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Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
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Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Vasquez-Martínez N, Guillen D, Andrea Moreno-Mendieta S, Medina-Granados P, Guadalupe Casañas-Pimentel R, San Martín-Martínez E, Ángel Morales M, Sanchez S, Rodríguez-Sanoja R. In vivo tracing of immunostimulatory raw starch microparticles after mucosal administration. Eur J Pharm Biopharm 2023; 187:96-106. [PMID: 37094693 DOI: 10.1016/j.ejpb.2023.04.013] [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: 11/15/2022] [Revised: 03/08/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Raw starch microparticles (SMPs) proved efficient antigen carriers with adjuvant properties when administered via the mucosal route; however, the underlying mechanisms associated with this bioactivity are unknown. In the present study, we explored the mucoadhesion properties, fate, and toxicity of starch microparticles after mucosal administration. Nasally administered microparticles were mainly retained in nasal turbinates, reaching the nasal-associated lymphoid tissue; this step is facilitated by the ability of the microparticles to penetrate through the mucous epithelium. Likewise, we found intraduodenally administered SMPs on the small intestinal villi, follicle-associated epithelium, and Peyer's patches. Furthermore, under simulated gastric and intestinal pH conditions, we detected mucoadhesion between the SMPs and mucins, regardless of microparticle swelling. SMPs' mucoadhesion and translocation to mucosal immune responses induction sites explain the previously reported role of these microparticles as vaccine adjuvants and immunostimulants.
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Affiliation(s)
- Nathaly Vasquez-Martínez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México; Programa de Doctorado en Ciencia Bioquímicas, Universidad Nacional Autónoma de México. Circuito de Posgrado, C.U, Coyoacán, 04510, CDMX, México.
| | - Daniel Guillen
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México.
| | - Silvia Andrea Moreno-Mendieta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México; Consejo Nacional de Ciencia y Tecnología (CONACyT).
| | - Pedro Medina-Granados
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México.
| | - Rocío Guadalupe Casañas-Pimentel
- Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Calzada Legaria 694, Irrigación, Miguel Hidalgo, 11500, Ciudad de México, México.
| | - Eduardo San Martín-Martínez
- Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Calzada Legaria 694, Irrigación, Miguel Hidalgo, 11500, Ciudad de México, México.
| | - Miguel Ángel Morales
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México.
| | - Sergio Sanchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México.
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito, Mario de La Cueva s/n, C.U, Coyoacán, 04510, Ciudad de México, México.
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3
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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: 6] [Impact Index Per Article: 6.0] [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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Yang T, Zhong L, Jiang G, Liu L, Wang P, Zhong Y, Yue Q, Ouyang L, Zhang A, Li Z, Cui Z, Jiang D, Zhou Q. Comparative study on bread quality and starch digestibility of normal and waxy wheat (Triticum aestivum L.) modified by maltohexaose producing α-amylases. Food Res Int 2022; 162:112034. [DOI: 10.1016/j.foodres.2022.112034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022]
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5
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Tong L, Huang H, Zheng J, Wang X, Bai Y, Wang X, Wang Y, Tu T, Yao B, Qin X, Luo H. Engineering a carbohydrate-binding module to increase the expression level of glucoamylase in Pichia pastoris. Microb Cell Fact 2022; 21:95. [PMID: 35643500 PMCID: PMC9148494 DOI: 10.1186/s12934-022-01833-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/13/2022] [Indexed: 12/04/2022] Open
Abstract
Background Glucoamylase is an important industrial enzyme for the saccharification of starch during sugar production, but the production cost of glucoamylase is a major limiting factor for the growth of the starch-based sugar market. Therefore, seeking strategies for high-level expression of glucoamylase in heterologous hosts are considered as the main way to reduce the enzyme cost. Results ReGa15A from Rasamsonia emersonii and TlGa15B-GA2 from Talaromyces leycettanus have similar properties. However, the secretion level of ReGa15A was significantly higher than TlGa15B-GA2 in Pichia pastoris. To explore the underlying mechanisms affecting the differential expression levels of glucoamylase in P. pastoris, the amino acid sequences and three-dimensional structures of them were compared and analyzed. First, the CBM region was identified by fragment replacement as the key region affecting the expression levels of ReGa15A and TlGa15B-GA2. Then, through the substitution and site-directed mutation of the motifs in the CBM region, three mutants with significantly increased expression levels were obtained. The eight-point mutant TlGA-M4 (S589D/Q599A/G600Y/V603Q/T607I/V608L/N609D/R613Q), the three-point mutant TlGA-M6 (Q599A/G600Y/V603Q) and the five-point mutant TlGA-M7 (S589D/T607I/V608L/N609D/R613Q) have the same specific activity with the wild-type, and the enzyme activity and secretion level have increased by 4–5 times, respectively. At the same time, the expression levels were 5.8-, 2.0- and 2.4-fold higher than that of wild type, respectively. Meanwhile, the expression of genes related to the unfolded protein responses (UPR) in the endoplasmic reticulum (ER) did not differ significantly between the mutants and wild type. In addition, the most highly expressed mutant, TlGA-M7 exhibits rapidly and effectively hydrolyze raw corn starch. Conclusions Our results constitute the first demonstration of improved expression and secretion of a glucoamylase in P. pastoris by introducing mutations within the non-catalytic CBM. This provides a novel and effective strategy for improving the expression of recombinant proteins in heterologous host expression systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01833-1.
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Liu Y, Wang P, Tian J, Seidi F, Guo J, Zhu W, Xiao H, Song J. Carbohydrate-Binding Modules of Potential Resources: Occurrence in Nature, Function, and Application in Fiber Recognition and Treatment. Polymers (Basel) 2022; 14:1806. [PMID: 35566977 PMCID: PMC9100146 DOI: 10.3390/polym14091806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 02/04/2023] Open
Abstract
Great interests have recently been aroused in the independent associative domain of glycoside hydrolases that utilize insoluble polysaccharides-carbohydrate-binding module (CBM), which responds to binding while the catalytic domain reacts with the substrate. In this mini-review, we first provide a brief introduction on CBM and its subtypes including the classifications, potential sources, structures, and functions. Afterward, the applications of CBMs in substrate recognition based on different types of CBMs have been reviewed. Additionally, the progress of CBMs in paper industry as a new type of environmentally friendly auxiliary agent for fiber treatment is summarized. At last, other applications of CBMs and the future outlook have prospected. Due to the specificity in substrate recognition and diversity in structures, CBM can be a prosperous and promising 'tool' for wood and fiber processing in the future.
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Affiliation(s)
- Yena Liu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Peipei Wang
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jing Tian
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Farzad Seidi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jiaqi Guo
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Wenyuan Zhu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB E3B 5A3, Canada;
| | - Junlong Song
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
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Ni G, Zhong L, Xia C, Zhang L, Dai L, Chen R, Zhao Y, Wang F. Phenylalanine 314 is essential for the activity of maltogenic amylase from Corallococcus sp. EGB. Biotechnol Appl Biochem 2021; 69:2240-2248. [PMID: 34775631 DOI: 10.1002/bab.2282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 11/06/2022]
Abstract
Maltogenic amylase CoMA from Corallococcus sp. strain EGB catalyzes the hydrolysis and transglycosylation of maltooligosaccharides and soluble starch into maltose, the sole hydrolysate. This process yields pure maltose with potentially wide applications. Here, we identified and evaluated the role of phenylalanine 314 (F314), a key amino acid located near the active center, in the catalytic activities of the CoMA. Site-directed mutagenesis analysis showed that the activity of a F314L mutant on potato starch substrate decreased to 26% of that of wild-type protein. Compared with the wild-type, F314L exhibited similar substrate specificity, hydrolysis pattern, pH, and temperature requirements. Circular dichroism spectrum data showed that the F314L mutation did not affect the structure of the folded protein. In addition, kinetic analysis demonstrated that F314L exhibited an increased Km value with lower substrate affinity. Homology modeling showed that the benzene ring structure of F314L was involved in π-π conjugation, which might potentially affect the affinity of CoMA toward starch. Taken together, these data demonstrated that F314 is essential for the hydrolytic activity of the CoMA from Corallococcus sp. strain EGB.
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Affiliation(s)
- Guorong Ni
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Lingli Zhong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Lixia Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Longhua Dai
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Ruyi Chen
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, China.,Institute of Botany Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Fei Wang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
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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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Synergistic effect of acetyl xylan esterase from Talaromyces leycettanus JCM12802 and xylanase from Neocallimastix patriciarum achieved by introducing carbohydrate-binding module-1. AMB Express 2019; 9:13. [PMID: 30694400 PMCID: PMC6351639 DOI: 10.1186/s13568-019-0740-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Wheat bran is an effective raw material for preparation xylooligosaccharides; however, current research mainly focuses on alkali extraction and enzymatic hydrolysis methods. Since ester bonds are destroyed during the alkali extraction process, xylanase and arabinofuranosidase are mainly used to hydrolyze xylooligosaccharides. However, alkali extraction costs are very high, and the method also causes pollution. Therefore, this study focuses on elucidating a method to efficiently and directly degrade destarched wheat bran. First, an acidic acetyl xylan esterase (AXE) containing a carbohydrate-binding module-1 (CBM1) domain was cloned from Talaromyces leycettanus JCM12802 and successfully expressed in Pichia pastoris. Characterization showed that the full-length acetyl xylan esterase AXE + CBM1 was similar toe uncovered AXE with an optimum temperature and pH of 55 °C and 6.5, respectively. Testing the acetyl xylan esterase and xylanase derived from Neocallimastix patriciarum in a starch-free wheat bran cooperative experiment revealed that AXE + CBM1 and AXE produced 29% and 16% reducing sugars respectively, compared to when only NPXYN11 was used. In addition, introduced the CBM1 domain into NPXYN11, and the results indicated that the CBM1 domain showed little effect on NPXYN11 properties. Finally, the systematically synergistic effects between acetyl xylan esterase and xylanase with/without the CBM1 domain demonstrated that the combined ratio of AXE + CBM1 coming in first and NPXYN11 + CBM1 s increased reducing sugars by almost 35% with AXE and NPXYN11. Furthermore, each component's proportion remained the same with respect to xylooligosaccharides, with the largest proportion (86%) containing of 49% xylobiose and 37% xylotriose.
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Armenta S, Sánchez-Cuapio Z, Munguia ME, Pulido NO, Farrés A, Manoutcharian K, Hernandez-Santoyo A, Moreno-Mendieta S, Sánchez S, Rodríguez-Sanoja R. The role of conserved non-aromatic residues in the Lactobacillus amylovorus α-amylase CBM26-starch interaction. Int J Biol Macromol 2019; 121:829-838. [DOI: 10.1016/j.ijbiomac.2018.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 10/28/2022]
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11
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Armenta S, Sánchez-Cuapio Z, Farrés A, Manoutcharian K, Hernandez-Santoyo A, Sánchez S, Rodríguez-Sanoja R. Data concerning secondary structure and alpha-glucans-binding capacity of the LaCBM26. Data Brief 2018; 21:1944-1949. [PMID: 30519620 PMCID: PMC6260227 DOI: 10.1016/j.dib.2018.11.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/20/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are auxiliary domains into glycoside-hydrolases that allow the interaction between the insoluble substrate and the solubilized enzyme, through hydrophobic, CH-π interactions and hydrogen bonds. Here, we present the data article related to the interaction of one LaCBM26 and some mutated proteins with soluble α-glucans determined by enzyme-linked carbohydrate-binding assay, isothermal titration calorimetry (ITC), and affinity gel electrophoresis (AGE). The data of the behavior of proteins in presence and absence of substrate analyzed by circular dichroism CD and thermofluor are also presented. These results are complementary to the research article “The role of conserved non-aromatic residues in the Lactobacillus amylovorus α-amylase CBM26-starch interaction” (Armenta et al., 2019).
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, Ciudad de México 04510, México
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, México DF 04510, Mexico
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, Ciudad de México 04510, México
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, México DF 04510, Mexico
| | - Amelia Farrés
- Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria, Ciudad de México 04510, México
| | - Karen Manoutcharian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, Ciudad de México 04510, México
| | - Alejandra Hernandez-Santoyo
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria, Ciudad de México 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, Ciudad de México 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), A.P. 70228, Ciudad Universitaria, Ciudad de México 04510, México
- Corresponding author.
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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: 61] [Impact Index Per Article: 8.7] [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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Kanpiengjai A, Nguyen TH, Haltrich D, Khanongnuch C. Expression and comparative characterization of complete and C-terminally truncated forms of saccharifying α-amylase from Lactobacillus plantarum S21. Int J Biol Macromol 2017; 103:1294-1301. [PMID: 28587961 DOI: 10.1016/j.ijbiomac.2017.05.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/16/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Abstract
Lactobacillus plantarum S21 α-amylase possesses 475 amino acids at the C-terminal region identified as the starch-binding domain (SBD) and has been previously reported to play a role in raw starch degradation. To understand the specific roles of this SBD, cloning and expression of the complete (AmyL9) and C-terminally truncated (AmyL9ΔSBD) forms of α-amylase were conducted for enzyme purification and comparative characterization. AmyL9 and AmyL9ΔSBD were overproduced in Escherichia coli at approximately 10- and 20-times increased values of volumetric productivity when compared to α-amylase produced by the wild type, respectively. AmyL9ΔSBD was unable to hydrolyze raw starch and exhibited substrate specificity in a similar manner to that of AmyL9, but it was weakly active toward amylopectin and glycogen. The hydrolysis products obtained from the amylaceous substrates of both enzymes were the same. In addition, AmyL9ΔSBD showed comparatively higher Km values than AmyL9 when it reacted with starch and amylopectin, and lower values for other kinetic constants namely vmax, kcat, and kcat/Km. The results indicated that the C-terminal SBDs of L. plantarum S21 α-amylase contribute to not only substrate preference but also substrate affinity and the catalytic efficiency of the α-amylase without any changes in the degradation mechanisms of the enzyme.
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Affiliation(s)
- Apinun Kanpiengjai
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand; Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Thu-Ha Nguyen
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Chartchai Khanongnuch
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand.
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Janeček Š, Majzlová K, Svensson B, MacGregor EA. The starch-binding domain family CBM41-Anin silicoanalysis of evolutionary relationships. Proteins 2017; 85:1480-1492. [DOI: 10.1002/prot.25309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/05/2017] [Accepted: 04/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Štefan Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Biology; Faculty of Natural Sciences, University of SS. Cyril and Methodius; Trnava Slovakia
| | - Katarína Majzlová
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
| | - Birte Svensson
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Kgs. Lyngby Denmark
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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Wei W, Qu K, Ren J, Qu X. Chiral detection using reusable fluorescent amylose-functionalized graphene. Chem Sci 2011. [DOI: 10.1039/c1sc00308a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Wayllace NZ, Valdez HA, Ugalde RA, Busi MV, Gomez-Casati DF. The starch-binding capacity of the noncatalytic SBD2 region and the interaction between the N- and C-terminal domains are involved in the modulation of the activity of starch synthase III from Arabidopsis thaliana. FEBS J 2009; 277:428-40. [PMID: 19968859 DOI: 10.1111/j.1742-4658.2009.07495.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Starch synthase III from Arabidopsis thaliana contains an N-terminal region, including three in-tandem starch-binding domains, followed by a C-terminal catalytic domain. We have reported previously that starch-binding domains may be involved in the regulation of starch synthase III function. In this work, we analyzed the existence of protein interactions between both domains using pull-down assays, far western blotting and co-expression of the full and truncated starch-binding domains with the catalytic domain. Pull-down assays and co-purification analysis showed that the D(316-344) and D(495-535) regions in the D2 and D3 domains, respectively, but not the individual starch-binding domains, are involved in the interaction with the catalytic domain. We also determined that the residues W366 and Y394 in the D2 domain are important in starch binding. Moreover, the co-purified catalytic domain plus site-directed mutants of the D123 protein lacking these aromatic residues showed that W366 was key to the apparent affinity for the polysaccharide substrate of starch synthase III, whereas either of these amino acid residues altered ADP-glucose kinetics. In addition, the analysis of full-length and truncated proteins showed an almost complete restoration of the apparent affinity for the substrates and V(max) of starch synthase III. The results presented here suggest that the interaction of the N-terminal starch-binding domains, particularly the D(316-344) and D(495-535) regions, with the catalytic domains, as well as the full integrity of the starch-binding capacity of the D2 domain, are involved in the modulation of starch synthase III activity.
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Affiliation(s)
- Nahuel Z Wayllace
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Argentina
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Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol 2009; 85:1241-9. [DOI: 10.1007/s00253-009-2331-y] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 10/23/2009] [Accepted: 10/24/2009] [Indexed: 10/20/2022]
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