1
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Du M, Wei L, Yuan M, Zou R, Xu Y, Wang X, Wang W, Li F. Enzymatic comparison of two homologous enzymes reveals N-terminal domain of chondroitinase ABC I regulates substrate selection and product generation. J Biol Chem 2023; 299:104692. [PMID: 37031818 DOI: 10.1016/j.jbc.2023.104692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/19/2023] [Accepted: 04/05/2023] [Indexed: 04/11/2023] Open
Abstract
Chondroitinase ABC-type I (CSase ABC I), which can digest both chondroitin sulfate (CS) and dermatan sulfate (DS) in an endolytic manner, is an essential tool in structural and functional studies of CS/DS. Although a few CSase ABC I have been identified from bacteria, the substrate-degrading pattern and regulatory mechanisms of them have rarely been investigated. Herein, two CSase ABC I, IM3796 and IM1634, were identified from the intestinal metagenome of CS-fed mice. They show high sequence homology (query coverage: 88.00%, percent identity: 90.10%) except for an extra peptide (Met1-His109) at the N-terminus in IM1634, but their enzymatic properties are very different. IM3796 prefers to degrade 6-O-sulfated GalNAc residue-enriched CS into tetra- and disaccharides. In contrast, IM1634 exhibits nearly a thousand times more activity than IM3796, and can completely digest CS/DS with various sulfation patterns to produce disaccharides, unlike most CSase ABC I. Structure modeling showed that IM3796 did not contain an N-terminal domain composed of two β-sheets, which is found in IM1634 and other CSase ABC I. Furthermore, deletion of the N-terminal domain (Met1-His109) from IM1634 caused the enzymatic properties of the variant IM1634-T109 to be similar to those of IM3796, and conversely, grafting this domain to IM3796 increased the similarity of the variant IM3796-A109 to IM1634. In conclusion, the comparative study of the new CSase ABC I provides two unique tools for CS/DS-related studies and applications and, more importantly, reveals the critical role of the N-terminal domain in regulating the substrate binding and degradation of these enzymes.
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Affiliation(s)
- Min Du
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lin Wei
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Min Yuan
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Ruyi Zou
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Yingying Xu
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Xu Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Wenshuang Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.
| | - Fuchuan Li
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China; College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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2
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Hungatella hathewayi, an Efficient Glycosaminoglycan-Degrading
Firmicutes
from Human Gut and Its Chondroitin ABC Exolyase with High Activity and Broad Substrate Specificity. Appl Environ Microbiol 2022; 88:e0154622. [PMID: 36342199 PMCID: PMC9680638 DOI: 10.1128/aem.01546-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An increased understanding of GAG metabolism by intestinal bacteria is critical in identifying the driving factors for the composition, modulation, and homeostasis of the human gut microbiota. In addition, GAG-depolymerizing polysaccharide lyases are highly desired enzymes for the production of GAG oligosaccharides and as therapeutics.
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3
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Moffat D, Ye K, Jin S. Decellularization for the retention of tissue niches. J Tissue Eng 2022; 13:20417314221101151. [PMID: 35620656 PMCID: PMC9128068 DOI: 10.1177/20417314221101151] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/01/2022] [Indexed: 12/25/2022] Open
Abstract
Decellularization of natural tissues to produce extracellular matrix is a promising method for three-dimensional scaffolding and for understanding microenvironment of the tissue of interest. Due to the lack of a universal standard protocol for tissue decellularization, recent investigations seek to develop novel methods for whole or partial organ decellularization capable of supporting cell differentiation and implantation towards appropriate tissue regeneration. This review provides a comprehensive and updated perspective on the most recent advances in decellularization strategies for a variety of organs and tissues, highlighting techniques of chemical, physical, biological, enzymatic, or combinative-based methods to remove cellular contents from tissues. In addition, the review presents modernized approaches for improving standard decellularization protocols for numerous organ types.
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Affiliation(s)
- Deana Moffat
- Department of Biomedical Engineering, Binghamton University, State University of New York (SUNY), Binghamton, NY, USA
| | - Kaiming Ye
- Department of Biomedical Engineering, Binghamton University, State University of New York (SUNY), Binghamton, NY, USA
- Center of Biomanufacturing for Regenerative Medicine, Binghamton University, State University of New York (SUNY), Binghamton, NY, USA
| | - Sha Jin
- Department of Biomedical Engineering, Binghamton University, State University of New York (SUNY), Binghamton, NY, USA
- Center of Biomanufacturing for Regenerative Medicine, Binghamton University, State University of New York (SUNY), Binghamton, NY, USA
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4
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Gheorghita AA, Wolfram F, Whitfield GB, Jacobs HM, Pfoh R, Wong SSY, Guitor AK, Goodyear MC, Berezuk AM, Khursigara CM, Parsek MR, Howell PL. The Pseudomonas aeruginosa homeostasis enzyme AlgL clears the periplasmic space of accumulated alginate during polymer biosynthesis. J Biol Chem 2022; 298:101560. [PMID: 34990713 PMCID: PMC8829089 DOI: 10.1016/j.jbc.2021.101560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen and a leading cause of chronic infection in the lungs of individuals with cystic fibrosis. After colonization, P. aeruginosa often undergoes a phenotypic conversion to mucoidy, characterized by overproduction of the alginate exopolysaccharide. This conversion is correlated with poorer patient prognoses. The majority of genes required for alginate synthesis, including the alginate lyase, algL, are located in a single operon. Previous investigations of AlgL have resulted in several divergent hypotheses regarding the protein’s role in alginate production. To address these discrepancies, we determined the structure of AlgL and, using multiple sequence alignments, identified key active site residues involved in alginate binding and catalysis. In vitro enzymatic analysis of active site mutants highlights R249 and Y256 as key residues required for alginate lyase activity. In a genetically engineered P. aeruginosa strain where alginate biosynthesis is under arabinose control, we found that AlgL is required for cell viability and maintaining membrane integrity during alginate production. We demonstrate that AlgL functions as a homeostasis enzyme to clear the periplasmic space of accumulated polymer. Constitutive expression of the AlgU/T sigma factor mitigates the effects of an algL deletion during alginate production, suggesting that an AlgU/T-regulated protein or proteins can compensate for an algL deletion. Together, our study demonstrates the role of AlgL in alginate biosynthesis, explains the discrepancies observed previously across other P. aeruginosa ΔalgL genetic backgrounds, and clarifies the existing divergent data regarding the function of AlgL as an alginate degrading enzyme.
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Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Francis Wolfram
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Holly M Jacobs
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Roland Pfoh
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven S Y Wong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Allison K Guitor
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mara C Goodyear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alison M Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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5
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Shin J, Kang EH, Choi S, Jeon EJ, Cho JH, Kang D, Lee H, Yun IS, Cho SW. Tissue-Adhesive Chondroitin Sulfate Hydrogel for Cartilage Reconstruction. ACS Biomater Sci Eng 2021; 7:4230-4243. [PMID: 33538598 DOI: 10.1021/acsbiomaterials.0c01414] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chondroitin sulfate (CS), the main component of cartilage extracellular matrix, has attracted attention as a biomaterial for cartilage tissue engineering. However, current CS hydrogel systems still have limitations for application in successful cartilage tissue engineering owing to their unsuitable degradation kinetics, insufficient mechanical similarity, and lack of integration with the native cartilage tissue. In this study, using mussel adhesive-inspired catechol chemistry, we developed a functional CS hydrogel that exhibits tunable physical and mechanical properties as well as excellent tissue adhesion for efficient integration with native tissues. Various properties of the developed catechol-functionalized CS (CS-CA) hydrogel, including swelling, degradation, mechanical properties, and adhesiveness, could be tailored by varying the conjugation ratio of the catechol group to the CS backbone and the concentration of the CS-CA conjugates. CS-CA hydrogels exhibited significantly increased modulus (∼10 kPa) and superior adhesive properties (∼3 N) over conventional CS hydrogels (∼hundreds Pa and ∼0.05 N). In addition, CS-CA hydrogels incorporating decellularized cartilage tissue dice promoted the chondrogenic differentiation of human adipose-derived mesenchymal stem cells by providing a cartilage-like microenvironment. Finally, the transplantation of autologous cartilage dice using tissue-adhesive CS-CA hydrogels enhanced cartilage integration with host tissue and neo-cartilage formation owing to favorable physical, mechanical, and biological properties for cartilage formation. In conclusion, our study demonstrated the potential utility of the CS-CA hydrogel system in cartilage tissue reconstruction.
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Affiliation(s)
- Jisoo Shin
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Eun Hye Kang
- Institute for Human Tissue Restoration, Department of Plastic and Reconstructive Surgery, Yonsei University College of Medicine, Severance Hospital, Seoul 03722, Republic of Korea
| | - Soojeong Choi
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Eun Je Jeon
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung Ho Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Donyoung Kang
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyungsuk Lee
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - In Sik Yun
- Department of Plastic and Reconstructive Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.,Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea.,Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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6
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Hettiaratchi MH, O’Meara MJ, O’Meara TR, Pickering AJ, Letko-Khait N, Shoichet MS. Reengineering biocatalysts: Computational redesign of chondroitinase ABC improves efficacy and stability. SCIENCE ADVANCES 2020; 6:eabc6378. [PMID: 32875119 PMCID: PMC7438101 DOI: 10.1126/sciadv.abc6378] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/08/2020] [Indexed: 05/24/2023]
Abstract
Maintaining biocatalyst stability and activity is a critical challenge. Chondroitinase ABC (ChABC) has shown promise in central nervous system (CNS) regeneration, yet its therapeutic utility is severely limited by instability. We computationally reengineered ChABC by introducing 37, 55, and 92 amino acid changes using consensus design and forcefield-based optimization. All mutants were more stable than wild-type ChABC with increased aggregation temperatures between 4° and 8°C. Only ChABC with 37 mutations (ChABC-37) was more active and had a 6.5 times greater half-life than wild-type ChABC, increasing to 106 hours (4.4 days) from only 16.8 hours. ChABC-37, expressed as a fusion protein with Src homology 3 (ChABC-37-SH3), was active for 7 days when released from a hydrogel modified with SH3-binding peptides. This study demonstrates the broad opportunity to improve biocatalysts through computational engineering and sets the stage for future testing of this substantially improved protein in the treatment of debilitating CNS injuries.
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Affiliation(s)
- Marian H. Hettiaratchi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave. #2017, Ann Arbor, MI 48109, USA
| | - Teresa R. O’Meara
- Department of Microbiology and Immunology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI 48109 USA
| | - Andrew J. Pickering
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Nitzan Letko-Khait
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College St., Toronto, ON M5S 3G9, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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7
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Ji Y, Zhang S, Qiao M, Jiao R, Li J, Song P, Zhang X, Huang H. Synthesis of structurally defined chondroitin sulfate: Paving the way to the structure-activity relationship studies. Carbohydr Polym 2020; 248:116796. [PMID: 32919534 DOI: 10.1016/j.carbpol.2020.116796] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/05/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
Abstract
Chondroitin sulfate (CS) is one of the major and widespread glycosaminoglycans, a family of structurally complex, linear, anionic hetero-co-polysaccharides. CS plays a vital role in various normal physiological and pathological processes, thus, showing varieties of biological activities, such as anti-oxidation, anti-atherosclerosis, anti-thrombosis, and insignificant immunogenicity. However, the heterogeneity of the naturally occurring CS potentially leads to function unspecific and limits further structure-activity relationship studies. Therefore, the synthesis of CS with well-defined and uniform chain lengths is of major interest for the development of reliable drugs. In this review, we examine the remarkable progress that has been made in the chemical, enzymatic and chemoenzymatic synthesis of CS and its derivatives, providing a broad spectrum of options to access CS of well controlled chain lengths.
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Affiliation(s)
- Yuan Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Shilin Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Meng Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ruoyu Jiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Ping Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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8
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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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9
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Ndeh D, Baslé A, Strahl H, Yates EA, McClurgg UL, Henrissat B, Terrapon N, Cartmell A. Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus. Nat Commun 2020; 11:646. [PMID: 32005816 PMCID: PMC6994673 DOI: 10.1038/s41467-020-14509-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/10/2020] [Indexed: 01/31/2023] Open
Abstract
The human gut microbiota (HGM), which is critical to human health, utilises complex glycans as its major carbon source. Glycosaminoglycans represent an important, high priority, nutrient source for the HGM. Pathways for the metabolism of various glycosaminoglycan substrates remain ill-defined. Here we perform a biochemical, genetic and structural dissection of the genetic loci that orchestrates glycosaminoglycan metabolism in the organism Bacteroides thetaiotaomicron. Here, we report: the discovery of two previously unknown surface glycan binding proteins which facilitate glycosaminoglycan import into the periplasm; distinct kinetic and genetic specificities of various periplasmic lyases which dictate glycosaminoglycan metabolic pathways; understanding of endo sulfatase activity questioning the paradigm of how the 'sulfation problem' is handled by the HGM; and 3D crystal structures of the polysaccharide utilisation loci encoded sulfatases. Together with comparative genomic studies, our study fills major gaps in our knowledge of glycosaminoglycan metabolism by the HGM.
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Affiliation(s)
- Didier Ndeh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Urszula L McClurgg
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 23218, Saudi Arabia
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
| | - Alan Cartmell
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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10
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Chondroitin Sulfate-Degrading Enzymes as Tools for the Development of New Pharmaceuticals. Catalysts 2019. [DOI: 10.3390/catal9040322] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chondroitin sulfates are linear anionic sulfated polysaccharides found in biological tissues, mainly within the extracellular matrix, which are degraded and altered by specific lyases depending on specific time points. These polysaccharides have recently acquired relevance in the pharmaceutical industry due to their interesting therapeutic applications. As a consequence, chondroitin sulfate (CS) lyases have been widely investigated as tools for the development of new pharmaceuticals based on these polysaccharides. This review focuses on the major breakthrough represented by chondroitin sulfate-degrading enzymes and their structures and mechanisms of function in addition to their major applications.
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11
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Omidi-Ardali H, Aminian M, Golestani A, Shahaboddin ME, Maleki M. N∆89 and C∆274 Truncated Enzymes of Chondroitinase ABC I Regain More Imperturbable Microenvironments Around Structural Components in Comparison to their Wild Type. Protein J 2019; 38:151-159. [DOI: 10.1007/s10930-019-09821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Jensen PF, Kadziola A, Comamala G, Segura DR, Anderson L, Poulsen JCN, Rasmussen KK, Agarwal S, Sainathan RK, Monrad RN, Svendsen A, Nielsen JE, Lo Leggio L, Rand KD. Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol 2019; 26:191-202.e6. [DOI: 10.1016/j.chembiol.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/14/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
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13
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Li Y, Zhou Z, Chen Z. High-level production of ChSase ABC I by co-expressing molecular chaperones in Escherichia coli. Int J Biol Macromol 2018; 119:779-784. [DOI: 10.1016/j.ijbiomac.2018.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
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14
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Konasani VR, Jin C, Karlsson NG, Albers E. A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901. Sci Rep 2018; 8:14713. [PMID: 30279430 PMCID: PMC6168547 DOI: 10.1038/s41598-018-32922-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/17/2018] [Indexed: 11/19/2022] Open
Abstract
Ulvan, which is one of the major structural polysaccharides of the cell walls of green macroalgae, is degraded by ulvan lyases via the β-elimination mechanism with the release of oligosaccharides that have unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid (∆) at the non-reducing end. These ulvan lyases belong to the PL24 or PL25 or PL28 family in the CAZy database. In this study, we identify and biochemically characterise a periplasmic novel broad-spectrum ulvan lyase from Formosa agariphila KMM 3901. The lyase was overexpressed in Escherichia coli, and the purified recombinant enzyme depolymerised ulvan in an endolytic manner with a Km of 0.77 mg/ml, and displayed optimum activity at 40 °C and pH 8. This lyase also degraded heparan sulphate and chondroitin sulphate. Detailed analyses of the end-products of the enzymatic degradation of ulvan using 1H- and 13C-NMR and LC-MS revealed an unsaturated disaccharide (∆Rha3S) and a tetrasaccharide (∆Rha3S-Xyl-Rha) as the principal end-products. In contrast to the previously described ulvan lyases, this novel lyase is mostly composed of α-helices that form an (α/α)6 incomplete toroid domain and displays a remarkably broad-spectrum activity. This novel lyase is the first member of a new family of ulvan lyases.
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Affiliation(s)
- Venkat Rao Konasani
- Industrial Biotechnology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Eva Albers
- Industrial Biotechnology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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15
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Establishment of Aromatic Pairs at the Surface of Chondroitinase ABC I: the Effect on Activity and Stability. Appl Biochem Biotechnol 2018; 186:358-370. [DOI: 10.1007/s12010-018-2741-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/18/2018] [Indexed: 10/17/2022]
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16
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Shahaboddin ME, Khajeh K, Maleki M, Golestani A. Improvement of activity and stability of Chondroitinase ABC I by introducing an aromatic cluster at the surface of protein. Enzyme Microb Technol 2017; 105:38-44. [DOI: 10.1016/j.enzmictec.2017.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/22/2017] [Accepted: 06/03/2017] [Indexed: 11/16/2022]
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17
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Woznica A, Gerdt JP, Hulett RE, Clardy J, King N. Mating in the Closest Living Relatives of Animals Is Induced by a Bacterial Chondroitinase. Cell 2017; 170:1175-1183.e11. [PMID: 28867285 DOI: 10.1016/j.cell.2017.08.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/07/2017] [Accepted: 08/03/2017] [Indexed: 01/08/2023]
Abstract
We serendipitously discovered that the marine bacterium Vibrio fischeri induces sexual reproduction in one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta. Although bacteria influence everything from nutrition and metabolism to cell biology and development in eukaryotes, bacterial regulation of eukaryotic mating was unexpected. Here, we show that a single V. fischeri protein, the previously uncharacterized EroS, fully recapitulates the aphrodisiac-like activity of live V. fischeri. EroS is a chondroitin lyase; although its substrate, chondroitin sulfate, was previously thought to be an animal synapomorphy, we demonstrate that S. rosetta produces chondroitin sulfate and thus extend the ancestry of this important glycosaminoglycan to the premetazoan era. Finally, we show that V. fischeri, purified EroS, and other bacterial chondroitin lyases induce S. rosetta mating at environmentally relevant concentrations, suggesting that bacteria likely regulate choanoflagellate mating in nature.
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Affiliation(s)
- Arielle Woznica
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joseph P Gerdt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan E Hulett
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Nicole King
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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18
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Expression, purification and characterization of GAPDH-ChSase ABC I from Proteus vulgaris in Escherichia coli. Protein Expr Purif 2016; 128:36-41. [DOI: 10.1016/j.pep.2016.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022]
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19
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Kale V, Friðjónsson Ó, Jónsson JÓ, Kristinsson HG, Ómarsdóttir S, Hreggviðsson GÓ. Chondroitin Lyase from a Marine Arthrobacter sp. MAT3885 for the Production of Chondroitin Sulfate Disaccharides. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:479-492. [PMID: 25912370 DOI: 10.1007/s10126-015-9629-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Chondroitin sulfate (CS) saccharides from cartilage tissues have potential application in medicine or as dietary supplements due to their therapeutic bioactivities. Studies have shown that depolymerized CS saccharides may display enhanced bioactivity. The objective of this study was to isolate a CS-degrading enzyme for an efficient production of CS oligo- or disaccharides. CS-degrading bacteria from marine environments were enriched using in situ artificial support colonization containing CS from shark cartilage as substrate. Subsequently, an Arthrobacter species (strain MAT3885) efficiently degrading CS was isolated from a CS enrichment culture. The genomic DNA from strain MAT3885 was pyro-sequenced by using the 454 FLX sequencing technology. Following assembly and annotation, an orf, annotated as family 8 polysaccharide lyase genes, was identified, encoding an amino acid sequence with a similarity to CS lyases according to NCBI blastX. The gene, designated choA1, was cloned in Escherichia coli and expressed downstream of and in frame with the E. coli malE gene for obtaining a high yield of soluble recombinant protein. Applying a dual-tag system (MalE-Smt3-ChoA1), the MalE domain was separated from ChoA1 with proteolytic cleavage using Ulp1 protease. ChoA1 was defined as an AC-type enzyme as it degraded chondroitin sulfate A, C, and hyaluronic acid. The optimum activity of the enzyme was at pH 5.5-7.5 and 40 °C, running a 10-min reaction. The native enzyme was estimated to be a monomer. As the recombinant chondroitin sulfate lyase (designated as ChoA1R) degraded chondroitin sulfate efficiently compared to a benchmark enzyme, it may be used for the production of chondroitin sulfate disaccharides for the food industry or health-promoting products.
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Affiliation(s)
- Varsha Kale
- Matís, Vínlandsleið 12, 113, Reykjavík, Iceland
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20
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Chen Z, Li Y, Feng Y, Chen L, Yuan Q. Enzyme activity enhancement of chondroitinase ABC I from Proteus vulgaris by site-directed mutagenesis. RSC Adv 2015. [DOI: 10.1039/c5ra15220h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arg660 was found as a new active site and Asn795Ala and Trp818Ala mutants showed higher activities than the wild type based on molecular docking simulation analysis for the first time.
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Affiliation(s)
- Zhenya Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Ye Li
- Department of Biotechnology
- Beijing Polytechnic
- Beijing 100029
- China
| | - Yue Feng
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Liang Chen
- Department of Biotechnology
- Beijing Polytechnic
- Beijing 100029
- China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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21
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Abstract
Over the sixty years since Koshland initially formulated the classical mechanisms for retaining and inverting glycosidases, researchers have assembled a large body of supporting evidence and have documented variations of these mechanisms. Recently, however, researchers have uncovered a number of completely distinct mechanisms for enzymatic cleavage of glycosides involving elimination and/or hydration steps. In family GH4 and GH109 glycosidases, the reaction proceeds via transient NAD(+)-mediated oxidation at C3, thereby acidifying the proton at C2 and allowing for elimination across the C1-C2 bond. Subsequent Michael-type addition of water followed by reduction at C3 generates the hydrolyzed product. Enzymes employing this mechanism can hydrolyze thioglycosides as well as both anomers of activated substrates. Sialidases employ a conventional retaining mechanism in which a tyrosine functions as the nucleophile, but in some cases researchers have observed off-path elimination end products. These reactions occur via the normal covalent intermediate, but instead of an attack by water on the anomeric center, the catalytic acid/base residue abstracts an adjacent proton. These enzymes can also catalyze hydration of the enol ether via the reverse pathway. Reactions of α-(1,4)-glucan lyases also proceed through a covalent intermediate with subsequent abstraction of an adjacent proton to give elimination. However, in this case, the departing carboxylate "nucleophile" serves as the base in a concerted but asynchronous syn-elimination process. These enzymes perform only elimination reactions. Polysaccharide lyases, which act on uronic acid-containing substrates, also catalyze only elimination reactions. Substrate binding neutralizes the charge on the carboxylate, which allows for abstraction of the proton on C5 and leads to an elimination reaction via an E1cb mechanism. These enzymes can also cleave thioglycosides, albeit slowly. The unsaturated product of polysaccharide lyases can then serve as a substrate for a hydration reaction carried out by unsaturated glucuronyl hydrolases. This hydration is initiated by protonation at C4 and proceeds in a Markovnikov fashion rather than undergoing a Michael-type addition, giving a hemiketal at C5. This hemiketal then undergoes a rearrangement that results in cleavage of the anomeric bond. These enzymes can also hydrolyze thioglycosides efficiently and slowly turn over substrates with inverted anomeric configuration. The mechanisms discussed in this Account proceed through transition states that involve either positive or negative charges, unlike the exclusively cationic transition states of the classical Koshland retaining and inverting glycosidases. In addition, the distribution of this charge throughout the substrate can vary substantially. The nature of these mechanisms and their transition states means that any inhibitors or inactivators of these unusual enzymes probably differ from those presently used for Koshland retaining or inverting glycosidases.
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Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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22
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Kawaguchi Y, Sugiura N, Kimata K, Kimura M, Kakuta Y. The crystal structure of novel chondroitin lyase ODV-E66, a baculovirus envelope protein. FEBS Lett 2013; 587:S0014-5793(13)00778-3. [PMID: 24512853 DOI: 10.1016/j.febslet.2013.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/01/2013] [Accepted: 10/15/2013] [Indexed: 11/28/2022]
Abstract
Chondroitin lyases have been known as pathogenic bacterial enzymes that degrade chondroitin. Recently, baculovirus envelope protein ODV-E66 was identified as the first reported viral chondroitin lyase. ODV-E66 has low sequence identity with bacterial lyases at <12%, and unique characteristics reflecting the life cycle of baculovirus. To understand ODV-E66's structural basis, the crystal structure was determined and it was found that the structural fold resembled that of polysaccharide lyase 8 proteins and that the catalytic residues were also conserved. This structure enabled discussion of the unique substrate specificity and the stability of ODV-E66 as well as the host specificity of baculovirus.
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Affiliation(s)
- Yoshirou Kawaguchi
- Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Nobuo Sugiura
- Institute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan
| | - Koji Kimata
- Research Complex for the Medicine Frontiers, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan
| | - Makoto Kimura
- Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan; Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Yoshimitu Kakuta
- Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan; Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan.
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23
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Nazari-Robati M, Khajeh K, Aminian M, Mollania N, Golestani A. Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:479-86. [DOI: 10.1016/j.bbapap.2012.11.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
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24
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Farrell EK, Tipton PA. Functional characterization of AlgL, an alginate lyase from Pseudomonas aeruginosa. Biochemistry 2012; 51:10259-66. [PMID: 23215237 DOI: 10.1021/bi301425r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alginate lyase (AlgL) catalyzes the cleavage of the polysaccharide alginate through a β-elimination reaction. In Pseudomonas aeruginosa, algL is part of the alginate biosynthetic operon, and although it is required for alginate biosynthesis, it is not clear why. Steady-state kinetic studies were performed to characterize its substrate specificity and revealed that AlgL operates preferentially on nonacetylated alginate or its precursor mannuronan. Mature alginate is secreted as a partially acetylated polysaccharide, so this observation is consistent with suggestions that AlgL serves to degrade mislocalized alginate that is trapped in the periplasmic space. The k(cat)/K(m) for the reaction increased linearly with the number of residues in the substrate, from 2.1 × 10(5) M(-1) s(-1) for the substrate containing 16 residues to 7.9 × 10(6) M(-1) s(-1) for the substrate with 280 residues. Over the same substrate size range, k(cat) varied between 10 and 30 s(-1). The variation in k(cat)/K(m) with substrate length suggests that AlgL operates in a processive manner. AlgL displayed a surprising lack of stereospecificity, in that it was able to catalyze cleavage adjacent to either mannuronate or guluronate residues in alginate. Thus, the enzyme is able to remove the C5 proton from both mannuronate and guluronate, which are C5 epimers. Exhaustive digestion of alginate by AlgL generated dimeric and trimeric products, which were characterized by (1)H nuclear magnetic resonance spectroscopy and mass spectrometry. Rapid-mixing chemical quench studies revealed that there was no lag in dimer or trimer production, indicating that AlgL operates as an exopolysaccharide lyase.
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Affiliation(s)
- Emma K Farrell
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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25
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Pomin VH, Park Y, Huang R, Heiss C, Sharp JS, Azadi P, Prestegard JH. Exploiting enzyme specificities in digestions of chondroitin sulfates A and C: production of well-defined hexasaccharides. Glycobiology 2012; 22:826-38. [PMID: 22345629 DOI: 10.1093/glycob/cws055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Interactions between proteins and glycosaminoglycans (GAGs) of the extracellular matrix are important to the regulation of cellular processes including growth, differentiation and migration. Understanding these processes can benefit greatly from the study of protein-GAG interactions using GAG oligosaccharides of well-defined structure. Materials for such studies have, however, been difficult to obtain because of challenges in synthetic approaches and the extreme structural heterogeneity in GAG polymers. Here, it is demonstrated that diversity in structures of oligosaccharides derived by limited enzymatic digestion of materials from natural sources can be greatly curtailed by a proper selection of combinations of source materials and digestive enzymes, a process aided by an improved understanding of the specificities of certain commercial preparations of hydrolases and lyases. Separation of well-defined oligosaccharides can then be accomplished by size-exclusion chromatography followed by strong anion-exchange chromatography. We focus here on two types of chondroitin sulfate (CS) as starting material (CS-A, and CS-C) and the use of three digestive enzymes with varying specificities (testicular hyaluronidase and bacterial chondroitinases ABC and C). Analysis using nuclear magnetic resonance and mass spectrometry focuses on isolated CS disaccharides and hexasaccharides. In all, 15 CS hexasaccharides have been isolated and characterized. These serve as useful contributions to growing libraries of well-defined GAG oligosaccharides that can be used in further biophysical assays.
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Affiliation(s)
- Vitor H Pomin
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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26
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Nyvall Collén P, Sassi JF, Rogniaux H, Marfaing H, Helbert W. Ulvan lyases isolated from the Flavobacteria Persicivirga ulvanivorans are the first members of a new polysaccharide lyase family. J Biol Chem 2011; 286:42063-42071. [PMID: 22009751 PMCID: PMC3234910 DOI: 10.1074/jbc.m111.271825] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 10/06/2011] [Indexed: 11/06/2022] Open
Abstract
Ulvans are complex sulfated polysaccharides found in the cell walls of green algae belonging to the genus Ulva. These polysaccharides are composed of disaccharide repetition moieties made up of sulfated rhamnose linked to either glucuronic acid, iduronic acid, or xylose. Two ulvan lyases of 30 and 46 kDa were purified from the culture supernatant of Persicivirga ulvanivorans. Based on peptide sequencing, the gene encoding the 46-kDa ulvan lyase was cloned. Sequence analysis revealed that the protein is modular and possesses a catalytic module similar to that of the 30-kDa ulvan lyase along with a module of unknown function. The ulvan-degrading function of the gene was confirmed by expression of the catalytic module in a heterologous system. The gene encoding the catalytic module has no sequence homolog in sequence databases and is likely to be the first member of a novel polysaccharide lyase family. Analysis of degradation products showed that both the 30- and 46-kDa ulvan lyases are endolytic and cleave the glycosidic bond between the sulfated rhamnose and a glucuronic or iduronic acid.
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Affiliation(s)
- Pi Nyvall Collén
- CNRS, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules," Station Biologique, F-29682 Roscoff Cedex, France
| | - Jean-François Sassi
- Centre d'Etudes et de Valorisation des Algues, Presqu'île de Pen Lan, BP3, 22610 Pleubian, France
| | - Hélène Rogniaux
- UR1268 Biopolymères Interactions Assemblages, Institut National de la Recherche Agronomique, Plate-forme Biopolymères Biologie Structurale, Rue de la Géraudière, BP 71627, 44316 Nantes, France
| | - Hélène Marfaing
- Centre d'Etudes et de Valorisation des Algues, Presqu'île de Pen Lan, BP3, 22610 Pleubian, France
| | - William Helbert
- CNRS, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules," Station Biologique, F-29682 Roscoff Cedex, France.
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27
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Sugiura N, Setoyama Y, Chiba M, Kimata K, Watanabe H. Baculovirus envelope protein ODV-E66 is a novel chondroitinase with distinct substrate specificity. J Biol Chem 2011; 286:29026-29034. [PMID: 21715327 DOI: 10.1074/jbc.m111.251157] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chondroitin sulfate is a linear polysaccharide of alternating D-glucuronic acid and N-acetyl-D-galactosamine residues with sulfate groups at various positions of the sugars. It interacts with and regulates cytokine and growth factor signal transduction, thus influencing development, organ morphogenesis, inflammation, and infection. We found chondroitinase activity in medium conditioned by baculovirus-infected insect cells and identified a novel chondroitinase. Sequence analysis revealed that the enzyme was a truncated form of occlusion-derived virus envelope protein 66 (ODV-E66) of Autographa californica nucleopolyhedrovirus. The enzyme was a novel chondroitin lyase with distinct substrate specificity. The enzyme was active over a wide range of pH (pH 4-9) and temperature (30-60 °C) and was unaffected by divalent metal ions. The ODV-E66 truncated protein digested chondroitin most efficiently followed by chondroitin 6-sulfate. It degraded hyaluronan to a minimal extent but did not degrade dermatan sulfate, heparin, and N-acetylheparosan. Further analysis using chemo-enzymatically synthesized substrates revealed that the enzyme specifically acted on glucuronate residues in non-sulfated and chondroitin 6-sulfate structures but not in chondroitin 4-sulfate structures. These results suggest that this chondroitinase is useful for detailed structural and compositional analysis of chondroitin sulfate, preparation of specific chondroitin oligosaccharides, and study of baculovirus infection mechanism.
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Affiliation(s)
- Nobuo Sugiura
- Institute for Molecular Science of Medicine, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan.
| | - Yuka Setoyama
- Institute for Molecular Science of Medicine, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan
| | - Mie Chiba
- Institute for Molecular Science of Medicine, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan
| | - Koji Kimata
- Research Complex for the Medicine Frontiers, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan
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28
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Abstract
Carbohydrate-active enzymes face huge substrate diversity in a highly selective manner using only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. In the present paper, a classification of polysaccharide lyases (the enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is shown thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (http://www.cazy.org).
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29
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Elmabrouk ZH, Vincent F, Zhang M, Smith NL, Turkenburg JP, Charnock SJ, Black GW, Taylor EJ. Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations. Proteins 2010; 79:965-74. [PMID: 21287626 DOI: 10.1002/prot.22938] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 10/22/2010] [Accepted: 10/29/2010] [Indexed: 11/06/2022]
Abstract
Bacterial enzymatic degradation of glycosaminoglycans such as hyaluronan and chondroitin is facilitated by polysaccharide lyases. Family 8 polysaccharide lyase (PL8) enzymes contain at least two domains: one predominantly composed of α-helices, the α-domain, and another predominantly composed of β-sheets, the β-domain. Simulation flexibility analyses indicate that processive exolytic cleavage of hyaluronan, by PL8 hyaluronate lyases, is likely to involve an interdomain shift, resulting in the opening/closing of the substrate-binding cleft between the α- and β-domains, facilitating substrate translocation. Here, the Streptomyces coelicolor A3(2) PL8 enzyme was recombinantly expressed in and purified from Escherichia coli and biochemically characterized as a hyaluronate lyase. By using X-ray crystallography its structure was solved in complex with hyaluronan and chondroitin disaccharides. These findings show key catalytic interactions made by the different substrates, and on comparison with all other PL8 structures reveals that the substrate-binding cleft of the S. coelicolor enzyme is highly occluded. A third structure of the enzyme, harboring a mutation of the catalytic tyrosine, created via site-directed mutagenesis, interestingly revealed an interdomain shift that resulted in the opening of the substrate-binding cleft. These results add further support to the proposed processive mechanism of action of PL8 hyaluronate lyases and may indicate that the mechanism of action is likely to be universally used by PL8 hyaluronate lyases.
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Affiliation(s)
- Zainab H Elmabrouk
- Department of Biomedical Sciences, School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
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30
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Garron ML, Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 2010; 20:1547-73. [PMID: 20805221 DOI: 10.1093/glycob/cwq122] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.
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Affiliation(s)
- Marie-Line Garron
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
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31
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Thompson JE, Pourhossein M, Waterhouse A, Hudson T, Goldrick M, Derrick JP, Roberts IS. The K5 lyase KflA combines a viral tail spike structure with a bacterial polysaccharide lyase mechanism. J Biol Chem 2010; 285:23963-9. [PMID: 20519506 DOI: 10.1074/jbc.m110.127571] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
K5 lyase A (KflA) is a tail spike protein (TSP) encoded by a K5A coliphage, which cleaves K5 capsular polysaccharide, a glycosaminoglycan with the repeat unit [-4)-betaGlcA-(1,4)- alphaGlcNAc(1-], displayed on the surface of Escherichia coli K5 strains. The crystal structure of KflA reveals a trimeric arrangement, with each monomer containing a right-handed, single-stranded parallel beta-helix domain. Stable trimer formation by the intertwining of strands in the C-terminal domain, followed by proteolytic maturation, is likely to be catalyzed by an autochaperone as described for K1F endosialidase. The structure of KflA represents the first bacteriophage tail spike protein combining polysaccharide lyase activity with a single-stranded parallel beta-helix fold. We propose a catalytic site and mechanism representing convergence with the syn-beta-elimination site of heparinase II from Pedobacter heparinus.
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Affiliation(s)
- James E Thompson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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32
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Prabhakar V, Capila I, Soundararajan V, Raman R, Sasisekharan R. Recombinant expression, purification, and biochemical characterization of chondroitinase ABC II from Proteus vulgaris. J Biol Chem 2009; 284:974-82. [PMID: 18849565 PMCID: PMC2613618 DOI: 10.1074/jbc.m806630200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 09/29/2008] [Indexed: 11/06/2022] Open
Abstract
Chondroitin lyases (or chondroitinases) are a family of enzymes that depolymerize chondroitin sulfate (CS) and dermatan sulfate (DS) galactosaminoglycans, which have gained prominence as important players in central nervous system biology. Two distinct chondroitinase ABC enzymes, cABCI and cABCII, were identified in Proteus vulgaris. Recently, cABCI was cloned, recombinantly expressed, and extensively characterized structurally and biochemically. This study focuses on recombinant expression, purification, biochemical characterization, and understanding the structure-function relationship of cABCII. The biochemical parameters for optimal activity and kinetic parameters associated with processing of various CS and DS substrates were determined. The profile of products formed by action of cABCII on different substrates was compared with product profile of cABCI. A homology-based structural model of cABCII and its complexes with CS oligosaccharides was constructed. This structural model provided molecular insights into the experimentally observed differences in the product profile of cABCII as compared with that of cABCI. The critical active site residues involved in the catalytic activity of cABCII identified based on the structural model were validated using site-directed mutagenesis and kinetic characterization of the mutants. The development of such a contaminant-free cABCII enzyme provides additional tools to decode the biologically important structure-function relationship of CS and DS galactosaminoglycans and offers novel therapeutic strategies for recovery after central nervous system injury.
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Affiliation(s)
- Vikas Prabhakar
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Pacheco B, Maccarana M, Goodlett DR, Malmström A, Malmström L. Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function. J Biol Chem 2008; 284:1741-7. [PMID: 19004833 DOI: 10.1074/jbc.m805479200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dermatan sulfate is a highly sulfated polysaccharide and has a variety of biological functions in development and disease. Iduronic acid domains in dermatan sulfate, which are formed by the action of two DS-epimerases, have a key role in mediating these functions. We have identified the catalytic site and three putative catalytic residues in DS-epimerase 1, His-205, Tyr-261, and His-450, by tertiary structure modeling and amino acid conservation to heparinase II. These residues were systematically mutated to alanine or more conserved residues, which resulted in complete loss of epimerase activity. Based on these data and the close relationship between lyase and epimerase reactions, we propose a model where His-450 functions as a general base abstracting the C5 proton from glucuronic acid. Subsequent cleavage of the glycosidic linkage by Tyr-261 generates a 4,5-unsaturated hexuronic intermediate, which is protonated at the C5 carbon by His-205 from the side of the sugar plane opposite to the side of previous proton abstraction. Concomitant recreation of the glycosidic linkage ends the reaction, generating iduronic acid. In addition, we show that proper N-glycosylation of DS-epimerase 1 is required for enzyme activity. This study represents the first description of the structural basis for epimerization by a glycosaminoglycan epimerase.
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Affiliation(s)
- Benny Pacheco
- Department of Experimental Medical Science, Lund University, Biomedical Center D12, SE-221 84 Lund, Sweden.
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Liquid chromatography-mass spectrometry to study chondroitin lyase action pattern. Anal Biochem 2008; 385:57-64. [PMID: 18992215 DOI: 10.1016/j.ab.2008.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 10/08/2008] [Accepted: 10/13/2008] [Indexed: 12/12/2022]
Abstract
Liquid chromatography-mass spectrometry was applied to determine the action pattern of different chondroitin lyases. Two commercial enzymes, chondroitinase ABC (Proteus vulgaris) and chondroitinase ACII (Arthrobacter aurescens), having action patterns previously determined by viscosimetry and gel electrophoresis were first examined. Next, the action patterns of recombinant lyases, chondroitinase ABC from Bacteroides thetaiotaomicron (expressed in Escherichia coli) and chondroitinase AC from Flavobacterium heparinum (expressed in its original host), were examined. Chondroitin sulfate A (CS-A, also known as chondroitin-4-sulfate) was used as the substrate for these four lyases. Aliquots taken at various time points were analyzed. The products of chondroitinase ABC (P. vulgaris) and chondroitinase AC (F. heparinum) contained unsaturated oligosaccharides of sizes ranging from disaccharide to decasaccharide, demonstrating that both are endolytic enzymes. The products afforded by chondroitinase ABC (B. thetaiotaomicron) and chondroitinase ACII (A. aurescens) contained primarily unsaturated disaccharide. These two exolytic enzymes showed different minor products, suggesting some subtle specificity differences between the actions of these two exolytic lyases on chondroitin sulfate A.
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Shaya D, Hahn BS, Park NY, Sim JS, Kim YS, Cygler M. Characterization of Chondroitin Sulfate Lyase ABC from Bacteroides thetaiotaomicron WAL2926. Biochemistry 2008; 47:6650-61. [DOI: 10.1021/bi800353g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Shaya
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Bum-Soo Hahn
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Nam Young Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Joon-Soo Sim
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Yeong Shik Kim
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Miroslaw Cygler
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
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