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Bains RK, Nasseri SA, Wardman JF, Withers SG. Advances in the understanding and exploitation of carbohydrate-active enzymes. Curr Opin Chem Biol 2024; 80:102457. [PMID: 38657391 DOI: 10.1016/j.cbpa.2024.102457] [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: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada.
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2
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Fujita K, Tsunomachi H, Lixia P, Maruyama S, Miyake M, Dakeshita A, Kitahara K, Tanaka K, Ito Y, Ishiwata A, Fushinobu S. Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans. Appl Microbiol Biotechnol 2024; 108:199. [PMID: 38324037 PMCID: PMC10850190 DOI: 10.1007/s00253-024-13014-8] [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: 11/16/2023] [Revised: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024]
Abstract
L-Arabinofuranosides with β-linkages are present in several plant molecules, such as arabinogalactan proteins (AGPs), extensin, arabinan, and rhamnogalacturonan-II. We previously characterized a β-L-arabinofuranosidase from Bifidobacterium longum subsp. longum JCM 1217, Bll1HypBA1, which was found to belong to the glycoside hydrolase (GH) family 127. This strain encodes two GH127 genes and two GH146 genes. In the present study, we characterized a GH146 β-L-arabinofuranosidase, Bll3HypBA1 (BLLJ_1848), which was found to constitute a gene cluster with AGP-degrading enzymes. This recombinant enzyme degraded AGPs and arabinan, which contain Araf-β1,3-Araf structures. In addition, the recombinant enzyme hydrolyzed oligosaccharides containing Araf-β1,3-Araf structures but not those containing Araf-β1,2-Araf and Araf-β1,5-Araf structures. The crystal structures of Bll3HypBA1 were determined at resolutions up to 1.7 Å. The monomeric structure of Bll3HypBA1 comprised a catalytic (α/α)6 barrel and two β-sandwich domains. A hairpin structure with two β-strands was observed in Bll3HypBA1, to extend from a β-sandwich domain and partially cover the active site. The active site contains a Zn2+ ion coordinated by Cys3-Glu and exhibits structural conservation of the GH127 cysteine glycosidase Bll1HypBA1. This is the first study to report on a β1,3-specific β-L-arabinofuranosidase. KEY POINTS: • β1,3-l-Arabinofuranose residues are present in arabinogalactan proteins and arabinans as a terminal sugar. • β-l-Arabinofuranosidases are widely present in intestinal bacteria. • Bll3HypBA1 is the first enzyme characterized as a β1,3-linkage-specific β-l-arabinofuranosidase.
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Affiliation(s)
- Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Pan Lixia
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
- National Key Laboratory of Non-food Biomass Energy Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Masayuki Miyake
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Aimi Dakeshita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-Cho, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
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Borlandelli V, Offen W, Moroz O, Nin-Hill A, McGregor N, Binkhorst L, Ishiwata A, Armstrong Z, Artola M, Rovira C, Davies GJ, Overkleeft HS. β-l- Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases. ACS Chem Biol 2023; 18:2564-2573. [PMID: 38051515 PMCID: PMC10728902 DOI: 10.1021/acschembio.3c00558] [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: 09/11/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023]
Abstract
GH127 and GH146 microorganismal retaining β-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by β-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of β-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The β-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label β-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified β-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance β-l-arabinofuranosidases in complex biological samples.
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Affiliation(s)
- Valentina Borlandelli
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Wendy Offen
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Olga Moroz
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Alba Nin-Hill
- 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
| | - Nicholas McGregor
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Lars Binkhorst
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Akihiro Ishiwata
- RIKEN
Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Zachary Armstrong
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marta Artola
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - 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
| | - Gideon J. Davies
- Department
of Chemistry, York Structural Biology Laboratory, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Herman S. Overkleeft
- Bio-organic
Synthesis, Leiden Institute of Chemistry (LIC), Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333
CC Leiden, The Netherlands
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Ishiwata A, Tsunomachi H, Kameyama K, Sophon K, Nakamura M, Kitahara K, Tanaka K, Ito Y, Fujita K. Bifidobacterial GH146 β-l-Arabinofuranosidase (Bll4HypBA1) as the Last Enzyme for the Complete Removal of Oligoarabinofuranosides from Hydroxyproline-Rich Glycoproteins. Chembiochem 2023; 24:e202200637. [PMID: 36579407 DOI: 10.1002/cbic.202200637] [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: 11/07/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
In plant cell walls, the hydroxyproline-rich glycoproteins (HRGPs) such as extensin contain oligoarabinofuranoside linked to a hydroxyproline (Hyp) residue. The mature arabinooligosaccharide was revealed to be a tetrasaccharide (α-l-Araf-(1→3)-β-l-Araf-(1→2)-β-l-Araf-(1→2)-β-l-Araf, l-Araf4 ), whose linkages are targets of the bifidobacterial and Xanthomonas arabinooligosaccharide-degrading enzymes. The l-Araf4 motif was cleaved by GH43 α-l-arabinofuranosidase (Arafase) and converted to an l-Araf3 -linked structure. The latter is then cleaved by GH121 β-l-arabinobiosidase (HypBA2), producing β-l-Araf-(1→2)-l-Ara (β-l-arabinobiose) and mono-β-l-Araf linked to the HRGP backbone. In bifidobacteria, the β-l-arabinobiose is then hydrolyzed by GH127 β-l-Arafase (Bll1HypBA1), a mechanistically unique cysteine glycosidase. We recently identified the distantly related homologue from Xanthomonas euvesicatoria as GH146 β-l-Arafase along with paralogues from Bifidobacterium longum, one of which, Bll4HypBA1 (BLLJ_0089), can degrade l-Araf1 -Hyp in a similar way to that of GH146. As the chemical synthesis of the extensin hydrophilic motif 1 a, which possesses three distinct linkages that connect four oligoAraf residues [Hyp(l-Arafn ) (n=4, 3, 1)], was achieved previously, we precisely monitored the step-wise enzymatic cleavage of 1 a in addition to that of potato lectin. The results unequivocally revealed that this enzyme specifically degrades the Hyp(l-Araf1 ) motif.
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kyohei Kameyama
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kaeothip Sophon
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masayuki Nakamura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
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Ishiwata A, Narita S, Kimura K, Tanaka K, Fujita K, Fushinobu S, Ito Y. Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides. Bioorg Med Chem 2022; 75:117054. [PMID: 36334492 DOI: 10.1016/j.bmc.2022.117054] [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: 08/18/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022]
Abstract
To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.
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Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan.
| | - Satoru Narita
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Department of Chemical Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8647, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8647, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
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Synthesis of naturally occurring β-l-arabinofuranosyl-l-arabinofuranoside structures towards the substrate specificity evaluation of β-l-arabinofuranosidase. Bioorg Med Chem 2022; 68:116849. [PMID: 35653870 DOI: 10.1016/j.bmc.2022.116849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/23/2022]
Abstract
Methyl β-l-arabinofuranosyl-(1 → 2)-, -(1 → 3)-, and -(1 → 5)-α-l-arabinofuranosides have been stereoselectively synthesized through 2-naphthylmethyl ether-mediated intramolecular aglycon delivery (NAP-IAD), whose β-linkages were confirmed by NMR analysis on the 3JH1-H2 coupling constant and 13C chemical shift of C1. The NAP-IAD approach was simply extended for the synthesis of trisaccharide motifs possessing β-l-arabinofuranosyl-(1 → 5)-l-arabinofuranosyl non-reducing terminal structure with the branched β-l-arabinofuranosyl-(1 → 5)-[α-l-arabinofuranosyl-(1 → 3)]-α-l-arabinofuranosyl and the liner β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl structures in olive arabinan and dinoflagellate polyethers, respectively. The results on the substrate specificity of a bifidobacterial β-l-arabinofuranosidase HypBA1 using the regioisomers indicated that HypBA1 could hydrolyze all three linkages however behaved clearly less active to β-(1 → 5)-linked disaccharide than other two regioisomers including the proposed natural degradation product, β-(1 → 2)-linked one from plant extracellular matrix such as extensin. On the other hand, Xanthomonas XeHypBA1 was found to hydrolyze all three disaccharides as the substrate with higher specificity to β-(1 → 2)-linkage than bifidobacterial HypBA1.
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