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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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2
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Structure of the Streptococcus pyogenes NADase translocation domain and its essential role in toxin binding to oropharyngeal keratinocytes. J Bacteriol 2021; 204:e0036621. [PMID: 34694903 DOI: 10.1128/jb.00366-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence and continued dominance of a Streptococcus pyogenes (group A Streptococcus, GAS) M1T1 clonal group is temporally correlated with acquisition of genomic sequences that confer high level expression of co-toxins streptolysin O (SLO) and NAD+-glycohydrolase (NADase). Experimental infection models have provided evidence that both toxins are important contributors to GAS virulence. SLO is a cholesterol-dependent pore-forming toxin capable of lysing virtually all types of mammalian cells. NADase, which is composed of an N-terminal translocation domain and C-terminal glycohydrolase domain, acts as an intracellular toxin that depletes host cell energy stores. NADase is dependent on SLO for internalization into epithelial cells, but its mechanism of interaction with the cell surface and details of its translocation mechanism remain unclear. In this study we found that NADase can bind oropharyngeal epithelial cells independently of SLO. This interaction is mediated by both domains of the toxin. We determined by NMR the structure of the translocation domain to be a β-sandwich with a disordered N-terminal region. The folded region of the domain has structural homology to carbohydrate binding modules. We show that excess NADase inhibits SLO-mediated hemolysis and binding to epithelial cells in vitro, suggesting NADase and SLO have shared surface receptors. This effect is abrogated by disruption of a putative carbohydrate binding site on the NADase translocation domain. Our data are consistent with a model whereby interactions of the NADase glycohydrolase domain and translocation domain with SLO and the cell surface increase avidity of NADase binding and facilitate toxin-toxin and toxin-cell surface interactions. Importance NADase and streptolysin O (SLO) are secreted toxins important for pathogenesis of group A Streptococcus, the agent of strep throat and severe invasive infections. The two toxins interact in solution and mutually enhance cytotoxic activity. We now find that NADase is capable of binding to the surface of human cells independently of SLO. Structural analysis of the previously uncharacterized translocation domain of NADase suggests that it contains a carbohydrate binding module. The NADase translocation domain and SLO appear to recognize similar glycan structures on the cell surface, which may be one mechanism through which NADase enhances SLO pore-forming activity during infection. Our findings provide new insight into the NADase toxin and its functional interactions with SLO during streptococcal infection.
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ŞahutoĞlu AS, Duman H, Frese SA, Karav S. Structural insights of two novel N-acetyl-glucosaminidase enzymes through in silico methods. Turk J Chem 2020; 44:1703-1712. [PMID: 33488263 PMCID: PMC7763110 DOI: 10.3906/kim-2006-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
EndoBI-1 and EndoBI-2 are two endo-
β-N-
acetylglucosaminidase isoenzymes that cleave
N-N’-
diacetylchitobiosyl moieties found in various types of native
N
-glycans. These
N
-glycans are indigestible by human infants and adults due to the lack of responsible glycosyl hydrolases and they act as selective prebiotics for a probiotic microorganism,
Bifidobacterium longum
subsp
. infantis
, in the large intestine. The selectivity and the thermostability of EndoBI-1 and EndoBI-2 suggest that these enzymes may be useful for many scientific and industrial applications. In this study, the growing numbers of homologous sequences in different databases were exploited in a comparative approach to investigate structural properties of EndoBI-1 and EndoBI-2 enzymes. Moreover, the complete and partial homology models of these two enzymes were generated and evaluated. Selected models were used for docking studies of the plus subsite ligand of these enzymes for further understanding on the substrate selectivity of EndoBI enzymes.
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Affiliation(s)
- Arif Sercan ŞahutoĞlu
- Department of Chemistry, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, Çanakkale Turkey
| | - Hatice Duman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, Çanakkale Turkey
| | - Steven Alex Frese
- Evolve Biosystems, Inc., Davis, CA USA.,Department of Food Science and Technology, University of Nebraska, Lincoln, NE USA
| | - Sercan Karav
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, Çanakkale Turkey
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4
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Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ. Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. ACS CENTRAL SCIENCE 2019; 5:524-538. [PMID: 30937380 PMCID: PMC6439443 DOI: 10.1021/acscentsci.8b00917] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 06/02/2023]
Abstract
Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen-deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.
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Affiliation(s)
- Erik H. Klontz
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Beatriz Trastoy
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Daniel Deredge
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - James K. Fields
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Chao Li
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Jared Orwenyo
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Alberto Marina
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Robert Beadenkopf
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Sebastian Günther
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Photon
Science, Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
| | - Jair Flores
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Patrick L. Wintrode
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Lai-Xi Wang
- Department
of Chemistry and Biochemistry, University
of Maryland, College Park, Maryland 20742, United States
| | - Marcelo E. Guerin
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
| | - Eric J. Sundberg
- Institute
of Human Virology, Department of Microbiology & Immunology, and Program in Molecular
Microbiology & Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department
of Medicine, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
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Hobbs JK, Pluvinage B, Boraston AB. Glycan-metabolizing enzymes in microbe-host interactions: the Streptococcus pneumoniae paradigm. FEBS Lett 2018; 592:3865-3897. [PMID: 29608212 DOI: 10.1002/1873-3468.13045] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the upper airways; however, it is also an accomplished pathogen capable of causing life-threatening diseases. To colonize and cause invasive disease, this bacterium relies on a complex array of factors to mediate the host-bacterium interaction. The respiratory tract is rich in functionally important glycoconjugates that display a vast range of glycans, and, thus, a key component of the pneumococcus-host interaction involves an arsenal of bacterial carbohydrate-active enzymes to depolymerize these glycans and carbohydrate transporters to import the products. Through the destruction of host glycans, the glycan-specific metabolic machinery deployed by S. pneumoniae plays a variety of roles in the host-pathogen interaction. Here, we review the processing and metabolism of the major host-derived glycans, including N- and O-linked glycans, Lewis and blood group antigens, proteoglycans, and glycogen, as well as some dietary glycans. We discuss the role of these metabolic pathways in the S. pneumoniae-host interaction, speculate on the potential of key enzymes within these pathways as therapeutic targets, and relate S. pneumoniae as a model system to glycan processing in other microbial pathogens.
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Affiliation(s)
- Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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Sjögren J, Collin M. Bacterial glycosidases in pathogenesis and glycoengineering. Future Microbiol 2015; 9:1039-51. [PMID: 25340834 DOI: 10.2217/fmb.14.71] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Glycosylation is a common post-translational protein modification and many key proteins of the immune system are glycosylated. As the true experts of our immune system, pathogenic bacteria produce enzymes that can modify the carbohydrates (glycans) of the defense mechanisms in order to favor bacterial survival and persistence. At the intersection between bacterial pathogenesis and glycobiology, there is an increased interest in studying the bacterial enzymes that modify the protein glycosylation of their colonized or infected hosts. This is of great importance in order to fully understand bacterial pathogenesis, but it also presents itself as a valuable source for glycoengineering and glycoanalysis tools. This article highlights the role of bacterial glycosidases during infections, introduces the use of such enzymes as glycoengineering tools and discusses the potential of further studies in this emerging field.
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Affiliation(s)
- Jonathan Sjögren
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, BMC B14, SE-221 84 Lund, Sweden
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Singh AK, Pluvinage B, Higgins MA, Dalia AB, Woodiga SA, Flynn M, Lloyd AR, Weiser JN, Stubbs KA, Boraston AB, King SJ. Unravelling the multiple functions of the architecturally intricate Streptococcus pneumoniae β-galactosidase, BgaA. PLoS Pathog 2014; 10:e1004364. [PMID: 25210925 PMCID: PMC4161441 DOI: 10.1371/journal.ppat.1004364] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell-surface proteins play integral roles in host-pathogen interactions. These proteins are often architecturally and functionally sophisticated and yet few studies of such proteins involved in host-pathogen interactions have defined the domains or modules required for specific functions. Streptococcus pneumoniae (pneumococcus), an opportunistic pathogen that is a leading cause of community acquired pneumonia, otitis media and bacteremia, is decorated with many complex surface proteins. These include β-galactosidase BgaA, which is specific for terminal galactose residues β-1-4 linked to glucose or N-acetylglucosamine and known to play a role in pneumococcal growth, resistance to opsonophagocytic killing, and adherence. This study defines the domains and modules of BgaA that are required for these distinct contributions to pneumococcal pathogenesis. Inhibitors of β-galactosidase activity reduced pneumococcal growth and increased opsonophagocytic killing in a BgaA dependent manner, indicating these functions require BgaA enzymatic activity. In contrast, inhibitors increased pneumococcal adherence suggesting that BgaA bound a substrate of the enzyme through a distinct module or domain. Extensive biochemical, structural and cell based studies revealed two newly identified non-enzymatic carbohydrate-binding modules (CBMs) mediate adherence to the host cell surface displayed lactose or N-acetyllactosamine. This finding is important to pneumococcal biology as it is the first adhesin-carbohydrate receptor pair identified, supporting the widely held belief that initial pneumococcal attachment is to a glycoconjugate. Perhaps more importantly, this is the first demonstration that a CBM within a carbohydrate-active enzyme can mediate adherence to host cells and thus this study identifies a new class of carbohydrate-binding adhesins and extends the paradigm of CBM function. As other bacterial species express surface-associated carbohydrate-active enzymes containing CBMs these findings have broad implications for bacterial adherence. Together, these data illustrate that comprehending the architectural sophistication of surface-attached proteins can increase our understanding of the different mechanisms by which these proteins can contribute to bacterial pathogenesis.
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Affiliation(s)
- Anirudh K. Singh
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Benjamin Pluvinage
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Melanie A. Higgins
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Ankur B. Dalia
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shireen A. Woodiga
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Matthew Flynn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Audrey R. Lloyd
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Jeffrey N. Weiser
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Keith A. Stubbs
- School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Alisdair B. Boraston
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (ABB); (SJK)
| | - Samantha J. King
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (ABB); (SJK)
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Pérez-Dorado I, Galan-Bartual S, Hermoso JA. Pneumococcal surface proteins: when the whole is greater than the sum of its parts. Mol Oral Microbiol 2012; 27:221-45. [PMID: 22759309 DOI: 10.1111/j.2041-1014.2012.00655.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Surface-exposed proteins of pathogenic bacteria are considered as potential virulence factors through their direct contribution to host-pathogen interactions. Four families of surface proteins decorate the cell surface of the human pathogen Streptococcus pneumoniae. Besides lipoproteins and LPXTG proteins, also present in other gram-positive bacteria, the pneumococcus presents the choline-binding protein (CBP) family and the non-classical surface proteins (NCSPs). The CBPs present specific structural features that allow their anchorage to the cell envelope through non-covalent interaction with choline residues of lipoteichoic acid and teichoic acid. NCSP is an umbrella term for less characterized proteins displaying moonlighting functions on the pneumococcal surface that lack a leader peptide and membrane-anchor motif. Considering the unceasing evolution of microbial species under the selective pressure of antibiotic use, detailed understanding of the interaction between pathogen and the host cells is required for the development of novel therapeutic strategies to combat pneumococcal infections. This article reviews recent progress in the investigation of the three-dimensional structures of surface-exposed pneumococcal proteins. The modular nature of some of them produces a great versatility and sophistication of the virulence functions that, in most cases, cannot be deduced by the structural analysis of the isolated modules.
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Affiliation(s)
- I Pérez-Dorado
- Department of Crystallography and Structural Biology, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
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