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Li K, Barrett K, Agger JW, Zeuner B, Meyer AS. Bioinformatics-based identification of GH12 endoxyloglucanases in citrus-pathogenic Penicillium spp. Enzyme Microb Technol 2024; 178:110441. [PMID: 38574421 DOI: 10.1016/j.enzmictec.2024.110441] [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: 12/21/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Millions of tons of citrus peel waste are produced every year as a byproduct of the juice industry. Citrus peel is rich in pectin and xyloglucan, but while the pectin is extracted for use in the food industry, the xyloglucan is currently not valorized. To target hydrolytic degradation of citrus peel xyloglucan into oligosaccharides, we have used bioinformatics to identify three glycoside hydrolase 12 (GH12) endoxyloglucanases (EC 3.2.1.151) from the citrus fruit pathogens Penicillium italicum GL-Gan1 and Penicillium digitatum Pd1 and characterized them on xyloglucan obtained by alkaline extraction from citrus peel. The enzymes displayed pH-temperature optima of pH 4.6-5.3 and 35-37°C. PdGH12 from P. digitatum and PiGH12A from P. italicum share 84% sequence identity and displayed similar kinetics, although kcat was highest for PdGH12. In contrast, PiGH12B from P. italicum, which has the otherwise conserved Trp in subsite -4 replaced with a Tyr, displayed a 3 times higher KM and a 4 times lower kcat/KM than PiGH12A, but was the most thermostable enzyme of the three Penicillium-derived endoxyloglucanases. The benchmark enzyme AnGH12 from Aspergillus nidulans was more thermally stable and had a higher pH-temperature optimum than the enzymes from Penicillum spp. The difference in structure of the xyloglucan oligosaccharides extracted from citrus peel xyloglucan and tamarind xyloglucan by the new endoxyloglucanases was determined by LC-MS. The inclusion of citrus peel xyloglucan demonstrated that the endoxyloglucanases liberated fucosylated xyloglucan oligomers, implying that these enzymes have the potential to upgrade citrus peel residues to produce oligomers useful as intermediates or bioactive compounds.
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Affiliation(s)
- Kai Li
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Jane W Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark.
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
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Rønne ME, Dybdahl Andersen C, Teze D, Beenfeldt Petersen A, Fredslund F, Stender EGP, Kirk Chaberski E, Holck J, Aachmann FL, Welner DH, Svensson B. Action and cooperation in alginate degradation by three enzymes from the human gut bacterium Bacteroides eggerthii DSM 20697. J Biol Chem 2024:107596. [PMID: 39032652 DOI: 10.1016/j.jbc.2024.107596] [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: 03/15/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Alginate is a polysaccharide consumed by humans in edible seaweed and different foods where it is applied as a texturizing hydrocolloid or in encapsulations of drugs and probiotics. While gut bacteria are found to utilize and ferment alginate to health beneficial short chain fatty acids, knowledge on details of the molecular reactions is sparse. Alginates are composed of mannuronic acid (M) and its C-5 epimer guluronic acid (G). An alginate related polysaccharide utilization locus (PUL) has been identified in the gut bacterium Bacteroides eggerthii DSM 20697. The PUL encodes two polysaccharide lyases (PLs) from the PL6 (BePL6) and PL17 (BePL17) families as well as a KdgF-like metalloprotein (BeKdgF) known to catalyze ring-opening of 4,5-unsaturated monouronates yielding 4-deoxy-l-erythro-5-hexoseulose uronate (DEH). B. eggerthii DSM 20697 does not grow on alginate, but readily proliferates with a lag phase of a few hours in the presence of an endo-acting alginate lyase A1-I from the marine bacterium Sphingomonas sp. A1. The B. eggerthii lyases are both exo-acting and while BePL6 is strictly G-block specific, BePL17 prefers M-blocks. BeKdgF retained 10-27% activity in the presence of 0.1-1 mM EDTA. X-ray crystallography was used to investigate the three-dimensional structure of BeKdgF, based on which a catalytic mechanism was proposed to involve Asp102, acting as acid/base having pKa of 5.9 as determined by NMR pH titration. BePL6 and BePL17 cooperate in alginate degradation with BeKdgF linearizing produced 4,5-unsaturated monouronates. Their efficiency of alginate degradation was much enhanced by addition of the A1-I alginate lyase.
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Affiliation(s)
- Mette E Rønne
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark; Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Christian Dybdahl Andersen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - David Teze
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark; Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Agnes Beenfeldt Petersen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Folmer Fredslund
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Emil G P Stender
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Evan Kirk Chaberski
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jesper Holck
- Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Ditte Hededam Welner
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
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Shen J, Li J, Zhang Y, Mei X, Xue C, Chang Y. Characterization of an α-L-fucosidase in marine bacterium Wenyingzhuangia fucanilytica: new evidence on the catalytic sites of GH95 family glycosidases. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38932571 DOI: 10.1002/jsfa.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/08/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND α-l-Fucose confers unique functions for fucose-containing biomolecules such as human milk oligosaccharides. α-l-Fucosidases can serve as desirable tools in the application of fucosylated saccharides. Discovering novel α-l-fucosidases and elucidating their enzyme properties are always worthy tasks. RESULTS A GH95 family α-l-fucosidase named Afc95A_Wf was cloned from the genome of the marine bacterium Wenyingzhuangia fucanilytica and expressed in Escherichia coli. It exhibited maximum activity at 40 °C and pH 7.5. Afc95A_Wf defined a different substrate specificity among reported α-l-fucosidases, which was capable of hydrolyzing α-fucoside in CNP-fucose, Fucα1-2Galβ1-4Glc and Galβ1-4(Fucα1-3)Glc, and showed a preference for α1,2-fucosidic linkage. It adopted Asp residue in the amino acid sequence at position 391, which was distinct from the previously acknowledged residue of Asn. The predicted tertiary structure and site-directed mutagenesis revealed that Asp391 participates in the catalysis of Afc95A_Wf. The differences in the substrate specificity and catalytic site shed light on that Afc95A_Wf adopted a novel mechanism in catalysis. CONCLUSION A GH95 family α-l-fucosidase (Afc95A_Wf) was cloned and expressed. It showed a cleavage preference for α1,2-fucosidic linkage to α1,3-fucosidic linkage. Afc95A_Wf demonstrated a different substrate specificity and a residue at an important catalytic site compared with known GH95 family proteins, which revealed the occurrence of diversity on catalytic mechanisms in the GH95 family. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jiajing Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Ye Q, Gong X, Li A, Shao S, Ji B. A typical acidic extracellular polysaccharide alludes to algae-bacteria-collaboration in microalgal-bacterial symbiosis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172545. [PMID: 38636868 DOI: 10.1016/j.scitotenv.2024.172545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Microalgal-bacterial symbioses are prevalent in aquatic ecosystems and play a pivotal role in carbon sequestration, significantly contributing to global carbon cycling. The understanding of the contribution of exopolysaccharides (EPSs), a crucial carbon-based component, to the structural integrity of microalgal-bacterial symbioses remains insufficiently elucidated. To address this gap, our study aims to enhance our comprehension of the composition and primary structure of EPSs within a specific type of granular microalgal-bacterial symbiosis named microalgal-bacterial granular sludge (MBGS). Our investigation reveals that the acidic EPSs characteristic of this symbiosis have molecular weights ranging from several hundred thousand to over one million Daltons, including components like glucopyranose, galactopyranose, mannose, and rhamnose. Our elucidation of the backbone linkage of a representative exopolysaccharide revealed a →3)-β-D-Galp-(1→4)-β-D-Glcp-(1→ glycosidic linkage. This linear structure closely resembles bacterial xanthan, while the branched chain structure bears similarities to algal EPSs. Our findings highlight the collaborative synthesis of acidic EPSs by both microalgae and bacteria, emphasizing their joint contribution in the production of macromolecules within microalgal-bacterial symbiosis. This collaborative synthesis underscores the intricate molecular interactions contributing to the stability and function of these symbiotic relationships.
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Affiliation(s)
- Qinyi Ye
- Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xiping Gong
- Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Anjie Li
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Senlin Shao
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Bin Ji
- Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China.
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Liu N, Odinot E, David H, Vita N, Otalvaro FM, Parsiegla G, Denis Y, Faulds C, Fierobe HP, Perret S. Intracellular removal of acetyl, feruloyl and p-coumaroyl decorations on arabinoxylo-oligosaccharides imported from lignocellulosic biomass degradation by Ruminiclostridium cellulolyticum. Microb Cell Fact 2024; 23:151. [PMID: 38789996 PMCID: PMC11127375 DOI: 10.1186/s12934-024-02423-z] [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: 02/13/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Xylans are polysaccharides that are naturally abundant in agricultural by-products, such as cereal brans and straws. Microbial degradation of arabinoxylan is facilitated by extracellular esterases that remove acetyl, feruloyl, and p-coumaroyl decorations. The bacterium Ruminiclostridium cellulolyticum possesses the Xua (xylan utilization associated) system, which is responsible for importing and intracellularly degrading arabinoxylodextrins. This system includes an arabinoxylodextrins importer, four intracellular glycosyl hydrolases, and two intracellular esterases, XuaH and XuaJ which are encoded at the end of the gene cluster. RESULTS Genetic studies demonstrate that the genes xuaH and xuaJ are part of the xua operon, which covers xuaABCDD'EFGHIJ. This operon forms a functional unit regulated by the two-component system XuaSR. The esterases encoded at the end of the cluster have been further characterized: XuaJ is an acetyl esterase active on model substrates, while XuaH is a xylan feruloyl- and p-coumaryl-esterase. This latter is active on oligosaccharides derived from wheat bran and wheat straw. Modelling studies indicate that XuaH has the potential to interact with arabinoxylobiose acylated with mono- or diferulate. The intracellular esterases XuaH and XuaJ are believed to allow the cell to fully utilize the complex acylated arabinoxylo-dextrins imported into the cytoplasm during growth on wheat bran or straw. CONCLUSIONS This study reports for the first time that a cytosolic feruloyl esterase is part of an intracellular arabinoxylo-dextrin import and degradation system, completing its cytosolic enzymatic arsenal. This system represents a new pathway for processing highly-decorated arabinoxylo-dextrins, which could provide a competitive advantage to the cell and may have interesting biotechnological applications.
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Affiliation(s)
- Nian Liu
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Elise Odinot
- OléoInnov, 19 rue du Musée, Marseille, 13001, France
| | - Hélène David
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Felipe Mejia Otalvaro
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, Konges Lyngby, 2800, Denmark
| | - Goetz Parsiegla
- Aix-Marseille Université, CNRS, BIP-UMR7281, Marseille, France
| | - Yann Denis
- Aix-Marseille Université, CNRS, IMM, Marseille, France
| | - Craig Faulds
- Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, UMR1163, 13009, France
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Lidbury IDEA, Hitchcock A, Groenhof SRM, Connolly AN, Moushtaq L. New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria. Adv Microb Physiol 2024; 84:1-49. [PMID: 38821631 DOI: 10.1016/bs.ampbs.2023.12.003] [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] [Indexed: 06/02/2024]
Abstract
In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.
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Affiliation(s)
- Ian D E A Lidbury
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
| | - Andrew Hitchcock
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Plants, Photosynthesis, and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Sophie R M Groenhof
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Alex N Connolly
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Laila Moushtaq
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
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Pfeilmeier S, Werz A, Ote M, Bortfeld-Miller M, Kirner P, Keppler A, Hemmerle L, Gäbelein CG, Petti GC, Wolf S, Pestalozzi CM, Vorholt JA. Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens. Nat Microbiol 2024; 9:136-149. [PMID: 38172620 PMCID: PMC10769872 DOI: 10.1038/s41564-023-01555-z] [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: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
In healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.
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Affiliation(s)
- Sebastian Pfeilmeier
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Molecular Plant Pathology, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Anja Werz
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Marine Ote
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Pascal Kirner
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Lucas Hemmerle
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | | | - Sarah Wolf
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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Matsuzawa T, Nakamichi Y, Shimada N. Identification and Characterization of Novel Intracellular α-Xylosidase in Aspergillus oryzae. J Appl Glycosci (1999) 2023; 70:119-125. [PMID: 38239767 PMCID: PMC10792220 DOI: 10.5458/jag.jag.jag-2023_0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/03/2023] [Indexed: 01/22/2024] Open
Abstract
α-Xylosidase releases xylopyranosyl side chains from xyloglucan oligosaccharides and is vital for xyloglucan degradation. Previously, we identified and characterized two α-xylosidases, intracellular AxyA and extracellular AxyB, in Aspergillus oryzae. In this study, we identified a third α-xylosidase, termed AxyC, in A. oryzae. These three A. oryzae α-xylosidases belong to the glycoside hydrolase family 31, but there are clear differences in substrate specificity. Both AxyA and AxyB showed much higher hydrolytic activity toward isoprimeverose (α-D-xylopyranosyl-1,6-glucose) than p-nitrophenyl α-D-xylopyranoside. In contrast, the specific activity of AxyC toward the p-nitrophenyl substrate was approximately 950-fold higher than that toward isoprimeverose. Our study revealed that there are multiple α-xylosidases with different substrate specificities in A. oryzae.
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Affiliation(s)
- Tomohiko Matsuzawa
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University
| | - Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Naoki Shimada
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University
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10
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Bonfim IM, Paixão DA, Andrade MDO, Junior JM, Persinoti GF, de Giuseppe PO, Murakami MT. Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens. Microbiol Spectr 2023; 11:e0228023. [PMID: 37855631 PMCID: PMC10714752 DOI: 10.1128/spectrum.02280-23] [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: 06/04/2023] [Accepted: 09/05/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Pathogenic Xanthomonas bacteria can affect a variety of economically relevant crops causing losses in productivity, limiting commercialization and requiring phytosanitary measures. These plant pathogens exhibit high level of host and tissue specificity through multiple molecular strategies including several secretion systems, effector proteins, and a broad repertoire of carbohydrate-active enzymes (CAZymes). Many of these CAZymes act on the plant cell wall and storage carbohydrates, such as cellulose and starch, releasing products used as nutrients and modulators of transcriptional responses to support host colonization by mechanisms yet poorly understood. Here, we reveal that structural and storage β-glucans from the plant cell function as spatial markers, providing distinct chemical stimuli that modulate the transition between higher and lower motility states in Xanthomonas citri, a key virulence trait for many bacterial pathogens.
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Affiliation(s)
- Isabela Mendes Bonfim
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Molecular and Morphofunctional Biology, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Douglas Alvarez Paixão
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Joaquim Martins Junior
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
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Wilson LFL, Neun S, Yu L, Tryfona T, Stott K, Hollfelder F, Dupree P. The biosynthesis, degradation, and function of cell wall β-xylosylated xyloglucan mirrors that of arabinoxyloglucan. THE NEW PHYTOLOGIST 2023; 240:2353-2371. [PMID: 37823344 PMCID: PMC10952531 DOI: 10.1111/nph.19305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/02/2023] [Indexed: 10/13/2023]
Abstract
Xyloglucan is an abundant polysaccharide in many primary cell walls and in the human diet. Decoration of its α-xylosyl sidechains with further sugars is critical for plant growth, even though the sugars themselves vary considerably between species. Plants in the Ericales order - prevalent in human diets - exhibit β1,2-linked xylosyl decorations. The biosynthetic enzymes responsible for adding these xylosyl decorations, as well as the hydrolases that remove them in the human gut, are unidentified. GT47 xyloglucan glycosyltransferase candidates were expressed in Arabidopsis and endo-xyloglucanase products from transgenic wall material were analysed by electrophoresis, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. The activities of gut bacterial hydrolases BoGH43A and BoGH43B on synthetic glycosides and xyloglucan oligosaccharides were measured by colorimetry and electrophoresis. CcXBT1 is a xyloglucan β-xylosyltransferase from coffee that can modify Arabidopsis xyloglucan and restore the growth of galactosyltransferase mutants. Related VmXST1 is a weakly active xyloglucan α-arabinofuranosyltransferase from cranberry. BoGH43A hydrolyses both α-arabinofuranosylated and β-xylosylated oligosaccharides. CcXBT1's presence in coffee and BoGH43A's promiscuity suggest that β-xylosylated xyloglucan is not only more widespread than thought, but might also nourish beneficial gut bacteria. The evolutionary instability of transferase specificity and lack of hydrolase specificity hint that, to enzymes, xylosides and arabinofuranosides are closely resemblant.
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Affiliation(s)
- Louis F. L. Wilson
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Stefanie Neun
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Li Yu
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Theodora Tryfona
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Katherine Stott
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Florian Hollfelder
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
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Alexandrino AV, Prieto EL, Nicolela NCS, da Silva Marin TG, Dos Santos TA, de Oliveira da Silva JPM, da Cunha AF, Behlau F, Novo-Mansur MTM. Xylose Isomerase Depletion Enhances Virulence of Xanthomonas citri subsp. citri in Citrus aurantifolia. Int J Mol Sci 2023; 24:11491. [PMID: 37511250 PMCID: PMC10380989 DOI: 10.3390/ijms241411491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 07/30/2023] Open
Abstract
Citrus canker, caused by the bacterium Xanthomonas citri (Xcc), is one of the most devastating diseases for the citrus industry. Xylose is a constituent of the cell wall of plants, and the ability of Xcc to use this carbohydrate may play a role in virulence. Xcc has two genes codifying for xylose isomerase (XI), a bifunctional enzyme that interconverts D-xylose into D-xylulose and D-glucose into D-fructose. The aim of this work was to investigate the functional role of the two putative XI ORFs, XAC1776 (xylA1) and XAC4225 (xylA2), in Xcc pathogenicity. XI-coding genes of Xcc were deleted, and the single mutants (XccΔxylA1 or XccΔxylA2) or the double mutant (XccΔxylA1ΔxylA2) remained viable. The deletion of one or both XI genes (xylA1 and/or xylA2) increased the aggressiveness of the mutants, causing disease symptoms. RT-qPCR analysis of wild strain and xylA deletion mutants grown in vivo and in vitro revealed that the highest expression level of hrpX and xylR was observed in vivo for the double mutant. The results indicate that XI depletion increases the expression of the hrp regulatory genes in Xcc. We concluded that the intracellular accumulation of xylose enhances Xcc virulence.
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Affiliation(s)
- André Vessoni Alexandrino
- Laboratório de Bioquímica e Biologia Molecular Aplicada-LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Programa de Pós-Graduação em Biotecnologia-PPGBiotec, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | - Evandro Luis Prieto
- Laboratório de Bioquímica e Biologia Molecular Aplicada-LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular-PPGGEv, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | - Nicole Castro Silva Nicolela
- Laboratório de Bioquímica e Biologia Molecular Aplicada-LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | | | | | - João Pedro Maia de Oliveira da Silva
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular-PPGGEv, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Laboratório de Bioquímica e Genética Aplicada-LBGA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | - Anderson Ferreira da Cunha
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular-PPGGEv, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Laboratório de Bioquímica e Genética Aplicada-LBGA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | - Franklin Behlau
- Fundo de Defesa da Citricultura-Fundecitrus, Araraquara 14807-040, SP, Brazil
| | - Maria Teresa Marques Novo-Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada-LBBMA, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Programa de Pós-Graduação em Biotecnologia-PPGBiotec, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular-PPGGEv, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
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13
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Saburi W, Ota T, Kato K, Tagami T, Yamashita K, Yao M, Mori H. Function and Structure of Lacticaseibacillus casei GH35 β-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N-biose I and Galacto- N-biose. J Appl Glycosci (1999) 2023; 70:43-52. [PMID: 37599861 PMCID: PMC10432377 DOI: 10.5458/jag.jag.jag-2022_0014] [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: 12/02/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
β-Galactosidase (EC 3.2.1.23) hydrolyzes β-D-galactosidic linkages at the non-reducing end of substrates to produce β-D-galactose. Lacticaseibacillus casei is one of the most widely utilized probiotic species of lactobacilli. It possesses a putative β-galactosidase belonging to glycoside hydrolase family 35 (GH35). This enzyme is encoded by the gene included in the gene cluster for utilization of lacto-N-biose I (LNB; Galβ1-3GlcNAc) and galacto-N-biose (GNB; Galβ1-3GalNAc) via the phosphoenolpyruvate: sugar phosphotransferase system. The GH35 protein (GnbG) from L. casei BL23 is predicted to be 6-phospho-β-galactosidase (EC 3.2.1.85). However, its 6-phospho-β-galactosidase activity has not yet been examined, whereas its hydrolytic activity against LNB and GNB has been demonstrated. In this study, L. casei JCM1134 LBCZ_0230, homologous to GnbG, was characterized enzymatically and structurally. A recombinant LBCZ_0230, produced in Escherichia coli, exhibited high hydrolytic activity toward o-nitrophenyl β-D-galactopyranoside, p-nitrophenyl β-D-galactopyranoside, LNB, and GNB, but not toward o-nitrophenyl 6-phospho-β-D-galactopyranoside. Crystal structure analysis indicates that the structure of subsite -1 of LBCZ_0230 is very similar to that of Streptococcus pneumoniae β-galactosidase BgaC and not suitable for binding to 6-phospho-β-D-galactopyranoside. These biochemical and structural analyses indicate that LBCZ_0230 is a β-galactosidase. According to the prediction of LNB's binding mode, aromatic residues, Trp190, Trp240, Trp243, Phe244, and Tyr458, form hydrophobic interactions with N-acetyl-D-glucosamine residue of LNB at subsite +1.
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Affiliation(s)
- Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University
| | - Tomoya Ota
- Research Faculty of Agriculture, Hokkaido University
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University
| | | | | | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University
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14
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Anso I, Naegeli A, Cifuente JO, Orrantia A, Andersson E, Zenarruzabeitia O, Moraleda-Montoya A, García-Alija M, Corzana F, Del Orbe RA, Borrego F, Trastoy B, Sjögren J, Guerin ME. Turning universal O into rare Bombay type blood. Nat Commun 2023; 14:1765. [PMID: 36997505 PMCID: PMC10063614 DOI: 10.1038/s41467-023-37324-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
AbstractRed blood cell antigens play critical roles in blood transfusion since donor incompatibilities can be lethal. Recipients with the rare total deficiency in H antigen, the Oh Bombay phenotype, can only be transfused with group Oh blood to avoid serious transfusion reactions. We discover FucOB from the mucin-degrading bacteria Akkermansia muciniphila as an α-1,2-fucosidase able to hydrolyze Type I, Type II, Type III and Type V H antigens to obtain the afucosylated Bombay phenotype in vitro. X-ray crystal structures of FucOB show a three-domain architecture, including a GH95 glycoside hydrolase. The structural data together with site-directed mutagenesis, enzymatic activity and computational methods provide molecular insights into substrate specificity and catalysis. Furthermore, using agglutination tests and flow cytometry-based techniques, we demonstrate the ability of FucOB to convert universal O type into rare Bombay type blood, providing exciting possibilities to facilitate transfusion in recipients/patients with Bombay phenotype.
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15
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Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota. Essays Biochem 2023; 67:443-454. [PMID: 36912209 PMCID: PMC10154613 DOI: 10.1042/ebc20220161] [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: 12/09/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid-base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.
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16
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The Glycoside Hydrolase Family 35 β-galactosidase from Trichoderma reesei debranches xyloglucan oligosaccharides from tamarind and jatobá. Biochimie 2023; 211:16-24. [PMID: 36828153 DOI: 10.1016/j.biochi.2023.02.009] [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: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Trichoderma reesei (anamorph Hypocrea jecorina) produces an extracellular beta-galactosidase from Glycoside Hydrolase Family 35 (TrBga1). Hydrolysis of xyloglucan oligosaccharides (XGOs) by TrBga1 has been studied by hydrolysis profile analysis of both tamarind (Tamarindus indica) and jatobá (Hymenaea courbaril) seed storage xyloglucans using PACE and MALDI-ToF-MS for separation, quantification and identification of the hydrolysis products. The TrBga1 substrate preference for galactosylated oligosaccharides from both the XXXG- and XXXXG-series of jatobá xyloglucan showed that the doubly galactosylated oligosaccharides were the first to be hydrolyzed. Furthermore, the TrBga1 showed more efficient hydrolysis against non-reducing end dexylosylated oligosaccharides (GLXG/GXLG and GLLG). This preference may play a key role in xyloglucan degradation, since galactosyl removal alleviates steric hindrance for other enzymes in the xyloglucanolytic complex resulting in complete xyloglucan mobilization. Indeed, mixtures of TrBga1 with the α-xylosidase from Escherichia coli (YicI), which shows a preference towards non-galactosylated xyloglucan oligosaccharides, reveals efficient depolymerization when either enzyme is applied first. This understanding of the synergistic depolymerization contributes to the knowledge of plant cell wall structure, and reveals possible evolutionary mechanisms directing the preferences of debranching enzymes acting on xyloglucan oligosaccharides.
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17
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Structure and function of microbial α-l-fucosidases: a mini review. Essays Biochem 2023; 67:399-414. [PMID: 36805644 PMCID: PMC10154630 DOI: 10.1042/ebc20220158] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.
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Du JJ, Sastre D, Trastoy B, Roberts B, Deredge D, Klontz EH, Flowers MW, Sultana N, Guerin ME, Sundberg EJ. Mass Spectrometry-Based Methods to Determine the Substrate Specificities and Kinetics of N-Linked Glycan Hydrolysis by Endo-β-N-Acetylglucosaminidases. Methods Mol Biol 2023; 2674:147-167. [PMID: 37258966 PMCID: PMC10988651 DOI: 10.1007/978-1-0716-3243-7_10] [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] [Indexed: 06/02/2023]
Abstract
Glycosylation is a common posttranslational modification of proteins and refers to the covalent addition of glycans, chains of polysaccharides, onto proteins producing glycoproteins. The glycans influence the structure, function, and stability of proteins. They also play an integral role in the immune system, and aberrantly glycosylated proteins have wide ranging effects, including leading to diseases such as autoimmune conditions and cancer. Carbohydrate-active enzymes (CAZymes) are produced in bacteria, fungi, and humans and are enzymes which modify glycans via the addition or subtraction of individual or multiple saccharides from glycans. One of the hurdles in studying these enzymes is determining the types of substrates each enzyme is specific for and the kinetics of enzymatic activity. In this chapter, we discuss methods which are currently used to study the substrate specificity and kinetics of CAZymes and introduce a novel mass spectrometry-based technique which enables the specificity and kinetics of CAZymes to be determined accurately and efficiently.
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Affiliation(s)
- Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
| | - Diego Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Blaine Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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Bligh M, Nguyen N, Buck-Wiese H, Vidal-Melgosa S, Hehemann JH. Structures and functions of algal glycans shape their capacity to sequester carbon in the ocean. Curr Opin Chem Biol 2022; 71:102204. [PMID: 36155346 DOI: 10.1016/j.cbpa.2022.102204] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023]
Abstract
Algae synthesise structurally complex glycans to build a protective barrier, the extracellular matrix. One function of matrix glycans is to slow down microorganisms that try to enzymatically enter living algae and degrade and convert their organic carbon back to carbon dioxide. We propose that matrix glycans lock up carbon in the ocean by controlling degradation of organic carbon by bacteria and other microbes not only while algae are alive, but also after death. Data revised in this review shows accumulation of algal glycans in the ocean underscoring the challenge bacteria and other microbes face to breach the glycan barrier with carbohydrate active enzymes. Briefly we also update on methods required to certify the uncertain magnitude and unknown molecular causes of glycan-controlled carbon sequestration in a changing ocean.
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Affiliation(s)
- Margot Bligh
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Nguyen Nguyen
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Hagen Buck-Wiese
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany.
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20
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Liu N, Gagnot S, Denis Y, Byrne D, Faulds C, Fierobe HP, Perret S. Selfish uptake versus extracellular arabinoxylan degradation in the primary degrader Ruminiclostridium cellulolyticum, a new string to its bow. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:127. [PMID: 36403068 PMCID: PMC9675976 DOI: 10.1186/s13068-022-02225-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Primary degraders of polysaccharides play a key role in anaerobic biotopes, where plant cell wall accumulates, providing extracellular enzymes to release fermentable carbohydrates to fuel themselves and other non-degrader species. Ruminiclostridium cellulolyticum is a model primary degrader growing amongst others on arabinoxylan. It produces large multi-enzymatic complexes called cellulosomes, which efficiently deconstruct arabinoxylan into fermentable monosaccharides. RESULTS Complete extracellular arabinoxylan degradation was long thought to be required to fuel the bacterium during this plant cell wall deconstruction stage. We discovered and characterized a second system of "arabinoxylan" degradation in R. cellulolyticum, which challenged this paradigm. This "selfish" system is composed of an ABC transporter dedicated to the import of large and possibly acetylated arabinoxylodextrins, and a set of four glycoside hydrolases and two esterases. These enzymes show complementary action modes on arabinoxylo-dextrins. Two α-L-arabinofuranosidases target the diverse arabinosyl side chains, and two exo-xylanases target the xylo-oligosaccharides backbone either at the reducing or the non-reducing end. Together, with the help of two different esterases removing acetyl decorations, they achieve the depolymerization of arabinoxylo-dextrins in arabinose, xylose and xylobiose. The in vivo study showed that this new system is strongly beneficial for the fitness of the bacterium when grown on arabinoxylan, leading to the conclusion that a part of arabinoxylan degradation is achieved in the cytosol, even if monosaccharides are efficiently provided by the cellulosomes in the extracellular space. These results shed new light on the strategies used by anaerobic primary degrader bacteria to metabolize highly decorated arabinoxylan in competitive environments. CONCLUSION The primary degrader model Ruminiclostridium cellulolyticum has developed a "selfish" strategy consisting of importing into the bacterium, large arabinoxylan-dextrin fractions released from a partial extracellular deconstruction of arabinoxylan, thus complementing its efficient extracellular arabinoxylan degradation system. Genetic studies suggest that this system is important to support fitness and survival in a competitive biotope. These results provide a better understanding of arabinoxylan catabolism in the primary degrader, with biotechnological application for synthetic microbial community engineering for the production of commodity chemicals from lignocellulosic biomass.
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Affiliation(s)
- Nian Liu
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Séverine Gagnot
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Yann Denis
- Aix Marseille Univ, CNRS, IMM, Marseille, France
| | | | - Craig Faulds
- INRAE, Aix Marseille Univ, INRAE, BBF, Marseille, France, 13009, Marseille, France
| | - Henri-Pierre Fierobe
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Stéphanie Perret
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France.
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21
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Martins MP, Morais MAB, Persinoti GF, Galinari RH, Yu L, Yoshimi Y, Passos Nunes FB, Lima TB, Barbieri SF, Silveira JLM, Lombard V, Terrapon N, Dupree P, Henrissat B, Murakami MT. Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:1358-1372. [DOI: 10.1107/s2059798322009561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-β-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-β-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing β6–α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the −1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.
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22
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Utilization of industrial citrus pectin side streams for enzymatic production of human milk oligosaccharides. Carbohydr Res 2022; 519:108627. [DOI: 10.1016/j.carres.2022.108627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022]
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23
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Sanya DRA, Syed-Ab-Rahman SF, Jia A, Onésime D, Kim KM, Ahohuendo BC, Rohr JR. A review of approaches to control bacterial leaf blight in rice. World J Microbiol Biotechnol 2022; 38:113. [PMID: 35578069 DOI: 10.1007/s11274-022-03298-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 01/16/2023]
Abstract
The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
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Affiliation(s)
| | | | - Aiqun Jia
- School of Environmental & Biological Engineering, Nanjing University of Science and Technology, Xiaolingwei No. 200, Xuanwu District, 210014, Nanjing, Jiangsu, China
| | - Djamila Onésime
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kyung-Min Kim
- School of Applied BioSciences, College of Agriculture & Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-Gu, 41566, Daegu, Korea
| | - Bonaventure Cohovi Ahohuendo
- Faculty of Agricultural Sciences, University of Abomey-Calavi, 526 Recette Principale, Cotonou 01, 01 BP, Abomey-Calavi, Benin
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Eck Institute of Global Health, Environmental Change Initiative, 178 Galvin Life Science Center, 46556, Notre Dame, IN, USA
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24
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Selective xyloglucan oligosaccharide hydrolysis by a GH31 α-xylosidase from Escherichia coli. Carbohydr Polym 2022; 284:119150. [DOI: 10.1016/j.carbpol.2022.119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022]
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25
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Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Front Microbiol 2022; 13:840308. [PMID: 35495725 PMCID: PMC9048695 DOI: 10.3389/fmicb.2022.840308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
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Affiliation(s)
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
- *Correspondence: Neha Potnis,
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26
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Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines. Microorganisms 2021; 9:microorganisms9102065. [PMID: 34683386 PMCID: PMC8538872 DOI: 10.3390/microorganisms9102065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas citri pv. glycines is a major pathogen of soybean in Korea. Here, we analyzed pathogenicity genes based on a comparative genome analysis of five Korean strains and one strain from the United States, 8ra. Whereas all six strains had nearly identical profiles of carbohydrate-active enzymes, they varied in diversity and number of candidate type III secretion system effector (T3SE) genes. The five Korean strains were similar in their effectors, but differed from the 8ra strain. Across the six strains, transcription activator-like effectors (TALEs) showed diverse repeat sizes and at least six forms of the repeat variable di-residue (RVD) sequences, with differences not correlated with the origin of the strains. However, a phylogenetic tree based on the alignment of RVD sequences showed two distinct clusters with 17.5 repeats, suggesting that two distinct 17.5 RVD clusters have evolved, potentially to adapt Xcg to growth on distinct soybean cultivars. The predicted effector binding elements of the TALEs fell into six groups and were strongly overlapping in sequence, suggesting evolving target specificity of the binding domains in soybean cultivars. Our findings reveal the variability and adaptability of T3SEs in the Xcg strains and enhance our understanding of Xcg pathogenicity in soybean.
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27
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Zhang W, Qin W, Li H, Wu AM. Biosynthesis and Transport of Nucleotide Sugars for Plant Hemicellulose. FRONTIERS IN PLANT SCIENCE 2021; 12:723128. [PMID: 34868108 PMCID: PMC8636097 DOI: 10.3389/fpls.2021.723128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/22/2021] [Indexed: 05/13/2023]
Abstract
Hemicellulose is entangled with cellulose through hydrogen bonds and meanwhile acts as a bridge for the deposition of lignin monomer in the secondary wall. Therefore, hemicellulose plays a vital role in the utilization of cell wall biomass. Many advances in hemicellulose research have recently been made, and a large number of genes and their functions have been identified and verified. However, due to the diversity and complexity of hemicellulose, the biosynthesis and regulatory mechanisms are yet unknown. In this review, we summarized the types of plant hemicellulose, hemicellulose-specific nucleotide sugar substrates, key transporters, and biosynthesis pathways. This review will contribute to a better understanding of substrate-level regulation of hemicellulose synthesis.
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Affiliation(s)
- Wenjuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Wenqi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
| | - Ai-min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Ai-min Wu,
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