1
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McNally R, Murali R. Structures of Cutibacterium acnes hyaluronate lyases suggest a correlation between active site opened/closed state and conformation of abutting loop. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001237. [PMID: 39144099 PMCID: PMC11322831 DOI: 10.17912/micropub.biology.001237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
The structures of hyaluronate lyases from two Cutibacterium acnes strains have been reported recently and show open catalytic clefts. We compared these open structures with more closed structures of homologous lyases and found that the conformation of a loop that abuts the catalytic cleft is seemingly correlated with the opening and closing of the cleft. We illustrate that the loop conformation seen in the open lyase appears incompatible with a closed catalytic cleft, and vice versa; however, mutations designed to disrupt the loop conformation did not significantly affect catalytic activity.
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Affiliation(s)
- Randall McNally
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, California, United States
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2
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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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3
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Han R, Baudrexl M, Ludwig C, Berezina OV, Rykov SV, Liebl W. Identification of a novel xanthan-binding module of a multi-modular Cohnella sp. xanthanase. Front Microbiol 2024; 15:1386552. [PMID: 38596379 PMCID: PMC11002231 DOI: 10.3389/fmicb.2024.1386552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
A new strain of xanthan-degrading bacteria identified as Cohnella sp. has been isolated from a xanthan thickener for food production. The strain was able to utilize xanthan as the only carbon source and to reduce the viscosity of xanthan-containing medium during cultivation. Comparative analysis of the secretomes of Cohnella sp. after growth on different media led to the identification of a xanthanase designated as CspXan9, which was isolated after recombinant production in Escherichia coli. CspXan9 could efficiently degrade the β-1,4-glucan backbone of xanthan after previous removal of pyruvylated mannose residues from the ends of the native xanthan side chains by xanthan lyase treatment (XLT-xanthan). Compared with xanthanase from Paenibacillus nanensis, xanthanase CspXan9 had a different module composition at the N- and C-terminal ends. The main putative oligosaccharides released from XLT-xanthan by CspXan9 cleavage were tetrasaccharides and octasaccharides. To explore the functions of the N- and C-terminal regions of the enzyme, truncated variants lacking some of the non-catalytic modules (CspXan9-C, CspXan9-N, CspXan9-C-N) were produced. Enzyme assays with the purified deletion derivatives, which all contained the catalytic glycoside hydrolase family 9 (GH9) module, demonstrated substantially reduced specific activity on XLT-xanthan of CspXan9-C-N compared with full-length CspXan9. The C-terminal module of CspXan9 was found to represent a novel carbohydrate-binding module of family CBM66 with binding affinity for XLT-xanthan, as was shown by native affinity polyacrylamide gel electrophoresis in the presence of various polysaccharides. The only previously known binding function of a CBM66 member is exo-type binding to the non-reducing fructose ends of the β-fructan polysaccharides inulin and levan.
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Affiliation(s)
- Rui Han
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Sergey V. Rykov
- National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, School of Life Sciences, Technical University of Munich, Freising, Germany
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4
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Berezina OV, Rykov SV, Schwarz WH, Liebl W. Xanthan: enzymatic degradation and novel perspectives of applications. Appl Microbiol Biotechnol 2024; 108:227. [PMID: 38381223 PMCID: PMC10881899 DOI: 10.1007/s00253-024-13016-6] [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: 01/04/2024] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
The extracellular heteropolysaccharide xanthan, synthesized by bacteria of the genus Xanthomonas, is widely used as a thickening and stabilizing agent across the food, cosmetic, and pharmaceutical sectors. Expanding the scope of its application, current efforts target the use of xanthan to develop innovative functional materials and products, such as edible films, eco-friendly oil surfactants, and biocompatible composites for tissue engineering. Xanthan-derived oligosaccharides are useful as nutritional supplements and plant defense elicitors. Development and processing of such new functional materials and products often necessitate tuning of xanthan properties through targeted structural modification. This task can be effectively carried out with the help of xanthan-specific enzymes. However, the complex molecular structure and intricate conformational behavior of xanthan create problems with its enzymatic hydrolysis or modification. This review summarizes and analyzes data concerning xanthan-degrading enzymes originating from microorganisms and microbial consortia, with a particular focus on the dependence of enzymatic activity on the structure and conformation of xanthan. Through a comparative study of xanthan-degrading pathways found within various bacterial classes, different microbial enzyme systems for xanthan utilization have been identified. The characterization of these new enzymes opens new perspectives for modifying xanthan structure and developing innovative xanthan-based applications. KEY POINTS: • The structure and conformation of xanthan affect enzymatic degradation. • Microorganisms use diverse multienzyme systems for xanthan degradation. • Xanthan-specific enzymes can be used to develop xanthan variants for novel applications.
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Affiliation(s)
- Oksana V Berezina
- National Research Centre «Kurchatov Institute», Academician Kurchatov Sq. 1, 123182, Moscow, Russian Federation
| | - Sergey V Rykov
- National Research Centre «Kurchatov Institute», Academician Kurchatov Sq. 1, 123182, Moscow, Russian Federation
| | - Wolfgang H Schwarz
- Chair of Microbiology, Technical University of Munich, TUM School of Life Sciences, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, TUM School of Life Sciences, Emil-Ramann-Str. 4, 85354, Freising, Germany.
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5
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Hajam IA, Katiki M, McNally R, Lázaro-Díez M, Kolar S, Chatterjee A, Gonzalez C, Paulchakrabarti M, Choudhury B, Caldera JR, Desmond T, Tsai CM, Du X, Li H, Murali R, Liu GY. Functional divergence of a bacterial enzyme promotes healthy or acneic skin. Nat Commun 2023; 14:8061. [PMID: 38052825 PMCID: PMC10697930 DOI: 10.1038/s41467-023-43833-8] [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: 04/06/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Acne is a dermatologic disease with a strong pathologic association with human commensal Cutibacterium acnes. Conspicuously, certain C. acnes phylotypes are associated with acne, whereas others are associated with healthy skin. Here we investigate if the evolution of a C. acnes enzyme contributes to health or acne. Two hyaluronidase variants exclusively expressed by C. acnes strains, HylA and HylB, demonstrate remarkable clinical correlation with acne or health. We show that HylA is strongly pro-inflammatory, and HylB is modestly anti-inflammatory in a murine (female) acne model. Structural and phylogenic studies suggest that the enzymes evolved from a common hyaluronidase that acquired distinct enzymatic activity. Health-associated HylB degrades hyaluronic acid (HA) exclusively to HA disaccharides leading to reduced inflammation, whereas HylA generates large-sized HA fragments that drive robust TLR2-dependent pathology. Replacing an amino acid, Serine to Glycine near the HylA catalytic site enhances the enzymatic activity of HylA and produces an HA degradation pattern intermediate to HylA and HylB. Selective targeting of HylA using peptide vaccine or inhibitors alleviates acne pathology. We suggest that the functional divergence of HylA and HylB is a major driving force behind C. acnes health- and acne- phenotype and propose targeting of HylA as an approach for acne therapy.
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Affiliation(s)
- Irshad A Hajam
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Madhusudhanarao Katiki
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Randall McNally
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Vault Pharma Inc., 570 Westwood Plaza, Los Angeles, CA, 90025, USA
| | - María Lázaro-Díez
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- AIDS Research Institute (IrsiCaixa). VIRus Immune Escape and VACcine Design (VIRIEVAC) Universitary Hospital German Trias i Pujol Crta Canyet s/n 08916, Badalona, Barcelona, Spain
| | - Stacey Kolar
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Pharmacology at Armata Pharmaceuticals, Inc., Marina del Rey, CA, 90292, USA
| | - Avradip Chatterjee
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Cesia Gonzalez
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | | | - Biswa Choudhury
- GlycoAnalytics Core, University of California San Diego, San Diego, CA, 92093, USA
| | - J R Caldera
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Pathology & Laboratory Medicine, UCLA Health & David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Trieu Desmond
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Chih-Ming Tsai
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Xin Du
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - George Y Liu
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA.
- Division of Infectious Diseases, Rady Children's Hospital, San Diego, CA, 92123, USA.
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6
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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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7
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Zhao J, Wang Q, Ni X, Shen S, Nan C, Li X, Chen X, Yang F. Dissecting the essential role of N-glycosylation in catalytic performance of xanthan lyase. BIORESOUR BIOPROCESS 2022; 9:129. [PMID: 38647758 PMCID: PMC10992191 DOI: 10.1186/s40643-022-00620-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Modified xanthan produced by xanthan lyase has broad application prospects in the food industry. However, the catalytic performance of xanthan lyase still needs to be improved through rational design. To address this problem, in this work, the glycosylation and its influences on the catalytic performance of a xanthan lyase (EcXly), which was heterologously expressed in Escherichia coli, were reported. Liquid chromatography coupled to tandem mass spectrometry analysis revealed that the N599 site of EcXly was modified by a single N-glycan chain. Based on sequence alignment and three-dimensional structure prediction, it could be deduced that the N599 site was located in the catalytic domain of EcXly and in close proximity to the catalytic residues. After site-directed mutagenesis of N599 with alanine, aspartic acid and glycine, respectively, the EcXly and its mutants were characterized and compared. The results demonstrated that elimination of the N-glycosylation had diminished the specific activity, pH stability, and substrate affinity of EcXly. Fluorescence spectra further revealed that the glycosylation could significantly affect the overall tertiary structure of EcXly. Therefore, in prokaryotic hosts, the N-glycosylation could influence the catalytic performance of the enzyme by changing its structure. To the best of our knowledge, this is the first report about the post-translational modification of xanthan lyase in prokaryotes. Overall, our work enriched research on the role of glycan chains in the functional performance of proteins expressed in prokaryotes and should be valuable for the rational design of xanthan lyase to produce modified xanthan for industrial application.
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Affiliation(s)
- Jingjing Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Qian Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Xin Ni
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Shaonian Shen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Chenchen Nan
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China.
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8
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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9
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Wang X, Zhang S, Wu H, Li Y, Yu W, Han F. Expression and characterization of a thermotolerant and pH-stable hyaluronate lyase from Thermasporomyces composti DSM22891. Protein Expr Purif 2021; 182:105840. [PMID: 33561520 DOI: 10.1016/j.pep.2021.105840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/10/2020] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
Hyaluronate lyases have received extensive attention due to their applications in medical science, drug and biochemical engineering. However, few thermotolerant and pH-stable hyaluronate lyases have been found. In this study, hyaluronate lyase TcHly8B from Thermasporomyces composti DSM22891 was expressed in Escherichia coli BL21(DE3), purified, and characterized. Phylogenetic analysis revealed that TcHly8B belonged to a new subfamily in PL8. The molecular mass of recombinant TcHly8B determined by SDS-PAGE was approximately 86 kDa. The optimal temperature of TcHly8B was 70 °C, which was higher than that of previously reported hyaluronate lyases. TcHly8B was very stable at temperatures from 0 to 60 °C. The optimal pH of TcHly8B was 6.6. It could retain more than 80% of its original enzyme activity after incubation for 12 h in the pH range of 3.0-10.6. TcHly8B degraded hyaluronic acid into unsaturated disaccharides as the end products. The amino acid sequence and structure analysis of TcHly8B demonstrated that the amino acid composition and salt bridges might contribute to the thermostability of TcHly8B. Overall, this study provides an excellent example for the discovery of thermotolerant hyaluronate lyases and can be applied to the industrialized production and basic research of hyaluronate oligosaccharides.
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Affiliation(s)
- Xiaoyi Wang
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shilong Zhang
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Hao Wu
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yujiao Li
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Feng Han
- Key Laboratory of Marine Drugs, Ministry of Education; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering; School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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10
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Shroff R, Cole AW, Diaz DJ, Morrow BR, Donnell I, Annapareddy A, Gollihar J, Ellington AD, Thyer R. Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning. ACS Synth Biol 2020; 9:2927-2935. [PMID: 33064458 DOI: 10.1021/acssynbio.0c00345] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the promise of deep learning accelerated protein engineering, examples of such improved proteins are scarce. Here we report that a 3D convolutional neural network trained to associate amino acids with neighboring chemical microenvironments can guide identification of novel gain-of-function mutations that are not predicted by energetics-based approaches. Amalgamation of these mutations improved protein function in vivo across three diverse proteins by at least 5-fold. Furthermore, this model provides a means to interrogate the chemical space within protein microenvironments and identify specific chemical interactions that contribute to the gain-of-function phenotypes resulting from individual mutations.
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Affiliation(s)
- Raghav Shroff
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Austin W. Cole
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Daniel J. Diaz
- The Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Barrett R. Morrow
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Isaac Donnell
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ankur Annapareddy
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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11
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Leth ML, Ejby M, Madland E, Kitaoku Y, Slotboom DJ, Guskov A, Aachmann FL, Abou Hachem M. Molecular insight into a new low‐affinity xylan binding module from the xylanolytic gut symbiont
Roseburia intestinalis. FEBS J 2019; 287:2105-2117. [DOI: 10.1111/febs.15117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Louise Leth
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
| | - Morten Ejby
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
| | - Eva Madland
- NOBIPOL Department of Biotechnology and Food Science NTNU Norwegian University of Science and Technology Trondheim Norway
| | - Yoshihito Kitaoku
- NOBIPOL Department of Biotechnology and Food Science NTNU Norwegian University of Science and Technology Trondheim Norway
| | - Dirk J. Slotboom
- Membrane Enzymology Institute for Biomolecular Sciences & Biotechnology University of Groningen Groningen The Netherlands
| | - Albert Guskov
- Membrane Enzymology Institute for Biomolecular Sciences & Biotechnology University of Groningen Groningen The Netherlands
| | - Finn Lillelund Aachmann
- NOBIPOL Department of Biotechnology and Food Science NTNU Norwegian University of Science and Technology Trondheim Norway
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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