel M, Ropartz D, Rogniaux H, Larocque R, Czjzek M, Tellier C, Michel G. The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily. J Biol Chem 2019; 294:6923-6939. [PMID: 30846563 DOI: 10.1074/jbc.ra118.006609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/28/2019] [Indexed: 01/09/2023] Open
Abstract
Agars are sulfated galactans from red macroalgae and are composed of a d-galactose (G unit) and l-galactose (L unit) alternatively linked by α-1,3 and β-1,4 glycosidic bonds. These polysaccharides display high complexity, with numerous modifications of their backbone (e.g. presence of a 3,6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (β-agarases and β-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium Zobellia galactanivorans (ZgAgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family β-agarases and β-porphyranases. Using a large red algae collection, we demonstrate that ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of ZgAgaC on agar extracted from Osmundea pinnatifida By resolving the crystal structure of ZgAgaC at high resolution (1.3 Å) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC recognizes agarose via a mechanism different from that of classical β-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that ZgAgaC homologs define a new GH16 subfamily distinct from β-porphyranases and classical β-agarases.
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Affiliation(s)
- Anaïs Naretto
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Mathieu Fanuel
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - David Ropartz
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - Hélène Rogniaux
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - Robert Larocque
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Mirjam Czjzek
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Charles Tellier
- the Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR 6286 CNRS, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, France
| | - Gurvan Michel
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France,
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14
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Schultz-Johansen M, Bech PK, Hennessy RC, Glaring MA, Barbeyron T, Czjzek M, Stougaard P. A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66 T Encoded in a Sizeable Polysaccharide Utilization Locus. Front Microbiol 2018; 9:839. [PMID: 29774012 PMCID: PMC5943477 DOI: 10.3389/fmicb.2018.00839] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66T is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both β-carrageenan and κ/β-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and κ/β-type carrageenan by P. hydrolytica S66T. The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.
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Affiliation(s)
- Mikkel Schultz-Johansen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Pernille K Bech
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rosanna C Hennessy
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mikkel A Glaring
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Peter Stougaard
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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15
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Thomas BR, Brandley BK, Rodriguez RL. Rapid Analysis of Saccharides in Beer via Fluorescence-Assisted Carbohydrate Electrophoresis. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-58-0124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Bruce R. Thomas
- Department of Vegetable Crops, University of California-Davis, Davis 95616
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16
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Ma Z, Boye JI. Research advances on structural characterization of resistant starch and its structure-physiological function relationship: A review. Crit Rev Food Sci Nutr 2017; 58:1059-1083. [DOI: 10.1080/10408398.2016.1230537] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Zhen Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Joyce I. Boye
- Food Research and Development Centre, Agriculture and Agri-Food Canada, St. Hyacinthe, Quebec, Canada
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17
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Danyluk HJ, Shum LK, Zandberg WF. A Rapid Procedure for the Purification of 8-Aminopyrene Trisulfonate (APTS)-Labeled Glycans for Capillary Electrophoresis (CE)-Based Enzyme Assays. Methods Mol Biol 2017; 1588:223-236. [PMID: 28417373 DOI: 10.1007/978-1-4939-6899-2_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Purified glycan standards are required for glycan arrays, characterizing substrate specificities of glycan-active enzymes, and to serve as retention-time or mobility standards for various separation techniques. This chapter describes a method for the rapid separation, and subsequent desalting, of glycans labeled with the highly fluorescent fluorophore 8-aminopyrene 1,3,6-trisulfonate (APTS). By using fluorophore-assisted carbohydrate electrophoresis (FACE) on polyacrylamide gels, which utilizes equipment readily available in most molecular biology laboratories, many APTS-labeled glycans can be simultaneously resolved. Excising specific gel bands containing the desired APTS-labeled glycans, followed by glycan elution from the gel and subsequent solid-phase extraction (SPE), yields single glycan species free of excess labeling reagents and buffer components. This chapter describes a FACE/SPE procedure ideal for preparing glycans for capillary electrophoresis (CE)-based enzyme assays, as well as for the purification of rare, commercially unavailable glycans from tissue culture samples.
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Affiliation(s)
- Hayden J Danyluk
- Simon Fraser University, Department of Molecular Biology and Biochemistry, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
| | - Leona K Shum
- Department of Chemistry, The University of British Columbia, Okanagan, Kelowna, BC, Canada
| | - Wesley F Zandberg
- Department of Chemistry, The University of British Columbia, Okanagan, Kelowna, BC, Canada.
- Department of Chemistry, Science Building, 1177 Research Road, Kelowna, BC, Canada, V1M 1V7.
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Separation and Visualization of Glycans by Fluorophore-Assisted Carbohydrate Electrophoresis. Methods Mol Biol 2017; 1588:215-221. [PMID: 28417372 DOI: 10.1007/978-1-4939-6899-2_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorophore-assisted carbohydrate electrophoresis (FACE) is a method in which a fluorophore is covalently attached to the reducing end of carbohydrates, thereby allowing visualization following high-resolution separation by electrophoresis. This method can be used for carbohydrate profiling and sequencing, as well as for the determination of the specificity of carbohydrate-active enzymes. Here, we describe and demonstrate the use of FACE to separate and visualize the glycans released following digestion of oligosaccharides by glycoside hydrolases (GHs) using two examples: (1) the digestion of chitobiose by the streptococcal β-hexosaminidase GH20C, and (2) the digestion of glycogen by the GH13 member SpuA.
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20
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Zhang Q, Zhang X, Wang P, Li D, Chen G, Gao P, Wang L. Determination of the action modes of cellulases from hydrolytic profiles over a time course using fluorescence-assisted carbohydrate electrophoresis. Electrophoresis 2015; 36:910-7. [PMID: 25546561 DOI: 10.1002/elps.201400563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/26/2014] [Accepted: 12/15/2014] [Indexed: 11/05/2022]
Abstract
Fluorescence-assisted carbohydrate electrophoresis (FACE) is a sensitive and simple method for the separation of oligosaccharides. It relies on labeling the reducing ends of oligosaccharides with a fluorophore, followed by PAGE. Concentration changes of oligosaccharides following hydrolysis of a carbohydrate polymer could be quantitatively measured continuously over time using the FACE method. Based on the quantitative analysis, we suggested that FACE was a relatively high-throughput, repeatable, and suitable method for the analysis of the action modes of cellulases. On account of the time courses of their hydrolytic profiles, the apparent processivity was used to show the different action modes of cellulases. Cellulases could be easily differentiated as exoglucanases, β-glucosidases, or endoglucanases. Moreover, endoglucanases from the same glycoside hydrolases family had a variety of apparent processivity, indicating the different modes of action. Endoglucanases with the same binding capacities and hydrolytic activities had similar oligosaccharide profiles, which aided in their classification. The hydrolytic profile of Trichoderma reesei Cel12A, an endoglucanases from T. reesei, contained glucose, cellobiose, and cellotriose, which revealed that it may have a new glucosidase activity, corresponding to that of EC 3.2.1.74. A hydrolysate study of a T. reesei Cel12A-N20A mutant demonstrated that the FACE method was sufficiently sensitive to detect the influence of a single-site mutation on enzymatic activity.
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Affiliation(s)
- Qing Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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22
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Volpi N, Galeotti F, Yang B, Linhardt RJ. Analysis of glycosaminoglycan-derived, precolumn, 2-aminoacridone–labeled disaccharides with LC-fluorescence and LC-MS detection. Nat Protoc 2014; 9:541-58. [DOI: 10.1038/nprot.2014.026] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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23
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Guo J, Yang S, Peng X, Li F, Zhou L, Pu Q. Microwave-assisted derivatization for fast and efficient analysis of saccharides on disposable microchips. RSC Adv 2014. [DOI: 10.1039/c4ra07934e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A domestic microwave oven was used to achieve rapid derivatization of saccharides for their microchip electrophoresis analysis.
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Affiliation(s)
- Jinxiu Guo
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
| | - Shenghong Yang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
| | - Xianglu Peng
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
| | - Fengyun Li
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
| | - Lei Zhou
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
| | - Qiaosheng Pu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- Department of Chemistry
- Lanzhou University
- Lanzhou, China
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Applications of organoboron compounds in carbohydrate chemistry and glycobiology: analysis, separation, protection, and activation. Carbohydr Res 2013; 381:112-22. [DOI: 10.1016/j.carres.2013.09.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 01/05/2023]
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25
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Benkeblia N. Fructooligosaccharides and fructans analysis in plants and food crops. J Chromatogr A 2013; 1313:54-61. [DOI: 10.1016/j.chroma.2013.08.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/28/2013] [Accepted: 08/03/2013] [Indexed: 12/30/2022]
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26
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Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol 2013; 16:598-610. [PMID: 23848955 DOI: 10.1111/1462-2920.12187] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022]
Abstract
The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.
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Affiliation(s)
- Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94025, USA
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27
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Reuel NF, Mu B, Zhang J, Hinckley A, Strano MS. Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. Chem Soc Rev 2013; 41:5744-79. [PMID: 22868627 DOI: 10.1039/c2cs35142k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.
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Affiliation(s)
- Nigel F Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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28
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Fossey JS, D'Hooge F, van den Elsen JMH, Pereira Morais MP, Pascu SI, Bull SD, Marken F, Jenkins ATA, Jiang YB, James TD. The development of boronic acids as sensors and separation tools. CHEM REC 2012; 12:464-78. [PMID: 22791631 DOI: 10.1002/tcr.201200006] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Indexed: 01/28/2023]
Abstract
Synthetic receptors for diols that incorporate boronic acid motifs have been developed as new sensors and separation tools. Utilizing the reversible interactions of diols with boronic acids to form boronic esters under new binding regimes has provided new hydrogel constructs that have found use as dye-displacement sensors and electrophoretic separation tools; similarly, molecular boronic-acid-containing chemosensors were constructed that offer applications in the sensing of diols. This review provides a somewhat-personal perspective of developments in boronic-acid-mediated sensing and separation, placed in the context of the seminal works of others in the area, as well as offering a concise summary of the contributions of the co-authors in the area.
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Affiliation(s)
- John S Fossey
- The School of Chemistry, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK..
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29
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Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J Biol Chem 2012; 287:30571-84. [PMID: 22778272 DOI: 10.1074/jbc.m112.377184] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the -2- and +1-binding subsites, PorB tolerates the presence of 3-6-anhydro-l-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Université Pierre et Marie Curie, Végétaux Marins et Biomolécules UMR 7139, Station Biologique de Roscoff, F 29682 Roscoff, France
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Functional Monolithic Materials for Boronate-Affinity Chromatography via Schrock Catalyst-Triggered Ring-Opening Metathesis Polymerization. Macromol Rapid Commun 2012; 33:1399-403. [DOI: 10.1002/marc.201200247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/07/2012] [Indexed: 11/07/2022]
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Enjalbert Q, Racaud A, Lemoine J, Redon S, Ayhan MM, Andraud C, Chambert S, Bretonnière Y, Loison C, Antoine R, Dugourd P. Optical Properties of a Visible Push–Pull Chromophore Covalently Bound to Carbohydrates: Solution and Gas-Phase Spectroscopy Combined to Theoretical Investigations. J Phys Chem B 2012; 116:841-51. [DOI: 10.1021/jp2099015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quentin Enjalbert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Amandine Racaud
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Jérôme Lemoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Sébastien Redon
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Mehmet Menaf Ayhan
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Chantal Andraud
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Stéphane Chambert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Yann Bretonnière
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Claire Loison
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Rodolphe Antoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Philippe Dugourd
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
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Riske F, Hamilton A, Zhang C, Hayes M. Remodeling the oligosaccharides on β-glucocerebrosidase using hydrophobic interaction chromatography and applications of hydroxyl ethyl starch for improving remodeling and enhancing protein stability. Biotechnol Bioeng 2011; 109:1217-27. [PMID: 22170377 DOI: 10.1002/bit.24406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 10/28/2011] [Accepted: 11/28/2011] [Indexed: 01/06/2023]
Abstract
In this article, we describe a hydrophobic interaction chromatography (HIC) method to remodel the carbohydrates on recombinant human β-glucocerebrosidase (GCR) and the use of hydroxyl ethyl starch (HES) an ethylated starch polymer, to improve this process. GCR is a therapeutic protein used in the treatment of Gaucher disease, a life threatening condition in which patients lack sufficient functional levels of this enzyme. Gaucher disease is the most common inherited lysosomal storage disorder resulting in hepatomegaly, splenomegaly, and bone and lung pathology due to the accumulation of glucosylceramide in the lysosomes of macrophages (Beutler and Grabowski, 2001). The oligosaccharide remodeling of GCR, performed on HIC using three enzymes that remove sugars, increases macrophage uptake through the mannose receptor and thereby lowers its therapeutic dose versus unmodified GCR (Furbish et al., 1981; Van Patten et al., 2007). In this article we describe findings that the addition of HES lowered the amounts of three deglycosylating enzymes needed for remodeling GCR. HES also stabilized the activity of α-glucosidase, α-galactosidase, and GCR under conditions in which these three enzymes rapidly lose activity in the absence of this polymer. Circular dichroism (CD) and second derivative UV spectroscopy revealed that the secondary and tertiary structure of α-glucosidase was unchanged while for GCR there was a slight compaction of the secondary structure but no apparent affect on the tertiary structure. The thermal stability of both GCR and α-glucosidase were enhanced by HES as both molecules showed an increased transition midpoint (T(m)).
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Affiliation(s)
- Frank Riske
- Purification Development, Genzyme Corporation, Framingham, Massachusetts 01701, USA.
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Harvey DJ. Derivatization of carbohydrates for analysis by chromatography; electrophoresis and mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:1196-225. [DOI: 10.1016/j.jchromb.2010.11.010] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 11/01/2010] [Accepted: 11/06/2010] [Indexed: 12/21/2022]
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34
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Nishiyabu R, Kubo Y, James TD, Fossey JS. Boronic acid building blocks: tools for sensing and separation. Chem Commun (Camb) 2011; 47:1106-23. [DOI: 10.1039/c0cc02920c] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010; 464:908-12. [PMID: 20376150 DOI: 10.1038/nature08937] [Citation(s) in RCA: 705] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 02/19/2010] [Indexed: 11/09/2022]
Abstract
Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.
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Zhang P, Wang Z, Xie M, Nie W, Huang L. Detection of carbohydrates using a pre-column derivatization reagent 1-(4-isopropyl) phenyl-3-methyl-5-pyrazolone by high-performance liquid chromatography coupled with electrospray ionization mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1135-44. [DOI: 10.1016/j.jchromb.2010.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/16/2010] [Accepted: 03/16/2010] [Indexed: 11/25/2022]
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Kazarian AA, Hilder EF, Breadmore MC. Capillary electrophoretic separation of mono- and di-saccharides with dynamic pH junction and implementation in microchips. Analyst 2010; 135:1970-8. [DOI: 10.1039/c0an00010h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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39
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Abstract
More than half of all human proteins are glycosylated. Glycosylation defines the adhesive properties of glycoconjugates and it is largely through glycan-protein interactions that cell-cell and cell-pathogen contacts occur. Not surprisingly, considering the central role they play in molecular encounters, glycoprotein and carbohydrate-based drugs and therapeutics represent a greater than $20 billion market. Glycomics, the study of glycan expression in biological systems, relies on effective analytical techniques for correlation of glycan structure with function. This overview summarizes techniques developed historically for glycan characterization as well as recent trends. Derivatization methods key to both traditional and modern approaches for glycoanalysis are described. Monosaccharide compositional analysis is fundamental to any effort to understand glycan structure-function relationships. Chromatographic and electrophoretic separations are key parts of any glycoanalytical workflow. Mass spectrometry and nuclear magnetic resonance are complementary instrumental techniques for glycan analysis. Finally, microarrays are emerging as powerful new tools for dynamic analysis of glycan expression.
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Affiliation(s)
- Alicia M Bielik
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
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40
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Buzzega D, Maccari F, Volpi N. Fluorophore-assisted carbohydrate electrophoresis for the determination of molecular mass of heparins and low-molecular-weight (LMW) heparins. Electrophoresis 2009; 29:4192-202. [PMID: 18844319 DOI: 10.1002/elps.200800165] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report the use of fluorophore-assisted carbohydrate electrophoresis (FACE) to determine the molecular mass (M) values of heparins (Heps) and low-molecular-weight (LMW)-Hep derivatives. Hep are labeled with 8-aminonaphthalene-1,3,6-trisulfonic acid and FACE is able to resolve each fraction as a discrete band depending on their M. After densitometric acquisition, the migration distance of each Hep standard is acquired and the third-grade polynomial calibration standard curve is determined by plotting the logarithms of the M values as a function of migration ratio. Purified Hep samples having different properties, pharmaceutical Heps and various LMW-Heps were analyzed by both FACE and conventional high-performance size-exclusion liquid chromatography (HPSEC) methods. The molecular weight value on the top of the chromatographic peak (Mp), the number-average Mn, weight-average Mw and polydispersity (Mw/Mn) were examined by both techniques and found to be similar. This approach offers certain advantages over the HPSEC method. The derivatization process with 8-aminonaphthalene-1,3,6-trisulfonic acid is complete after 4 h so that many samples may be analyzed in a day also considering that multiple samples can be run simultaneously and in parallel and that a single FACE analysis requires approx. 15 min. Furthermore, FACE is a very sensitive method as it requires approx. 5-10 microg of Heps, about 10-100-fold lower than samples and standards used in HPSEC evaluation. Finally, the utilization of mini-gels allows the use of very low amounts of reagents with neither expensive equipment nor any complicated procedures having to be applied. This study demonstrates that FACE analysis is a sensitive method for the determination of the M values of Heps and LMW-Heps with possible utilization in virtually any kind of research and development such as quality control laboratories due to its rapid, parallel analysis of multiple samples by means of common and simple largely used analytical laboratory equipment.
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Affiliation(s)
- Dania Buzzega
- Department of Biologia Animale, University of Modena and Reggio Emilia, Modena, Italy
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41
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Yuan Chuan L. Tracing the development of Structural Elucidation of N-glycans. TRENDS GLYCOSCI GLYC 2009. [DOI: 10.4052/tigg.21.53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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42
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Jackson TR, Springall JS, Rogalle D, Masumoto N, Ching Li H, D'Hooge F, Perera SP, Jenkins ATA, James TD, Fossey JS, van den Elsen JMH. Boronate affinity saccharide electrophoresis: a novel carbohydrate analysis tool. Electrophoresis 2008; 29:4185-91. [PMID: 18925583 DOI: 10.1002/elps.200800178] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The incorporation of specialised carbohydrate affinity ligand methacrylamido phenylboronic acid in polyacrylamide gels for fluorophore-assisted carbohydrate electrophoresis greatly improved the effective separation of saccharides that show similar mobilities in standard electrophoresis. Polyacrylamide gel electrophoresis using methacrylamido phenylboronic acid in low loading (typically 0.5-1% dry weight) was unequivocally shown to alter retention of labelled saccharides depending on their boronate affinity. While conventional fluorophore-assisted carbohydrate electrophoresis of 2-aminoacridone labelled glucose oligomers showed an inverted parabolic migration, an undesired trait of small oligosaccharides labelled with this neutral fluorophore, boron affinity saccharide electrophoresis separation of these carbohydrates completely restored their predicted running order, based on their charge/mass ratio, and resulted in improved separation of the analyte saccharides. These results exemplify boron affinity saccharide electrophoresis as an important new technique for analysing carbohydrates and sugar-containing molecules.
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Affiliation(s)
- Thomas R Jackson
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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43
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Quantification and characterization of enzymatically produced hyaluronan with fluorophore-assisted carbohydrate electrophoresis. Anal Biochem 2008; 384:329-36. [PMID: 18948072 DOI: 10.1016/j.ab.2008.09.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 09/24/2008] [Accepted: 09/29/2008] [Indexed: 11/23/2022]
Abstract
Hyaluronan (HA) is a polysaccharide with high-potential medical applications, depending on the chain length and the chain length distribution. Special interest goes to homogeneous HA oligosaccharides, which can be enzymatically produced using Pasteurella multocida hyaluronan synthase (PmHAS). We have developed a sensitive, simple, and fast method, based on fluorophore-assisted carbohydrate electrophoresis (FACE), for characterization and quantification of polymerization products. A chromatographic pure fluorescent template was synthesized from HA tetrasaccharide (HA4) and 2-aminobenzoic acid. HA4-fluor and HA4 were used as template for PmHAS-mediated polymerization of nucleotide sugars. All products, fluorescent and nonfluorescent, were analyzed with gel electrophoresis and quantified using lane densitometry. Comparison of HA4- and HA4-fluor-derived polymers showed that the fluorophore did not negatively influence the PmHAS-mediated polymerization. Only even-numbered oligosaccharide products were observed using HA4-fluor or HA4 as template. The fluorophore intensity was linearly related to its concentration, and the limit of detection was determined to be 7.4pmol per product band. With this assay, we can now differentiate oligosaccharides of size range DP2 (degree of polymerization 2) to approximately DP400, monitor the progress of polymerization reactions, and measure subtle differences in polymerization rate. Quantifying polymerization products enables us to study the influence of experimental conditions on HA synthesis.
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15 Capillary electrophoresis and bioanalysis. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0149-6395(07)00015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Lehrman MA. Teaching dolichol-linked oligosaccharides more tricks with alternatives to metabolic radiolabeling. Glycobiology 2007; 17:75R-85R. [PMID: 17384121 DOI: 10.1093/glycob/cwm029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The dolichol cycle involves synthesis of the lipid-linked oligosaccharide (LLO) Glc(3)Man(9)GlcNAc(2)-P-P-dolichol (G(3)M(9)Gn(2)-P-P-Dol), transfer of G(3)M(9)Gn(2) to asparaginyl residues of nascent endoplasmic reticulum (ER) polypeptides by oligosaccharyltransferase (OT), and recycling of the resultant Dol-P-P to Dol-P for new rounds of LLO synthesis. The importance of the dolichol cycle in secretory and membrane protein biosynthesis, ER function, and human genetic disease is now widely accepted. Elucidation of the fundamental properties of the dolichol cycle in intact cells was achieved through the use of radioactive sugar precursors, typically [(3)H]-labeled or [(14)C]-labeled d-mannose, d-galactose, or d-glucosamine. However, difficulties were encountered with cells or tissues not amenable to metabolic labeling, or in experiments influenced by isotope dilution, variable rates of LLO turnover, or special culture conditions required for the use of radioactive sugars. This article will review recently developed alternatives for LLO analysis that do not rely upon metabolic labeling with radioactive precursors, and thereby circumvent these problems. New information revealed by these methods with regard to regulation, genetic disorders, and evolution of the dolichol cycle, as well as caveats of radiolabeling techniques, will be discussed.
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Affiliation(s)
- Mark A Lehrman
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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Krupa JC, Shaya D, Chi L, Linhardt RJ, Cygler M, Withers SG, Mort JS. Quantitative continuous assay for hyaluronan synthase. Anal Biochem 2006; 361:218-25. [PMID: 17173853 PMCID: PMC4114249 DOI: 10.1016/j.ab.2006.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 10/20/2006] [Accepted: 11/03/2006] [Indexed: 01/15/2023]
Abstract
A rapid, continuous, and convenient three-enzyme coupled UV absorption assay was developed to quantitate the glucuronic acid and N-acetylglucosamine transferase activities of hyaluronan synthase from Pasteurella multocida (PmHAS). Activity was measured by coupling the UDP produced from the PmHAS-catalyzed transfer of UDP-GlcNAc and UDP-GlcUA to a hyaluronic acid tetrasaccharide primer with the oxidation of NADH. Using a fluorescently labeled primer, the products were characterized by gel electrophoresis. Our results show that a truncated soluble form of recombinant PmHAS (residues 1-703) can catalyze the glycosyl transfers in a time- and concentration-dependent manner. The assay can be used to determine kinetic parameters, inhibition constants, and mechanistic aspects of this enzyme. In addition, it can be used to quantify PmHAS during purification of the enzyme from culture media.
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Affiliation(s)
- Joanne C. Krupa
- Joint Diseases Laboratory, Shriners Hospital for Children, Montreal, Que., Canada H3G 1A6
| | - David Shaya
- Department of Biochemistry, McGill University, Montreal, Que., Canada H3G 1Y6
| | - Lianli Chi
- Rensselaer Polytechnic Institute, Biotechnology Center 4005, Troy, NY 12180, USA
| | - Robert J. Linhardt
- Rensselaer Polytechnic Institute, Biotechnology Center 4005, Troy, NY 12180, USA
| | - Miroslaw Cygler
- Department of Biochemistry, McGill University, Montreal, Que., Canada H3G 1Y6
- Biotechnology Research Institute, NRC, Montreal, Que., Canada H4P 2R2
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - John S. Mort
- Joint Diseases Laboratory, Shriners Hospital for Children, Montreal, Que., Canada H3G 1A6
- Department of Surgery, McGill University, Montreal, Que., Canada H3G 1A4
- Corresponding author. Fax: +1 514 842 5581. (J.S. Mort)
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Gao N, Lehrman MA. Non-radioactive analysis of lipid-linked oligosaccharide compositions by fluorophore-assisted carbohydrate electrophoresis. Methods Enzymol 2006; 415:3-20. [PMID: 17116464 DOI: 10.1016/s0076-6879(06)15001-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lipid-linked oligosaccharides (LLOs) are the donors of glycans that modify newly synthesized proteins in the endoplasmic reticulum (ER) of eukaryotes, resulting in formation of N-linked glycoproteins. The vast majority of LLO analyses have relied on metabolic labeling with radioactive sugar precursors, but these approaches have technical limitations resulting in many important questions about LLO synthesis being left unanswered. Here we describe the application of a facile non-radioactive technique, fluorophore-assisted carbohydrate electrophoresis (FACE), which circumvents these limitations. With FACE, steady-state LLO compositions can be determined quantitatively from cell cultures and animal tissues. We also present FACE methods for analysis of phosphosugars and nucleotide sugars, which are metabolic precursors of LLOs.
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Affiliation(s)
- Ningguo Gao
- Department of Pharmacology, UT-Southwestern Medical Center, Dallas, TX, USA
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48
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de Rezende CE, Anriany Y, Carr LE, Joseph SW, Weiner RM. Capsular polysaccharide surrounds smooth and rugose types of Salmonella enterica serovar Typhimurium DT104. Appl Environ Microbiol 2005; 71:7345-51. [PMID: 16269777 PMCID: PMC1287654 DOI: 10.1128/aem.71.11.7345-7351.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biofilms and rugose colony morphology of Salmonella enterica serovar Typhimurium strains are usually associated with at least two different exopolymeric substances (EPS), curli and cellulose. In this study, another EPS, a capsular polysaccharide (CP) synthesized constitutively in S. enterica serovar Typhimurium strain DT104 at 25 and 37 degrees C, has been recognized as a biofilm matrix component as well. Fluorophore-assisted carbohydrate electrophoresis (FACE) analysis indicated that the CP is comprised principally of glucose and mannose, with galactose as a minor constituent. The composition differs from that of known colanic acid-containing CP that is isolated from cells of Escherichia coli and other enteric bacteria grown at 37 degrees C. The reactivity of carbohydrate-specific lectins conjugated to fluorescein isothiocyanate or gold particles with cellular carbohydrates demonstrated the cell surface localization of CP. Further, lectin binding also correlated with the FACE analysis of CP. Immunoelectron microscopy, using specific antibodies against CP, confirmed that CP surrounds the cells. Confocal microscopy of antibody-labeled cells showed greater biofilm formation at 25 degrees C than at 37 degrees C. Since the CP was shown to be produced at both 37 degrees C and 25 degrees C, it does not appear to be significantly involved in attachment during the early formation of the biofilm matrix. Although the attachment of S. enterica serovar Typhimurium DT104 does not appear to be mediated by its CP, the capsule does contribute to the biofilm matrix and may have a role in other features of this organism, such as virulence, as has been shown previously for the capsules of other gram-negative and gram-positive bacteria.
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Affiliation(s)
- C Eriksson de Rezende
- Department of Cell Biology and Molecular Genetics, Microbiology Building, University of Maryland, College Park, MD 20742, USA
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49
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Anumula KR. Advances in fluorescence derivatization methods for high-performance liquid chromatographic analysis of glycoprotein carbohydrates. Anal Biochem 2005; 350:1-23. [PMID: 16271261 DOI: 10.1016/j.ab.2005.09.037] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Accepted: 09/26/2005] [Indexed: 11/28/2022]
Affiliation(s)
- Kalyan R Anumula
- Analytical Biochemistry, Inhibitex Inc., Alpharetta, GA 30004, USA.
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50
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Ramsay SL, Meikle PJ, Hopwood JJ, Clements PR. Profiling oligosaccharidurias by electrospray tandem mass spectrometry: Quantifying reducing oligosaccharides. Anal Biochem 2005; 345:30-46. [PMID: 16111643 DOI: 10.1016/j.ab.2005.06.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 06/14/2005] [Accepted: 06/27/2005] [Indexed: 11/15/2022]
Abstract
A method to semiquantify urinary oligosaccharides from patients suffering from oligosaccharidurias is presented. 1-Phenyl-3-methyl-5-pyrazolone has been used to derivatize urinary oligosaccharides prior to analysis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Disease-specific oligosaccharides were identified for several oligosaccharidurias, including GM1 gangliosidosis, GM2 gangliosidosis, sialic acid storage disease, sialidase/neuraminidase deficiency, galactosialidosis, I-cell disease, fucosidosis, Pompe and Gaucher diseases, and alpha-mannosidosis. The oligosaccharides were referenced against the internal standard, methyl lactose, to produce ratios for comparison with control samples. Elevations in specific urinary oligosaccharides were indicative of lysosomal disease and the defective catabolic enzyme. This method has been adapted to enable assay of large sample numbers and could readily be extended to other oligosaccharidurias and to monitor oligosaccharide levels in patients receiving treatment. It also has immediate potential for incorporation into a newborn screening program.
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Affiliation(s)
- Steven L Ramsay
- Lysosomal Diseases Research Unit, Department of Genetic Medicine, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
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