1
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Sumida T, Hiraoka S, Usui K, Ishiwata A, Sengoku T, Stubbs KA, Tanaka K, Deguchi S, Fushinobu S, Nunoura T. Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun 2024; 15:3543. [PMID: 38730244 PMCID: PMC11087588 DOI: 10.1038/s41467-024-47653-2] [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: 08/23/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Keiko Usui
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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2
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Moreno Prieto ES, Fjermedal S, Siebenhaar S, Vuillemin M, Holck J, Vincentelli R, Gippert GP, Wilkens C, Morth JP, Henrissat B. Characterization and structural study of a novel β-N-acetylgalactosaminidase from Niabella aurantiaca. FEBS J 2024; 291:1439-1456. [PMID: 38129294 DOI: 10.1111/febs.17042] [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: 08/31/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
We report here the identification, characterization and three-dimensional (3D) structure determination of NaNga, a newly identified β-N-acetylgalactosaminidase from the Gram-negative soil bacterium Niabella aurantiaca DSM 17617. When recombinantly expressed in Escherichia coli, the enzyme selectively cleaved 4-nitrophenyl-N-acetyl-β-d-galactosamine (pNP-β-d-GalpNAc). The X-ray crystal structure of the protein was refined to 2.5 Å and consists of an N-terminal β-sandwich domain and a (β/α)8 barrel catalytic domain. Despite a mere 22% sequence identity, the 3D structure of NaNga is similar to those previously determined for family GH123 members, suggesting it also employs the same substrate-assisted catalytic mechanism. Inhibition by N-acetyl-galactosamine thiazoline (GalNAc-thiazoline) supports the suggested mechanism. A phylogenetic analysis of its proximal sequence space shows significant clustering of unknown sequences around NaNga with sufficient divergence with previously identified GH123 members to subdivide this family into distinct subfamilies. Although the actual biological substrate of our enzyme remains unknown, examination of the active site pocket suggests that it may be a β-N-acetylgalactosaminide substituted by a monosaccharide at O-3. Analysis of the genomic context suggests, in turn, that this substituted β-N-acetylgalactosaminide may be appended to a d-arabinan from an environmental Actinomycete.
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Affiliation(s)
| | - Sune Fjermedal
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, France
| | - Garry P Gippert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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3
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Li X, Chen Y, Song L, Wang J, Song Z, Zhao X, Zhou C, Wu Y. Partial enzymolysis affects the digestion of tamarind seed polysaccharides in vitro: Degradation accelerates and gut microbiota regulates. Int J Biol Macromol 2023; 237:124175. [PMID: 37003195 DOI: 10.1016/j.ijbiomac.2023.124175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023]
Abstract
Two hydrolyzed fractions of tamarind seed polysaccharide (TSP), denoted ETSP1 (176.68 kDa) and ETSP2 (34.34 kDa), were prepared by partial degradation via endo-xyloglucanase, and then characterized and evaluated by simulated gastrointestinal digestion in vitro. The results showed that the hydrolyzed TSPs remained indigestible in gastric and small intestinal media, and were fermented by gut microbiota, similar to the native TSP (Mw = 481.52 kDa). Although the degradation of hydrolyzed TSPs was accelerated during fermentation with a decreasing degree of polymerization, the content of produced total short-chain fatty acids (SCFAs) decreased. After fermentation, the gut microbiota composition was modified, esp. the Firmicutes/Bacteroidetes ratio decreased (1.06 vs. 0.96 vs. 0.80) with a decreasing degree of polymerization, which implied that the potential anti-obesity prebiotic effect was enhanced. At the genus level, hydrolyzed TSPs maintained similar roles as native TSP, including promoting beneficial bacteria (Bifidobacterium, Parabacteroides, and Faecalibacterium) and inhibiting enteropathogenic bacteria (Escherichia-Shigella and Dorea). Moreover, ETSP1 had additional potential due to abundant Bacteroides vulgatus (LDA = 4.68), and ETSP2 might perform better as related to Bacteroides xylanisolvens (LDA = 4.40). All these results indicated the prebiotic potential of hydrolyzed TSP with detailed information about changes in degradation and gut microbiota based on enzyme-hydrolysis.
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Affiliation(s)
- Xujiao Li
- Institute for Agro-food Standards and Testing Technology, Laboratory of Quality & Safety Risk Assessment for Agro-products (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Shanghai Engineering Research Center of Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yinan Chen
- Shanghai Engineering Research Center of Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Lihua Song
- Shanghai Engineering Research Center of Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jiangmei Wang
- Weifang Ecological Environment Monitoring Center, Weifang 261041, China.
| | - Zibo Song
- Yunnan Maoduoli Group Food Co., Ltd., Yuxi 653100, China.
| | - Xiaoyan Zhao
- Institute for Agro-food Standards and Testing Technology, Laboratory of Quality & Safety Risk Assessment for Agro-products (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Changyan Zhou
- Institute for Agro-food Standards and Testing Technology, Laboratory of Quality & Safety Risk Assessment for Agro-products (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Yan Wu
- Shanghai Engineering Research Center of Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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4
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Nekvasilová P, Kulik N, Kotik M, Petrásková L, Slámová K, Křen V, Bojarová P. Mutation Hotspot for Changing the Substrate Specificity of β- N-Acetylhexosaminidase: A Library of GlcNAcases. Int J Mol Sci 2022; 23:12456. [PMID: 36293310 PMCID: PMC9604439 DOI: 10.3390/ijms232012456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 12/27/2023] Open
Abstract
β-N-Acetylhexosaminidase from Talaromyces flavus (TfHex; EC 3.2.1.52) is an exo-glycosidase with dual activity for cleaving N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) units from carbohydrates. By targeting a mutation hotspot of the active site residue Glu332, we prepared a library of ten mutant variants with their substrate specificity significantly shifted towards GlcNAcase activity. Suitable mutations were identified by in silico methods. We optimized a microtiter plate screening method in the yeast Pichia pastoris expression system, which is required for the correct folding of tetrameric fungal β-N-acetylhexosaminidases. While the wild-type TfHex is promiscuous with its GalNAcase/GlcNAcase activity ratio of 1.2, the best single mutant variant Glu332His featured an 8-fold increase in selectivity toward GlcNAc compared with the wild-type. Several prepared variants, in particular Glu332Thr TfHex, had significantly stronger transglycosylation capabilities than the wild-type, affording longer chitooligomers - they behaved like transglycosidases. This study demonstrates the potential of mutagenesis to alter the substrate specificity of glycosidases.
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Affiliation(s)
- Pavlína Nekvasilová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843 Praha 2, Czech Republic
| | - Natalia Kulik
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, CZ-37333 Nové Hrady, Czech Republic
| | - Michael Kotik
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Lucie Petrásková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
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5
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Cuxart I, Coines J, Esquivias O, Faijes M, Planas A, Biarnés X, Rovira C. Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto- N-biosidase. ACS Catal 2022; 12:4737-4743. [PMID: 35465242 PMCID: PMC9016705 DOI: 10.1021/acscatal.2c00309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/26/2022] [Indexed: 12/22/2022]
Abstract
![]()
Bifidobacterium
bifidum lacto-N-biosidase (LnbB)
is a critical enzyme for the degradation
of human milk oligosaccharides in the gut microbiota of breast-fed
infants. Guided by recent crystal structures, we unveil its molecular
mechanism of catalysis using QM/MM metadynamics. We show that the
oligosaccharide substrate follows 1S3/1,4B → [4E]‡ → 4C1/4H5 and 4C1/4H5 → [4E/4H5]‡ → 1,4B conformational itineraries for the two
successive reaction steps, with reaction free energy barriers in agreement
with experiments. The simulations also identify a critical histidine
(His263) that switches between two orientations to modulate the pKa of the acid/base residue, facilitating catalysis.
The reaction intermediate of LnbB is best depicted as an oxazolinium
ion, with a minor population of neutral oxazoline. The present study
sheds light on the processing of oligosaccharides of the early life
microbiota and will be useful for the engineering of LnbB and similar
glycosidases for biocatalysis.
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Affiliation(s)
- Irene Cuxart
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Oriol Esquivias
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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6
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Teze D, Zhao J, Wiemann M, Kazi ZGA, Lupo R, Zeuner B, Vuillemin M, Rønne ME, Carlström G, Duus JØ, Sanejouand YH, O'Donohue MJ, Nordberg Karlsson E, Fauré R, Stålbrand H, Svensson B. Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases. Chemistry 2021; 27:10323-10334. [PMID: 33914359 DOI: 10.1002/chem.202100110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.
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Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Jiao Zhao
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Mathias Wiemann
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Zubaida G A Kazi
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Rossana Lupo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Mette E Rønne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Göran Carlström
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Jens Ø Duus
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bulding 207, DK-2800, Kongens Lyngby, Denmark
| | - Yves-Henri Sanejouand
- UFIP, UMR 6286, Université de Nantes, CNRS, 2, chemin de la Houssiniere, Nantes, France
| | - Michael J O'Donohue
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | | | - Régis Fauré
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
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7
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The Core and Distinction of the Gut Microbiota in Chinese Populations across Geography and Ethnicity. Microorganisms 2020; 8:microorganisms8101579. [PMID: 33066420 PMCID: PMC7602275 DOI: 10.3390/microorganisms8101579] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/26/2020] [Accepted: 10/12/2020] [Indexed: 12/26/2022] Open
Abstract
The diversity of the human gut microbiota constitutes a fundamental health indicator of different populations. The relative importance of geographical location and ethnicity on the gut microbiota, however, has not been previously addressed. Due to unique ethnic distributions across China, we recruited distinct minority ethnic groups, including Han populations, in each of the seven cities that were explored in this study. We investigated the gut microbiota of 394 healthy subjects (14 groups) from these seven different cities using 16S rRNA sequencing. Our results indicated that both geographical location and ethnicity were major factors. However, geographical location exhibited greater influence than ethnicity on both the composition and diversity of the gut microbiota. In addition, a total of 15 shared biomarkers at the genus level were identified in three distinct locations, including seven in Inner Mongolia, seven in Xinjiang and one in Gansu. Furthermore, 65 unique biomarkers were found in 14 population groups, which indicated specific communities in different populations. Based on the gut microbiota species, two main enterotypes—namely Prevotella (ETP) and Bacteroides (ETB), which consist of Prevotella and Bacteroides as the core bacterial genus, were observed in Chinese populations. Our unique experimental design using the same ethnic group—Han, as a control in different locations, enables delineating the importance of geographical location and ethnicity on the gut microbiota, and provides the fundamental characteristics of gut microbiota diversity in Chinese populations.
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8
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Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. MICROBIOME 2020; 8:141. [PMID: 33004077 PMCID: PMC7531118 DOI: 10.1186/s40168-020-00911-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/23/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. RESULTS Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. CONCLUSION By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.
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Affiliation(s)
- Alexandra S Tauzin
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- CAPES Foundation, Ministry of Education of Brazil, BrasÍlia, DF, 70040-020, Brazil
| | - Liisa D Van Vliet
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Drop-Tech, Canterbury Court, Cambridge, CB4 3QU, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Sandrine Laguerre
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Terrapon
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Marion Leclerc
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
- Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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9
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Nekvasilová P, Kulik N, Rychlá N, Pelantová H, Petrásková L, Bosáková Z, Cvačka J, Slámová K, Křen V, Bojarová P. How Site‐Directed Mutagenesis Boosted Selectivity of a Promiscuous Enzyme. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pavlína Nekvasilová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Genetics and Microbiology Faculty of Science Charles University Viničná 5 CZ-12843 Praha 2 Czech Republic
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Natalia Kulik
- Center for Nanobiology and Structural Biology Institute of Microbiology Czech Academy of Sciences Zámek 136 CZ-37333 Nové Hrady Czech Republic
| | - Nikola Rychlá
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
| | - Helena Pelantová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Lucie Petrásková
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Zuzana Bosáková
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nám. 2 CZ-16610 Praha 6 Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Vladimír Křen
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
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Intestinal microbiota characteristics of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress. 3 Biotech 2020; 10:180. [PMID: 32231961 DOI: 10.1007/s13205-020-02172-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/17/2020] [Indexed: 01/30/2023] Open
Abstract
To investigate the characteristics of the intestinal microbiota of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress. Ten healthy male Kunming mice were chosen and randomly divided into control group and model group, with five mice in each group. Mice in the control group were raised regularly, while mice in the model group were treated by feeding with Folium senna decoction, restraint in a constraint tube and tail pinch with a clip for 7 days. Intestinal contents from the jejunum to ileum were collected, and DNA was extracted from each mouse. The characteristics of the intestinal microbial species were analysed by PacBio Sequel-based 16S rRNA sequencing. Result showed that alpha diversity indices in the model group were higher than those in the control group, and the Simpson index differed significantly (P < 0.05). Based on the composition and abundances of species, there were differences between the control group and model group at the species level, but these differences were not significant (P > 0.05). In the control group, Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii were the dominant species. In the model group, Staphylococcus lentus, Lactobacillus johnsonii, Candidatus arthromitus sp. SFB-mouse and Lactobacillus murinus were included. Furthermore, LEfSe analysis showed that the relative abundances of Escherichia sp. BBDP27, Helicobacter ganmani, Bacteroides vulgatus and Lactobacillus intestinalis in the model group were higher than those in the control group (P < 0.05 or P < 0.01). In conclusion, Folium senna decoction gavage combined with restraint and tail pinch stress increased the intestinal microbiota diversity. Strains associated with intestinal diseases, including Bacteroides vulgatus, Helicobacter ganmani, Staphylococcus lentus and Lactobacillus murinus, were significantly enriched, while strains beneficial to health, such as Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii, were significantly depleted.
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11
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Teze D, Coines J, Raich L, Kalichuk V, Solleux C, Tellier C, André-Miral C, Svensson B, Rovira C. A Single Point Mutation Converts GH84 O-GlcNAc Hydrolases into Phosphorylases: Experimental and Theoretical Evidence. J Am Chem Soc 2020; 142:2120-2124. [DOI: 10.1021/jacs.9b09655] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
- UFIP, CNRS, Université de Nantes, 44300 Nantes, France
| | - Joan Coines
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | | | | | | | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 224, DK-2800 Kongens Lyngby, Denmark
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Rovira C, Males A, Davies GJ, Williams SJ. Mannosidase mechanism: at the intersection of conformation and catalysis. Curr Opin Struct Biol 2019; 62:79-92. [PMID: 31891872 DOI: 10.1016/j.sbi.2019.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Mannosidases are a diverse group of enzymes that are important in the biological processing of mannose-containing polysaccharides and complex glycoconjugates. They are found in 12 of the >160 sequence-based glycosidase families. We discuss evidence that nature has evolved a small set of common mechanisms that unite almost all of these mannosidase families. Broadly, mannosidases (and the closely related rhamnosidases) perform catalysis through just two conformations of the oxocarbenium ion-like transition state: a B2,5 (or enantiomeric 2,5B) boat and a 3H4 half-chair. This extends to a new family (GT108) of GDPMan-dependent β-1,2-mannosyltransferases/phosphorylases that perform mannosyl transfer through a boat conformation as well as some mannosidases that are metalloenzymes and require divalent cations for catalysis. Yet, among this commonality lies diversity. New evidence shows that one unique family (GH99) of mannosidases use an unusual mechanism involving anchimeric assistance via a 1,2-anhydro sugar (epoxide) intermediate.
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Affiliation(s)
- Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandra Males
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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Delahaye M, Winne JM, Du Prez FE. Internal Catalysis in Covalent Adaptable Networks: Phthalate Monoester Transesterification As a Versatile Dynamic Cross-Linking Chemistry. J Am Chem Soc 2019; 141:15277-15287. [DOI: 10.1021/jacs.9b07269] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Maarten Delahaye
- Polymer Chemistry Research Group (PCR), Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
| | - Johan M. Winne
- Laboratory for Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Filip E. Du Prez
- Polymer Chemistry Research Group (PCR), Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4-bis, B-9000 Ghent, Belgium
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β-N-Acetylhexosaminidases-the wizards of glycosylation. Appl Microbiol Biotechnol 2019; 103:7869-7881. [PMID: 31401752 DOI: 10.1007/s00253-019-10065-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022]
Abstract
β-N-Acetylhexosaminidases (EC 3.2.1.52) are a unique family of glycoside hydrolases with dual substrate specificity and a particular reaction mechanism. Though hydrolytic enzymes per se, their good stability, easy recombinant production, absolute stereoselectivity, and a broad substrate specificity predestine these enzymes for challenging applications in carbohydrate synthesis. This mini-review aims to demonstrate the catalytic potential of β-N-acetylhexosaminidases in a range of unusual reactions, processing of unnatural substrates, formation of unexpected products, and demanding reaction designs. The use of unconventional media can considerably alter the progress of transglycosylation reactions. By means of site-directed mutagenesis, novel catalytic machineries can be constructed. Glycosylation of difficult substrates such as sugar nucleotides was accomplished, and the range of afforded glycosidic bonds comprises unique non-reducing sugars. Specific functional groups may be tolerated in the substrate molecule, which makes β-N-acetylhexosaminidases invaluable allies in difficult synthetic problems.
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15
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The Effects of Glucosamine and Chondroitin Sulfate on Gut Microbial Composition: A Systematic Review of Evidence from Animal and Human Studies. Nutrients 2019; 11:nu11020294. [PMID: 30704054 PMCID: PMC6412843 DOI: 10.3390/nu11020294] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Oral glucosamine sulfate (GS) and chondroitin sulfate (CS), while widely marketed as joint-protective supplements, have limited intestinal absorption and are predominantly utilized by gut microbiota. Hence the effects of these supplements on the gut microbiome are of great interest, and may clarify their mode of action, or explain heterogeneity in therapeutic responses. We conducted a systematic review of animal and human studies reporting the effects of GS or CS on gut microbial composition. We searched MEDLINE, EMBASE, and Scopus databases for journal articles in English from database inception until July 2018, using search terms microbiome, microflora, intestinal microbiota/flora, gut microbiota/flora and glucosamine or chondroitin. Eight original articles reported the effects of GS or CS on microbiome composition in adult humans (four articles) or animals (four articles). Studies varied significantly in design, supplementation protocols, and microbiome assessment methods. There was moderate-quality evidence for an association between CS exposure and increased abundance of genus Bacteroides in the murine and human gut, and low-quality evidence for an association between CS exposure and an increase in Desulfovibrio piger species, an increase in Bacteroidales S24-7 family, and a decrease in Lactobacillus. We discuss the possible metabolic implications of these changes for the host. For GS, evidence of effects on gut microbiome was limited to one low-quality study. This review highlights the importance of considering the potential influence of oral CS supplements on gut microbiota when evaluating their effects and safety for the host.
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Coines J, Alfonso‐Prieto M, Biarnés X, Planas A, Rovira C. Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited. Chemistry 2018; 24:19258-19265. [DOI: 10.1002/chem.201803905] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/29/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) and Institut de Química Teòrica i, Computacional (IQTCUB)Universitat de Barcelona, Martí i Franquès 1 08028 Barcelona Spain
| | - Mercedes Alfonso‐Prieto
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) and Institut de Química Teòrica i, Computacional (IQTCUB)Universitat de Barcelona, Martí i Franquès 1 08028 Barcelona Spain
- Current address: INM-9/IAS-5Forschungszentrum Jülich, 52425 Jülich (Germany) and C. and O. Vogt Institute for Brain Research, Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany
| | - Xevi Biarnés
- Laboratory of BiochemistryInstitut Químic de SarriàUniversitat Ramon Llull Via Augusta, 390 08017 Barcelona Spain
| | - Antoni Planas
- Laboratory of BiochemistryInstitut Químic de SarriàUniversitat Ramon Llull Via Augusta, 390 08017 Barcelona Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica, (secció de Química Orgànica) and Institut de Química Teòrica i, Computacional (IQTCUB)Universitat de Barcelona, Martí i Franquès 1 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 23 08010 Barcelona Spain
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Mechanism of the Escherichia coli MltE lytic transglycosylase, the cell-wall-penetrating enzyme for Type VI secretion system assembly. Sci Rep 2018. [PMID: 29515200 PMCID: PMC5841429 DOI: 10.1038/s41598-018-22527-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lytic transglycosylases (LTs) catalyze the non-hydrolytic cleavage of the bacterial cell wall by an intramolecular transacetalization reaction. This reaction is critically and broadly important in modifications of the bacterial cell wall in the course of its biosynthesis, recycling, manifestation of virulence, insertion of structural entities such as the flagellum and the pili, among others. The first QM/MM analysis of the mechanism of reaction of an LT, that for the Escherichia coli MltE, is undertaken. The study reveals a conformational itinerary consistent with an oxocarbenium-like transition state, characterized by a pivotal role for the active-site glutamic acid in proton transfer. Notably, an oxazolinium intermediate, as a potential intermediate, is absent. Rather, substrate-assisted catalysis is observed through a favorable dipole provided by the N-acetyl carbonyl group of MurNAc saccharide. This interaction stabilizes the incipient positive charge development in the transition state. This mechanism coincides with near-synchronous acetal cleavage and acetal formation.
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Slámová K, Bojarová P. Engineered N-acetylhexosamine-active enzymes in glycoscience. Biochim Biophys Acta Gen Subj 2017; 1861:2070-2087. [PMID: 28347843 DOI: 10.1016/j.bbagen.2017.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND In recent years, enzymes modifying N-acetylhexosamine substrates have emerged in numerous theoretical studies as well as practical applications from biology, biomedicine, and biotechnology. Advanced enzyme engineering techniques converted them into potent synthetic instruments affording a variety of valuable glycosides. SCOPE OF REVIEW This review presents the diversity of engineered enzymes active with N-acetylhexosamine carbohydrates: from popular glycoside hydrolases and glycosyltransferases to less known oxidases, epimerases, kinases, sulfotransferases, and acetylases. Though hydrolases in natura, engineered chitinases, β-N-acetylhexosaminidases, and endo-β-N-acetylglucosaminidases were successfully employed in the synthesis of defined natural and derivatized chitooligomers and in the remodeling of N-glycosylation patterns of therapeutic antibodies. The genes of various N-acetylhexosaminyltransferases were cloned into metabolically engineered microorganisms for producing human milk oligosaccharides, Lewis X structures, and human-like glycoproteins. Moreover, mutant N-acetylhexosamine-active glycosyltransferases were applied, e.g., in the construction of glycomimetics and complex glycostructures, industrial production of low-lactose milk, and metabolic labeling of glycans. In the synthesis of biotechnologically important compounds, several innovative glycoengineered systems are presented for an efficient bioproduction of GlcNAc, UDP-GlcNAc, N-acetylneuraminic acid, and of defined glycosaminoglycans. MAJOR CONCLUSIONS The above examples demonstrate that engineering of N-acetylhexosamine-active enzymes was able to solve complex issues such as synthesis of tailored human-like glycoproteins or industrial-scale production of desired oligosaccharides. Due to the specific catalytic mechanism, mutagenesis of these catalysts was often realized through rational solutions. GENERAL SIGNIFICANCE Specific N-acetylhexosamine glycosylation is crucial in biological, biomedical and biotechnological applications and a good understanding of its details opens new possibilities in this fast developing area of glycoscience.
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Affiliation(s)
- Kristýna Slámová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic.
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