1
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Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584156. [PMID: 38496653 PMCID: PMC10942478 DOI: 10.1101/2024.03.08.584156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.
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Affiliation(s)
- Zhenrun J Zhang
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Michael J Coyne
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Jessica C Little
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Amber Rose
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emma McSpadden
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
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2
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Sobala ŁF. Evolution and phylogenetic distribution of endo-α-mannosidase. Glycobiology 2023; 33:687-699. [PMID: 37202179 PMCID: PMC11025385 DOI: 10.1093/glycob/cwad041] [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: 12/23/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
While glycans underlie many biological processes, such as protein folding, cell adhesion, and cell-cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL, is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step toward this goal.
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Affiliation(s)
- Łukasz F Sobala
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
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3
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Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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4
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Panwar D, Shubhashini A, Kapoor M. Complex alpha and beta mannan foraging by the human gut bacteria. Biotechnol Adv 2023; 66:108166. [PMID: 37121556 DOI: 10.1016/j.biotechadv.2023.108166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
The human gut microbiota (HGM), a community of trillions of microbes, underscores its contribution by impacting many facets of host health and disease. In the HGM, Bacteroidota and Bacillota represent dominant bacterial phyla, which mainly rely on the glycans recalcitrant to host digestion to meet their energy requirements. Accordingly, the impact of dietary and host-derived glycans in the assembly and operation of these dominant microbial communities continues to be an area of active research. Among various glycans, mannans represent an integral component of the human diet. Apart from their health effects, the diverse and complex mannan structures bears molecular signatures that alter the expression of specific gene clusters in selected Bacteroidota and Bacillota species. Both the phyla possess variable and sophisticated loci of mannan recognition proteins, hydrolytic enzymes, transporters, and other metabolic proteins to sense, capture and utilize mannans as an energy source. The current review summarizes mannan structural diversity, and strategies adopted by select species of the HGM bacteria to forage mannans by focusing primarily on glycoside hydrolases and their effects on host health and metabolism.
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Affiliation(s)
- Deepesh Panwar
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - A Shubhashini
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India
| | - Mukesh Kapoor
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India.
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5
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Maranha A, Costa M, Ripoll-Rozada J, Manso JA, Miranda V, Mendes VM, Manadas B, Macedo-Ribeiro S, Ventura MR, Pereira PJB, Empadinhas N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 2023; 6:108. [PMID: 36707645 PMCID: PMC9883506 DOI: 10.1038/s42003-023-04448-3] [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: 05/20/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) so far detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria such as Mycobacterium avium, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a previously undescribed α-endomannosidase that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1→4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, whose disruption affected mycobacterial growth rate at low temperature.
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Affiliation(s)
- Ana Maranha
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mafalda Costa
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jorge Ripoll-Rozada
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal ,grid.507090.b0000 0004 5303 6218Present Address: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, Spain
| | - José A. Manso
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vanessa Miranda
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Vera M. Mendes
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - M. Rita Ventura
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro José Barbosa Pereira
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Empadinhas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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6
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Burchill L, Males A, Kaur A, Davies GJ, Williams SJ. Structure, Function and Mechanism of N‐Glycan Processing Enzymes:
endo
‐α‐1,2‐Mannanase and
endo
‐α‐1,2‐Mannosidase. Isr J Chem 2022. [DOI: 10.1002/ijch.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Alexandra Males
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Gideon J. Davies
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
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7
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Alonso‐Gil S, Parkan K, Kaminský J, Pohl R, Miyazaki T. Unlocking the Hydrolytic Mechanism of GH92 α‐1,2‐Mannosidases: Computation Inspires the use of C‐Glycosides as Michaelis Complex Mimics. Chemistry 2022; 28:e202200148. [PMID: 35049087 PMCID: PMC9305736 DOI: 10.1002/chem.202200148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 11/28/2022]
Abstract
The conformational changes in a sugar moiety along the hydrolytic pathway are key to understand the mechanism of glycoside hydrolases (GHs) and to design new inhibitors. The two predominant itineraries for mannosidases go via OS2→B2,5→1S5 and 3S1→3H4→1C4. For the CAZy family 92, the conformational itinerary was unknown. Published complexes of Bacteroides thetaiotaomicron GH92 catalyst with a S‐glycoside and mannoimidazole indicate a 4C1→4H5/1S5→1S5 mechanism. However, as observed with the GH125 family, S‐glycosides may not act always as good mimics of GH's natural substrate. Here we present a cooperative study between computations and experiments where our results predict the E5→B2,5/1S5→1S5 pathway for GH92 enzymes. Furthermore, we demonstrate the Michaelis complex mimicry of a new kind of C‐disaccharides, whose biochemical applicability was still a chimera.
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Affiliation(s)
- Santiago Alonso‐Gil
- Department of Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Dr.-Bohr-Gasse 9 1030 Vienna Austria
| | - Kamil Parkan
- Department of Chemistry of Natural Compounds University of Chemistry and Technology Technická 5 166 28 Prague Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Gilead Sciences & IOCB Research Centre Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Gilead Sciences & IOCB Research Centre Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Takatsugu Miyazaki
- Research Institute of Green Science and Technology Shizuoka University 836 Ohya, Suruga-ku Shizuoka 422-8529 Japan
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8
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Farren-Dai M, Sannikova N, Świderek K, Moliner V, Bennet AJ. Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marco Farren-Dai
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalia Sannikova
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón 12071, Spain
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón 12071, Spain
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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9
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Viinikangas T, Khosrowabadi E, Kellokumpu S. N-Glycan Biosynthesis: Basic Principles and Factors Affecting Its Outcome. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:237-257. [PMID: 34687012 DOI: 10.1007/978-3-030-76912-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Carbohydrate chains are the most abundant and diverse of nature's biopolymers and represent one of the four fundamental macromolecular building blocks of life together with proteins, nucleic acids, and lipids. Indicative of their essential roles in cells and in multicellular organisms, genes encoding proteins associated with glycosylation account for approximately 2% of the human genome. It has been estimated that 50-80% of all human proteins carry carbohydrate chains-glycans-as part of their structure. Despite cells utilize only nine different monosaccharides for making their glycans, their order and conformational variation in glycan chains together with chain branching differences and frequent post-synthetic modifications can give rise to an enormous repertoire of different glycan structures of which few thousand is estimated to carry important structural or functional information for a cell. Thus, glycans are immensely versatile encoders of multicellular life. Yet, glycans do not represent a random collection of unpredictable structures but rather, a collection of predetermined but still dynamic entities that are present at defined quantities in each glycosylation site of a given protein in a cell, tissue, or organism.In this chapter, we will give an overview of what is currently known about N-glycan synthesis in higher eukaryotes, focusing not only on the processes themselves but also on factors that will affect or can affect the final outcome-the dynamicity and heterogeneity of the N-glycome. We hope that this review will help understand the molecular details underneath this diversity, and in addition, be helpful for those who plan to produce optimally glycosylated antibody-based therapeutics.
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Affiliation(s)
- Teemu Viinikangas
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Elham Khosrowabadi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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10
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Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Proc Natl Acad Sci U S A 2020; 117:29595-29601. [PMID: 33154157 PMCID: PMC7703563 DOI: 10.1073/pnas.2013620117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc3Man9GlcNAc2 precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo-acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.
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11
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Brown HA, Koropatkin NM. Host glycan utilization within the Bacteroidetes Sus-like paradigm. Glycobiology 2020; 31:697-706. [PMID: 32518945 DOI: 10.1093/glycob/cwaa054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022] Open
Abstract
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
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12
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Rowland RJ, Wu L, Liu F, Davies GJ. A baculoviral system for the production of human β-glucocerebrosidase enables atomic resolution analysis. Acta Crystallogr D Struct Biol 2020; 76:565-580. [PMID: 32496218 PMCID: PMC7271948 DOI: 10.1107/s205979832000501x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
The lysosomal glycoside hydrolase β-glucocerebrosidase (GBA; sometimes called GBA1 or GCase) catalyses the hydrolysis of glycosphingolipids. Inherited deficiencies in GBA cause the lysosomal storage disorder Gaucher disease (GD). Consequently, GBA is of considerable medical interest, with continuous advances in the development of inhibitors, chaperones and activity-based probes. The development of new GBA inhibitors requires a source of active protein; however, the majority of structural and mechanistic studies of GBA today rely on clinical enzyme-replacement therapy (ERT) formulations, which are incredibly costly and are often difficult to obtain in adequate supply. Here, the production of active crystallizable GBA in insect cells using a baculovirus expression system is reported, providing a nonclinical source of recombinant GBA with comparable activity and biophysical properties to ERT preparations. Furthermore, a novel crystal form of GBA is described which diffracts to give a 0.98 Å resolution unliganded structure. A structure in complex with the inactivator 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-D-glucopyranoside was also obtained, demonstrating the ability of this GBA formulation to be used in ligand-binding studies. In light of its purity, stability and activity, the GBA production protocol described here should circumvent the need for ERT formulations for structural and biochemical studies and serve to support GD research.
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Affiliation(s)
- Rhianna J. Rowland
- Department of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Liang Wu
- Department of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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13
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Sobala L, Speciale G, Zhu S, Raich L, Sannikova N, Thompson AJ, Hakki Z, Lu D, Shamsi Kazem Abadi S, Lewis AR, Rojas-Cervellera V, Bernardo-Seisdedos G, Zhang Y, Millet O, Jiménez-Barbero J, Bennet AJ, Sollogoub M, Rovira C, Davies GJ, Williams SJ. An Epoxide Intermediate in Glycosidase Catalysis. ACS CENTRAL SCIENCE 2020; 6:760-770. [PMID: 32490192 PMCID: PMC7256955 DOI: 10.1021/acscentsci.0c00111] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Indexed: 05/18/2023]
Abstract
Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope (E 3) conformation. Kinetic isotope effects (k cat/K M) for anomeric-2H and anomeric-13C support an oxocarbenium ion-like transition state, and that for C2-18O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.
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Affiliation(s)
- Lukasz
F. Sobala
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sha Zhu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Lluís Raich
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Natalia Sannikova
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Thompson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Zalihe Hakki
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan Lu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Saeideh Shamsi Kazem Abadi
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew R. Lewis
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Víctor Rojas-Cervellera
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Ganeko Bernardo-Seisdedos
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Yongmin Zhang
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Oscar Millet
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- Ikerbasque,
Basque Foundation for Science, Marıá Dıáz de Haro 3, 48013 Bilbao, Spain
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- E-mail:
| | - Matthieu Sollogoub
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
- E-mail:
| | - Carme Rovira
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys
23, 08010 Barcelona, Spain
- E-mail:
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- E-mail:
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
- E-mail:
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14
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Vocadlo DJ. A Shut-and-Open Case: An Epoxide Intermediate Spotted in the Reaction Coordinate of a Family of Glycoside Hydrolases. ACS CENTRAL SCIENCE 2020; 6:619-621. [PMID: 32490180 PMCID: PMC7256941 DOI: 10.1021/acscentsci.0c00482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- David J. Vocadlo
- Department of
Chemistry and Department of Molecular
Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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15
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Large-Scale Differential Gene Expression Transcriptomic Analysis Identifies a Metabolic Signature Shared by All Cancer Cells. Biomolecules 2020; 10:biom10050701. [PMID: 32365991 PMCID: PMC7277211 DOI: 10.3390/biom10050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer-dependent metabolic rewiring is often manifested by selective expression of enzymes essential for the transformed cells’ viability. However, the metabolic variations between normal and transformed cells are not fully characterized, and therefore, a systematic analysis will result in the identification of unknown cellular mechanisms crucial for tumorigenesis. Here, we applied differential gene expression transcriptome analysis to examine the changes in metabolic gene profiles between a wide range of normal tissues and cancer samples. We found that, in contrast to normal tissues which exhibit a tissue-specific expression profile, cancer samples are more homogenous despite their diverse origins. This similarity is due to a “proliferation metabolic signature” (PMS), composed of 158 genes (87 upregulated and 71 downregulated gene sets), where 143 are common to all proliferative cells but 15 are cancer specific. Intriguingly, the PMS gene set is enriched for genes encoding rate-limiting enzymes, and its upregulated set with genes associated with poor patient outcome and essential genes. Among these essential genes is ribulose-5-phosphate-3-epimerase (RPE), which encodes a pentose phosphate pathway enzyme and whose role in cancer is still unclear. Collectively, we identified a set of metabolic genes that can serve as novel cancer biomarkers and potential targets for drug development.
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16
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Vanbeselaere J, Jin C, Eckmair B, Wilson IBH, Paschinger K. Sulfated and sialylated N-glycans in the echinoderm Holothuria atra reflect its marine habitat and phylogeny. J Biol Chem 2020; 295:3159-3172. [PMID: 31969392 DOI: 10.1074/jbc.ra119.011701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/17/2020] [Indexed: 01/14/2023] Open
Abstract
Among the earliest deuterostomes, the echinoderms are an evolutionary important group of ancient marine animals. Within this phylum, the holothuroids (sea cucumbers) are known to produce a wide range of glycoconjugate biopolymers with apparent benefits to health; therefore, they are of economic and culinary interest throughout the world. Other than their highly modified glycosaminoglycans (e.g. fucosylated chondroitin sulfate and fucoidan), nothing is known about their protein-linked glycosylation. Here we used multistep N-glycan fractionation to efficiently separate anionic and neutral N-glycans before analyzing the N-glycans of the black sea cucumber (Holothuria atra) by MS in combination with enzymatic and chemical treatments. These analyses showed the presence of various fucosylated, phosphorylated, sialylated, and multiply sulfated moieties as modifications of oligomannosidic, hybrid, and complex-type N-glycans. The high degree of sulfation and fucosylation parallels the modifications observed previously on holothuroid glycosaminoglycans. Compatible with its phylogenetic position, H. atra not only expresses vertebrate motifs such as sulfo- and sialyl-Lewis A epitopes but displays a high degree of anionic substitution of its glycans, as observed in other marine invertebrates. Thus, as for other echinoderms, the phylum- and order-specific aspects of this species' N-glycosylation reveal both invertebrate- and vertebrate-like features.
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Affiliation(s)
- Jorick Vanbeselaere
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Chunsheng Jin
- Institute of Biomedicine, Sahlgrenska Academy, Göteborg University, 405 30 Göteborg, Sweden
| | - Barbara Eckmair
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Iain B H Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
| | - Katharina Paschinger
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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17
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Rovira C, Males A, Davies GJ, Williams SJ. Mannosidase mechanism: at the intersection of conformation and catalysis. Curr Opin Struct Biol 2019; 62:79-92. [PMID: 31891872 DOI: 10.1016/j.sbi.2019.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Mannosidases are a diverse group of enzymes that are important in the biological processing of mannose-containing polysaccharides and complex glycoconjugates. They are found in 12 of the >160 sequence-based glycosidase families. We discuss evidence that nature has evolved a small set of common mechanisms that unite almost all of these mannosidase families. Broadly, mannosidases (and the closely related rhamnosidases) perform catalysis through just two conformations of the oxocarbenium ion-like transition state: a B2,5 (or enantiomeric 2,5B) boat and a 3H4 half-chair. This extends to a new family (GT108) of GDPMan-dependent β-1,2-mannosyltransferases/phosphorylases that perform mannosyl transfer through a boat conformation as well as some mannosidases that are metalloenzymes and require divalent cations for catalysis. Yet, among this commonality lies diversity. New evidence shows that one unique family (GH99) of mannosidases use an unusual mechanism involving anchimeric assistance via a 1,2-anhydro sugar (epoxide) intermediate.
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Affiliation(s)
- Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandra Males
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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18
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Nakamura T, Fahmi M, Tanaka J, Seki K, Kubota Y, Ito M. Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico. Int J Mol Sci 2019; 20:E6290. [PMID: 31847093 PMCID: PMC6940844 DOI: 10.3390/ijms20246290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.
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Affiliation(s)
- Takahiro Nakamura
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Jun Tanaka
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Kaito Seki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
| | - Yukihiro Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan;
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan; (T.N.); (M.F.); (J.T.); (K.S.)
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan;
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19
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Coines J, Raich L, Rovira C. Modeling catalytic reaction mechanisms in glycoside hydrolases. Curr Opin Chem Biol 2019; 53:183-191. [PMID: 31731209 DOI: 10.1016/j.cbpa.2019.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023]
Abstract
Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA) Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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20
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Colombo C, Bennet AJ. The physical organic chemistry of glycopyranosyl transfer reactions in solution and enzyme-catalyzed. Curr Opin Chem Biol 2019; 53:145-157. [PMID: 31689605 DOI: 10.1016/j.cbpa.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Our understanding of the mechanisms of glycopyranosyl transfer that occur in solution, both for the chemical synthesis of complex structures and that for the cleavage of glycosidic bonds has allowed us to design biologically active molecules. Recent efforts on the reactivity of glycopyranosides, which are critical entities in all biological systems, coupled with the advent of modern spectroscopic instrumentation have allowed physical organic chemists to broaden our knowledge of glycosyl transfer reaction transition states, both in solution and for enzyme-catalyzed processes, and of critical high energy intermediates. This review details recent physical organic, kinetic and structural studies that have led to elucidation of several different mechanism for the transfer of glycopyranosyl moieties from various substrates to acceptors, such as water or a sugar hydroxyl group.
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21
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Sano K, Kuribara T, Ishii N, Kuroiwa A, Yoshihara T, Tobita S, Totani K, Matsuo I. Fluorescence Quenching-based Assay for Measuring Golgi endo-α-Mannosidase. Chem Asian J 2019; 14:1965-1969. [PMID: 30884161 DOI: 10.1002/asia.201900240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/13/2019] [Indexed: 11/11/2022]
Abstract
Golgi endo-α-mannosidase (G-EM) catalyzes an alternative deglucosylation process for N-glycans and plays important roles in the post-endoplasmic reticulum (ER) quality control pathway. To understand the post-ER quality control mechanism, we synthesized a tetrasaccharide probe for the detection of the hydrolytic activity of G-EM based on a fluorescence quenching assay. The probe was labeled with an N-methylanthraniloyl group as a reporter dye at the non-reducing end and a 2,4-dinitrophenyl group as a quencher at the reducing end. This probe is hydrolyzed to disaccharide derivatives by G-EM, resulting in increased fluorescence intensity. Thus, the fluorescence signal is directly proportional to the amount of disaccharide derivative present, allowing the G-EM activity to be evaluated easily and quantitatively.
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Affiliation(s)
- Kanae Sano
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Taiki Kuribara
- Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino, Tokyo, 180-8633, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Ayumi Kuroiwa
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Kiichiro Totani
- Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino, Tokyo, 180-8633, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
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22
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Lu D, Zhu S, Sobala LF, Bernardo-Seisdedos G, Millet O, Zhang Y, Jiménez-Barbero J, Davies GJ, Sollogoub M. From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-α-mannosidase. Org Lett 2018; 20:7488-7492. [PMID: 30427198 DOI: 10.1021/acs.orglett.8b03260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the enzyme reaction mechanism can lead to the design of enzyme inhibitors. A Claisen rearrangement was used to allow conversion of an α-1,4-disaccharide into an α-1,3-linked glycosyl carbasugar to target the endo-α-mannosidase from the GH99 glycosidase family, which, unusually, is believed to act through a 1,2-anhydrosugar "epoxide" intermediate. Using NMR and X-ray crystallography, it is shown that glucosyl carbasugar α-aziridines can act as reasonably potent endo-α-mannosidase inhibitors, likely by virtue of their shape mimicry and the interactions of the aziridine nitrogen with the conserved catalytic acid/base of the enzyme active site.
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Affiliation(s)
- Dan Lu
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Sha Zhu
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Lukasz F Sobala
- York Structural Biology Laboratory, Department of Chemistry , University of York , York YO10 5DD , U.K
| | | | | | - Yongmin Zhang
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Jesus Jiménez-Barbero
- Ikerbasque, Basque Foundation for Science , Maria Diaz de Haro 3 , 48013 Bilbao , Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry , University of York , York YO10 5DD , U.K
| | - Matthieu Sollogoub
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
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23
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Schröder SP, Kallemeijn WW, Debets MF, Hansen T, Sobala LF, Hakki Z, Williams SJ, Beenakker TJM, Aerts JMFG, van der Marel GA, Codée JDC, Davies GJ, Overkleeft HS. Spiro-epoxyglycosides as Activity-Based Probes for Glycoside Hydrolase Family 99 Endomannosidase/Endomannanase. Chemistry 2018; 24:9983-9992. [PMID: 29797675 PMCID: PMC6055899 DOI: 10.1002/chem.201801902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022]
Abstract
N-Glycans direct protein function, stability, folding and targeting, and influence immunogenicity. While most glycosidases that process N-glycans cleave a single sugar residue at a time, enzymes from glycoside hydrolase family 99 are endo-acting enzymes that cleave within complex N-glycans. Eukaryotic Golgi endo-1,2-α-mannosidase cleaves glucose-substituted mannose within immature glucosylated high-mannose N-glycans in the secretory pathway. Certain bacteria within the human gut microbiota produce endo-1,2-α-mannanase, which cleaves related structures within fungal mannan, as part of nutrient acquisition. An unconventional mechanism of catalysis was proposed for enzymes of this family, hinted at by crystal structures of imino/azasugars complexed within the active site. Based on this mechanism, we developed the synthesis of two glycosides bearing a spiro-epoxide at C-2 as electrophilic trap, to covalently bind a mechanistically important, conserved GH99 catalytic residue. The spiro-epoxyglycosides are equipped with a fluorescent tag, and following incubation with recombinant enzyme, allow concentration, time and pH dependent visualization of the bound enzyme using gel electrophoresis.
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Affiliation(s)
- Sybrin P. Schröder
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marjoke F. Debets
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Hansen
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Lukasz F. Sobala
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Thomas J. M. Beenakker
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gijsbert A. van der Marel
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Herman S. Overkleeft
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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24
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Fernandes PZ, Petricevic M, Sobala L, Davies GJ, Williams SJ. Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. Chemistry 2018; 24:7464-7473. [PMID: 29508463 PMCID: PMC6001782 DOI: 10.1002/chem.201800435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Indexed: 11/06/2022]
Abstract
endo-α-1,2-Mannosidases and -mannanases, members of glycoside hydrolase family 99 (GH99), cleave α-Glc/Man-1,3-α-Man-OR structures within mammalian N-linked glycans and fungal α-mannan, respectively. They are proposed to act through a two-step mechanism involving a 1,2-anhydrosugar "epoxide" intermediate incorporating two conserved catalytic carboxylates. In the first step, one carboxylate acts as a general base to deprotonate the 2-hydroxy group adjacent to the fissile glycosidic bond, and the other provides general acid assistance to the departure of the aglycon. We report herein the synthesis of two inhibitors designed to interact with either the general base (α-mannosyl-1,3-(2-aminodeoxymannojirimycin), Man2NH2 DMJ) or the general acid (α-mannosyl-1,3-mannoimidazole, ManManIm). Modest affinities were observed for an endo-α-1,2-mannanase from Bacteroides thetaiotaomicron. Structural studies revealed that Man2NH2 DMJ binds like other iminosugar inhibitors, which suggests that the poor inhibition shown by this compound is not a result of a failure to achieve the expected interaction with the general base, but rather the reduction in basicity of the endocyclic nitrogen caused by introduction of a vicinal, protonated amine at C2. ManManIm binds with the imidazole headgroup distorted downwards, a result of an unfavourable interaction with a conserved active site tyrosine. This study has identified important limitations associated with mechanism-inspired inhibitor design for GH99 enzymes.
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Affiliation(s)
- Pearl Z. Fernandes
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Marija Petricevic
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Lukasz Sobala
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Gideon J. Davies
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Spencer J. Williams
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
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25
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Liu YF, Liao CT, Chiang YC, Li CE, Hsiao YM. WxcX is involved in bacterial attachment and virulence in Xanthomonas campestris pv. campestris. J Basic Microbiol 2018; 58:403-413. [PMID: 29504631 DOI: 10.1002/jobm.201700591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 11/08/2022]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers. Here, one EZ-Tn5 transposon mutant of Xcc, altered in bacterial attachment, was isolated. Further analysis revealed that the transposon was inserted in the wxcX gene (encodes a hypothetical protein) of the transposon mutant. Sequence analysis revealed that WxcX is highly conserved in Xanthomonas, but none has been characterized. In this study, it was indicated that mutation of wxcX resulted in enhanced bacterial attachment, reduced virulence on the host cabbage, and increased sensitivity to sodium dodecyl sulfate. The affected phenotypes of the wxcX mutant could be complemented to wild-type levels by the intact wxcX gene. Site-directed mutagenesis revealed that E408 and E411 are critical amino acid residues for WxcX function in bacterial attachment. Taken together, our results demonstrate the roles of wxcX in attachment, virulence, and tolerance to sodium dodecyl sulfate in Xanthomonas for the first time.
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Affiliation(s)
- Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan.,Division of Allergy, Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Ying-Chuan Chiang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Chih-En Li
- Graduate Institute of Biotechnology and Biomedical Engineering, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
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26
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Robb CS, Mystkowska AA, Hehemann JH. Crystal structure of a marine glycoside hydrolase family 99-related protein lacking catalytic machinery. Protein Sci 2017; 26:2445-2450. [PMID: 28884852 DOI: 10.1002/pro.3291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022]
Abstract
Algal polysaccharides of diverse structures are one of the most abundant carbon resources for heterotrophic, marine bacteria with coevolved digestive enzymes. A putative sulfo-mannan polysaccharide utilization locus, which is conserved in marine flavobacteria, contains an unusual GH99-like protein that lacks the conserved catalytic residues of glycoside hydrolase family 99. Using X-ray crystallography, we structurally characterized this protein from the marine flavobacterium Ochrovirga pacifica to help elucidate its molecular function. The structure reveals the absence of potential catalytic residues for polysaccharide hydrolysis, which-together with additional structural features-suggests this protein may be noncatalytic and involved in carbohydrate binding.
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Affiliation(s)
- Craig S Robb
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Agata Anna Mystkowska
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
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27
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Hykollari A, Malzl D, Yan S, Wilson IBH, Paschinger K. Hydrophilic interaction anion exchange for separation of multiply modified neutral and anionic Dictyostelium N-glycans. Electrophoresis 2017; 38:2175-2183. [PMID: 28556908 DOI: 10.1002/elps.201700073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 11/05/2022]
Abstract
The unusual nature of the N-glycans of the cellular slime mould Dictyostelium discoideum has been revealed by a number of studies, primarily based on examination of radiolabeled glycopeptides but more recently also by MS. The complexity of the N-glycomes of even glycosylation mutants is compounded by the occurrence of anionic modifications, which also present an analytical challenge. In this study, we have employed hydrophilic interaction anion exchange (HIAX) HPLC in combination with MALDI-TOF MS/MS to explore the anionic N-glycome of the M31 (modA) strain, which lacks endoplasmic reticulum α-glucosidase II, an enzyme conserved in most eukaryotes including Homo sapiens. Prefractionation with HIAX chromatography enabled the identification of N-glycans with unusual oligo-α1,2-mannose extensions as well as others with up to four anionic modifications. Due to the use of hydrofluoric acid treatment, we were able to discriminate isobaric glycans differing in the presence of sulphate or phosphate on intersected structures as opposed to those carrying GlcNAc-phosphodiesters. The latter represent biosynthetic intermediates during the pathway leading to formation of the methylphosphorylated mannose epitope, which may have a similar function in intracellular targeting of hydrolases as the mannose-6-phosphate modification of lysosomal enzymes in mammals. In conclusion, HIAX in combination with MS is a highly sensitive approach for both fine separation and definition of neutral and anionic N-glycan structures.
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Affiliation(s)
- Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | - Daniel Malzl
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
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28
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Iwamoto S, Kasahara Y, Yoshimura Y, Seko A, Takeda Y, Ito Y, Totani K, Matsuo I. Endo-α-Mannosidase-Catalyzed Transglycosylation. Chembiochem 2017; 18:1376-1378. [PMID: 28444927 DOI: 10.1002/cbic.201700111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 02/04/2023]
Abstract
In order for facilitating the synthesis of oligosaccharides, transglycosylation reactions mediated by glycoside hydrolases have been studied in various contexts. In this study, we examined the transglycosylating activity of a Golgi endo-α-mannosidase. We prepared various glycosyl donors and acceptors, and recombinant human Golgi endo-α-mannosidase and its various mutants were expressed. The enzyme was able to mediate transglycosylation from α-glycosyl-fluorides. Systematic screening of various point mutants revealed that the E407D mutant had excellent transglycosylation activity and extremely low hydrolytic activity. Substrate specificity analysis revealed that minimum motif required for glycosyl acceptor is Manα1- 2Man. The synthetic utility of the enzyme was demonstrated by generation of a high-mannose-type undecasaccharide (Glc1 Man9 GlcNAc2 ).
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Affiliation(s)
- Shogo Iwamoto
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Yuta Kasahara
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Yayoi Yoshimura
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Akira Seko
- ERATO Science and Technology Agency, JST), Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- Department of Biotechnology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yukishige Ito
- ERATO Science and Technology Agency, JST), Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kiichiro Totani
- Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino, Tokyo, 180-8633, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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29
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Czjzek M, Michel G. Innovating glycoside hydrolase activity on a same structural scaffold. Proc Natl Acad Sci U S A 2017; 114:4857-4859. [PMID: 28465442 PMCID: PMC5441738 DOI: 10.1073/pnas.1704802114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mirjam Czjzek
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, 29688 Roscoff, France;
- Laboratory for Integrative Biology of Marine Models, UMR8227, CNRS, 29688 Roscoff, France
| | - Gurvan Michel
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, 29688 Roscoff, France
- Laboratory for Integrative Biology of Marine Models, UMR8227, CNRS, 29688 Roscoff, France
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30
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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31
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Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Proc Natl Acad Sci U S A 2017; 114:4936-4941. [PMID: 28396425 DOI: 10.1073/pnas.1701130114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human gut microbiota use complex carbohydrates as major nutrients. The requirement for an efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that these bacteria represent a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis, we focused on enzymes that hydrolyze rhamnosidic bonds, as cleavage of these linkages is chemically challenging and there is a paucity of information on l-rhamnosidases. Here we screened the activity of enzymes derived from the human gut microbiota bacterium Bacteroides thetaiotaomicron, which are up-regulated in response to rhamnose-containing glycans. We identified an α-l-rhamnosidase, BT3686, which is the founding member of a glycoside hydrolase (GH) family, GH145. In contrast to other rhamnosidases, BT3686 cleaved l-Rha-α1,4-d-GlcA linkages through a retaining double-displacement mechanism. The crystal structure of BT3686 showed that the enzyme displayed a type A seven-bladed β-propeller fold. Mutagenesis and crystallographic studies, including the structure of BT3686 in complex with the reaction product GlcA, revealed a location for the active site among β-propeller enzymes cited on the posterior surface of the rhamnosidase. In contrast to the vast majority of GH, the catalytic apparatus of BT3686 does not comprise a pair of carboxylic acid residues but, uniquely, a single histidine functions as the only discernable catalytic amino acid. Intriguingly, the histidine, His48, is not invariant in GH145; however, when engineered into structural homologs lacking the imidazole residue, α-l-rhamnosidase activity was established. The potential contribution of His48 to the catalytic activity of BT3686 is discussed.
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32
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Petricevic M, Sobala LF, Fernandes PZ, Raich L, Thompson AJ, Bernardo-Seisdedos G, Millet O, Zhu S, Sollogoub M, Jiménez-Barbero J, Rovira C, Davies GJ, Williams SJ. Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase. J Am Chem Soc 2017; 139:1089-1097. [PMID: 27992199 PMCID: PMC5269645 DOI: 10.1021/jacs.6b10075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Inhibitor
design incorporating features of the reaction coordinate
and transition-state structure has emerged as a powerful approach
for the development of enzyme inhibitors. Such inhibitors find use
as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases,
members of glycoside hydrolase family 99 (GH99), are interesting targets
for inhibitor development as they play key roles in N-glycan maturation
and microbiotal yeast mannan degradation, respectively. These enzymes
are proposed to act via a 1,2-anhydrosugar “epoxide”
mechanism that proceeds through an unusual conformational itinerary.
Here, we explore how shape and charge contribute to binding of diverse
inhibitors of these enzymes. We report the synthesis of neutral dideoxy,
glucal and cyclohexenyl disaccharide inhibitors, their binding to
GH99 endo-α-1,2-mannanases, and their structural
analysis by X-ray crystallography. Quantum mechanical calculations
of the free energy landscapes reveal how the neutral inhibitors provide
shape but not charge mimicry of the proposed intermediate and transition
state structures. Building upon the knowledge of shape and charge
contributions to inhibition of family GH99 enzymes, we design and
synthesize α-Man-1,3-noeuromycin, which is revealed to be the
most potent inhibitor (KD 13 nM for Bacteroides xylanisolvens GH99 enzyme) of these enzymes
yet reported. This work reveals how shape and charge mimicry of transition
state features can enable the rational design of potent inhibitors.
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Affiliation(s)
- Marija Petricevic
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
| | - Lukasz F Sobala
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Pearl Z Fernandes
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
| | - Lluís Raich
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain
| | - Andrew J Thompson
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Ganeko Bernardo-Seisdedos
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Sha Zhu
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France
| | - Matthieu Sollogoub
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, Marı́a Dı́az de Haro 3, 48013 Bilbao, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
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33
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Alonso-Gil S, Males A, Fernandes PZ, Williams SJ, Davies GJ, Rovira C. Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 α-Mannosidases. J Am Chem Soc 2017; 139:1085-1088. [DOI: 10.1021/jacs.6b11247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Santiago Alonso-Gil
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alexandra Males
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Pearl Z. Fernandes
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5DD York, United Kingdom
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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34
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Speciale G, Farren-Dai M, Shidmoossavee FS, Williams SJ, Bennet AJ. C2-Oxyanion Neighboring Group Participation: Transition State Structure for the Hydroxide-Promoted Hydrolysis of 4-Nitrophenyl α-d-Mannopyranoside. J Am Chem Soc 2016; 138:14012-14019. [DOI: 10.1021/jacs.6b07935] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Marco Farren-Dai
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Fahimeh S. Shidmoossavee
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
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35
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Dedola S, Izumi M, Makimura Y, Seko A, Kanamori A, Takeda Y, Ito Y, Kajihara Y. Direct assay for endo-α-mannosidase substrate preference on correctly folded and misfolded model glycoproteins. Carbohydr Res 2016; 434:94-98. [PMID: 27623439 DOI: 10.1016/j.carres.2016.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/06/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
We previously reported a unique assay system for UDP-glucose glycoprotein glucosyltransferase (UGGT) toward glycoprotein folding intermediates during the folding process. The assay involved the in vitro folding of both high-mannose type oligosaccharyl crambin, which yielded only the correctly folded glycoprotein form (M9-glycosyl-native-crambin), and its mutant, which yielded misfolded glycoproteins (M9-glycosyl-misfolded-crambin), in the presence of UGGT. The process successfully yielded both mono-glucosylated M9-glycosyl-native-crambin (G1M9-glycosyl-native-crambin) and M9-glycosyl-misfolded-crambin (G1M9-glycosyl-misfolded-crambin). Here, we report the use of our in vitro folding system to evaluate the substrate preference of Golgi endo-α-mannosidase against G1M9-native and -misfolded glycoprotein forms. In our assay Golgi endo-α-mannosidase removed Glc-α-1-3-Man unit from G1M9-native and -misfolded-crambins clearly proving that Golgi endo-α-mannosidase does not have specific preference for correctly folded or misfolded protein structure.
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Affiliation(s)
- Simone Dedola
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Yutaka Makimura
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akira Seko
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akiko Kanamori
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yukishige Ito
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yasuhiro Kajihara
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan.
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36
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Abstract
The enzyme-catalysed degradation of oligo and polysaccharides is of considerable interest in many fields ranging from the fundamental–understanding the intrinsic chemical beauty–through to the applied, including diverse practical applications in medicine and biotechnology. Carbohydrates are the most stereochemically-complex biopolymer, and myriad different natural polysaccharides have led to evolution of multifaceted enzyme consortia for their degradation. The glycosidic bonds that link sugar monomers are among the most chemically-stable, yet enzymatically-labile, bonds in the biosphere. That glycoside hydrolases can achieve a rate enhancement (kcat/kuncat) >1017-fold provides testament to their remarkable proficiency and the sophistication of their catalysis reaction mechanisms. The last two decades have seen significant advances in the discovery of new glycosidase sequences, sequence-based classification into families and clans, 3D structures and reaction mechanisms, providing new insights into enzymatic catalysis. New impetus to these studies has been provided by the challenges inherent in plant and microbial polysaccharide degradation, both in the context of environmentally-sustainable routes to foods and biofuels, and increasingly in human nutrition. Study of the reaction mechanism of glycoside hydrolases has also inspired the development of enzyme inhibitors, both as mechanistic probes and increasingly as therapeutic agents. We are on the cusp of a new era where we are learning how to dovetail powerful computational techniques with structural and kinetic data to provide an unprecedented view of conformational details of enzyme action.
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37
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Qian BC, Kamori A, Kinami K, Kato A, Li YX, Fleet GWJ, Yu CY. Epimerization of C5 of an N-hydroxypyrrolidine in the synthesis of swainsonine related iminosugars. Org Biomol Chem 2016; 14:4488-98. [DOI: 10.1039/c6ob00531d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Cuskin F, Baslé A, Ladevèze S, Day AM, Gilbert HJ, Davies GJ, Potocki-Véronèse G, Lowe EC. The GH130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases That Target β-1,2-Mannosidic Linkages in Candida Mannan. J Biol Chem 2015; 290:25023-33. [PMID: 26286752 PMCID: PMC4599007 DOI: 10.1074/jbc.m115.681460] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/12/2015] [Indexed: 11/06/2022] Open
Abstract
The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. β-Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by glycoside hydrolases, although recently, a family of glycoside phosphorylases, GH130, have also been shown to target β-1,2- and β-1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as glycoside hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed β-mannosidases that hydrolyze β-1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast α-mannans, it is likely that the two enzymes target the β-1,2-mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed that a pair of glutamates, Glu(227) and Glu(268), hydrogen bond to O1 of α-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and β-1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys(199) in BT3780, as a key specificity determinant for β-1,2-mannosidic linkages.
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Affiliation(s)
- Fiona Cuskin
- From the Institute for Cell and Molecular Biosciences, Medical School Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Medical School Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Simon Ladevèze
- Université de Toulouse, INSA/UPS/INP, LISBP, F-31077 Toulouse, France, CNRS, UMR5504 and INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France, and
| | - Alison M Day
- From the Institute for Cell and Molecular Biosciences, Medical School Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Medical School Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
| | - Gideon J Davies
- the York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gabrielle Potocki-Véronèse
- Université de Toulouse, INSA/UPS/INP, LISBP, F-31077 Toulouse, France, CNRS, UMR5504 and INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France, and
| | - Elisabeth C Lowe
- From the Institute for Cell and Molecular Biosciences, Medical School Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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39
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Li J, Zhang J, Lai B, Zhao Y, Li Q. Cloning, Expression, and Characterization of Capra hircus Golgi α-Mannosidase II. Appl Biochem Biotechnol 2015; 177:1241-51. [PMID: 26306528 DOI: 10.1007/s12010-015-1810-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/13/2015] [Indexed: 11/28/2022]
Abstract
Golgi α-mannosidase II (GMII), a key glycosyl hydrolase in the N-linked glycosylation pathway, has been demonstrated to be closely associated with the genesis and development of cancer. In this study, we cloned cDNA-encoding Capra hircus GMII (chGMII) and expressed it in Pichia pastoris expression system. The chGMII cDNA contains an open reading frame of 3432 bp encoding a polypeptide of 1144 amino acids. The deduced molecular mass and pI of chGMII was 130.5 kDa and 8.04, respectively. The gene expression profile analysis showed GMII was the highest expressed gene in the spleen. The recombinant chGMII showed maximum activity at pH 5.4 and 42 °C and was activated by Fe(2+), Zn(2+), Ca(2+), and Mn(2+) and strongly inhibited by Co(2+), Cu(2+), and EDTA. By homology modeling and molecular docking, we obtained the predicted 3D structure of chGMII and the probable binding modes of chGMII-GnMan5Gn, chGMII-SW. A small cavity containing Tyr355 and zinc ion fixed by residues Asp290, His176, Asp178, and His570 was identified as the active center of chGMII. These results not only provide a clue for clarifying the catalytic mechanism of chGMII but also lay a theoretical foundation for subsequent investigations in the field of anticancer therapy for mammals.
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Affiliation(s)
- Jianfei Li
- College of Veterinary Medicine, Northwest A&F University, Xian, China
| | - Jiangye Zhang
- College of Veterinary Medicine, Northwest A&F University, Xian, China
| | - Bi Lai
- College of Veterinary Medicine, Northwest A&F University, Xian, China
| | - Ying Zhao
- College of Veterinary Medicine, Northwest A&F University, Xian, China
| | - Qinfan Li
- College of Veterinary Medicine, Northwest A&F University, Xian, China.
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40
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Thompson AJ, Speciale G, Iglesias-Fernández J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ. Evidence for a Boat Conformation at the Transition State of GH76 α-1,6-Mannanases-Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Thompson AJ, Speciale G, Iglesias-Fernández J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ. Evidence for a boat conformation at the transition state of GH76 α-1,6-mannanases--key enzymes in bacterial and fungal mannoprotein metabolism. Angew Chem Int Ed Engl 2015; 54:5378-82. [PMID: 25772148 DOI: 10.1002/anie.201410502] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/29/2015] [Indexed: 01/21/2023]
Abstract
α-Mannosidases and α-mannanases have attracted attention for the insight they provide into nucleophilic substitution at the hindered anomeric center of α-mannosides, and the potential of mannosidase inhibitors as cellular probes and therapeutic agents. We report the conformational itinerary of the family GH76 α-mannanases studied through structural analysis of the Michaelis complex and synthesis and evaluation of novel aza/imino sugar inhibitors. A Michaelis complex in an (O) S2 conformation, coupled with distortion of an azasugar in an inhibitor complex to a high energy B2,5 conformation are rationalized through ab initio QM/MM metadynamics that show how the enzyme surface restricts the conformational landscape of the substrate, rendering the B2,5 conformation the most energetically stable on-enzyme. We conclude that GH76 enzymes perform catalysis using an itinerary that passes through (O) S2 and B2,5 (≠) conformations, information that should inspire the development of new antifungal agents.
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Affiliation(s)
- Andrew J Thompson
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
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42
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Dupoiron S, Zischek C, Ligat L, Carbonne J, Boulanger A, Dugé de Bernonville T, Lautier M, Rival P, Arlat M, Jamet E, Lauber E, Albenne C. The N-Glycan cluster from Xanthomonas campestris pv. campestris: a toolbox for sequential plant N-glycan processing. J Biol Chem 2015. [PMID: 25586188 DOI: 10.1074/jbc.m114.62459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
N-Glycans are widely distributed in living organisms but represent only a small fraction of the carbohydrates found in plants. This probably explains why they have not previously been considered as substrates exploited by phytopathogenic bacteria during plant infection. Xanthomonas campestris pv. campestris, the causal agent of black rot disease of Brassica plants, possesses a specific system for GlcNAc utilization expressed during host plant infection. This system encompasses a cluster of eight genes (nixE to nixL) encoding glycoside hydrolases (GHs). In this paper, we have characterized the enzymatic activities of these GHs and demonstrated their involvement in sequential degradation of a plant N-glycan using a N-glycopeptide containing two GlcNAcs, three mannoses, one fucose, and one xylose (N2M3FX) as a substrate. The removal of the α-1,3-mannose by the α-mannosidase NixK (GH92) is a prerequisite for the subsequent action of the β-xylosidase NixI (GH3), which is involved in the cleavage of the β-1,2-xylose, followed by the α-mannosidase NixJ (GH125), which removes the α-1,6-mannose. These data, combined to the subcellular localization of the enzymes, allowed us to propose a model of N-glycopeptide processing by X. campestris pv. campestris. This study constitutes the first evidence suggesting N-glycan degradation by a plant pathogen, a feature shared with human pathogenic bacteria. Plant N-glycans should therefore be included in the repertoire of molecules putatively metabolized by phytopathogenic bacteria during their life cycle.
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Affiliation(s)
- Stéphanie Dupoiron
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Claudine Zischek
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Laetitia Ligat
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Julien Carbonne
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Alice Boulanger
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Thomas Dugé de Bernonville
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Martine Lautier
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and the Université de Toulouse, UPS, F-31062 Toulouse, France
| | - Pauline Rival
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France, INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Matthieu Arlat
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and the Université de Toulouse, UPS, F-31062 Toulouse, France
| | - Elisabeth Jamet
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Emmanuelle Lauber
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Cécile Albenne
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
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43
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Dupoiron S, Zischek C, Ligat L, Carbonne J, Boulanger A, Dugé de Bernonville T, Lautier M, Rival P, Arlat M, Jamet E, Lauber E, Albenne C. The N-Glycan cluster from Xanthomonas campestris pv. campestris: a toolbox for sequential plant N-glycan processing. J Biol Chem 2015; 290:6022-36. [PMID: 25586188 DOI: 10.1074/jbc.m114.624593] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-Glycans are widely distributed in living organisms but represent only a small fraction of the carbohydrates found in plants. This probably explains why they have not previously been considered as substrates exploited by phytopathogenic bacteria during plant infection. Xanthomonas campestris pv. campestris, the causal agent of black rot disease of Brassica plants, possesses a specific system for GlcNAc utilization expressed during host plant infection. This system encompasses a cluster of eight genes (nixE to nixL) encoding glycoside hydrolases (GHs). In this paper, we have characterized the enzymatic activities of these GHs and demonstrated their involvement in sequential degradation of a plant N-glycan using a N-glycopeptide containing two GlcNAcs, three mannoses, one fucose, and one xylose (N2M3FX) as a substrate. The removal of the α-1,3-mannose by the α-mannosidase NixK (GH92) is a prerequisite for the subsequent action of the β-xylosidase NixI (GH3), which is involved in the cleavage of the β-1,2-xylose, followed by the α-mannosidase NixJ (GH125), which removes the α-1,6-mannose. These data, combined to the subcellular localization of the enzymes, allowed us to propose a model of N-glycopeptide processing by X. campestris pv. campestris. This study constitutes the first evidence suggesting N-glycan degradation by a plant pathogen, a feature shared with human pathogenic bacteria. Plant N-glycans should therefore be included in the repertoire of molecules putatively metabolized by phytopathogenic bacteria during their life cycle.
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Affiliation(s)
- Stéphanie Dupoiron
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Claudine Zischek
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Laetitia Ligat
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Julien Carbonne
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Alice Boulanger
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Thomas Dugé de Bernonville
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Martine Lautier
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and the Université de Toulouse, UPS, F-31062 Toulouse, France
| | - Pauline Rival
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France, INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Matthieu Arlat
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and the Université de Toulouse, UPS, F-31062 Toulouse, France
| | - Elisabeth Jamet
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Emmanuelle Lauber
- INRA and CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR 2594, F-31326 Castanet-Tolosan, France, and
| | - Cécile Albenne
- From the Université de Toulouse and CNRS, Laboratoire de Recherches en Sciences Végétales, UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
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44
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Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, Gilbert HJ. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 2015; 517:165-169. [PMID: 25567280 PMCID: PMC4978465 DOI: 10.1038/nature13995] [Citation(s) in RCA: 358] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 10/22/2014] [Indexed: 12/28/2022]
Abstract
Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.
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Affiliation(s)
- Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Elisabeth C. Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Max J. Temple
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Yanping Zhu
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Elizabeth Cameron
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan T. Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alan Cartmell
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Brian S. Hamilton
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | - Rui Chen
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | - Thomas J. Tolbert
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | | | | | | | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jose L. Munōz-Munōz
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Andrew Day
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Maria J. Peña
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Michael D. Suits
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Alisdair B. Boraston
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Todd Atherly
- USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, Iowa, USA
| | - Cherie J. Ziemer
- USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, Iowa, USA
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - D. Wade Abbott
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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Hakki Z, Thompson AJ, Bellmaine S, Speciale G, Davies GJ, Williams SJ. Structural and Kinetic Dissection of theendo-α-1,2-Mannanase Activity of Bacterial GH99 Glycoside Hydrolases fromBacteroides spp. Chemistry 2014; 21:1966-77. [DOI: 10.1002/chem.201405539] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 01/14/2023]
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Speciale G, Thompson AJ, Davies GJ, Williams SJ. Dissecting conformational contributions to glycosidase catalysis and inhibition. Curr Opin Struct Biol 2014; 28:1-13. [PMID: 25016573 PMCID: PMC4220041 DOI: 10.1016/j.sbi.2014.06.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/15/2023]
Abstract
The conformational itinerary describes the changes in sugar shape during catalysis. Stereoelectronic requirements for glycoside hydrolysis are discussed. Major and emerging approaches to define conformational itineraries are reviewed. New assignments of glycosidase conformational itineraries are summarized.
Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed.
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Affiliation(s)
- Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew J Thompson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A. Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. BMC Bioinformatics 2014; 15:196. [PMID: 24938123 PMCID: PMC4071793 DOI: 10.1186/1471-2105-15-196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/10/2014] [Indexed: 01/24/2023] Open
Abstract
Background Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain. Results Genomic context and domain architecture analyses support a role for the GxGYxYP domain in carbohydrate metabolism. Sparse occurrences in eukaryotes are the result of lateral gene transfer. The structure of the GxGYxYP domain-containing protein encoded by the BT2193 locus reveals two structural domains, the first composed of three divergent repeats with no recognisable homology to previously solved structures, the second a more familiar seven-stranded β/α barrel. Structure-based analyses including conservation mapping localise a presumed functional site to a cleft between the two domains of BT2193. Matching to a catalytic site template from a GH9 cellulase and other analyses point to a putative catalytic triad composed of Glu272, Asp331 and Asp333. Conclusions We suggest that GxGYxYP-containing proteins constitute a novel glycoside hydrolase family of as yet unknown specificity.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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Iwamoto S, Kasahara Y, Kamei KI, Seko A, Takeda Y, Ito Y, Matsuo I. Measurement of endo-α-mannosidase activity using a fluorescently labeled oligosaccharide derivative. Biosci Biotechnol Biochem 2014; 78:927-36. [DOI: 10.1080/09168451.2014.910101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Endo-α-mannosidase, a GH99-family glycoside hydrolase, cleaves α-mannoside linkages with glucose residues. This enzyme is proposed to play a critical role in N-glycan processing for deglucosylation. To measure endo-α-mannosidase activity, we synthesized a fluorescently labeled tetrasaccharide derivative (Glcα1-3Manα1-2Manα1-2Manα1-O–C3H6–NH-Dansyl) in a stereocontrolled manner. The tetrasaccharide skeleton was prepared by step-wise coupling using mannose donors 4 and 7. The 1,2-cis α-glycosidic linkage on the non-reducing end of the glucose residue was constructed by inversion of the stereochemistry of the C-2 hydroxyl group in the α-mannose residue. Finally, the dansyl group was introduced at the reducing end via an aminopropyl linker. This probe successfully measured endo-α-mannosidase activity.
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Affiliation(s)
- Shogo Iwamoto
- Division of Molecular Science, Gunma University, Kiryu, Japan
| | - Yuta Kasahara
- Division of Molecular Science, Gunma University, Kiryu, Japan
| | - Ken-ichi Kamei
- Division of Molecular Science, Gunma University, Kiryu, Japan
| | - Akira Seko
- ERATO Ito Glycotrilogy Project, JST, Saitama, Japan
| | | | - Yukishige Ito
- ERATO Ito Glycotrilogy Project, JST, Saitama, Japan
- RIKEN Synthetic Cellular Chemistry Laboratory, Saitama, Japan
| | - Ichiro Matsuo
- Division of Molecular Science, Gunma University, Kiryu, Japan
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Hykollari A, Dragosits M, Rendić D, Wilson IBH, Paschinger K. N-glycomic profiling of a glucosidase II mutant of Dictyostelium discoideum by ''off-line'' liquid chromatography and mass spectrometry. Electrophoresis 2014; 35:2116-29. [PMID: 24574058 DOI: 10.1002/elps.201300612] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/09/2014] [Indexed: 01/27/2023]
Abstract
In this study, we have performed the first mass spectrometric analysis of N-glycans of the M31 mutant strain of the cellular slime mould Dictyostelium discoideum, previously shown to have a defect in glucosidase II. Together with glucosidase I, this enzyme mediates part of the initial processing of N-glycans; defects in either glucosidase are associated with human diseases and result in an accumulation of incorrectly processed oligosaccharides which are not, or only poor, substrates for a range of downstream enzymes. To examine the effect of the glucosidase II mutation in Dictyostelium, we employed off-line LC-MALDI-TOF MS in combination with chemical and enzymatic treatments and MS/MS to analyze the neutral and anionic N-glycans of the mutant as compared to the wild type. The major neutral species were, as expected, of the composition Hex10-11 HexNAc2-3 with one or two terminal glucose residues. Consistent with the block in processing of neutral N-glycans caused by the absence of glucosidase II, fucose was apparently absent from the N-glycans and bisecting N-acetylglucosamine was rare. The major anionic oligosaccharides were sulfated and/or methylphosphorylated forms of Hex8-11 HexNAc2-3 , many of which surprisingly lacked glucose residues entirely. As anionic N-glycans are considered to be mostly associated with lysosomal enzymes in Dictyostelium, we hypothesise that glycosidases present in the acidic compartments may act on the oligosaccharides attached to such slime mould proteins. Furthermore, our chosen analytical approach enabled us, via observation of diagnostic negative-mode MS/MS fragments, to determine the fine structure of the methylphosphorylated and sulfated N-glycans of the M31 glucosidase mutant in their native state.
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Affiliation(s)
- Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
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