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Durand T, Dodge GJ, Siuda RP, Higinbotham HR, Arbour CA, Ghosh S, Allen KN, Imperiali B. Proteome-Wide Bioinformatic Annotation and Functional Validation of the Monotopic Phosphoglycosyl Transferase Superfamily. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602977. [PMID: 39026775 PMCID: PMC11257628 DOI: 10.1101/2024.07.10.602977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Phosphoglycosyl transferases (PGTs) are membrane proteins that initiate glycoconjugate biosynthesis by transferring a phospho-sugar moiety from a soluble nucleoside diphosphate sugar to a membrane-embedded polyprenol phosphate acceptor. The centrality of PGTs in complex glycan assembly and the current lack of functional information make these enzymes high-value targets for biochemical investigation. In particular, the small monotopic PGT family is exclusively bacterial and represents the minimal functional unit of the monotopic PGT superfamily. Here, we combine a sequence similarity network (SSN) analysis with a generalizable, luminescence-based activity assay to probe the substrate specificity of this family of monoPGTs in a bacterial cell-membrane fraction. This strategy allows us to identify specificity on a far more significant scale than previously achievable and correlate preferred substrate specificities with predicted structural differences within the conserved monoPGT fold. Finally, we present the proof-of-concept for a small-scale inhibitor screen (eight nucleoside analogs) with four monoPGTs of diverse substrate specificity, thus building a foundation for future inhibitor discovery initiatives.
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Affiliation(s)
- Theo Durand
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Imperial College London, Exhibition Rd, South Kensington, London SW7 2AZ, UK
| | - Greg J. Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Current address Biogen, 225 Binney Street, Cambridge MA 02139, USA
| | - Roxanne P. Siuda
- Department of Chemistry, Boston University, 590 Commonwealth Ave, Boston MA 02215, USA
- Dept. of Pharmacology Physiology, and Biophysics, Boston University Chobanian & Avedisian School of Medicine, 72 E Concord St L-630D, Boston, MA 02215, USA
| | - Hugh R. Higinbotham
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine A. Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Soumi Ghosh
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, 590 Commonwealth Ave, Boston MA 02215, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Sijmons D, Collett S, Soliman C, Guy AJ, Scott AM, Durrant LG, Elbourne A, Walduck AK, Ramsland PA. Probing the expression and adhesion of glycans involved in Helicobacter pylori infection. Sci Rep 2024; 14:8587. [PMID: 38615147 PMCID: PMC11016089 DOI: 10.1038/s41598-024-59234-w] [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: 12/19/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Helicobacter pylori infects approximately half the human population and has an unusual infective niche of the human stomach. Helicobacter pylori is a major cause of gastritis and has been classified as a group 1 carcinogen by the WHO. Treatment involves triple or quadruple antibiotic therapy, but antibiotic resistance is becoming increasingly prevalent. Helicobacter pylori expresses certain blood group related antigens (Lewis system) as a part of its lipopolysaccharide (LPS), which is thought to assist in immune evasion. Additionally, H. pylori LPS participates in adhesion to host cells alongside several adhesion proteins. This study profiled the carbohydrates of H. pylori reference strains (SS1 and 26695) using monoclonal antibodies (mAbs) and lectins, identifying interactions between two carbohydrate-targeting mAbs and multiple lectins. Atomic force microscopy (AFM) scans were used to probe lectin and antibody interactions with the bacterial surfaces. The selected mAb and lectins displayed an increased adhesive force over the surface of the curved H. pylori rods. Furthermore, this study demonstrates the ability of anti-carbohydrate antibodies to reduce the adhesion of H. pylori 26695 to human gastric adenocarcinoma cells via AFM. Targeting bacterial carbohydrates to disrupt crucial adhesion and immune evasion mechanisms represents a promising strategy for combating H. pylori infection.
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Affiliation(s)
- Daniel Sijmons
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Simon Collett
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Caroline Soliman
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Andrew J Guy
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- ZiP Diagnostics, Collingwood, VIC, 3066, Australia
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Molecular Imaging and Therapy, Austin Health and Faculty of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Lindy G Durrant
- Scancell Limited, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Anna K Walduck
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Paul A Ramsland
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Department of Immunology, Monash University, Melbourne, VIC, 3004, Australia.
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia.
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3
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Liu J, Zhang Z, Deng Y, Chen G. Effect of extraction method on the structure and bioactivity of polysaccharides from activated sludge. WATER RESEARCH 2024; 253:121196. [PMID: 38394931 DOI: 10.1016/j.watres.2024.121196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
Resource recovery is a pivotal facet of waste activated sludge treatment, particularly within the framework of carbon neutrality and the circular economy. Polysaccharides are emerging as a valuable resource from waste activated sludge, and the choice of extraction method affects the properties of the polysaccharides, which is of utmost importance for subsequent application. This investigation examined the effects of six extraction methods (i.e., acidic, alkaline, ultrasonication, hot-water, microwave, and electric treatments) on the yield, chemical composition, structural characteristics, and bioactivities of polysaccharides extracted from sludge. For each extraction method, two operational parameters, namely the treatment time and strength (e.g., the acid and alkali concentration), were initially optimized in terms of the polysaccharide yield. The polysaccharide yield varied from 1.03 ± 0.12 % to 5.34 ± 0.10 % adopting the extraction methods under optimized conditions, and the alkaline extraction method had the highest yield of polysaccharides with a treatment time of 120 min and NaOH concentration of 1 %. At least one polysaccharide fraction was successfully purified from the crude polysaccharide of each extraction method. The compositions and structures of these fractions, including carbohydrate, protein, sulfate, uronic acid contents, and monosaccharide compositions, were determined. Carbohydrate was the dominant component, with the hot-water-2 fraction having the highest carbohydrate content (77.90 % ± 2.02 %). Monosaccharides in the polysaccharides were measured, with mannose, rhamnose, glucose, and xylose being found in all fractions, whereas ribose was exclusively found in the acid-1 fraction. The molecular weights of these fractions ranged between 1.60 × 104 Da and 7.11 × 106 Da. Furthermore, the bioactivities of the polysaccharides, encompassing five anti-oxidant and three anti-coagulant properties, were assessed, with the ultrasonication-1 fraction having superior performance in seven of the assays. Finally, the association among the fractions in terms of composition and bioactivity was assessed adopting cluster analysis and regression methods. The findings underscore the effect of the extraction method on the properties of polysaccharides extracted from sludge, thereby providing valuable insights for the prospective applications of polysaccharides.
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Affiliation(s)
- Jie Liu
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zi Zhang
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yangfan Deng
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Guanghao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Wastewater Treatment Laboratory, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangzhou, China.
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Prinčič L, Orsi RH, Martin NH, Wiedmann M, Trmčić A. Phenotypic and genomic characterizations of Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata strains reveal no clear association between genetic content and ropy phenotype. J Dairy Sci 2024; 107:1370-1385. [PMID: 37944807 DOI: 10.3168/jds.2023-23922] [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: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This defect has, among other causes, been attributed to the growth, proliferation and exopolysaccharide production by coliform bacteria, which are most commonly introduced in milk as post-pasteurization contaminants. As we identified both Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata that were linked to a ropy defect, the goal of this study was to characterize 3 K. pneumoniae ssp. pneumoniae strains and 2 R. inusitata for (1) their ability to grow and cause ropy defect in milk at 6°C and 21°C and to (2) probe the genetic basis for observed ropy phenotype. Although all K. pneumoniae ssp. pneumoniae and R. inusitata strains showed net growth of >4 log10 over 48 h in UHT milk at 21°C, only R. inusitata strains displayed growth during 28-d incubation period at 6°C (>6 log10). Two out of 3 K. pneumoniae ssp. pneumoniae strains were capable of causing the ropy defect in milk at 21°C, as supported by an increase in the viscosity of milk and string-like flow during pouring; these 2 strains were originally isolated from raw milk. Only one R. inusitata strains was able to cause the ropy defect in milk; this strain was able to cause the defect at both 6°C and 21°C, and was originally isolated from a pasteurized milk. These findings suggest that the potential of K. pneumoniae ssp. pneumoniae and R. inusitata to cause ropy defect in milk is a strain-dependent characteristic. Comparative genomics provided no definitive answer on genetic basis for the ropy phenotype. However, for K. pneumoniae ssp. pneumoniae, genes rffG, rffH, rfbD, and rfbC involved in biosynthesis and secretion of enterobacterial common antigen (ECA) could only be found in the 2 strains that produced ropy defect, and for R. inusitata a set of 2 glycosyltransferase- and flippase genes involved in nucleotide sugar biosynthesis and export could only be identified in the ropy strain. Although these results provide some initial information for potential markers for strains that can cause ropy milk, the relationship between genetic content and ropiness in milk remains poorly understood and merits further investigation.
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Affiliation(s)
- Lucija Prinčič
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria 1190
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Aljoša Trmčić
- Department of Food Science, Cornell University, Ithaca, NY 14853.
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Kay EJ, Dooda MK, Bryant JC, Reid AJ, Wren BW, Troutman JM, Jorgenson MA. Engineering Escherichia coli for increased Und-P availability leads to material improvements in glycan expression technology. Microb Cell Fact 2024; 23:72. [PMID: 38429691 PMCID: PMC10908060 DOI: 10.1186/s12934-024-02339-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Bacterial surface glycans are assembled by glycosyltransferases (GTs) that transfer sugar monomers to long-chained lipid carriers. Most bacteria employ the 55-carbon chain undecaprenyl phosphate (Und-P) to scaffold glycan assembly. The amount of Und-P available for glycan synthesis is thought to be limited by the rate of Und-P synthesis and by competition for Und-P between phosphoglycosyl transferases (PGTs) and GTs that prime glycan assembly (which we collectively refer to as PGT/GTs). While decreasing Und-P availability disrupts glycan synthesis and promotes cell death, less is known about the effects of increased Und-P availability. RESULTS To determine if cells can maintain higher Und-P levels, we first reduced intracellular competition for Und-P by deleting all known non-essential PGT/GTs in the Gram-negative bacterium Escherichia coli (hereafter called ΔPGT/GT cells). We then increased the rate of Und-P synthesis in ΔPGT/GT cells by overexpressing the Und-P(P) synthase uppS from a plasmid (puppS). Und-P quantitation revealed that ΔPGT/GT/puppS cells can be induced to maintain 3-fold more Und-P than wild type cells. Next, we determined how increasing Und-P availability affects glycan expression. Interestingly, increasing Und-P availability increased endogenous and recombinant glycan expression. In particular, ΔPGT/GT/puppS cells could be induced to express 7-fold more capsule from Streptococcus pneumoniae serotype 4 than traditional E. coli cells used to express recombinant glycans. CONCLUSIONS We demonstrate that the biotechnology standard bacterium E. coli can be engineered to maintain higher levels of Und-P. The results also strongly suggest that Und-P pathways can be engineered to increase the expression of potentially any Und-P-dependent polymer. Given that many bacterial glycans are central to the production of vaccines, diagnostics, and therapeutics, increasing Und-P availability should be a foremost consideration when designing bacterial glycan expression systems.
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Affiliation(s)
- Emily J Kay
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Manoj K Dooda
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Joseph C Bryant
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 West Markham St. / Biomed I, Room 511 / Little Rock, Little Rock, AR, 72205, USA
| | - Amanda J Reid
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jerry M Troutman
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Matthew A Jorgenson
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301 West Markham St. / Biomed I, Room 511 / Little Rock, Little Rock, AR, 72205, USA.
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6
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Lemos TJDS, Silva HGDS, Previato JO, Mendonça-Previato L, Freitas EOD, Barbosa AS, Franzolin MR, Santos LFD, Melo BDS, Anjos GFD, Gonçalves RHN, Domingos MDO. O26 Polysaccharides as Key Players in Enteropathogenic E. coli Immune Evasion and Vaccine Development. Int J Mol Sci 2024; 25:2878. [PMID: 38474124 DOI: 10.3390/ijms25052878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) produce a capsule of polysaccharides identical to those composing the O-antigen polysaccharide of its LPS (lipopolysaccharide) molecules. In light of this, the impact of O26 polysaccharides on the immune evasion mechanisms of capsulated O26 EPEC compared to non-capsulated enterohemorrhagic Escherichia coli (EHEC) was investigated. Our findings reveal that there was no significant difference between the levels in EPEC and EHEC of rhamnose (2.8:2.5), a molecule considered to be a PAMP (Pathogen Associated Molecular Patterns). However, the levels of glucose (10:1.69), heptose (3.6:0.89) and N-acetylglucosamine (4.5:2.10), were significantly higher in EPEC than EHEC, respectively. It was also observed that the presence of a capsule in EPEC inhibited the deposition of C3b on the bacterial surface and protected the pathogen against lysis by the complement system. In addition, the presence of a capsule also protected EPEC against phagocytosis by macrophages. However, the immune evasion provided by the capsule was overcome in the presence of anti-O26 polysaccharide antibodies, and additionally, these antibodies were able to inhibit O26 EPEC adhesion to human epithelial cells. Finally, the results indicate that O26 polysaccharides can generate an effective humoral immune response, making them promising antigens for the development of a vaccine against capsulated O26 E. coli.
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Affiliation(s)
| | | | - José Osvaldo Previato
- Instituto de Biofísica Carlos Chagas Filho, UFRJ, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
| | - Lucia Mendonça-Previato
- Instituto de Biofísica Carlos Chagas Filho, UFRJ, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
| | - Elisangela Oliveira de Freitas
- Instituto de Biofísica Carlos Chagas Filho, UFRJ, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
| | - Angela Silva Barbosa
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, SP, Brazil
| | - Marcia Regina Franzolin
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, SP, Brazil
| | - Luis Fernando Dos Santos
- Centro de Bacteriologia, Núcleo de Doenças Entéricas, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 355, São Paulo 01246-000, SP, Brazil
| | - Bruna de Sousa Melo
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, SP, Brazil
| | - Geovana Ferreira Dos Anjos
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, SP, Brazil
| | | | - Marta de Oliveira Domingos
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo 05503-900, SP, Brazil
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7
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Nieto-Fabregat F, Marseglia A, Thépaut M, Kleman JP, Abbas M, Le Roy A, Ebel C, Maalej M, Simorre JP, Laguri C, Molinaro A, Silipo A, Fieschi F, Marchetti R. Molecular recognition of Escherichia coli R1-type core lipooligosaccharide by DC-SIGN. iScience 2024; 27:108792. [PMID: 38299112 PMCID: PMC10828809 DOI: 10.1016/j.isci.2024.108792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
Due to their ability to recognize carbohydrate structures, lectins emerged as potential receptors for bacterial lipopolysaccharides (LPS). Despite growing interest in investigating the association between host receptor lectins and exogenous glycan ligands, the molecular mechanisms underlying bacterial recognition by human lectins are still not fully understood. We contributed to fill this gap by unveiling the molecular basis of the interaction between the lipooligosaccharide of Escherichia coli and the dendritic cell-specific intracellular adhesion molecules (ICAM)-3 grabbing non-integrin (DC-SIGN). Specifically, a combination of different techniques, including fluorescence microscopy, surface plasmon resonance, NMR spectroscopy, and computational studies, demonstrated that DC-SIGN binds to the purified deacylated R1 lipooligosaccharide mainly through the recognition of its outer core pentasaccharide, which acts as a crosslinker between two different tetrameric units of DC-SIGN. Our results contribute to a better understanding of DC-SIGN-LPS interaction and may support the development of pharmacological and immunostimulatory strategies for bacterial infections, prevention, and therapy.
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Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
| | - Angela Marseglia
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
| | - Michel Thépaut
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Jean-Philippe Kleman
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Massilia Abbas
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Aline Le Roy
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Christine Ebel
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Meriem Maalej
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Jean-Pierre Simorre
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Cedric Laguri
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonio Molinaro
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
| | - Alba Silipo
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
| | - Franck Fieschi
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 41 Avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France (IUF), Paris, France
| | - Roberta Marchetti
- Department of Chemical Science, University of Naples Federico II Via Cinthia 4, 80126 Naples, Italy
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8
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Dodge GJ, Anderson AJ, He Y, Liu W, Viner R, Imperiali B. Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle. eLife 2024; 12:RP91125. [PMID: 38358918 PMCID: PMC10942596 DOI: 10.7554/elife.91125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the Salmonella enterica (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs.
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Affiliation(s)
- Greg J Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Alyssa J Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yi He
- Thermo Fisher ScientificSan JoseUnited States
| | - Weijing Liu
- Thermo Fisher ScientificSan JoseUnited States
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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9
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Xu Y, Wagner GK. A cell-permeable probe for the labelling of a bacterial glycosyltransferase and virulence factor. RSC Chem Biol 2024; 5:55-62. [PMID: 38179196 PMCID: PMC10763556 DOI: 10.1039/d3cb00092c] [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: 06/15/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical probes for bacterial glycosyltransferases are of interest for applications such as tracking of expression levels, and strain profiling and identification. Existing probes for glycosyltransferases are typically based on sugar-nucleotides, whose charged nature limits their applicability in intact cells. We report the development of an uncharged covalent probe for the bacterial galactosyltransferase LgtC, and its application for the fluorescent labelling of this enzyme in recombinant form, cell lysates, and intact cells. The probe was designed by equipping a previously reported covalent LgtC inhibitor based on a pyrazol-3-one scaffold with a 7-hydroxycoumarin fluorophore. We show that this pyrazol-3-ones scaffold is surprisingly stable in aqueous media, which may have wider implications for the use of pyrazol-3-ones as chemical probes. We also show that the 7-hydroxycoumarin fluorophore leads to an unexpected improvement in activity, which could be exploited for the development of second generation analogues. These results will provide a basis for the development of LgtC-specific probes for the detection of LgtC-expressing bacterial strains.
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Affiliation(s)
- Yong Xu
- Department of Chemistry, King's College London UK
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road Belfast BT9 7BL UK
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10
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Vuksanovic N, Clasman JR, Imperiali B, Allen KN. Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Protein Sci 2024; 33:e4848. [PMID: 38019455 PMCID: PMC10731488 DOI: 10.1002/pro.4848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
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Affiliation(s)
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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11
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Luo H, Tu C, He D, Zhang A, Sun J, Li J, Xu J, Pan X. Interactions between microplastics and contaminants: A review focusing on the effect of aging process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165615. [PMID: 37481081 DOI: 10.1016/j.scitotenv.2023.165615] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Microplastics (MPs) in the environment are a major global concern due to their persistent nature and wide distribution. The aging of MPs is influenced by several processes including photodegradation, thermal degradation, biodegradation and mechanical fragmentation, which affect their interaction with contaminants. This comprehensive review aims to summarize the aging process of MPs and the factors that impact their aging, and to discuss the effects of aging on the interaction of MPs with contaminants. A range of characterization methods that can effectively elucidate the mechanistic processes of these interactions are outlined. The rate and extent of MPs aging are influenced by their physicochemical properties and other environmental factors, which ultimately affect the adsorption and aggregation of aged MPs with environmental contaminants. Pollutants such as heavy metals, organic matter and microorganisms have a tendency to accumulate on MPs through adsorption and the interactions between them impact their environmental behavior. Aging enhances the specific surface area and oxygen-containing functional groups of MPs, thereby affecting the mechanism of interaction between MPs and contaminants. To obtain a more comprehensive understanding of how aging affects the interactions, this review also provides an overview of the mechanisms by which MPs interact with contaminants. In the future, there should be further in-depth studies of the potential hazards of aged MPs in different environments e.g., soil, sediment, aquatic environment, and effects of their interaction with environmental pollutants on human health and ecology.
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Affiliation(s)
- Hongwei Luo
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Chaolin Tu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dongqin He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Anping Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianqiang Sun
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Juan Xu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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12
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Hulbert SW, Desai P, Jewett MC, DeLisa MP, Williams AJ. Glycovaccinology: The design and engineering of carbohydrate-based vaccine components. Biotechnol Adv 2023; 68:108234. [PMID: 37558188 DOI: 10.1016/j.biotechadv.2023.108234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Vaccines remain one of the most important pillars in preventative medicine, providing protection against a wide array of diseases by inducing humoral and/or cellular immunity. Of the many possible candidate antigens for subunit vaccine development, carbohydrates are particularly appealing because of their ubiquitous presence on the surface of all living cells, viruses, and parasites as well as their known interactions with both innate and adaptive immune cells. Indeed, several licensed vaccines leverage bacterial cell-surface carbohydrates as antigens for inducing antigen-specific plasma cells secreting protective antibodies and the development of memory T and B cells. Carbohydrates have also garnered attention in other aspects of vaccine development, for example, as adjuvants that enhance the immune response by either activating innate immune responses or targeting specific immune cells. Additionally, carbohydrates can function as immunomodulators that dampen undesired humoral immune responses to entire protein antigens or specific, conserved regions on antigenic proteins. In this review, we highlight how the interplay between carbohydrates and the adaptive and innate arms of the immune response is guiding the development of glycans as vaccine components that act as antigens, adjuvants, and immunomodulators. We also discuss how advances in the field of synthetic glycobiology are enabling the design, engineering, and production of this new generation of carbohydrate-containing vaccine formulations with the potential to prevent infectious diseases, malignancies, and complex immune disorders.
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Affiliation(s)
- Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Primit Desai
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Asher J Williams
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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13
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Cummings RD. Glycosphingolipids in human parasites. FEBS Open Bio 2023; 13:1625-1635. [PMID: 37335950 PMCID: PMC10476572 DOI: 10.1002/2211-5463.13662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
Glycosphingolipids (GSLs) are comprised of glycans (oligosaccharides) linked to a lipid containing a sphingosine moiety. They are major membrane components in cells of most animals, and importantly, they also occur in parasitic protozoans and worms that infect people. While the endogenous functions of the GSLs in most parasites are elusive, many of these GSLs are recognized by antibodies in infected human and animal hosts, and thus, their structures, biosynthesis, and functions are of great interest. Such knowledge of GSLs could lead to new drugs and diagnostics for treating infections, as well as novel vaccine strategies. The diversity of GSLs recently identified in such infectious organisms and aspects of their immune recognition are major topics of this review. It is not intended to be exhaustive but to highlight aspects of GSL glycans in human parasites.
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Affiliation(s)
- Richard D. Cummings
- Division of Surgical Sciences, Department of Surgery, Beth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMAUSA
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14
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McPherson RL, Isabella CR, Walker RL, Sergio D, Bae S, Gaca T, Raman S, Nguyen LTT, Wesener DA, Halim M, Wuo MG, Dugan A, Kerby R, Ghosh S, Rey FE, Dhennezel C, Pishchany G, Lensch V, Vlamakis H, Alm EJ, Xavier RJ, Kiessling LL. Lectin-Seq: A method to profile lectin-microbe interactions in native communities. SCIENCE ADVANCES 2023; 9:eadd8766. [PMID: 37506208 PMCID: PMC10381928 DOI: 10.1126/sciadv.add8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.
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Affiliation(s)
- Robert L. McPherson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine R. Isabella
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Dallis Sergio
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sunhee Bae
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tony Gaca
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Smrithi Raman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Le Thanh Tu Nguyen
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Melanie Halim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael G. Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amanda Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Kerby
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Soumi Ghosh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine Dhennezel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Gleb Pishchany
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Valerie Lensch
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric J. Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ramnik J. Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Dodge GJ, Anderson AJ, He Y, Liu W, Viner R, Imperiali B. Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545297. [PMID: 37398332 PMCID: PMC10312794 DOI: 10.1101/2023.06.16.545297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from Salmonella enterica (LT2) O-antigen biosynthesis without detergent solubilization from the lipid bilayer. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for oligomerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying small membrane proteins embedded in liponanoparticles beyond PGTs.
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Affiliation(s)
- Greg J. Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alyssa J. Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi He
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Weijing Liu
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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Giardino L, Generali L, Del Fabbro M, Tartaglia GM, Bidossi A, Savadori P. Detection of bacteria in dental samples using the Periodic acid-Schiff (PAS) histological stain. Micron 2023; 172:103498. [PMID: 37295188 DOI: 10.1016/j.micron.2023.103498] [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: 03/24/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
The bacterial cell wall mainly consists of glycoproteins and polysaccharides, which could be detected in dental tissue with specific stain protocols. The present study aimed to investigate bacteria stainability in dental histological samples of human teeth by a histochemical method. Eight extracted teeth, because severely decayed, were decalcified, dehydrated, paraffin-embedded, and serially sectioned at 4 µm thickness each. The serial sections were then stained with Periodic acid-Schiff (PAS). Furthermore, SEM analysis was performed on the same slide of one previously histologically investigated tooth to acquire more details on the structures stained by the PAS method obtained from the histological procedures. Afterward, some American Type Culture Collection (ATCC) strains, smeared on glass slides, were stained following the staining method used in histological samples. Stained rod and cocci forms by PAS stain, observed under light microscopy, were predominantly detected inside dentinal tubules and root canal space of histologically examined specimens, suggesting their bacterial origin. Additional SEM analysis on the identical histological stained slide showed the precise nature of these forms (bacteria) and supplemental information regarding their vitality status. In addition, ATCC smeared strain samples showed variable PAS stainability of microorganisms investigated. Due to its properties, the PAS histochemical stain could be a valid and helpful aid for non- or weakly stainable microorganisms in infected tissues to be associated with other methods of investigation.
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Affiliation(s)
| | - Luigi Generali
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Massimo Del Fabbro
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università Degli Studi di Milano, 20122 Milan, Italy; IRCCS Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, 20133, Milano, Italy
| | - Gianluca Martino Tartaglia
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università Degli Studi di Milano, 20122 Milan, Italy; IRCCS Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, 20133, Milano, Italy
| | | | - Paolo Savadori
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Università Degli Studi di Milano, 20122 Milan, Italy; IRCCS Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, 20133, Milano, Italy.
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17
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Anderson AJ, Dodge GJ, Allen KN, Imperiali B. Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases. Protein Sci 2023; 32:e4646. [PMID: 37096962 PMCID: PMC10186338 DOI: 10.1002/pro.4646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Monotopic phosphoglycosyl transferases (monoPGTs) are an expansive superfamily of enzymes that catalyze the first membrane-committed step in the biosynthesis of bacterial glycoconjugates. MonoPGTs show a strong preference for their cognate nucleotide diphospho-sugar (NDP-sugar) substrates. However, despite extensive characterization of the monoPGT superfamily through previous development of a sequence similarity network comprising >38,000 nonredundant sequences, the connection between monoPGT sequence and NDP-sugar substrate specificity has remained elusive. In this work, we structurally characterize the C-terminus of a prototypic monoPGT for the first time and show that 19 C-terminal residues play a significant structural role in a subset of monoPGTs. This new structural information facilitated the identification of co-conserved sequence "fingerprints" that predict NDP-sugar substrate specificity for this subset of monoPGTs. A Hidden Markov model was generated that correctly assigned the substrate of previously unannotated monoPGTs. Together, these structural, sequence, and biochemical analyses have delivered new insight into the determinants guiding substrate specificity of monoPGTs and have provided a strategy for assigning the NDP-sugar substrate of a subset of enzymes in the superfamily that use UDP-di-N-acetyl bacillosamine. Moving forward, this approach may be applied to identify additional sequence motifs that serve as fingerprints for monoPGTs of differing UDP-sugar substrate specificity.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Greg J. Dodge
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
| | - Barbara Imperiali
- Department of Biology and Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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18
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Dodge GJ, Bernstein HM, Imperiali B. A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles. Protein Expr Purif 2023; 207:106273. [PMID: 37068720 DOI: 10.1016/j.pep.2023.106273] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Phosphoglycosyl transferases (PGTs) are among the first membrane-bound enzymes involved in the biosynthesis of bacterial glycoconjugates. Robust expression and purification protocols for an abundant subfamily of PGTs remains lacking. Recent advancements in detergent-free methods for membrane protein solubilization open the door for purification of difficult membrane proteins directly from cell membranes into native-like liponanoparticles. By leveraging autoinduction, in vivo SUMO tag cleavage, styrene maleic acid co-polymer liponanoparticles (SMALPs), and Strep-Tag purification, we have established a robust workflow for expression and purification of previously unobtainable PGTs. The material generated from this workflow is extremely pure and can be directly visualized by Cryogenic Electron Microscopy (CryoEM). The methods presented here promise to be generalizable to additional membrane proteins recombinantly expressed in E. coli and should be of interest to the greater membrane proteomics community.
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Affiliation(s)
- Greg J Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hannah M Bernstein
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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19
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Anderson AJ, Seebald LM, Arbour CA, Imperiali B. Probing Monotopic Phosphoglycosyl Transferases from Complex Cellular Milieu. ACS Chem Biol 2022; 17:3191-3197. [PMID: 36346917 PMCID: PMC9703085 DOI: 10.1021/acschembio.2c00648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Monotopic phosphoglycosyl transferase enzymes (monoPGTs) initiate the assembly of prokaryotic glycoconjugates essential for bacterial survival and proliferation. MonoPGTs belong to an expansive superfamily with a diverse and richly annotated sequence space; however, the biochemical roles of most monoPGTs in glycoconjugate biosynthesis pathways remain elusive. To better understand these critical enzymes, we have implemented activity-based protein profiling (ABPP) probes as protein-centric, membrane protein compatible tools that lay the groundwork for understanding the activity and regulation of the monoPGT superfamily from a cellular proteome. With straightforward gel-based readouts, we demonstrate robust, covalent labeling at the active site of various representative monoPGTs from cell membrane fractions using 3-phenyl-2H-azirine probes.
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Affiliation(s)
- Alyssa J. Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah M. Seebald
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine A. Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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Widhani A, Djauzi S, Suyatna FD, Dewi BE. Changes in Gut Microbiota and Systemic Inflammation after Synbiotic Supplementation in Patients with Systemic Lupus Erythematosus: A Randomized, Double-Blind, Placebo-Controlled Trial. Cells 2022; 11:3419. [PMID: 36359816 PMCID: PMC9658918 DOI: 10.3390/cells11213419] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 08/04/2023] Open
Abstract
Gut dysbiosis has a role in the pathogenesis of lupus. Synbiotic supplementation may restore the balance of gut microbiota. This study investigated whether synbiotics could improve gut microbiota and systemic inflammation in lupus patients. This randomized, double-blind, placebo-controlled trial was conducted in adult systemic lupus erythematosus (SLE) patients. Subjects were randomized to receive either synbiotics or a placebo. Fecal microbiota, hs-CRP, IL-6, and IL-17 were measured at baseline and after 60 days. Patients who fulfilled the inclusion criteria were randomized into synbiotic (n = 23) and placebo groups (n = 23). In the synbiotic group, hs-CRP was not significantly increased (1.8 [0.9; 4.85] vs. 2.1 [0.9; 4.25] mg/L; pre vs. post; p = 0.23), whereas in the placebo group hs-CRP was increased significantly (1.75 [0.4; 4.45] vs. 3.75 [0.58; 7.05] mg/L; pre vs. post; p = 0.005). In the synbiotic group, IL-6 decreased significantly (8.76 [6.62; 11.39] vs. 6.59 [4.96; 8.01]; pre vs. post; p = 0.02), while there was no significant change in IL-17 level. In the placebo group, there was no significant change in IL-6 and IL-17. Synbiotic supplementation increased the Firmicutes:Bacteroidetes ratio (0.05 ± 0.60 vs. -0.08 ± 0.63, synbiotic vs. placebo p = 0.48) and butyrate metabolism (p = 0.037) and decreased amino sugar and nucleotide sugar metabolism (p = 0.040). There was improvement in the SLE disease activity index 2K (SLEDAI-2K) score in the synbiotic group (14 [9; 16] vs. 8 [2; 12]; pre vs. post; p < 0.001), while no change in the placebo group (9 [8; 18.25] vs. 9 [5.5; 15]; pre vs. post; p = 0.31). Synbiotic supplementation could reduce systemic inflammation and SLE disease activity and alter the composition and functions of gut microbiota.
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Affiliation(s)
- Alvina Widhani
- Allergy and Clinical Immunology Division, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Dr. Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
- Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Samsuridjal Djauzi
- Allergy and Clinical Immunology Division, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Dr. Cipto Mangunkusumo Hospital, Jakarta 10430, Indonesia
| | | | - Beti Ernawati Dewi
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
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21
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Guérin H, Kulakauskas S, Chapot-Chartier MP. Structural variations and roles of rhamnose-rich cell wall polysaccharides in Gram-positive bacteria. J Biol Chem 2022; 298:102488. [PMID: 36113580 PMCID: PMC9574508 DOI: 10.1016/j.jbc.2022.102488] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Abstract
Rhamnose-rich cell wall polysaccharides (Rha-CWPSs) have emerged as crucial cell wall components of numerous Gram-positive, ovoid-shaped bacteria—including streptococci, enterococci, and lactococci—of which many are of clinical or biotechnological importance. Rha-CWPS are composed of a conserved polyrhamnose backbone with side-chain substituents of variable size and structure. Because these substituents contain phosphate groups, Rha-CWPS can also be classified as polyanionic glycopolymers, similar to wall teichoic acids, of which they appear to be functional homologs. Recent advances have highlighted the critical role of these side-chain substituents in bacterial cell growth and division, as well as in specific interactions between bacteria and infecting bacteriophages or eukaryotic hosts. Here, we review the current state of knowledge on the structure and biosynthesis of Rha-CWPS in several ovoid-shaped bacterial species. We emphasize the role played by multicomponent transmembrane glycosylation systems in the addition of side-chain substituents of various sizes as extracytoplasmic modifications of the polyrhamnose backbone. We provide an overview of the contribution of Rha-CWPS to cell wall architecture and biogenesis and discuss current hypotheses regarding their importance in the cell division process. Finally, we sum up the critical roles that Rha-CWPS can play as bacteriophage receptors or in escaping host defenses, roles that are mediated mainly through their side-chain substituents. From an applied perspective, increased knowledge of Rha-CWPS can lead to advancements in strategies for preventing phage infection of lactococci and streptococci in food fermentation and for combating pathogenic streptococci and enterococci.
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Affiliation(s)
- Hugo Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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22
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Sanozky-Dawes R, Barrangou R. Lactobacillus, glycans and drivers of health in the vaginal microbiome. MICROBIOME RESEARCH REPORTS 2022; 1:18. [PMID: 38046360 PMCID: PMC10688826 DOI: 10.20517/mrr.2022.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/08/2022] [Accepted: 04/29/2022] [Indexed: 12/05/2023]
Abstract
A microbiome consists of microbes and their genomes, encompassing bacteria, viruses, fungi, protozoa, archaea, and eukaryotes. These elements interact dynamically in the specific environment in which they reside and evolve. In the past decade, studies of various microbiomes have been prevalent in the scientific literature, accounting for the shift from culture-dependent to culture-independent identification of microbes using new high-throughput sequencing technologies that decipher their composition and sometimes provide insights into their functions. Despite tremendous advances in understanding the gut microbiome, relatively little attention has been devoted to the vaginal environment, notably regarding the ubiquity and diversity of glycans which denote the significant role they play in the maintenance of homeostasis. Hopefully, emerging technologies will aid in the determination of what is a healthy vaginal microbiome, and provide insights into the roles of Lactobacillus, glycans and microbiome-related drivers of health and disease.
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Affiliation(s)
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
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Suban S, Sendersky E, Golden SS, Schwarz R. Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:218-229. [PMID: 35172394 PMCID: PMC9306852 DOI: 10.1111/1758-2229.13050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/03/2022] [Indexed: 05/03/2023]
Abstract
A biofilm inhibiting mechanism operates in the cyanobacterium Synechococcus elongatus. Here, we demonstrate that the glycosyltransferase homologue, Ogt, participates in the inhibitory process - inactivation of ogt results in robust biofilm formation. Furthermore, a mutational approach shows requirement of the glycosyltransferase activity for biofilm inhibition. This enzyme is necessary for glycosylation of the pilus subunit and for adequate pilus formation. In contrast to wild-type culture in which most cells exhibit several pili, only 25% of the mutant cells are piliated, half of which possess a single pilus. In spite of this poor piliation, natural DNA competence was similar to that of wild-type; therefore, we propose that the unglycosylated pili facilitate DNA transformation. Additionally, conditioned medium from wild-type culture, which contains a biofilm inhibiting substance(s), only partially blocks biofilm development by the ogt-mutant. Thus, we suggest that inactivation of ogt affects multiple processes including production or secretion of the inhibitor as well as the ability to sense or respond to it.
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Affiliation(s)
- Shiran Suban
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Susan S. Golden
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCA92093USA
- Center for Circadian BiologyUniversity of California, San DiegoLa JollaCA92093USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
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24
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Furevi A, Ruda A, Angles d’Ortoli T, Mobarak H, Ståhle J, Hamark C, Fontana C, Engström O, Apostolica P, Widmalm G. Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER. Carbohydr Res 2022; 513:108528. [DOI: 10.1016/j.carres.2022.108528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/02/2023]
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25
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Fischer S, Stegmann F, Gnanapragassam VS, Lepenies B. From structure to function – Ligand recognition by myeloid C-type lectin receptors. Comput Struct Biotechnol J 2022; 20:5790-5812. [DOI: 10.1016/j.csbj.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
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26
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Onyango SO, Juma J, De Paepe K, Van de Wiele T. Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease. Front Microbiol 2021; 12:653448. [PMID: 34956106 PMCID: PMC8702856 DOI: 10.3389/fmicb.2021.653448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inter-individual variability in the microbial gene complement encoding for carbohydrate-active enzymes (CAZymes) can profoundly regulate how the host interacts with diverse carbohydrate sources thereby influencing host health. CAZy-typing, characterizing the microbiota-associated CAZyme-coding genes within a host individual, can be a useful tool to predict carbohydrate pools that the host can metabolize, or identify which CAZyme families are underrepresented requiring supplementation via microbiota transplantation or probiotics. CAZy-typing, moreover, provides a novel framework to search for disease biomarkers. As a proof of concept, we used publicly available metagenomes (935) representing 310 type strain bacterial genomes to establish the link between disease status and CAZymes in the oral and gut microbial ecosystem. The abundance and distribution of 220 recovered CAZyme families in saliva and stool samples from patients with colorectal cancer, rheumatoid arthritis, and type 1 diabetes were compared with healthy subjects. Based on the multivariate discriminant analysis, the disease phenotype did not alter the CAZyme profile suggesting a functional conservation in carbohydrate metabolism in a disease state. When disease and healthy CAZyme profiles were contrasted in differential analysis, CAZyme markers that were underrepresented in type 1 diabetes (15), colorectal cancer (12), and rheumatoid arthritis (5) were identified. Of interest, are the glycosyltransferase which can catalyze the synthesis of glycoconjugates including lipopolysaccharides with the potential to trigger inflammation, a common feature in many diseases. Our analysis has also confirmed the expansive carbohydrate metabolism in the gut as evidenced by the overrepresentation of CAZyme families in the gut compared to the oral site. Nevertheless, each site exhibited specific CAZyme markers. Taken together, our analysis provides an insight into the CAZyme landscape in health and disease and has demonstrated the diversity in carbohydrate metabolism in host-microbiota which can be a sound basis for optimizing the selection of pre, pro, and syn-biotic candidate products.
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Affiliation(s)
- Stanley O Onyango
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Kim De Paepe
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
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Zhu H, Rollier CS, Pollard AJ. Recent advances in lipopolysaccharide-based glycoconjugate vaccines. Expert Rev Vaccines 2021; 20:1515-1538. [PMID: 34550840 DOI: 10.1080/14760584.2021.1984889] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION The public health burden caused by pathogenic Gram-negative bacteria is increasingly prominent due to antimicrobial resistance. The surface carbohydrates are potential antigens for vaccines against Gram-negative bacteria. The enhanced immunogenicity of the O-specific polysaccharide (O-SP) moiety of LPS when coupled to a carrier protein may protect against bacterial pathogens. However, because of the toxic lipid A moiety and relatively high costs of O-SP isolation, LPS has not been a popular vaccine antigen until recently. AREAS COVERED In this review, we discuss the rationales for developing LPS-based glycoconjugate vaccines, principles of glycoconjugate-induced immunity, and highlight the recent developments and challenges faced by LPS-based glycoconjugate vaccines. EXPERT OPINION Advances in LPS harvesting, LPS chemical synthesis, and newer carrier proteins in the past decade have propelled LPS-based glycoconjugate vaccines toward further development, through to clinical evaluation. The development of LPS-based glycoconjugates offers a new horizon for vaccine prevention of Gram-negative bacterial infection.
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Affiliation(s)
- Henderson Zhu
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (Nihr) Oxford Biomedical Research Centre, Oxford, UK
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (Nihr) Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (Nihr) Oxford Biomedical Research Centre, Oxford, UK
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28
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Utility of Bioluminescent Homogeneous Nucleotide Detection Assays in Measuring Activities of Nucleotide-Sugar Dependent Glycosyltransferases and Studying Their Inhibitors. Molecules 2021; 26:molecules26206230. [PMID: 34684811 PMCID: PMC8539010 DOI: 10.3390/molecules26206230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/22/2023] Open
Abstract
Traditional glycosyltransferase (GT) activity assays are not easily configured for rapid detection nor for high throughput screening because they rely on radioactive product isolation, the use of heterogeneous immunoassays or mass spectrometry. In a typical glycosyltransferase biochemical reaction, two products are generated, a glycosylated product and a nucleotide released from the sugar donor substrate. Therefore, an assay that detects the nucleotide could be universal to monitor the activity of diverse glycosyltransferases in vitro. Here we describe three homogeneous and bioluminescent glycosyltransferase activity assays based on UDP, GDP, CMP, and UMP detection. Each of these assays are performed in a one-step detection that relies on converting the nucleotide product to ATP, then to bioluminescence using firefly luciferase. These assays are highly sensitive, robust and resistant to chemical interference. Various applications of these assays are presented, including studies on the specificity of sugar transfer by diverse GTs and the characterization of acceptor substrate-dependent and independent nucleotide-sugar hydrolysis. Furthermore, their utility in screening for specific GT inhibitors and the study of their mode of action are described. We believe that the broad utility of these nucleotide assays will enable the investigation of a large number of GTs and may have a significant impact on diverse areas of Glycobiology research.
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29
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Yakovlieva L, Fülleborn JA, Walvoort MTC. Opportunities and Challenges of Bacterial Glycosylation for the Development of Novel Antibacterial Strategies. Front Microbiol 2021; 12:745702. [PMID: 34630370 PMCID: PMC8498110 DOI: 10.3389/fmicb.2021.745702] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
Glycosylation is a ubiquitous process that is universally conserved in nature. The various products of glycosylation, such as polysaccharides, glycoproteins, and glycolipids, perform a myriad of intra- and extracellular functions. The multitude of roles performed by these molecules is reflected in the significant diversity of glycan structures and linkages found in eukaryotes and prokaryotes. Importantly, glycosylation is highly relevant for the virulence of many bacterial pathogens. Various surface-associated glycoconjugates have been identified in bacteria that promote infectious behavior and survival in the host through motility, adhesion, molecular mimicry, and immune system manipulation. Interestingly, bacterial glycosylation systems that produce these virulence factors frequently feature rare monosaccharides and unusual glycosylation mechanisms. Owing to their marked difference from human glycosylation, bacterial glycosylation systems constitute promising antibacterial targets. With the rise of antibiotic resistance and depletion of the antibiotic pipeline, novel drug targets are urgently needed. Bacteria-specific glycosylation systems are especially promising for antivirulence therapies that do not eliminate a bacterial population, but rather alleviate its pathogenesis. In this review, we describe a selection of unique glycosylation systems in bacterial pathogens and their role in bacterial homeostasis and infection, with a focus on virulence factors. In addition, recent advances to inhibit the enzymes involved in these glycosylation systems and target the bacterial glycan structures directly will be highlighted. Together, this review provides an overview of the current status and promise for the future of using bacterial glycosylation to develop novel antibacterial strategies.
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Affiliation(s)
- Liubov Yakovlieva
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Julius A Fülleborn
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Marthe T C Walvoort
- Faculty of Science and Engineering, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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30
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Glueck NK, O'Brien KM, Seguin DC, Starai VJ. Legionella pneumophila LegC7 effector protein drives aberrant endoplasmic reticulum:endosome contacts in yeast. Traffic 2021; 22:284-302. [PMID: 34184807 DOI: 10.1111/tra.12807] [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: 11/19/2020] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/28/2022]
Abstract
Legionella pneumophila is a facultative intracellular bacterial pathogen, causing the severe form of pneumonia known as Legionnaires' disease. Legionella actively alters host organelle trafficking through the activities of "effector" proteins secreted via a type-IVB secretion system, in order to construct the bacteria-laden Legionella-containing vacuole (LCV) and prevent lysosomal degradation. The LCV is created with membrane derived from host endoplasmic reticulum (ER), secretory vesicles and phagosomes, although the precise molecular mechanisms that drive its synthesis remain poorly understood. In an effort to characterize the in vivo activity of the LegC7/YlfA SNARE-like effector protein from Legionella in the context of eukaryotic membrane trafficking in yeast, we find that LegC7 interacts with the Emp46p/Emp47p ER-to-Golgi glycoprotein cargo adapter complex, alters ER morphology and induces aberrant ER:endosome interactions, as measured by visualization of ER cargo degradation, reconstitution of split-GFP proteins and enhanced oxidation of the ER lumen. LegC7-dependent toxicity, disruption of ER morphology and ER:endosome fusion events were dependent upon endosomal VPS class C tethering complexes and the endosomal t-SNARE, Pep12p. This work establishes a model in which LegC7 functions to recruit host ER material to the bacterial phagosome during infection by driving ER:endosome contacts, potentially through interaction with host membrane tethering complexes and/or cargo adapters.
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Affiliation(s)
- Nathan K Glueck
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Kevin M O'Brien
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Danielle C Seguin
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Vincent J Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, USA.,Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
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31
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Willcocks SJ, Denman C, Cia F, McCarthy E, Cuccui J, Wren BW. Virulence of the emerging pathogen, Burkholderia pseudomallei, depends upon the O-linked oligosaccharyltransferase, PglL. Future Microbiol 2021; 15:241-257. [PMID: 32271107 PMCID: PMC7611010 DOI: 10.2217/fmb-2019-0165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim We sought to characterize the contribution of the O-OTase, PglL, to virulence in two Burkholderia spp. by comparing isogenic mutants in Burkholderia pseudomallei with the related species, Burkholderia thailandensis. Materials & methods We utilized an array of in vitro assays in addition to Galleria mellonella and murine in vivo models to assess virulence of the mutant and wild-type strains in each Burkholderia species. Results We found that pglL contributes to biofilm and twitching motility in both species. PglL uniquely affected morphology; cell invasion; intracellular motility; plaque formation and intergenus competition in B. pseudomallei. This mutant was attenuated in the murine model, and extended survival in a vaccine-challenge experiment. Conclusion Our data support a broad role for pglL in bacterial fitness and virulence, particularly in B. pseudomallei.
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Affiliation(s)
| | - Carmen Denman
- The London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK
| | - Felipe Cia
- The London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK
| | | | - Jon Cuccui
- The London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK
| | - Brendan W Wren
- The London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK
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32
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Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases. Proc Natl Acad Sci U S A 2021; 118:2018289118. [PMID: 33472976 DOI: 10.1073/pnas.2018289118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc oligosaccharide biosynthetic pathways, transferring a phosphosugar from a soluble nucleoside diphosphosugar to a membrane-resident polyprenol phosphate. The singularity of the monoPGT fold and its employment in the pivotal first membrane-committed step allows confident assignment of both protein and corresponding pathway. The diversity of the family is revealed by the generation and analysis of a sequence similarity network for the superfamily, with fusion of monoPGTs with other pathway members being the most frequent and extensive elaboration. Three common fusions were identified: sugar-modifying enzymes, glycosyl transferases, and regulatory domains. Additionally, unexpected fusions of the monoPGT with members of the polytopic PGT superfamily were discovered, implying a possible evolutionary link through the shared polyprenol phosphate substrate. Notably, a phylogenetic reconstruction of the monoPGT superfamily shows a radial burst of functionalization, with a minority of members comprising only the minimal PGT catalytic domain. The commonality and identity of the fusion partners in the monoPGT superfamily is consistent with advantageous colocalization of pathway members at membrane interfaces.
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33
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The surprising structural and mechanistic dichotomy of membrane-associated phosphoglycosyl transferases. Biochem Soc Trans 2021; 49:1189-1203. [PMID: 34100892 DOI: 10.1042/bst20200762] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022]
Abstract
Phosphoglycosyl transferases (PGTs) play a pivotal role at the inception of complex glycoconjugate biosynthesis pathways across all domains of life. PGTs promote the first membrane-committed step in the en bloc biosynthetic strategy by catalyzing the transfer of a phospho-sugar from a nucleoside diphospho-sugar to a membrane-resident polyprenol phosphate. Studies on the PGTs have been hampered because they are integral membrane proteins, and often prove to be recalcitrant to expression, purification and analysis. However, in recent years exciting new information has been derived on the structures and the mechanisms of PGTs, revealing the existence of two unique superfamilies of PGT enzymes that enact catalysis at the membrane interface. Genome neighborhood analysis shows that these superfamilies, the polytopic PGT (polyPGT) and monotopic PGT (monoPGT), may initiate different pathways within the same organism. Moreover, the same fundamental two-substrate reaction is enacted through two different chemical mechanisms with distinct modes of catalysis. This review highlights the structural and mechanistic divergence between the PGT enzyme superfamilies and how this is reflected in differences in regulation in their varied glycoconjugate biosynthesis pathways.
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34
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Arega AM, Mahapatra RK. Glycoconjugates, hypothetical proteins, and post-translational modification: Importance in host-pathogen interaction and antitubercular intervention development. Chem Biol Drug Des 2021; 98:30-48. [PMID: 33838076 DOI: 10.1111/cbdd.13845] [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: 11/20/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022]
Abstract
With the emergence of multidrug-resistant bacteria, insufficiency of the established chemotherapy, and the existing vaccine BCG, tuberculosis (TB) subsists as the chief cause of death in different parts of the world. Thus, identification of novel target proteins is urgently required to develop more effective TB interventions. However, the novel vaccine and drug target knowledge based on the essentiality of the pathogen cell envelope components such as glycoconjugates, glycans, and the peptidoglycan layer of the lipid-rich capsule are limited. Furthermore, most of the genes encoding proteins are characterized as hypothetical and functionally unknown. Correspondingly, some researchers have shown that the lipid and sugar components of the envelope glycoconjugates are largely in charge of TB pathogenesis and encounter many drugs and vaccines. Therefore, in this review we provide an insight into a comprehensive study concerning the importance of cell envelope glycoconjugates and hypothetical proteins, the impact of post-translational modification, and the bioinformatics-based implications for better antitubercular intervention development.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, India.,National Veterinary Institute, Debre Zeit, Ethiopia
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35
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Macedo-da-Silva J, Santiago VF, Rosa-Fernandes L, Marinho CRF, Palmisano G. Protein glycosylation in extracellular vesicles: Structural characterization and biological functions. Mol Immunol 2021; 135:226-246. [PMID: 33933815 DOI: 10.1016/j.molimm.2021.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed particles involved in intercellular communication, delivery of biomolecules from donor to recipient cells, cellular disposal and homeostasis, potential biomarkers and drug carriers. The content of EVs includes DNA, lipids, metabolites, proteins, and microRNA, which have been studied in various diseases, such as cancer, diabetes, pregnancy, neurodegenerative, and cardiovascular disorders. EVs are enriched in glycoconjugates and exhibit specific glycosignatures. Protein glycosylation is a co- and post-translational modification (PTM) that plays an important role in the expression and function of exosomal proteins. N- and O-linked protein glycosylation has been mapped in exosomal proteins. The purpose of this review is to highlight the importance of glycosylation in EVs proteins. Initially, we describe the main PTMs in EVs with a focus on glycosylation. Then, we explore glycan-binding proteins describing the main findings of studies that investigated the glycosylation of EVs in cancer, pregnancy, infectious diseases, diabetes, mental disorders, and animal fluids. We have highlighted studies that have developed innovative methods for studying the content of EVs. In addition, we present works related to lipid glycosylation. We explored the content of studies deposited in public databases, such as Exocarta and Vesiclepedia. Finally, we discuss analytical methods for structural characterization of glycoconjugates and present an overview of the critical points of the study of glycosylation EVs, as well as perspectives in this field.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Verônica F Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil.
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36
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Williams GT, Kedge JL, Fossey JS. Molecular Boronic Acid-Based Saccharide Sensors. ACS Sens 2021; 6:1508-1528. [PMID: 33844515 PMCID: PMC8155662 DOI: 10.1021/acssensors.1c00462] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
Boronic acids can reversibly bind diols, a molecular feature that is ubiquitous within saccharides, leading to their use in the design and implementation of sensors for numerous saccharide species. There is a growing understanding of the importance of saccharides in many biological processes and systems; while saccharide or carbohydrate sensing in medicine is most often associated with detection of glucose in diabetes patients, saccharides have proven to be relevant in a range of disease states. Herein the relevance of carbohydrate sensing for biomedical applications is explored, and this review seeks to outline how the complexity of saccharides presents a challenge for the development of selective sensors and describes efforts that have been made to understand the underpinning fluorescence and binding mechanisms of these systems, before outlining examples of how researchers have used this knowledge to develop ever more selective receptors.
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Affiliation(s)
- George T. Williams
- School of Chemistry, University
of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, United Kingdom
| | - Jonathan L. Kedge
- School of Chemistry, University
of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, United Kingdom
| | - John S. Fossey
- School of Chemistry, University
of Birmingham, Edgbaston, Birmingham, West Midlands, B15 2TT, United Kingdom
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37
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Qin R, Mahal LK. The host glycomic response to pathogens. Curr Opin Struct Biol 2021; 68:149-156. [PMID: 33529786 DOI: 10.1016/j.sbi.2020.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/28/2022]
Abstract
Glycans play important roles in the biology of infectious diseases. Although glycans are expressed on both the pathogens and the host, the functions and dynamics of the host glycome during infection are not well understood. Recent years have witnessed new discoveries on the host glycome respsonse to infection, as well as related mechanisms and their implications. Herein, we present a brief review on the latest findings in this field and put them in the context of host immunity.
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Affiliation(s)
- Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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38
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Metier C, Dow J, Wootton H, Lynham S, Wren B, Wagner GK. Profiling of Haemophilus influenzae strain R2866 with carbohydrate-based covalent probes. Org Biomol Chem 2021; 19:476-485. [PMID: 33355321 DOI: 10.1039/d0ob01971b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the application of four covalent probes based on anomerically pure d-galactosamine and d-glucosamine scaffolds for the profiling of Haemophilus influenzae strain R2866. The probes have been used successfully for the labelling of target proteins not only in cell lysates, but also in intact cells. Differences in the labelling patterns between lysates and intact cells indicate that the probes can penetrate into the periplasm, but not the cytoplasm of H. influenzae. Analysis of selected target proteins by LC-MS/MS suggests predominant labelling of nucleotide-binding proteins, including several known antibacterial drug targets. Our protocols will aid the identification of molecular determinants of bacterial pathogenicity in Haemophilus influenzae and other bacterial pathogens.
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Affiliation(s)
- Camille Metier
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Jennifer Dow
- London School of Hygiene and Tropical Medicine, Department of Infection Biology, Keppel Street, London, WC1E, 7HT, UK
| | - Hayley Wootton
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Brendan Wren
- London School of Hygiene and Tropical Medicine, Department of Infection Biology, Keppel Street, London, WC1E, 7HT, UK
| | - Gerd K Wagner
- Queen's University Belfast, School of Pharmacy, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK.
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39
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Metier CC, Peng J, Xu Y, Wootton H, Riesi V, Lynham S, Zadi S, Turner C, Wand ME, Mark Sutton J, Wagner GK. Profiling protein expression in Klebsiella pneumoniae with a carbohydrate-based covalent probe. Bioorg Med Chem 2021; 30:115900. [PMID: 33352389 DOI: 10.1016/j.bmc.2020.115900] [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: 09/22/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
We report the application of a covalent probe based on a d-glucosamine scaffold for the profiling of the bacterial pathogen Klebsiella pneumoniae. Incubation of K. pneumoniae lysates with the probe followed by electrophoretic separation and in-gel fluorescence detection allowed the generation of strain-specific signatures and the differentiation of a carbapenem-resistant strain. The labelling profile of the probe was independent of its anomeric configuration and included several low-abundance proteins not readily detectable by conventional protein staining. Initial target identification experiments by mass spectrometry suggest that target proteins include several carbohydrate-recognising proteins, which indicates that the sugar scaffold may have a role for target recognition.
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Affiliation(s)
- Camille C Metier
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Jiaming Peng
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Yong Xu
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Hayley Wootton
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Victoire Riesi
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Steven Lynham
- King's College London, Proteomics Facility, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Sirine Zadi
- Public Health England, Technology Development Group, Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Carrie Turner
- Public Health England, Technology Development Group, Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Matthew E Wand
- Public Health England, Technology Development Group, Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - J Mark Sutton
- Public Health England, Technology Development Group, Porton Down, Salisbury, Wiltshire SP4 0JG, United Kingdom
| | - Gerd K Wagner
- Queen's University Belfast, School of Pharmacy, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
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40
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Hansen T, Ofman TP, Vlaming JGC, Gagarinov IA, van Beek J, Goté TA, Tichem JM, Ruijgrok G, Overkleeft HS, Filippov DV, van der Marel GA, Codée JDC. Reactivity-Stereoselectivity Mapping for the Assembly of Mycobacterium marinum Lipooligosaccharides. Angew Chem Int Ed Engl 2021; 60:937-945. [PMID: 32856761 PMCID: PMC7821131 DOI: 10.1002/anie.202010280] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Indexed: 01/08/2023]
Abstract
The assembly of complex bacterial glycans presenting rare structural motifs and cis-glycosidic linkages is significantly obstructed by the lack of knowledge of the reactivity of the constituting building blocks and the stereoselectivity of the reactions in which they partake. We here report a strategy to map the reactivity of carbohydrate building blocks and apply it to understand the reactivity of the bacterial sugar, caryophyllose, a rare C12-monosaccharide, containing a characteristic tetrasubstituted stereocenter. We mapped reactivity-stereoselectivity relationships for caryophyllose donor and acceptor glycosides by a systematic series of glycosylations in combination with the detection and characterization of different reactive intermediates using experimental and computational techniques. The insights garnered from these studies enabled the rational design of building blocks with the required properties to assemble mycobacterial lipooligosaccharide fragments of M. marinum.
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Affiliation(s)
- Thomas Hansen
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Tim P. Ofman
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Joey G. C. Vlaming
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Ivan A. Gagarinov
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jessey van Beek
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Tessa A. Goté
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jacoba M. Tichem
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gijs Ruijgrok
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Dmitri V. Filippov
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | | | - Jeroen D. C. Codée
- Leiden UniversityLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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41
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Hansen T, Ofman TP, Vlaming JGC, Gagarinov IA, Beek J, Goté TA, Tichem JM, Ruijgrok G, Overkleeft HS, Filippov DV, Marel GA, Codée JDC. Reactivity–Stereoselectivity Mapping for the Assembly of
Mycobacterium marinum
Lipooligosaccharides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Thomas Hansen
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Tim P. Ofman
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Joey G. C. Vlaming
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Ivan A. Gagarinov
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jessey Beek
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Tessa A. Goté
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jacoba M. Tichem
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijs Ruijgrok
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. Marel
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D. C. Codée
- Leiden University Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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42
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Chan JM, Gori A, Nobbs AH, Heyderman RS. Streptococcal Serine-Rich Repeat Proteins in Colonization and Disease. Front Microbiol 2020; 11:593356. [PMID: 33193266 PMCID: PMC7661464 DOI: 10.3389/fmicb.2020.593356] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
Glycosylation of proteins, previously thought to be absent in prokaryotes, is increasingly recognized as important for both bacterial colonization and pathogenesis. For mucosal pathobionts, glycoproteins that function as cell wall-associated adhesins facilitate interactions with mucosal surfaces, permitting persistent adherence, invasion of deeper tissues and transition to disease. This is exemplified by Streptococcus pneumoniae and Streptococcus agalactiae, which can switch from being relatively harmless members of the mucosal tract microbiota to bona fide pathogens that cause life-threatening diseases. As part of their armamentarium of virulence factors, streptococci encode a family of large, glycosylated serine-rich repeat proteins (SRRPs) that facilitate binding to various tissue types and extracellular matrix proteins. This minireview focuses on the roles of S. pneumoniae and S. agalactiae SRRPs in persistent colonization and the transition to disease. The potential of utilizing SRRPs as vaccine targets will also be discussed.
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Affiliation(s)
- Jia Mun Chan
- NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Andrea Gori
- NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Angela H. Nobbs
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Robert S. Heyderman
- NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, United Kingdom
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43
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Synthetic Route to Glycosyl β-1C-(phosphino)-phosphonates as Unprecedented Stable Glycosyl Diphosphate Analogs and Their Preliminary Biological Evaluation. Molecules 2020; 25:molecules25214969. [PMID: 33121078 PMCID: PMC7663146 DOI: 10.3390/molecules25214969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022] Open
Abstract
The synthesis of glycosyl-β-1C-(phosphino)-phosphonates is a challenge since it has not yet been described. In this paper, we report an innovative synthetic method for their preparation from Glc-, Man-, and GlcNAc- lactone derivatives. The proposed original strategy involves the addition of the corresponding δ-hexonolactones onto the dianion of (methylphosphino) phosphonate as a key step, followed by dehydration and stereoselective addition of dihydrogen on the resulting double bond. Final deprotection provides the new glycosyl diphosphate analogs in 35%, 36%, and 10% yield over 6 steps from the corresponding δ-hexonolactones. The synthetized compounds were evaluated as inhibitors of phosphatase and diphosphatase activities and found to have complex concentration-dependent activatory and inhibitory properties on alkaline phosphatase. The synthetized tools should be useful to study other enzymes such as transferases.
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44
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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45
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Abstract
The outer membrane (OM) of Gram-negative bacteria poses a barrier to antibiotic entry due to its high impermeability. Thus, there is an urgent need to study the function and biogenesis of the OM. In Enterobacterales, an order of bacteria with many pathogenic members, one of the components of the OM is enterobacterial common antigen (ECA). We have known of the presence of ECA on the cell surface of Enterobacterales for many years, but its properties have only more recently begun to be unraveled. ECA is a carbohydrate antigen built of repeating units of three amino sugars, the structure of which is conserved throughout Enterobacterales. There are three forms of ECA, two of which (ECAPG and ECALPS) are located on the cell surface, while one (ECACYC) is located in the periplasm. Awareness of the importance of ECA has increased due to studies of its function that show it plays a vital role in bacterial physiology and interaction with the environment. Here, we review the discovery of ECA, the pathways for the biosynthesis of ECA, and the interactions of its various forms. In addition, we consider the role of ECA in the host immune response, as well as its potential roles in host-pathogen interaction. Furthermore, we explore recent work that offers insights into the cellular function of ECA. This review provides a glimpse of the biological significance of this enigmatic molecule.
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Affiliation(s)
- Ashutosh K Rai
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Angela M Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, USA
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46
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Kappler K, Hennet T. Emergence and significance of carbohydrate-specific antibodies. Genes Immun 2020; 21:224-239. [PMID: 32753697 PMCID: PMC7449879 DOI: 10.1038/s41435-020-0105-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Carbohydrate-specific antibodies are widespread among all classes of immunoglobulins. Despite their broad occurrence, little is known about their formation and biological significance. Carbohydrate-specific antibodies are often classified as natural antibodies under the assumption that they arise without prior exposure to exogenous antigens. On the other hand, various carbohydrate-specific antibodies, including antibodies to ABO blood group antigens, emerge after the contact of immune cells with the intestinal microbiota, which expresses a vast diversity of carbohydrate antigens. Here we explore the development of carbohydrate-specific antibodies in humans, addressing the definition of natural antibodies and the production of carbohydrate-specific antibodies upon antigen stimulation. We focus on the significance of the intestinal microbiota in shaping carbohydrate-specific antibodies not just in the gut, but also in the blood circulation. The structural similarity between bacterial carbohydrate antigens and surface glycoconjugates of protists, fungi and animals leads to the production of carbohydrate-specific antibodies protective against a broad range of pathogens. Mimicry between bacterial and human glycoconjugates, however, can also lead to the generation of carbohydrate-specific antibodies that cross-react with human antigens, thereby contributing to the development of autoimmune disorders.
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Affiliation(s)
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland.
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47
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Abstract
Cordyceps is a parasitic edible fungus with a variety of metabolically active ingredients. The main active ingredient, extracellular polysaccharide (EPS), shows favourable application prospects in prevention and treatment of certain diseases. EPS extracted from different parts of various Cordyceps species can be used in health foods or medicinal preparations because of the structural diversity and multiple bioactivities. In terms of the complexity of composition and structure, researchers have speculated on the anabolic pathways of EPSs and the genes involved in the synthesis process. Studies to increase the yield of polysaccharides are limited because the synthesis pathways and anabolic regulation mechanisms of Cordyceps exopolysaccharide remain unknown. This review summarises the current researches in the yield of Cordyceps polysaccharides. A mechanism for the biosynthesis of Cordyceps polysaccharides was proposed by referring to the polysaccharide synthesis in other species. Furthermore, we also discuss the future perspective and ongoing challenges of EPS in uses of health foods and pharmaceutics.
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Affiliation(s)
- Shengli Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Xi Yang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Hui Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
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48
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Kightlinger W, Warfel KF, DeLisa MP, Jewett MC. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synth Biol 2020; 9:1534-1562. [PMID: 32526139 PMCID: PMC7372563 DOI: 10.1021/acssynbio.0c00210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Protein glycosylation, the attachment of sugars to amino acid side chains, can endow proteins with a wide variety of properties of great interest to the engineering biology community. However, natural glycosylation systems are limited in the diversity of glycoproteins they can synthesize, the scale at which they can be harnessed for biotechnology, and the homogeneity of glycoprotein structures they can produce. Here we provide an overview of the emerging field of synthetic glycobiology, the application of synthetic biology tools and design principles to better understand and engineer glycosylation. Specifically, we focus on how the biosynthetic and analytical tools of synthetic biology have been used to redesign glycosylation systems to obtain defined glycosylation structures on proteins for diverse applications in medicine, materials, and diagnostics. We review the key biological parts available to synthetic biologists interested in engineering glycoproteins to solve compelling problems in glycoscience, describe recent efforts to construct synthetic glycoprotein synthesis systems, and outline exemplary applications as well as new opportunities in this emerging space.
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Affiliation(s)
- Weston Kightlinger
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, 123 Wing Drive, Ithaca, New York 14853, United States
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, New York 14853, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
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49
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Mnich ME, van Dalen R, van Sorge NM. C-Type Lectin Receptors in Host Defense Against Bacterial Pathogens. Front Cell Infect Microbiol 2020; 10:309. [PMID: 32733813 PMCID: PMC7358460 DOI: 10.3389/fcimb.2020.00309] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Antigen-presenting cells (APCs) are present throughout the human body—in tissues, at barrier sites and in the circulation. They are critical for processing external signals to instruct both local and systemic responses toward immune tolerance or immune defense. APCs express an extensive repertoire of pattern-recognition receptors (PRRs) to detect and transduce these signals. C-type lectin receptors (CLRs) comprise a subfamily of PRRs dedicated to sensing glycans, including those expressed by commensal and pathogenic bacteria. This review summarizes recent findings on the recognition of and responses to bacteria by membrane-expressed CLRs on different APC subsets, which are discussed according to the primary site of infection. Many CLR-bacterial interactions promote bacterial clearance, whereas other interactions are exploited by bacteria to enhance their pathogenic potential. The discrimination between protective and virulence-enhancing interactions is essential to understand which interactions to target with new prophylactic or treatment strategies. CLRs are also densely concentrated at APC dendrites that sample the environment across intact barrier sites. This suggests an–as yet–underappreciated role for CLR-mediated recognition of microbiota-produced glycans in maintaining tolerance at barrier sites. In addition to providing a concise overview of identified CLR-bacteria interactions, we discuss the main challenges and potential solutions for the identification of new CLR-bacterial interactions, including those with commensal bacteria, and for in-depth structure-function studies on CLR-bacterial glycan interactions. Finally, we highlight the necessity for more relevant tissue-specific in vitro, in vivo and ex vivo models to develop therapeutic applications in this area.
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Affiliation(s)
- Malgorzata E Mnich
- Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, Netherlands.,GSK, Siena, Italy
| | - Rob van Dalen
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, Amsterdam, Netherlands
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50
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Naseri R, Navabi SJ, Samimi Z, Mishra AP, Nigam M, Chandra H, Olatunde A, Tijjani H, Morais-Urano RP, Farzaei MH. Targeting Glycoproteins as a therapeutic strategy for diabetes mellitus and its complications. Daru 2020; 28:333-358. [PMID: 32006343 PMCID: PMC7095136 DOI: 10.1007/s40199-020-00327-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES Glycoproteins are organic compounds formed from proteins and carbohydrates, which are found in many parts of the living systems including the cell membranes. Furthermore, impaired metabolism of glycoprotein components plays the main role in the pathogenesis of diabetes mellitus. The aim of this study is to investigate the influence of glycoprotein levels in the treatment of diabetes mellitus. METHODS All relevant papers in the English language were compiled by searching electronic databases, including Scopus, PubMed and Cochrane library. The keywords of glycoprotein, diabetes mellitus, glycan, glycosylation, and inhibitor were searched until January 2019. RESULTS Glycoproteins are pivotal elements in the regulation of cell proliferation, growth, maturation and signaling pathways. Moreover, they are involved in drug binding, drug transportation, efflux of chemicals and stability of therapeutic proteins. These functions, structure, composition, linkages, biosynthesis, significance and biological effects are discussed as related to their use as a therapeutic strategy for the treatment of diabetes mellitus and its complications. CONCLUSIONS The findings revealed several chemical and natural compounds have significant beneficial effects on glycoprotein metabolism. The comprehension of glycoprotein structure and functions are very essential and inevitable to enhance the knowledge of glycoengineering for glycoprotein-based therapeutics as may be required for the treatment of diabetes mellitus and its associated complications. Graphical abstract.
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Affiliation(s)
- Rozita Naseri
- Internal Medicine Department, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seyed Jafar Navabi
- Internal Medicine Department, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zeinab Samimi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abhay Prakash Mishra
- Department of Pharmaceutical Chemistry, Hemwati Nandan Bahuguna Garhwal (A Central) University, Srinagar Garhwal, Uttarakhand, 246174, India.
| | - Manisha Nigam
- Department of Biochemistry, Hemwati Nandan Bahuguna Garhwal University, Srinagar Garhwal, Uttarakhand, 246174, India
| | - Harish Chandra
- Department of Microbiology, Gurukul Kangri Vishwavidhyalya, Haridwar, Uttarakhand, 249404, India
| | - Ahmed Olatunde
- Department of Biochemistry, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Habibu Tijjani
- Natural Product Research Laboratory, Department of Biochemistry, Bauchi State University, Gadau, Nigeria
| | - Raquel P Morais-Urano
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970, São Carlos, SP, Brasil
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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