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Zawaira A, Shibayama Y. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2012; 13:185-200. [PMID: 22956349 DOI: 10.1007/s10969-012-9141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/08/2012] [Indexed: 06/01/2023]
Abstract
The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.
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Affiliation(s)
- Alexander Zawaira
- Gene Expression and Biophysics Group, Synthetic Biology, ERA, CSIR Biosciences, Brummeria, Pretoria, South Africa.
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52
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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53
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Arab-Jaziri F, Bissaro B, Barbe S, Saurel O, Débat H, Dumon C, Gervais V, Milon A, André I, Fauré R, O’Donohue MJ. Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l
-arabinofuranosidase from Thermobacillus xylanilyticus. FEBS J 2012; 279:3598-3611. [DOI: 10.1111/j.1742-4658.2012.08720.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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54
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Chlubnova I, Legentil L, Dureau R, Pennec A, Almendros M, Daniellou R, Nugier-Chauvin C, Ferrières V. Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis. Carbohydr Res 2012; 356:44-61. [PMID: 22554502 DOI: 10.1016/j.carres.2012.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.
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Affiliation(s)
- Ilona Chlubnova
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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55
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Kim YS, Lim YR, Oh DK. l-Arabinose production from sugar beet arabinan by immobilized endo- and exo-arabinanases from Caldicellulosiruptor saccharolyticus in a packed-bed reactor. J Biosci Bioeng 2012; 113:239-41. [DOI: 10.1016/j.jbiosc.2011.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/01/2022]
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56
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Amore A, Amoresano A, Birolo L, Henrissat B, Leo G, Palmese A, Faraco V. A family GH51 α-L-arabinofuranosidase from Pleurotus ostreatus: identification, recombinant expression and characterization. Appl Microbiol Biotechnol 2011; 94:995-1006. [PMID: 22080345 DOI: 10.1007/s00253-011-3678-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/29/2011] [Accepted: 10/27/2011] [Indexed: 11/26/2022]
Abstract
An α-L-arabinofuranosidase produced by Pleurotus ostreatus (PoAbf) during solid state fermentation on tomato pomace was identified and the corresponding gene and cDNA were cloned and sequenced. Molecular analysis showed that the poabf gene carries 26 exons interrupted by 25 introns and has an open reading frame encoding a protein of 646 amino acid residues, including a signal peptide of 20 amino acid residues. The amino acid sequence similar to the other α-L-arabinofuranosidases indicated that the enzyme encoded by poabf can be classified as a family 51 glycoside hydrolase. Heterologous recombinant expression of PoAbf was carried out in the yeasts Pichia pastoris and Kluyveromyces lactis achieving the highest production level of the secreted enzyme (180 mg L(-1)) in the former host. rPoAbf produced in P. pastoris was purified and characterized. It is a glycosylated monomer with a molecular weight of 81,500 Da in denaturing conditions. Mass spectral analyses led to the localization of a single O-glycosylation site at the level of Ser160. The enzyme is highly specific for α-L-arabinofuranosyl linkages and when assayed with p-nitrophenyl α-L-arabinofuranoside it follows Michaelis-Menten kinetics with a K (M) of 0.64 mM and a k (cat) of 3,010 min(-1). The optimum pH is 5 and the optimal temperature 40°C. It is worth noting that the enzyme shows a very high stability in a broad range of pH. The more durable activity showed by rPoAbf in comparison to the other α-L-arabinofuranosidases enhances its potential for biotechnological applications and increases interest in elucidating the molecular bases of its peculiar properties.
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Affiliation(s)
- Antonella Amore
- Department of Organic Chemistry and Biochemistry, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia 4, Naples, Italy
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57
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Lee JH, Hyun YJ, Kim DH. Cloning and characterization of α-L-arabinofuranosidase and bifunctional α-L-arabinopyranosidase/β-D-galactopyranosidase from Bifidobacterium longum H-1. J Appl Microbiol 2011; 111:1097-107. [PMID: 21851513 DOI: 10.1111/j.1365-2672.2011.05128.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS This study focused on the cloning, expression and characterization of recombinant α-l-arabinosidases from Bifidobacterium longum H-1. METHODS AND RESULTS α-l-Arabinofuranosidase (AfuB-H1) and bifunctional α-l-arabinopyranosidase/β-d-galactosidase (Apy-H1) from B. longum H-1 were identified by Southern blotting, and their recombinant enzymes were overexpressed in Escherichia coli BL21 (DE3). Recombinant AfuB-H1 (rAfuB-H1) was purified by single-step Ni(2+) -affinity column chromatography, whereas recombinant Apy-H1 (rApy-H1) was purified by serial Q-HP and Ni(2+) -affinity column chromatography. Enzymatic properties and substrate specificities of the two enzymes were assessed, and their kinetic constants were calculated. According to the results, rAfuB-H1 hydrolysed p-nitrophenyl-α-l-arabinofuranoside (pNP-αL-Af) and ginsenoside Rc, but did not hydrolyse p-nitrophenyl-α-l-arabinopyranoside (pNP-αL-Ap). On the other hand, rApy-H1 hydrolysed pNP-αL-Ap, p-nitrophenyl-β-d-galactopyranoside (pNP-βD-Ga) and ginsenoside Rb2. CONCLUSIONS Ginsenoside-metabolizing bifidobacterial rAfuB-H1 and rApy-H1 were successfully cloned, expressed, and characterized. rAfuB-H1 specifically recognized the α-l-arabinofuranoside, whereas rApy-H1 had dual functions, that is, it could hydrolyse both β-d-galactopyranoside and α-l-arabinopyranoside. SIGNIFICANCE AND IMPACT OF THE STUDY These findings suggest that the biochemical properties and substrate specificities of these recombinant enzymes differ from those of previously identified α-l-arabinosidases from Bifidobacterium breve K-110 and Clostridium cellulovorans.
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Affiliation(s)
- J H Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Korea
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58
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Souza TACB, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MT. Structure of a novel thermostable GH51 α-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Protein Sci 2011; 20:1632-7. [PMID: 21796714 PMCID: PMC3190157 DOI: 10.1002/pro.693] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/01/2011] [Indexed: 11/09/2022]
Abstract
α-L-arabinofuranosidases (EC 3.2.1.55) participate in the degradation of a variety of L-arabinose-containing polysaccharides and interact synergistically with other hemicellulases in the production of oligosaccharides and bioconversion of lignocellulosic biomass into biofuels. In this work, the structure of a novel thermostable family 51 (GH51) α-L-arabinofuranosidase from Thermotoga petrophila RKU-1 (TpAraF) was determined at 3.1 Å resolution. The TpAraF tertiary structure consists of an (α/β)-barrel catalytic core associated with a C-terminal β-sandwich domain, which is stabilized by hydrophobic contacts. In contrast to other structurally characterized GH51 AraFs, the accessory domain of TpAraF is intimately linked to the active site by a long β-hairpin motif, which modifies the catalytic cavity in shape and volume. Sequence and structural analyses indicate that this motif is unique to Thermotoga AraFs. Small angle X-ray scattering investigation showed that TpAraF assembles as a hexamer in solution and is preserved at the optimum catalytic temperature, 65°C, suggesting functional significance. Crystal packing analysis shows that the biological hexamer encompasses a dimer of trimers and the multiple oligomeric interfaces are predominantly fashioned by polar and electrostatic contacts.
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Affiliation(s)
- Tatiana ACB Souza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Camila R Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Angelica R Souza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Daiane P Oldiges
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Rolf A Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State UniversityStillwater, Oklahoma
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
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59
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Islam SM, Richards MR, Taha HA, Byrns SC, Lowary TL, Roy PN. Conformational Analysis of Oligoarabinofuranosides: Overcoming Torsional Barriers with Umbrella Sampling. J Chem Theory Comput 2011; 7:2989-3000. [DOI: 10.1021/ct200333p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Shahidul M. Islam
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Michele R. Richards
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Simon C. Byrns
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
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60
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Gandhi NS, Freeman C, Parish CR, Mancera RL. Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-d-glucuronidase (heparanase). Glycobiology 2011; 22:35-55. [DOI: 10.1093/glycob/cwr095] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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61
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Almendros M, Danalev D, François-Heude M, Loyer P, Legentil L, Nugier-Chauvin C, Daniellou R, Ferrières V. Exploring the synthetic potency of the first furanothioglycoligase through original remote activation. Org Biomol Chem 2011; 9:8371-8. [DOI: 10.1039/c1ob06227a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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62
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Heterologously expressed family 51 alpha-L-arabinofuranosidases from Oenococcus oeni and Lactobacillus brevis. Appl Environ Microbiol 2010; 77:1528-31. [PMID: 21169445 DOI: 10.1128/aem.01385-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Putative α-L-arabinofuranosidases of Oenococcus oeni and Lactobacillus brevis were heterologously expressed and characterized. We report the basic functional properties of the recombinant enzymes in comparison to those of a commercial family 51 arabinosidase of Aspergillus niger.
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63
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St John FJ, González JM, Pozharski E. Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups. FEBS Lett 2010; 584:4435-41. [PMID: 20932833 DOI: 10.1016/j.febslet.2010.09.051] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/23/2010] [Accepted: 09/30/2010] [Indexed: 12/26/2022]
Abstract
In this work glycosyl hydrolase (GH) family 30 (GH30) is analyzed and shown to consist of its currently classified member sequences as well as several homologous sequence groups currently assigned within family GH5. A large scale amino acid sequence alignment and a phylogenetic tree were generated and GH30 groups and subgroups were designated. A partial rearrangement in the GH30 defining side-associated β-domain contributes to the differentiation of two major groups that contain up to eight subgroups. For this CAZy family of Clan A enzymes the dual domain fold is conserved, suggesting that it may be a requirement for evolved function. This work redefines GH family 30 and serves as a guide for future efforts regarding enzymes classified within this family.
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Affiliation(s)
- Franz J St John
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, USA
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64
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Seo ES, Lim YR, Kim YS, Park CS, Oh DK. Characterization of a recombinant endo-1,5-α-l-arabinanase from the isolated bacterium Bacillus licheniformis. BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-3138-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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65
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Squina FM, Santos CR, Ribeiro DA, Cota J, de Oliveira RR, Ruller R, Mort A, Murakami MT, Prade RA. Substrate cleavage pattern, biophysical characterization and low-resolution structure of a novel hyperthermostable arabinanase from Thermotoga petrophila. Biochem Biophys Res Commun 2010; 399:505-11. [DOI: 10.1016/j.bbrc.2010.07.097] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 07/25/2010] [Indexed: 10/19/2022]
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66
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Lim YR, Yoon RY, Seo ES, Kim YS, Park CS, Oh DK. Hydrolytic properties of a thermostable α-l-arabinofuranosidase from Caldicellulosiruptor saccharolyticus. J Appl Microbiol 2010; 109:1188-97. [DOI: 10.1111/j.1365-2672.2010.04744.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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67
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Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases. Appl Microbiol Biotechnol 2010; 87:9-19. [DOI: 10.1007/s00253-010-2567-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/09/2010] [Accepted: 03/15/2010] [Indexed: 10/19/2022]
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68
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Yeoman CJ, Han Y, Dodd D, Schroeder CM, Mackie RI, Cann IKO. Thermostable enzymes as biocatalysts in the biofuel industry. ADVANCES IN APPLIED MICROBIOLOGY 2010; 70:1-55. [PMID: 20359453 DOI: 10.1016/s0065-2164(10)70001-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lignocellulose is the most abundant carbohydrate source in nature and represents an ideal renewable energy source. Thermostable enzymes that hydrolyze lignocellulose to its component sugars have significant advantages for improving the conversion rate of biomass over their mesophilic counterparts. We review here the recent literature on the development and use of thermostable enzymes for the depolymerization of lignocellulosic feedstocks for biofuel production. Furthermore, we discuss the protein structure, mechanisms of thermostability, and specific strategies that can be used to improve the thermal stability of lignocellulosic biocatalysts.
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Affiliation(s)
- Carl J Yeoman
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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69
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Chlubnová I, Filipp D, Spiwok V, Dvořáková H, Daniellou R, Nugier-Chauvin C, Králová B, Ferrières V. Enzymatic synthesis of oligo-d-galactofuranosides and l-arabinofuranosides: from molecular dynamics to immunological assays. Org Biomol Chem 2010; 8:2092-102. [DOI: 10.1039/b926988f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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70
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Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, Phalip V. Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. J Biol Chem 2009; 284:12285-96. [PMID: 19269961 PMCID: PMC2673297 DOI: 10.1074/jbc.m900439200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/19/2009] [Indexed: 11/06/2022] Open
Abstract
The phytopathogenic fungus Fusarium graminearum secretes a very diverse pool of glycoside hydrolases (GHs) aimed at degrading plant cell walls. alpha-l-Arabinanases are essential GHs participating in the complete hydrolysis of hemicellulose, a natural resource for various industrial processes, such as bioethanol or pharmaceuticals production. Arb93A, the exo-1,5-alpha-l-arabinanase of F. graminearum encoded by the gene fg03054.1, belongs to the GH93 family, for which no structural data exists. The enzyme is highly active (1065 units/mg) and displays a strict substrate specificity for linear alpha-1,5-l-arabinan. Biochemical assays and NMR experiments demonstrated that the enzyme releases alpha-1,5-l-arabinobiose from the nonreducing end of the polysaccharide. We determined the crystal structure of the native enzyme and its complex with alpha-1,5-l-arabinobiose, a degradation product of alpha-Me-1,5-l-arabinotetraose, at 1.85 and 2.05A resolution, respectively. Arb93A is a monomeric enzyme, which presents the six-bladed beta-propeller fold characteristic of sialidases of clan GHE. The configuration of the bound arabinobiose is consistent with the retaining mechanism proposed for the GH93 family. Catalytic residues were proposed from the structural analysis, and site-directed mutagenesis was used to validate their role. They are significantly different from those observed for GHE sialidases.
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Affiliation(s)
- Raphaël Carapito
- UMR 7175, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg-CNRS, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch-Graffenstaden, France
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71
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Inácio JM, Correia IL, de Sá-Nogueira I. Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis. MICROBIOLOGY-SGM 2008; 154:2719-2729. [PMID: 18757805 DOI: 10.1099/mic.0.2008/018978-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus subtilis produces alpha-l-arabinofuranosidases (EC 3.2.1.55; AFs) capable of releasing arabinosyl oligomers and l-arabinose from plant cell walls. Here, we show by insertion-deletion mutational analysis that genes abfA and xsa(asd), herein renamed abf2, encode AFs responsible for the majority of the intracellular AF activity in B. subtilis. Both enzyme activities were shown to be cytosolic and functional studies indicated that arabino-oligomers are natural substrates for the AFs. The products of the two genes were overproduced in Escherichia coli, purified and characterized. The molecular mass of the purified AbfA and Abf2 was about 58 kDa and 57 kDa, respectively. However, native PAGE gradient gel analysis and cross-linking assays detected higher-order structures (>250 kDa), suggesting a multimeric organization of both enzymes. Kinetic experiments at 37 degrees C, with p-nitrophenyl-alpha-l-arabinofuranoside as substrate, gave an apparent K(m) of 0.498 mM and 0.421 mM, and V(max) of 317 U mg(-1) and 311 U mg(-1) for AbfA and Abf2, respectively. The two enzymes displayed maximum activity at 50 degrees C and 60 degrees C, respectively, and both proteins were most active at pH 8.0. AbfA and Abf2 both belong to family 51 of the glycoside hydrolases but have different substrate specificity. AbfA acts preferentially on (1-->5) linkages of linear alpha-1,5-l-arabinan and alpha-1,5-linked arabino-oligomers, and is much less effective on branched sugar beet arabinan and arabinoxylan and arabinogalactan. In contrast, Abf2 is most active on (1-->2) and (1-->3) linkages of branched arabinan and arabinoxylan, suggesting a concerted contribution of these enzymes to optimal utilization of arabinose-containing polysaccharides by B. subtilis.
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Affiliation(s)
- José Manuel Inácio
- Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
| | - Isabel Lopes Correia
- Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
| | - Isabel de Sá-Nogueira
- Departamento de CiÁncias da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal.,Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
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72
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Fritz M, Ravanal MC, Braet C, eyzaguirre J. A family 51 α-l-arabinofuranosidase from Penicillium purpurogenum: purification, properties and amino acid sequence. ACTA ACUST UNITED AC 2008; 112:933-42. [DOI: 10.1016/j.mycres.2008.01.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 12/24/2007] [Accepted: 01/24/2008] [Indexed: 10/22/2022]
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Ichinose H, Yoshida M, Fujimoto Z, Kaneko S. Characterization of a modular enzyme of exo-1,5-alpha-L-arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893. Appl Microbiol Biotechnol 2008; 80:399-408. [PMID: 18665359 PMCID: PMC2518083 DOI: 10.1007/s00253-008-1551-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 05/19/2008] [Accepted: 05/20/2008] [Indexed: 11/26/2022]
Abstract
A gene encoding an α-l-arabinofuranosidase, designated SaAraf43A, was cloned from Streptomyces avermitilis. The deduced amino acid sequence implies a modular structure consisting of an N-terminal glycoside hydrolase family 43 module and a C-terminal family 42 carbohydrate-binding module (CBM42). The recombinant enzyme showed optimal activity at pH 6.0 and 45°C and was stable over the pH range of 5.0–6.5 at 30°C. The enzyme hydrolyzed p-nitrophenol (PNP)-α-l-arabinofuranoside but did not hydrolyze PNP-α-l-arabinopyranoside, PNP-β-d-xylopyranoside, or PNP-β-d-galactopyranoside. Debranched 1,5-arabinan was hydrolyzed by the enzyme but arabinoxylan, arabinogalactan, gum arabic, and arabinan were not. Among the synthetic regioisomers of arabinofuranobiosides, only methyl 5-O-α-l-arabinofuranosyl-α-l-arabinofuranoside was hydrolyzed by the enzyme, while methyl 2-O-α-l-arabinofuranosyl-α-l-arabinofuranoside and methyl 3-O-α-l-arabinofuranosyl-α-l-arabinofuranoside were not. These data suggested that the enzyme only cleaves α-1,5-linked arabinofuranosyl linkages. The analysis of the hydrolysis product of arabinofuranopentaose suggested that the enzyme releases arabinose in exo-acting manner. These results indicate that the enzyme is definitely an exo-1,5-α-l-arabinofuranosidase. The C-terminal CBM42 did not show any affinity for arabinogalactan and debranched arabinan, although it bound arabinan and arabinoxylan, suggesting that the CBM42 bound to branched arabinofuranosyl residues. Removal of the module decreased the activity of the enzyme with regard to debranched arabinan. The CBM42 plays a role in enhancing the debranched arabinan hydrolytic action of the catalytic module in spite of its preference for binding arabinofuranosyl side chains.
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Affiliation(s)
- Hitomi Ichinose
- Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan
| | - Makoto Yoshida
- Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan
- Present Address: Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 Japan
| | - Zui Fujimoto
- Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Satoshi Kaneko
- Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan
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74
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Paës G, Skov LK, O’Donohue MJ, Rémond C, Kastrup JS, Gajhede M, Mirza O. The Structure of the Complex between a Branched Pentasaccharide and Thermobacillus xylanilyticus GH-51 Arabinofuranosidase Reveals Xylan-Binding Determinants and Induced Fit. Biochemistry 2008; 47:7441-51. [DOI: 10.1021/bi800424e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriel Paës
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Lars K. Skov
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Michael J. O’Donohue
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Caroline Rémond
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jette S. Kastrup
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Michael Gajhede
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Osman Mirza
- INRA—UMR FARE 614, 8, rue Gabriel Voisin, BP 316, 51688 Reims cedex 2, France, Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsvaerd, Denmark, and Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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75
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Rémond C, Boukari I, Chambat G, O’Donohue M. Action of a GH 51 α-l-arabinofuranosidase on wheat-derived arabinoxylans and arabino-xylooligosaccharides. Carbohydr Polym 2008. [DOI: 10.1016/j.carbpol.2007.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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76
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Lopez G, Nugier-Chauvin C, Rémond C, O'Donohue M. Investigation of the specificity of an α-l-arabinofuranosidase using C-2 and C-5 modified α-l-arabinofuranosides. Carbohydr Res 2007; 342:2202-11. [PMID: 17601513 DOI: 10.1016/j.carres.2007.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 05/25/2007] [Accepted: 06/02/2007] [Indexed: 10/23/2022]
Abstract
The synthesis of three novel glycosyl donors presenting the same scaffold as alpha-L-arabinofuranose but modified at the C-2 or C-5 positions has been achieved. Furthermore, chemoenzymatic syntheses using the alpha-L-arabinofuranosidase AbfD3 and these unnatural furanosides were investigated. The use of the novel p-nitrophenyl furanoside donors revealed that AbfD3 can perform transglycosylation with the C-5 deoxygenated donor but not with the C-2 modified one. These results emphasize the vital role for OH-2 in AbfD3 substrate recognition.
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Affiliation(s)
- Gérald Lopez
- Ecole Nationale Supérieure de Chimie de Rennes, UMR CNRS 6226 Sciences Chimiques de Rennes, Equipe Synthèse Organique et Systèmes Organisés, Avenue du Général Leclerc, F-35700 Rennes, France
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77
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Rademacher C, Shoemaker GK, Kim HS, Zheng RB, Taha H, Liu C, Nacario RC, Schriemer DC, Klassen JS, Peters T, Lowary TL. Ligand specificity of CS-35, a monoclonal antibody that recognizes mycobacterial lipoarabinomannan: a model system for oligofuranoside-protein recognition. J Am Chem Soc 2007; 129:10489-502. [PMID: 17672460 DOI: 10.1021/ja0723380] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The CS-35 antibody is widely used in the characterization of glycans containing D-arabinofuranose residues, in particular polysaccharides present in the mycobacterial cell wall. A detailed understanding of the combining site of this antibody and the measurement of its binding to different ligands is of interest as this knowledge will have implications in the characterization of arabinofuranose-containing glycoconjugates that are increasingly recognized as important biological molecules. Of even greater significance is that an in-depth study of this carbohydrate-protein interaction will provide insights into the mechanisms by which oligosaccharides containing furanose rings are bound by proteins, an area that has, to date, received little attention. This system has been refractory to X-ray crystallography, and thus we report here a study of the interaction of CS-35 with its ligands using a combination of chemical synthesis, mass spectrometry, titration microcalorimetry, and NMR spectroscopy. Through these investigations we have established that the binding pocket recognizes, as a minimum epitope, a linear tetrasaccharide motif and that the residues at the reducing and non-reducing end of the oligosaccharide are essential for tight binding. The residue at the non-reducing end appears to be bound in an aliphatic pocket, whereas the rest of the tetrasaccharide interacts more strongly with aromatic amino acids.
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Affiliation(s)
- Christoph Rademacher
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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78
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Berger E, Zhang D, Zverlov VV, Schwarz WH. Two noncellulosomal cellulases of Clostridium thermocellum, Cel9I and Cel48Y, hydrolyse crystalline cellulose synergistically. FEMS Microbiol Lett 2007; 268:194-201. [PMID: 17227469 DOI: 10.1111/j.1574-6968.2006.00583.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The genome of Clostridium thermocellum contains a number of genes for polysaccharide degradation-associated proteins that are not cellulosome bound. The list includes beta-glucanases, glycosidases, chitinases, amylases and a xylanase. One of these 'soluble'-enzyme genes codes for a second glycosyl hydrolase (GH)48 cellulase, Cel48Y, which was expressed in Escherichia coli and biochemically characterized. It is a cellobiohydrolyse with activity on native cellulose such as microcrystalline and bacterial cellulose, and low activity on carboxymethylcellulose. It is about 100 times as active on amorphic cellulose and mixed-linkage barley beta-glucan compared with cellulase Cel9I. The enzyme Cel48Y shows a distinct synergism of 2.1 times with the noncellulosomal processive endoglucanase Cel9I on highly crystalline bacterial cellulose at a 17-fold excess of Cel48Y over Cel9I. These data show that C. thermocellum has, besides the cellulosome, the genes for a second cellulase system for the hydrolysis of crystalline cellulose that is not particle bound.
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Affiliation(s)
- Emanuel Berger
- Dept of Microbiology Technische Universitaet Muenchen, Am Hochanger, Freising-Weihenstephan, Germany
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79
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Lopez G, Daniellou R, O'Donohue M, Ferrières V, Nugier-Chauvin C. Thioimidoyl furanosides as first inhibitors of the α-l-arabinofuranosidase AbfD3. Bioorg Med Chem Lett 2007; 17:434-8. [PMID: 17071084 DOI: 10.1016/j.bmcl.2006.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 10/12/2006] [Accepted: 10/12/2006] [Indexed: 10/24/2022]
Abstract
Two sets of five thioimidoyl alpha-L-arabino- and beta-D-galactofuranosides were designed, synthesized and subjected to docking studies to evaluate their ability to be recognized by the active site of the alpha-L-arabinofuranosidase AbfD3. Further in vitro assays showed that the targeted furanosides are the first potent inhibitors of this furanosyl hydrolase and that the most efficient one, the thiazolyl alpha-L-arabinofuranoside 1, is a competitive inhibitor having a KI of 1.4 microM.
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Affiliation(s)
- Gérald Lopez
- Ecole Nationale Supérieure de Chimie de Rennes, UMR CNRS 6226, Team Organic Synthesis and Organized Systems, Avenue du Général Leclerc, F-35700 Rennes, France
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