1
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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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D'Arminio N, Ruggiero V, Pierri G, Marabotti A, Tedesco C. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns. Protein Sci 2024; 33:e4868. [PMID: 38100281 PMCID: PMC10806932 DOI: 10.1002/pro.4868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types.
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Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Valentina Ruggiero
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
- Present address:
Department of PharmacyUniversity of SalernoFiscianoItaly
| | - Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
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3
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Liu G, Chang Y, Mei X, Chen G, Zhang Y, Jiang X, Tao W, Xue C. Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100. Int J Biol Macromol 2024; 255:127959. [PMID: 37951443 DOI: 10.1016/j.ijbiomac.2023.127959] [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: 09/22/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
Chondroitin sulfate is a biologically and commercially important polysaccharide with a variety of applications. Carbohydrate-binding module (CBM) is an important class of carbohydrate-binding protein, which could be utilized as a promising tool for the applications of polysaccharides. In the present study, an unknown function domain was explored from a putative chondroitin sulfate lyase in PL29 family. Recombinant PhCBM100 demonstrated binding capacity to chondroitin sulfates with Ka values of 2.1 ± 0.2 × 106 M-1 and 6.0 ± 0.1 × 106 M-1 to chondroitin sulfate A and chondroitin sulfate C, respectively. The 1.55 Å resolution X-ray crystal structure of PhCBM100 exhibited a β-sandwich fold formed by two antiparallel β-sheets. A binding groove in PhCBM100 interacting with chondroitin sulfate was subsequently identified, and the potential of PhCBM100 for visualization of chondroitin sulfate was evaluated. PhCBM100 is the first characterized chondroitin sulfate-specific CBM. The novelty of PhCBM100 proposed a new CBM family of CBM100.
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Affiliation(s)
- Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xiaoxiao Jiang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Wenwen Tao
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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4
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Shi Q, Abdel-Hamid AM, Sun Z, Cheng Y, Tu T, Cann I, Yao B, Zhu W. Carbohydrate-binding modules facilitate the enzymatic hydrolysis of lignocellulosic biomass: Releasing reducing sugars and dissociative lignin available for producing biofuels and chemicals. Biotechnol Adv 2023; 65:108126. [PMID: 36921877 DOI: 10.1016/j.biotechadv.2023.108126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
The microbial decomposition and utilization of lignocellulosic biomass present in the plant tissues are driven by a series of carbohydrate active enzymes (CAZymes) acting in concert. As the non-catalytic domains widely found in the modular CAZymes, carbohydrate-binding modules (CBMs) are intimately associated with catalytic domains (CDs) that effect the diverse hydrolytic reactions. The CBMs function as auxiliary components for the recognition, adhesion, and depolymerization of the complex substrate mediated by the associated CDs. Therefore, CBMs are deemed as significant biotools available for enzyme engineering, especially to facilitate the enzymatic hydrolysis of dense and insoluble plant tissues to acquire more fermentable sugars. This review aims at presenting the taxonomies and biological properties of the CBMs currently curated in the CAZy database. The molecular mechanisms that CBMs use in assisting the enzymatic hydrolysis of plant polysaccharides and the regulatory factors of CBM-substrate interactions are outlined in detail. In addition, guidelines for the rational designs of CBM-fused CAZymes are proposed. Furthermore, the potential to harness CBMs for industrial applications, especially in enzymatic pretreatment of the recalcitrant lignocellulose, is evaluated. It is envisaged that the ideas outlined herein will aid in the engineering and production of novel CBM-fused enzymes to facilitate efficient degradation of lignocellulosic biomass to easily fermentable sugars for production of value-added products, including biofuels.
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Affiliation(s)
- Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed M Abdel-Hamid
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Animal Science, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA; Center for East Asian and Pacific Studies, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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5
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Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. NATURE PLANTS 2023; 9:486-500. [PMID: 36849618 PMCID: PMC10115243 DOI: 10.1038/s41477-023-01358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/25/2023] [Indexed: 05/18/2023]
Abstract
Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the β-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.
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Affiliation(s)
- Pradeep Kumar Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA
| | - Jose Henrique Pereira
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Wanchen Shao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA.
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6
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Goulet A, Mahony J, Cambillau C, van Sinderen D. Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2. Microorganisms 2022; 10:2278. [PMID: 36422348 PMCID: PMC9692632 DOI: 10.3390/microorganisms10112278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 01/16/2024] Open
Abstract
Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding.
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Affiliation(s)
- Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université—CNRS, UMR 7255, 13288 Marseille, France
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
| | - Christian Cambillau
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
- AlphaGraphix, 24 Carrer d’Amont, 66210 Formiguères, France
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7
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Xu J, Xu R, Jia M, Su Y, Zhu W. Metatranscriptomic analysis of colonic microbiota's functional response to different dietary fibers in growing pigs. Anim Microbiome 2021; 3:45. [PMID: 34217374 PMCID: PMC8254964 DOI: 10.1186/s42523-021-00108-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/23/2021] [Indexed: 01/30/2023] Open
Abstract
Background Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis. Results The results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin. Conclusion The results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00108-1.
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Affiliation(s)
- Jie Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Menglan Jia
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
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8
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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9
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Kim CC, Healey GR, Kelly WJ, Patchett ML, Jordens Z, Tannock GW, Sims IM, Bell TJ, Hedderley D, Henrissat B, Rosendale DI. Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon. ISME JOURNAL 2019; 13:1437-1456. [PMID: 30728469 PMCID: PMC6776006 DOI: 10.1038/s41396-019-0363-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 01/07/2019] [Accepted: 01/19/2019] [Indexed: 12/16/2022]
Abstract
Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.
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Affiliation(s)
- Caroline C Kim
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand. .,Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.
| | - Genelle R Healey
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand.,Massey Institute of Food Science and Technology, School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | | | - Mark L Patchett
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Zoe Jordens
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, Microbiome Otago, University of Otago, Dunedin, 9016, New Zealand
| | - Ian M Sims
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt, 5040, New Zealand
| | - Tracey J Bell
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt, 5040, New Zealand
| | - Duncan Hedderley
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Douglas I Rosendale
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand.
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10
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Broeker J, Mechelke M, Baudrexl M, Mennerich D, Hornburg D, Mann M, Schwarz WH, Liebl W, Zverlov VV. The hemicellulose-degrading enzyme system of the thermophilic bacterium Clostridium stercorarium: comparative characterisation and addition of new hemicellulolytic glycoside hydrolases. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:229. [PMID: 30159029 PMCID: PMC6106730 DOI: 10.1186/s13068-018-1228-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND The bioconversion of lignocellulosic biomass in various industrial processes, such as the production of biofuels, requires the degradation of hemicellulose. Clostridium stercorarium is a thermophilic bacterium, well known for its outstanding hemicellulose-degrading capability. Its genome comprises about 50 genes for partially still uncharacterised thermostable hemicellulolytic enzymes. These are promising candidates for industrial applications. RESULTS To reveal the hemicellulose-degrading potential of 50 glycoside hydrolases, they were recombinantly produced and characterised. 46 of them were identified in the secretome of C. stercorarium cultivated on cellobiose. Xylanases Xyn11A, Xyn10B, Xyn10C, and cellulase Cel9Z were among the most abundant proteins. The secretome of C. stercorarium was active on xylan, β-glucan, xyloglucan, galactan, and glucomannan. In addition, the recombinant enzymes hydrolysed arabinan, mannan, and galactomannan. 20 enzymes are newly described, degrading xylan, galactan, arabinan, mannan, and aryl-glycosides of β-d-xylose, β-d-glucose, β-d-galactose, α-l-arabinofuranose, α-l-rhamnose, β-d-glucuronic acid, and N-acetyl-β-d-glucosamine. The activities of three enzymes with non-classified glycoside hydrolase (GH) family modules were determined. Xylanase Xyn105F and β-d-xylosidase Bxl31D showed activities not described so far for their GH families. 11 of the 13 polysaccharide-degrading enzymes were most active at pH 5.0 to pH 6.5 and at temperatures of 57-76 °C. Investigation of the substrate and product specificity of arabinoxylan-degrading enzymes revealed that only the GH10 xylanases were able to degrade arabinoxylooligosaccharides. While Xyn10C was inhibited by α-(1,2)-arabinosylations, Xyn10D showed a degradation pattern different to Xyn10B and Xyn10C. Xyn11A released longer degradation products than Xyn10B. Both tested arabinose-releasing enzymes, Arf51B and Axh43A, were able to hydrolyse single- as well as double-arabinosylated xylooligosaccharides. CONCLUSIONS The obtained results lead to a better understanding of the hemicellulose-degrading capacity of C. stercorarium and its involved enzyme systems. Despite similar average activities measured by depolymerisation tests, a closer look revealed distinctive differences in the activities and specificities within an enzyme class. This may lead to synergistic effects and influence the enzyme choice for biotechnological applications. The newly characterised glycoside hydrolases can now serve as components of an enzyme platform for industrial applications in order to reconstitute synthetic enzyme systems for complete and optimised degradation of defined polysaccharides and hemicellulose.
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Affiliation(s)
- Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Matthias Mechelke
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Melanie Baudrexl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Denise Mennerich
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Daniel Hornburg
- Present Address: School of Medicine, Stanford University, Stanford, CA 94305 USA
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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11
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Dunne M, Hupfeld M, Klumpp J, Loessner MJ. Molecular Basis of Bacterial Host Interactions by Gram-Positive Targeting Bacteriophages. Viruses 2018; 10:v10080397. [PMID: 30060549 PMCID: PMC6115969 DOI: 10.3390/v10080397] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/29/2022] Open
Abstract
The inherent ability of bacteriophages (phages) to infect specific bacterial hosts makes them ideal candidates to develop into antimicrobial agents for pathogen-specific remediation in food processing, biotechnology, and medicine (e.g., phage therapy). Conversely, phage contaminations of fermentation processes are a major concern to dairy and bioprocessing industries. The first stage of any successful phage infection is adsorption to a bacterial host cell, mediated by receptor-binding proteins (RBPs). As the first point of contact, the binding specificity of phage RBPs is the primary determinant of bacterial host range, and thus defines the remediative potential of a phage for a given bacterium. Co-evolution of RBPs and their bacterial receptors has forced endless adaptation cycles of phage-host interactions, which in turn has created a diverse array of phage adsorption mechanisms utilizing an assortment of RBPs. Over the last decade, these intricate mechanisms have been studied intensely using electron microscopy and X-ray crystallography, providing atomic-level details of this fundamental stage in the phage infection cycle. This review summarizes current knowledge surrounding the molecular basis of host interaction for various socioeconomically important Gram-positive targeting phage RBPs to their protein- and saccharide-based receptors. Special attention is paid to the abundant and best-characterized Siphoviridae family of tailed phages. Unravelling these complex phage-host dynamics is essential to harness the full potential of phage-based technologies, or for generating novel strategies to combat industrial phage contaminations.
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Affiliation(s)
- Matthew Dunne
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Mario Hupfeld
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Jochen Klumpp
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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12
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Rydahl MG, Hansen AR, Kračun SK, Mravec J. Report on the Current Inventory of the Toolbox for Plant Cell Wall Analysis: Proteinaceous and Small Molecular Probes. FRONTIERS IN PLANT SCIENCE 2018; 9:581. [PMID: 29774041 PMCID: PMC5943554 DOI: 10.3389/fpls.2018.00581] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Plant cell walls are highly complex structures composed of diverse classes of polysaccharides, proteoglycans, and polyphenolics, which have numerous roles throughout the life of a plant. Significant research efforts aim to understand the biology of this cellular organelle and to facilitate cell-wall-based industrial applications. To accomplish this, researchers need to be provided with a variety of sensitive and specific detection methods for separate cell wall components, and their various molecular characteristics in vitro as well as in situ. Cell wall component-directed molecular detection probes (in short: cell wall probes, CWPs) are an essential asset to the plant glycobiology toolbox. To date, a relatively large set of CWPs has been produced-mainly consisting of monoclonal antibodies, carbohydrate-binding modules, synthetic antibodies produced by phage display, and small molecular probes. In this review, we summarize the state-of-the-art knowledge about these CWPs; their classification and their advantages and disadvantages in different applications. In particular, we elaborate on the recent advances in non-conventional approaches to the generation of novel CWPs, and identify the remaining gaps in terms of target recognition. This report also highlights the addition of new "compartments" to the probing toolbox, which is filled with novel chemical biology tools, such as metabolic labeling reagents and oligosaccharide conjugates. In the end, we also forecast future developments in this dynamic field.
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Affiliation(s)
- Maja G. Rydahl
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Aleksander R. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Stjepan K. Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- GlycoSpot IVS, Frederiksberg, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Jozef Mravec
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13
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Carbohydrate-binding architecture of the multi-modular α-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces α-1,6-glucosyl-α-glucosaccharides from starch. Biochem J 2017; 474:2763-2778. [DOI: 10.1042/bcj20170152] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 11/17/2022]
Abstract
Paenibacillus sp. 598K α-1,6-glucosyltransferase (Ps6TG31A), a member of glycoside hydrolase family 31, catalyzes exo-α-glucohydrolysis and transglucosylation and produces α-1,6-glucosyl-α-glucosaccharides from α-glucan via its disproportionation activity. The crystal structure of Ps6TG31A was determined by an anomalous dispersion method using a terbium derivative. The monomeric Ps6TG31A consisted of one catalytic (β/α)8-barrel domain and six small domains, one on the N-terminal and five on the C-terminal side. The structures of the enzyme complexed with maltohexaose, isomaltohexaose, and acarbose demonstrated that the ligands were observed in the catalytic cleft and the sugar-binding sites of four β-domains. The catalytic site was structured by a glucose-binding pocket and an aglycon-binding cleft built by two sidewalls. The bound acarbose was located with its non-reducing end pseudosugar docked in the pocket, and the other moieties along one sidewall serving three subsites for the α-1,4-glucan. The bound isomaltooligosaccharide was found on the opposite sidewall, which provided the space for the acceptor molecule to be positioned for attack of the catalytic intermediate covalent complex during transglucosylation. The N-terminal domain recognized the α-1,4-glucan in a surface-binding mode. Two of the five C-terminal domains belong to the carbohydrate-binding modules family 35 and one to family 61. The sugar complex structures indicated that the first family 35 module preferred α-1,6-glucan, whereas the second family 35 module and family 61 module preferred α-1,4-glucan. Ps6TG31A appears to have enhanced transglucosylation activity facilitated by its carbohydrate-binding modules and substrate-binding cleft that positions the substrate and acceptor sugar for the transglucosylation.
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14
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Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV. Function of bacteriophage G7C esterase tailspike in host cell adsorption. Mol Microbiol 2017; 105:385-398. [PMID: 28513100 DOI: 10.1111/mmi.13710] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs show a great variability in their shapes, sizes, and location on the particle. Some RBPs are known to depolymerize surface polysaccharides of the host while others show no enzymatic activity. Here we report that both RBPs of podovirus G7C - tailspikes gp63.1 and gp66 - are essential for infection of its natural host bacterium E. coli 4s that populates the equine intestinal tract. We characterize the structure and function of gp63.1 and show that unlike any previously described RPB, gp63.1 deacetylates surface polysaccharides of E. coli 4s leaving the backbone of the polysaccharide intact. We demonstrate that gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The esterase domain of gp63.1 as well as domains mediating the gp63.1-gp66 interaction is widespread among all three families of tailed bacteriophages.
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Affiliation(s)
- Nikolai S Prokhorov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, 7b2 pr. 60-letiya Oktyabrya, Moscow, 117312, Russia
| | - Cristian Riccio
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Evelina L Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky pr, Moscow, 119991, Russia
| | - Mikhail M Shneider
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland.,Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya St, Moscow, 117997, Russia
| | - Christopher Browning
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky pr, Moscow, 119991, Russia
| | - Petr G Leiman
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Andrey V Letarov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, 7b2 pr. 60-letiya Oktyabrya, Moscow, 117312, Russia.,Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119991, Russia
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15
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Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R. Advances in molecular engineering of carbohydrate-binding modules. Proteins 2017; 85:1602-1617. [PMID: 28547780 DOI: 10.1002/prot.25327] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Silvia Moreno-Mendieta
- CONACYT, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
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16
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Paenibacillus sp. 598K 6-α-glucosyltransferase is essential for cycloisomaltooligosaccharide synthesis from α-(1 → 4)-glucan. Appl Microbiol Biotechnol 2017; 101:4115-4128. [DOI: 10.1007/s00253-017-8174-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/29/2017] [Accepted: 02/01/2017] [Indexed: 11/26/2022]
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17
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Back CR, Sztukowska MN, Till M, Lamont RJ, Jenkinson HF, Nobbs AH, Race PR. The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. J Biol Chem 2017; 292:1538-1549. [PMID: 27920201 PMCID: PMC5290933 DOI: 10.1074/jbc.m116.760975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/01/2016] [Indexed: 11/06/2022] Open
Abstract
Adherence of bacteria to biotic or abiotic surfaces is a prerequisite for host colonization and represents an important step in microbial pathogenicity. This attachment is facilitated by bacterial adhesins at the cell surface. Because of their size and often elaborate multidomain architectures, these polypeptides represent challenging targets for detailed structural and functional characterization. The multifunctional fibrillar adhesin CshA, which mediates binding to both host molecules and other microorganisms, is an important determinant of colonization by Streptococcus gordonii, an oral commensal and opportunistic pathogen of animals and humans. CshA binds the high-molecular-weight glycoprotein fibronectin (Fn) via an N-terminal non-repetitive region, and this protein-protein interaction has been proposed to promote S. gordonii colonization at multiple sites within the host. However, the molecular details of how these two proteins interact have yet to be established. Here we present a structural description of the Fn binding N-terminal region of CshA, derived from a combination of X-ray crystallography, small angle X-ray scattering, and complementary biophysical methods. In vitro binding studies support a previously unreported two-state "catch-clamp" mechanism of Fn binding by CshA, in which the disordered N-terminal domain of CshA acts to "catch" Fn, via formation of a rapidly assembled but also readily dissociable pre-complex, enabling its neighboring ligand binding domain to tightly clamp the two polypeptides together. This study presents a new paradigm for target binding by a bacterial adhesin, the identification of which will inform future efforts toward the development of anti-adhesive agents that target S. gordonii and related streptococci.
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Affiliation(s)
- Catherine R Back
- From the School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, United Kingdom
| | - Maryta N Sztukowska
- the Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky 40202; the Department of Dentistry, University of Information Technology and Management, 35-225 Rzeszow, Poland
| | - Marisa Till
- the School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom; the BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
| | - Richard J Lamont
- the Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky 40202
| | - Howard F Jenkinson
- From the School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, United Kingdom
| | - Angela H Nobbs
- From the School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, United Kingdom.
| | - Paul R Race
- the School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom; the BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom.
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18
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Andersen MCF, Kračun SK, Rydahl MG, Willats WGT, Clausen MH. Synthesis of β-1,4-Linked Galactan Side-Chains of Rhamnogalacturonan I. Chemistry 2016; 22:11543-8. [PMID: 27305141 DOI: 10.1002/chem.201602197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 11/05/2022]
Abstract
The synthesis of linear- and (1→6)-branched β-(1→4)-d-galactans, side-chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n-pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction with a covalent linker and immobilization on N-hydroxysuccinimide (NHS)-modified glass surfaces allows the generation of carbohydrate microarrays. The glycan arrays enable the study of protein-carbohydrate interactions in a high-throughput fashion, demonstrated herein with binding studies of mAbs and a CBM.
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Affiliation(s)
- Mathias C F Andersen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs., Lyngby, Denmark
| | - Stjepan K Kračun
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Maja G Rydahl
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - William G T Willats
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.,School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs., Lyngby, Denmark.
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19
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Carvalho CC, Phan NN, Chen Y, Reilly PJ. Carbohydrate-binding module tribes. Biopolymers 2016; 103:203-14. [PMID: 25381933 DOI: 10.1002/bip.22584] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/28/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022]
Abstract
At present, 69 families of carbohydrate-binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences (primary structures) of their members, with most members of different families showing little if any homology. On the other hand, members of the same family have primary and tertiary (three-dimensional) structures that can be computationally aligned, suggesting that they are descended from common protein ancestors. Members of the large majority of CBM families are β-sandwiches. This raises the question of whether members of different families are descended from distant common ancestors, and therefore are members of the same tribe. We have attacked this problem by attempting to computationally superimpose tertiary structure representatives of each of the 53 CBM families that have members with known tertiary structures. When successful, we have aligned locations of secondary structure elements and determined root mean square deviations and percentages of similarity between adjacent amino acid residues in structures from similar families. Further criteria leading to tribal membership are amino acid chain lengths and bound ligands. These considerations have led us to assign 27 families to nine tribes. Eight of the tribes have members with β-sandwich structures, while the ninth is composed of structures with β-trefoils.
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Affiliation(s)
- Caio C Carvalho
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011
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20
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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Esaka K, Aburaya S, Morisaka H, Kuroda K, Ueda M. Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation. AMB Express 2015; 5:2. [PMID: 25642399 PMCID: PMC4305082 DOI: 10.1186/s13568-014-0089-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/23/2014] [Indexed: 02/03/2023] Open
Abstract
Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its known metabolic functions, that contribute to effective degradation of natural soft biomass.
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Pattathil S, Avci U, Zhang T, Cardenas CL, Hahn MG. Immunological Approaches to Biomass Characterization and Utilization. Front Bioeng Biotechnol 2015; 3:173. [PMID: 26579515 PMCID: PMC4623462 DOI: 10.3389/fbioe.2015.00173] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Plant biomass is the major renewable feedstock resource for sustainable generation of alternative transportation fuels to replace fossil carbon-derived fuels. Lignocellulosic cell walls are the principal component of plant biomass. Hence, a detailed understanding of plant cell wall structure and biosynthesis is an important aspect of bioenergy research. Cell walls are dynamic in their composition and structure, varying considerably among different organs, cells, and developmental stages of plants. Hence, tools are needed that are highly efficient and broadly applicable at various levels of plant biomass-based bioenergy research. The use of plant cell wall glycan-directed probes has seen increasing use over the past decade as an excellent approach for the detailed characterization of cell walls. Large collections of such probes directed against most major cell wall glycans are currently available worldwide. The largest and most diverse set of such probes consists of cell wall glycan-directed monoclonal antibodies (McAbs). These McAbs can be used as immunological probes to comprehensively monitor the overall presence, extractability, and distribution patterns among cell types of most major cell wall glycan epitopes using two mutually complementary immunological approaches, glycome profiling (an in vitro platform) and immunolocalization (an in situ platform). Significant progress has been made recently in the overall understanding of plant biomass structure, composition, and modifications with the application of these immunological approaches. This review focuses on such advances made in plant biomass analyses across diverse areas of bioenergy research.
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Affiliation(s)
- Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
| | - Utku Avci
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
| | - Tiantian Zhang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Claudia L. Cardenas
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
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Toubai T, Guoqing H, Rossi C, Mathewson N, Oravecz-Wilson K, Cummings E, Wu J, Sun Y, Choi S, Reddy P. Ikaros deficiency in host hematopoietic cells separates GVL from GVHD after experimental allogeneic hematopoietic cell transplantation. Oncoimmunology 2015; 4:e1016699. [PMID: 26140241 PMCID: PMC4485841 DOI: 10.1080/2162402x.2015.1016699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 10/25/2022] Open
Abstract
The graft-versus-leukemia (GVL) effect following allogeneic hematopoietic stem cell transplantation (allo-HCT) is critical for its curative potential. Hwever, GVL is tightly linked to graft-versus-host disease (GVHD). Among hematological malignancies, acute lymphoblastic leukemia (ALL) is the most resistant to GVL, although the reasons for this remain poorly understood. Clinical studies have identified alterations in Ikaros (Ik) transcription factor as the major marker associated with poor outcomes in ALL. We have shown that the absence of Ik in professional host-derived hematopoietic antigen-presenting cells (APCs) exacerbates GVHD. However, whether Ik expression plays a role in resistance to GVL is not known. In this study we used multiple clinically relevant murine models of allo-HCT to explore whether Ik expression in hematopoietic APCs and/or leukemic cells is critical for increasing resistance to GVL and thus inducing relapse. We found that Ik deficiency in host APCs failed to enhance GVL despite increased GVHD severity. Mechanistic studies with bone marrow (BM) chimeras and tetramer analyses demonstrated reduced tumor-specific immunodominant (gag+) antigen responses in the [B6Ik-/-→B6] group. Loss of GVL was observed when both the leukemia cells and the host APCs were deficient in Ik. We found that calreticulin (CRT) expression in host antigen-presenting dendritic cells (DCs) of Ik-/- animals was significantly lower than in wild-type animals. Rescuing CRT expression in Ik-/- DCs improved leukemic-specific cytotoxic T cell function. Together, our data demonstrate that the absence of Ikaros in host hematopoietic cells promotes resistance to GVL despite increasing GVHD and thus provides a potential mechanism for the poor outcome of Ik-/- ALL patients.
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Key Words
- 51Cr, Chromium-51
- ALL, acute lymphoblastic leukemia
- APC, allophycocyanin
- APCs, antigen-presenting cells
- Allo-HCT, allogeneic hematopoietic stem cell transplantation
- BC, blast crisis
- BLI, bioluminescence imaging
- BM, bone marrow
- BMDCs, bone marrow derived dendritic cells
- BMT, bone marrow transplantation
- CML, chronic myeloid leukemia
- CRT, calreticulin
- CTL, cytotoxic T cell
- DCs, dendritic cells
- FACS, Fluorescence-activated cell sorting
- FBS, fatal bovine serum
- FITC, fluorescein isothiocyanate
- GVHD, graft-versus-host-disease
- GVL, graft-versus-leukemia
- HCT, hematopoietic stem cell transplantation
- ICAM-1, intracellular adhesion molecule 1
- Ik DN, Ikaros dominant negative
- Ik, Ikaros
- Ikaros
- MACS, magnetic- activated cell sorting
- MBL-2, moloney-murine sarcoma virus-induced MBL-2 lymphoma cells
- MHC, major histocompatibility complex
- MLR, mixed lymphocyte reaction
- MiHAs, multiple minor histocompatibility antigens
- PBS, phosphate buffered saline
- PE, phycoerythrin
- SIRP-α, signal regulatory protein α
- TCD-BM, T cell depleted bone marrow
- TSA, tumor specific antigen
- Tregs, regulatory T cells
- UCUCA, University Committee on Use and Care of Animals
- WT, wild-type
- antigen-presenting cells
- bone marrow transplantation
- graft-versus-leukemia
- luc+, luciferase+
- mAbs, monoclonal antibodies
- mCRT, murine calreticulin
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Affiliation(s)
- Tomomi Toubai
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Hou Guoqing
- Department of Pediatrics and Communicable Diseases; University of Michigan Medical School ; Ann Arbor, MI USA
| | - Corrine Rossi
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Nathan Mathewson
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Katherine Oravecz-Wilson
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Emily Cummings
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Julia Wu
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Yaping Sun
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
| | - Sung Choi
- Department of Pediatrics and Communicable Diseases; University of Michigan Medical School ; Ann Arbor, MI USA
| | - Pavan Reddy
- Department of Internal Medicine; University of Michigan Comprehensive Cancer Center ; Ann Arbor, MI USA
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24
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Mikshina PV, Idiyatullin BZ, Petrova AA, Shashkov AS, Zuev YF, Gorshkova TA. Physicochemical properties of complex rhamnogalacturonan I from gelatinous cell walls of flax fibers. Carbohydr Polym 2015; 117:853-861. [DOI: 10.1016/j.carbpol.2014.10.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/29/2014] [Accepted: 10/11/2014] [Indexed: 11/27/2022]
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25
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Evdokimov AG, Moshiri F, Sturman EJ, Rydel TJ, Zheng M, Seale JW, Franklin S. Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals. Protein Sci 2014; 23:1491-7. [PMID: 25139047 PMCID: PMC4241100 DOI: 10.1002/pro.2536] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 01/07/2023]
Abstract
For almost half a century, the structure of the full-length Bacillus thuringiensis (Bt) insecticidal protein Cry1Ac has eluded researchers, since Bt-derived crystals were first characterized in 1965. Having finally solved this structure we report intriguing details of the lattice-based interactions between the toxic core of the protein and the protoxin domains. The structure provides concrete evidence for the function of the protoxin as an enhancer of native crystal packing and stability.
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Affiliation(s)
- Artem G Evdokimov
- *Correspondence to: Artem G. Evdokimov; Monsanto, GG4D 700 Chesterfield Parkway West, Chesterfield, MO 63017. E-mail:
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26
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Abbott DW, van Bueren AL. Using structure to inform carbohydrate binding module function. Curr Opin Struct Biol 2014; 28:32-40. [PMID: 25108190 DOI: 10.1016/j.sbi.2014.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/24/2014] [Accepted: 07/16/2014] [Indexed: 10/24/2022]
Abstract
Generally, non-catalytic carbohydrate binding module (CBM) specificity has been shown to parallel the catalytic activity of the carbohydrate active enzyme (CAZyme) module it is appended to. With the rapid expansion in metagenomic sequence space for the potential discovery of new CBMs in addition to the recent emergence of several new CBM families that display diverse binding profiles and novel functions, elucidating the function of these protein modules has become a much more challenging task. This review summarizes several approaches that have been reported for using primary structure to inform CBM specificity and streamlining their biophysical characterization. In addition we discuss general trends in binding site architecture and several newly identified functions for CBMs. Streams of investigation that will facilitate the development and refinement of sequence-based prediction tools are suggested.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403-1st Ave, Lethbridge, AB, Canada T1J4B1.
| | - Alicia Lammerts van Bueren
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747AG, The Netherlands
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27
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Grant OC, Woods RJ. Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol 2014; 28:47-55. [PMID: 25108191 DOI: 10.1016/j.sbi.2014.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023]
Abstract
Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States; School of Chemistry, University Road, National University of Ireland, Galway, Ireland.
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28
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Yaniv O, Fichman G, Borovok I, Shoham Y, Bayer EA, Lamed R, Shimon LJW, Frolow F. Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σI factors. ACTA ACUST UNITED AC 2014; 70:522-34. [PMID: 24531486 DOI: 10.1107/s139900471302926x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/23/2013] [Indexed: 11/11/2022]
Abstract
The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism of the cellulosomal genes was unknown until recently, when genomic analysis revealed a set of putative operons in C. thermocellum that encode σI factors (i.e. alternative σ factors that control specialized regulon activation) and their cognate anti-σI factor (RsgI). These putative anti-σI-factor proteins have modules that are believed to be carbohydrate sensors. Three of these modules were crystallized and their three-dimensional structures were solved. The structures show a high overall degree of sequence and structural similarity to the cellulosomal family 3 carbohydrate-binding modules (CBM3s). The structures of the three carbohydrate sensors (RsgI-CBM3s) and a reference CBM3 are compared in the context of the structural determinants for the specificity of cellulose and complex carbohydrate binding. Fine structural variations among the RsgI-CBM3s appear to result in alternative substrate preferences for each of the sensors.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Galit Fichman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
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29
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Cornuault V, Knox J. Sandwich Enzyme-linked Immunosorbent Assay (ELISA) Analysis of Plant Cell Wall Glycan Connections. Bio Protoc 2014. [DOI: 10.21769/bioprotoc.1106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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30
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Gilbert HJ, Knox JP, Boraston AB. Advances in understanding the molecular basis of plant cell wall polysaccharide recognition by carbohydrate-binding modules. Curr Opin Struct Biol 2013; 23:669-77. [DOI: 10.1016/j.sbi.2013.05.005] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 11/25/2022]
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31
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Lee KJD, Cornuault V, Manfield IW, Ralet MC, Paul Knox J. Multi-scale spatial heterogeneity of pectic rhamnogalacturonan I (RG-I) structural features in tobacco seed endosperm cell walls. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:1018-27. [PMID: 23789903 PMCID: PMC3824205 DOI: 10.1111/tpj.12263] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/24/2013] [Accepted: 06/10/2013] [Indexed: 05/23/2023]
Abstract
Plant cell walls are complex configurations of polysaccharides that fulfil a diversity of roles during plant growth and development. They also provide sets of biomaterials that are widely exploited in food, fibre and fuel applications. The pectic polysaccharides, which comprise approximately a third of primary cell walls, form complex supramolecular structures with distinct glycan domains. Rhamnogalacturonan I (RG-I) is a highly structurally heterogeneous branched glycan domain within the pectic supramolecule that contains rhamnogalacturonan, arabinan and galactan as structural elements. Heterogeneous RG-I polymers are implicated in generating the mechanical properties of cell walls during cell development and plant growth, but are poorly understood in architectural, biochemical and functional terms. Using specific monoclonal antibodies to the three major RG-I structural elements (arabinan, galactan and the rhamnogalacturonan backbone) for in situ analyses and chromatographic detection analyses, the relative occurrences of RG-I structures were studied within a single tissue: the tobacco seed endosperm. The analyses indicate that the features of the RG-I polymer display spatial heterogeneity at the level of the tissue and the level of single cell walls, and also heterogeneity at the biochemical level. This work has implications for understanding RG-I glycan complexity in the context of cell-wall architectures and in relation to cell-wall functions in cell and tissue development.
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Affiliation(s)
- Kieran JD Lee
- Centre for Plant Sciences, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Valérie Cornuault
- Centre for Plant Sciences, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Marie-Christine Ralet
- UR1268 Biopolymères, Interactions et Assemblages, Institut National de la Recherche AgronomiqueRue de la Géraudière, BP 71627, F–44316, Nantes, France
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
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32
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Sakamoto T, Ishimaru M. Peculiarities and applications of galactanolytic enzymes that act on type I and II arabinogalactans. Appl Microbiol Biotechnol 2013; 97:5201-13. [PMID: 23666442 DOI: 10.1007/s00253-013-4946-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022]
Abstract
Arabinogalactans (AGs) are branched galactans to which arabinose residues are bound as side chains and are widely distributed in plant cell walls. They can be grouped into two types based on the structures of their backbones. Type I AGs have β-1,4-galactan backbones and are often covalently linked to the rhamnogalacturonan-I region of pectins. Type II AGs have β-1,3-galactan backbones and are often covalently linked to proteins. The main enzymes involved in the degradation of AGs are endo-β-galactanases, exo-β-galactanases, and β-galactosidases, although other enzymes such as α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases are required to remove the side chains for efficient degradation of the polysaccharides. Galactanolytic enzymes have a wide variety of potential uses, including the bioconversion of AGs to fermentable sugars for production of commodity chemicals like ethanol, biobleaching of cellulose pulp, modulation of pectin properties, improving animal feed, and determining the chemical structure of AGs. This review summarizes our current knowledge about the biochemical properties and potential applications of AG-degrading enzymes.
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Affiliation(s)
- Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
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33
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Abstract
The stability of the MHC (major histocompatibility complex) class I peptide repertoire is optimized during assembly in the endoplasmic reticulum (ER) and depends on the collective function of components of the peptide-loading complex (PLC). The chaperone-like molecule tapasin is the cornerstone of this complex and acts directly on the MHC class I molecule to promote high-affinity peptide loading. Optimal tapasin activity, however, relies on the ability of ERp57 and calreticulin, two proteins involved in general ER glycoprotein folding, to bridge and thereby stabilize its otherwise weak interaction with the MHC class I heavy chain. Here, we describe methods for the recombinant expression of soluble components of the PLC specifically tailored to generate the post-translational modifications required to support subcomplex assembly in vitro. Using recombinant MHC class I molecules bearing monoglucosylated N-linked glycans, calreticulin, and disulfide-linked tapasin/ERp57 heterodimers, this soluble PLC subcomplex can be employed to study the mechanism of peptide loading or the principles governing peptide selection for particular MHC class I alleles.
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Affiliation(s)
- Pamela A Wearsch
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Peter Cresswell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, USA.
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34
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Abstract
Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities.
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35
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Cao R, Jin Y, Xu D. Recognition of Cello-Oligosaccharides by CBM17 from Clostridium cellulovorans: Molecular Dynamics Simulation. J Phys Chem B 2012; 116:6087-96. [DOI: 10.1021/jp3010647] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ruyin Cao
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Yongdong Jin
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Dingguo Xu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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36
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Sakamoto T, Nishimura Y, Makino Y, Sunagawa Y, Harada N. Biochemical characterization of a GH53 endo-β-1,4-galactanase and a GH35 exo-β-1,4-galactanase from Penicillium chrysogenum. Appl Microbiol Biotechnol 2012; 97:2895-906. [DOI: 10.1007/s00253-012-4154-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 11/27/2022]
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37
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Abbott DW, Boraston AB. Quantitative approaches to the analysis of carbohydrate-binding module function. Methods Enzymol 2012; 510:211-31. [PMID: 22608728 DOI: 10.1016/b978-0-12-415931-0.00011-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbohydrate-binding modules (CBMs) are important components of carbohydrate-active enzymes. Their primary functions are to assist in substrate turnover by targeting appended catalytic modules to substrate and concentrating appended catalytic modules on the surface of substrate. Presented here are four well-established methodologies for investigating and quantifying the CBM-polysaccharide binding relationship. These methods include: (1) the solid state depletion assay, (2) affinity gel electrophoresis, (3) UV difference and fluorescence spectroscopy, and (4) isothermal titration calorimetry. In addition, entropy-driven CBM-crystalline cellulose binding events and differential approaches to calculating stoichiometry with polyvalent polysaccharide ligands are also discussed.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Station, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
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