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Koval'ová T, Kovaľ T, Stránský J, Kolenko P, Dušková J, Švecová L, Vodičková P, Spiwok V, Benešová E, Lipovová P, Dohnálek J. The first structure–function study of GH151 α‐
l
‐fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity. FEBS J 2022; 289:4998-5020. [DOI: 10.1111/febs.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/21/2021] [Accepted: 02/02/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Terézia Koval'ová
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Tomáš Kovaľ
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Jan Stránský
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Leona Švecová
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
| | - Patricie Vodičková
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Eva Benešová
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology University of Chemistry and Technology Prague Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules Institute of Biotechnology of the Czech Academy of Sciences Vestec Czech Republic
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2
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You J, Lin S, Jiang T. Origins and Evolution of the α-L-Fucosidases: From Bacteria to Metazoans. Front Microbiol 2019; 10:1756. [PMID: 31507539 PMCID: PMC6718869 DOI: 10.3389/fmicb.2019.01756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022] Open
Abstract
α-L-fucosidases (EC 3.2.1.51, FUC), belonging to the glycoside hydrolase family 29 (GH29), play important roles in several biological processes and are markers used for detecting hepatocellular carcinoma. In this study, a protein sequence similarity network (SSN) was generated and a subsequent evolutionary analysis was performed to understand the enzymes comprehensively. The SSN indicated that the proteins in the FUC family are mainly present in bacteria, fungi, metazoans, plants, as well as in archaea, but less abundantly. The sequences in bacteria were found to be more diverse than those in other taxonomic groups. The SSN and a phylogenetic tree both supported that the proteins in the FUC family can be classified into 3 subfamilies. FUCs in each subfamily are under the pressure of negative selection. The enzymes from metazoans, fungi, and plants separated into the three subfamilies and shared high similarity with the bacterial homologs. The multiple sequence alignment results indicated that the amino acid residues for binding α-L-fucosidase and catalysis are highly conserved in the 3 subfamilies; however, the evolutionary patterns were different, based on the coevolution analysis in the subfamily of metazoans and bacteria. Finally, gene duplication plays an important role for α-L-fucosidase evolution, not only in metazoans, but also in bacteria and fungi.
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Affiliation(s)
- Jia You
- Department of Hepatology, The Liver Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shujin Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Tao Jiang
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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3
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Kovalová T, Koval T, Benešová E, Vodicková P, Spiwok V, Lipovová P, Dohnálek J. Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Glycobiology 2019; 29:59-73. [PMID: 30544181 DOI: 10.1093/glycob/cwy078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022] Open
Abstract
α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crystal structure of this protein revealing a novel quaternary state within this family. The protein is in a unique hexameric assembly revealing the first observed case of active site complementation by a residue from an adjacent monomer in this family. Mutation of the complementing tryptophan residue caused changes in the catalytic properties including a shift of the pH optimum, a change of affinity to an artificial chromogenic substrate and a decreased reaction rate for a natural substrate. The wild-type enzyme was active on most of the tested naturally occurring oligosaccharides and capable of transglycosylation on a variety of acceptor molecules, including saccharides, alcohols or chromogenic substrates. Mutation of the complementing residue changed neither substrate specificity nor the preference for the type of transglycosylation acceptor molecule; however, the yields of the reactions were lower in both cases. Maltose molecules bound to the enzyme in the crystal structure identified surface carbohydrate-binding sites, possibly participating in binding of larger oligosaccharides.
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Affiliation(s)
- Terézia Kovalová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Koval
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic
| | - Eva Benešová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Patricie Vodicková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Vojtech Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic
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4
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Liu T, Liu R, Zhu L, Zou X, Guan H, Xu Z. Development of a UHPLC-MS method for inhibitor screening against α-L-1,3-fucosidase. Anal Bioanal Chem 2019; 411:1467-1477. [PMID: 30706074 DOI: 10.1007/s00216-019-01575-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/27/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
α-L-Fucosidase (AFU) is a promising therapeutic target for the treatment of inflammation, cancer, cystic fibrosis, and fucosidosis. Some of the existing analytical methods for the assessment of AFU activity are lacking in sensitivity and selectivity, since most of them are based on spectrofluorimetric methods. More recently, mass spectrometry (MS) has evolved as a key technology for enzyme assays and inhibitor screening as it enables accurate monitoring of the conversion of substrate to product in enzymatic reactions. In this study, UHPLC-MS has been utilized to develop a simple, sensitive, and accurate assay for enzyme kinetics and inhibition studies of AFU3, a member of the AFU family. A reported method for analyzing saccharide involving a porous graphitic carbon column, combined with reduction by NaBH4/CH3OH, was used to improve sensitivity. The conversion of saccharide into alditol could reach nearly 100% in the NaBH4 reduction reaction. In addition, the bioanalytical quantitative screening method was validated according to US-FDA guidance, including selectivity, linearity, precision, accuracy, stability, and matrix effect. The developed method displayed a good accuracy, high sensitivity (LOD = 0.05 mg L-1), and good reproducibility (RSD < 15%). The assay accurately measured an IC50 value of 0.40 μM for the known AFU inhibitor, deoxyfuconojirimycin, which was consistent with results reported in the literature. Further validation of the assay was achieved through the determination of a high Z'-factor value of 0.89. The assay was applied to screen a marine-derived chemical library against AFU3, which revealed two marine-oriented pyrimidine alkaloids as potential AFU3 inhibitors. Graphical abstract.
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Affiliation(s)
- Tangrong Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China.,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Ruonan Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China.,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Li Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China.,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Xuan Zou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China.,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China.,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.,Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, Shandong, China
| | - Zhe Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, Shandong, China. .,Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China. .,Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, Shandong, China.
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5
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Carmona AT, Carrión-Jiménez S, Pingitore V, Moreno-Clavijo E, Robina I, Moreno-Vargas AJ. Harnessing pyrrolidine iminosugars into dimeric structures for the rapid discovery of divalent glycosidase inhibitors. Eur J Med Chem 2018; 151:765-776. [PMID: 29674295 DOI: 10.1016/j.ejmech.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/12/2018] [Accepted: 04/03/2018] [Indexed: 11/29/2022]
Abstract
The synthesis of three libraries (1a-l, 1a'-l' and 2a-l) of dimeric iminosugars through CuAAC reaction between three different alkynyl pyrrolidines and a set of diazides was carried out. The resulting crude dimers were screened in situ against two α-fucosidases (libraries 1a-l and 1a'-l') and one β-galactosidase (2a-l). This method is pioneer in the search of divalent glycosidase inhibitors. It has allowed the rapid identification of dimer 1i as the best inhibitor of α-fucosidases from bovine kidney (Ki = 0.15 nM) and Homo sapiens (Ki = 60 nM), and dimer 2e as the best inhibitor of β-galactosidase from bovine liver (Ki = 5.8 μM). In order to evaluate a possible divalent effect in the inhibition, the synthesis and biological analysis of the reference monomers were also performed. Divalent effect was only detected in the inhibition of bovine liver β-galactosidase by dimer 2e.
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Affiliation(s)
- Ana T Carmona
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain
| | - Sebastián Carrión-Jiménez
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain
| | - Valeria Pingitore
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain
| | - Elena Moreno-Clavijo
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain
| | - Inmaculada Robina
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain
| | - Antonio J Moreno-Vargas
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, C/ Prof. García González, 1, 41012, Seville, Spain.
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6
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Martínez-Bailén M, Carmona AT, Moreno-Clavijo E, Robina I, Ide D, Kato A, Moreno-Vargas AJ. Tuning of β-glucosidase and α-galactosidase inhibition by generation and in situ screening of a library of pyrrolidine-triazole hybrid molecules. Eur J Med Chem 2017; 138:532-542. [DOI: 10.1016/j.ejmech.2017.06.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/17/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
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7
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Tsai TI, Li ST, Liu CP, Chen KY, Shivatare SS, Lin CW, Liao SF, Lin CW, Hsu TL, Wu YT, Tsai MH, Lai MY, Lin NH, Wu CY, Wong CH. An Effective Bacterial Fucosidase for Glycoprotein Remodeling. ACS Chem Biol 2017; 12:63-72. [PMID: 28103685 DOI: 10.1021/acschembio.6b00821] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fucose is an important component of many oligo- and polysaccharide structures as well as glycoproteins and glycolipids, which are often associated with a variety of physiological processes ranging from fertilization, embryogenesis, signal transduction, and disease progression, such as rheumatoid arthritis, inflammation, and cancer. The enzyme α-l-fucosidase is involved in the cleavage of the fucosidic bond in glycans and glycoconjugates, particularly the Fuc-α-1,2-Gal, Fuc-α-1,3/4-GlcNAc, and Fuc-α-1,6-GlcNAc linkages. Here, we report a highly efficient fucosidase, designated as BfFucH identified from a library of bacterial glycosidases expressed in E. coli from the CAZy database, which is capable of hydrolyzing the aforementioned fucosidic linkages, especially the α-1,6-linkage from the N-linked Fuc-α-1,6-GlcNAc residue on glycoproteins. Using BfFucH coupled with endoglycosidases and the emerging glycosynthases allows glycoengineering of IgG antibodies to provide homogeneous glycoforms with well-defined glycan structures and optimal effector functions.
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Affiliation(s)
- Tsung-I Tsai
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
- Institute
of Biotechnology, National Taiwan University, Taipei 106, Taiwan
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shiou-Ting Li
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Chiu-Ping Liu
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
- Institute
of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Karen Y. Chen
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sachin S. Shivatare
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Chin-Wei Lin
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Shih-Fen Liao
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Chih-Wei Lin
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Tsui-Ling Hsu
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Ying-Ta Wu
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | | | | | | | - Chung-Yi Wu
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
| | - Chi-Huey Wong
- Genomics
Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 115, Taiwan
- Institute
of Biotechnology, National Taiwan University, Taipei 106, Taiwan
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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8
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Yu C, Harrold DR, Claypool JT, Simmons BA, Singer SW, Simmons CW, VanderGheynst JS. Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Stütz AE, Wrodnigg TM. Carbohydrate-Processing Enzymes of the Lysosome: Diseases Caused by Misfolded Mutants and Sugar Mimetics as Correcting Pharmacological Chaperones. Adv Carbohydr Chem Biochem 2016; 73:225-302. [PMID: 27816107 DOI: 10.1016/bs.accb.2016.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysosomal storage diseases are hereditary disorders caused by mutations on genes encoding for one of the more than fifty lysosomal enzymes involved in the highly ordered degradation cascades of glycans, glycoconjugates, and other complex biomolecules in the lysosome. Several of these metabolic disorders are associated with the absence or the lack of activity of carbohydrate-processing enzymes in this cell compartment. In a recently introduced therapy concept, for susceptible mutants, small substrate-related molecules (so-called pharmacological chaperones), such as reversible inhibitors of these enzymes, may serve as templates for the correct folding and transport of the respective protein mutant, thus improving its concentration and, consequently, its enzymatic activity in the lysosome. Carbohydrate-processing enzymes in the lysosome, related lysosomal diseases, and the scope and limitations of reported reversible inhibitors as pharmacological chaperones are discussed with a view to possibly extending and improving research efforts in this area of orphan diseases.
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Affiliation(s)
- Arnold E Stütz
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Tanja M Wrodnigg
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
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10
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A second-generation ferrocene–iminosugar hybrid with improved fucosidase binding properties. Bioorg Med Chem Lett 2016; 26:1546-1549. [DOI: 10.1016/j.bmcl.2016.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 11/23/2022]
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11
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Hottin A, Carrión-Jiménez S, Moreno-Clavijo E, Moreno-Vargas AJ, Carmona AT, Robina I, Behr JB. Expanding the library of divalent fucosidase inhibitors with polyamino and triazole-benzyl bridged bispyrrolidines. Org Biomol Chem 2016; 14:3212-20. [DOI: 10.1039/c6ob00212a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A small library of divalent fucosidase inhibitors containing pyrrolidine motifs were prepared and evaluated as α-fucosidase inhibitors.
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Affiliation(s)
- Audrey Hottin
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- CNRS UMR 7312
- UFR des Sciences Exactes et Naturelles
- 51687 Reims Cedex 2
| | | | - Elena Moreno-Clavijo
- Departamento de Química Orgánica
- Facultad de Química
- Universidad de Sevilla
- Sevilla
- Spain
| | | | - Ana T. Carmona
- Departamento de Química Orgánica
- Facultad de Química
- Universidad de Sevilla
- Sevilla
- Spain
| | - Inmaculada Robina
- Departamento de Química Orgánica
- Facultad de Química
- Universidad de Sevilla
- Sevilla
- Spain
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims
- CNRS UMR 7312
- UFR des Sciences Exactes et Naturelles
- 51687 Reims Cedex 2
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12
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Hottin A, Wright DW, Davies GJ, Behr JB. Exploiting the Hydrophobic Terrain in Fucosidases with Aryl-Substituted Pyrrolidine Iminosugars. Chembiochem 2014; 16:277-83. [DOI: 10.1002/cbic.201402509] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 12/16/2022]
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13
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Jiménez DJ, Dini-Andreote F, van Elsas JD. Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:92. [PMID: 24955113 PMCID: PMC4064818 DOI: 10.1186/1754-6834-7-92] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/23/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. RESULTS In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions. CONCLUSION In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
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14
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Moreno-Clavijo E, Carmona AT, Moreno-Vargas AJ, Molina L, Wright DW, Davies GJ, Robina I. Exploring a Multivalent Approach to α-L-Fucosidase Inhibition. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300878] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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