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Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem 2024; 300:107352. [PMID: 38723750 PMCID: PMC11157272 DOI: 10.1016/j.jbc.2024.107352] [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: 01/23/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/21/2024] Open
Abstract
In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pierce T O'Neil
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kelly S Harrison
- The Department of Molecular Biosciences, The University of Kansas - Lawrence, Lawrence, Kansas, USA
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cole L Bird
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Aron W Fenton
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - P Scott Hefty
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jeffrey L Bose
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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2
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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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3
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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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Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022; 8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.
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Affiliation(s)
- Elizabeth A. Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chris Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - James O. McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,*Correspondence: Alan McNally,
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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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Characterization of an extracellular α-xylosidase involved in xyloglucan degradation in Aspergillus oryzae. Appl Microbiol Biotechnol 2021; 106:675-687. [PMID: 34971412 DOI: 10.1007/s00253-021-11744-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 10/19/2022]
Abstract
α-Xylosidases release the α-D-xylopyranosyl side chain from di- and oligosaccharides derived from xyloglucans and are involved in xyloglucan degradation. In this study, an extracellular α-xylosidase, named AxyB, is identified and characterized in Aspergillus oryzae. AxyB belongs to the glycoside hydrolase family 31 and releases D-xylose from isoprimeverose (α-D-xylopyranosyl-(1 → 6)-D-glucopyranose) and xyloglucan oligosaccharides. In the hydrolysis of xyloglucan oligosaccharides (XLLG, Glc4Xyl3Gal2 nonasaccharide; XLXG/XXLG, Glc4Xyl3Gal1 octasaccharide; and XXXG, Glc4Xyl3 heptasaccharide), AxyB releases one molecule of the xylopyranosyl side chain attached to the non-reducing end of the β-1,4-glucan main chain of these xyloglucan oligosaccharides to yield GLLG (Glc4Xyl2Gal2), GLXG/GXLG (Glc4Xyl2Gal1), and GXXG (Glc4Xyl2). A. oryzae has both extracellular and intracellular α-xylosidase, suggesting that xyloglucan oligosaccharides are degraded by a combination of isoprimeverose-producing oligoxyloglucan hydrolase and intracellular α-xylosidase and a combination of extracellular α-xylosidase and β-glucosidase(s) in A. oryzae. KEY POINTS: • An extracellular α-xylosidase, AxyB, is identified in Aspergillus oryzae. • AxyB releases the xylopyranosyl side chain from xyloglucan oligosaccharides. • Different sets of glycosidases degrade xyloglucan oligosaccharides in A. oryzae.
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Matsuzawa T, Kameyama A, Nakamichi Y, Yaoi K. Identification and characterization of two xyloglucan-specific endo-1,4-glucanases in Aspergillus oryzae. Appl Microbiol Biotechnol 2020; 104:8761-8773. [PMID: 32910269 DOI: 10.1007/s00253-020-10883-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/13/2020] [Accepted: 09/02/2020] [Indexed: 02/03/2023]
Abstract
Aspergillus oryzae produces glycoside hydrolases to degrade xyloglucan. We identified and characterized two xyloglucan-specific endo-1,4-glucanases (xyloglucanases) named Xeg12A and Xeg5A. Based on their amino acid sequences, Xeg12A and Xeg5A were classified into glycoside hydrolase families GH12 and GH5, respectively. Xeg12A degrades tamarind seed xyloglucan polysaccharide into xyloglucan oligosaccharides containing four glucopyranosyl residues as main chains, including heptasaccharides (XXXG: Glc4Xyl3), octasaccharides (XXLG and XLXG: Glc4Xyl3Gal1), and nonasaccharides (XLLG: Glc4Xyl3Gal2). By contrast, Xeg5A produces various xyloglucan oligosaccharides from xyloglucan. Xeg5A hydrolyzes xyloglucan into not only XXXG, XXLG/XLXG, and XLLG but also disaccharides (isoprimeverose: Glc1Xyl1), tetrasaccharides (XX: Glc2Xyl2 and LG: Glc2Xyl1Gal1), and so on. Xeg12A is a typical endo-dissociative-type xyloglucanase that repeats hydrolysis and desorption from xyloglucan. Conversely, Xeg5A acts as an endo-processive-type xyloglucanase that hydrolyzes xyloglucan progressively without desorption. These results indicate that although both Xeg12A and Xeg5A contribute to the degradation of xyloglucan, they have different modes of activity toward xyloglucan, and the hydrolysis machinery of Xeg5A is unique compared with that of other known GH5 enzymes. KEY POINTS: • We identified two xyloglucanases, Xeg12A and Xeg5A, in A. oryzae. • Modes of activity and regiospecificities of Xeg12A and Xeg5A were clearly different. • Xeg5A is a unique xyloglucanase that produces low-molecular-weight oligosaccharides.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, HigashiHiroshima, Hiroshima, 739-0046, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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Development of a thermophilic coculture for corn fiber conversion to ethanol. Nat Commun 2020; 11:1937. [PMID: 32321909 PMCID: PMC7176698 DOI: 10.1038/s41467-020-15704-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that Clostridium thermocellum can solubilize over 90% of the carbohydrate in autoclaved corn fiber, including its hemicellulose component glucuronoarabinoxylan (GAX). However, Thermoanaerobacterium thermosaccharolyticum or several other described hemicellulose-fermenting thermophilic bacteria can only partially utilize this GAX. We describe the isolation of a previously undescribed organism, Herbinix spp. strain LL1355, from a thermophilic microbiome that can consume 85% of the recalcitrant GAX. We sequence its genome, and based on structural analysis of the GAX, identify six enzymes that hydrolyze GAX linkages. Combinations of up to four enzymes are successfully expressed in T. thermosaccharolyticum. Supplementation with these enzymes allows T. thermosaccharolyticum to consume 78% of the GAX compared to 53% by the parent strain and increases ethanol yield from corn fiber by 24%. Corn fiber is a difficult feedstock to utilize due to its recalcitrant hemicellulose. Here, the authors characterize the recalcitrant structures, isolate a new bacterium to consume the hemicellulose, identify its enzymes, and show the benefit with increased conversion of corn fiber to ethanol.
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Matsuzawa T, Kameyama A, Yaoi K. Identification and characterization of α-xylosidase involved in xyloglucan degradation in Aspergillus oryzae. Appl Microbiol Biotechnol 2019; 104:201-210. [PMID: 31781819 DOI: 10.1007/s00253-019-10244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022]
Abstract
Aspergillus oryzae produces hydrolases involved in xyloglucan degradation and induces the expression of genes encoding xyloglucan oligosaccharide hydrolases in the presence of xyloglucan oligosaccharides. A gene encoding α-xylosidase (termed AxyA), which is induced in the presence of xyloglucan oligosaccharides, is identified and expressed in Pichia pastoris. AxyA is a member of the glycoside hydrolase family 31 (GH31). AxyA hydrolyzes isoprimeverose (α-D-xylopyranosyl-(1→6)-D-glucopyranose) into D-xylose and D-glucose and shows hydrolytic activity with other xyloglucan oligosaccharides such as XXXG (heptasaccharide, Glc4Xyl3) and XLLG (nonasaccharide, Glc4Xyl3Gal2). Isoprimeverose is a preferred AxyA substrate over other xyloglucan oligosaccharides. In the hydrolysis of XXXG, AxyA releases one molecule of D-xylose from one molecule of XXXG to yield GXXG (hexasaccharide, Glc4Xyl2). AxyA does not contain a signal peptide for secretion and remains within the cell. The intracellular localization of AxyA may help determine the order of hydrolases acting on xyloglucan oligosaccharides.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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10
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Rossoni AW, Price DC, Seger M, Lyska D, Lammers P, Bhattacharya D, Weber APM. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 2019; 8:e45017. [PMID: 31149898 PMCID: PMC6629376 DOI: 10.7554/elife.45017] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.
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Affiliation(s)
- Alessandro W Rossoni
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Dana C Price
- Department of Plant BiologyRutgers UniversityNew BrunswickUnited States
| | - Mark Seger
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | - Dagmar Lyska
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Peter Lammers
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | | | - Andreas PM Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
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11
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Matsuzawa T, Watanabe M, Kameda T, Kameyama A, Yaoi K. Cooperation between β-galactosidase and an isoprimeverose-producing oligoxyloglucan hydrolase is key for xyloglucan degradation in Aspergillus oryzae. FEBS J 2019; 286:3182-3193. [PMID: 30980597 DOI: 10.1111/febs.14848] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/07/2019] [Accepted: 04/10/2019] [Indexed: 11/30/2022]
Abstract
The galactosylation of xyloglucan blocks many of the enzymatic processes targeting this oligosaccharide. We found that the expression of a gene encoding Aspergillus oryzae β-galactosidase (LacA) is induced in the presence of xyloglucan oligosaccharides. With detailed analyses of the substrate specificity of purified recombinant LacA, we show that LacA cleaves galactopyranosyl residues from xyloglucan oligosaccharides, but not from xyloglucan polysaccharide, and plays a vital role in xyloglucan degradation. LacA acts cooperatively with the isoprimeverose-producing oligoxyloglucan hydrolase IpeA to hydrolyze xyloglucan oligosaccharides. Galactosylation of the xylopyranosyl side chain at the nonreducing end of oligoxyloglucan saccharides completely abolishes IpeA activity while LacA efficiently removes the galactopyranosyl residue. Conversely, an isoprimeverose unit at the nonreducing end of the main chain of xyloglucan oligosaccharides blocks LacA activity, while IpeA can still remove the isoprimeverose moiety. This is the first study reporting the cooperative action of β-galactosidase and isoprimeverose-producing oligoxyloglucan hydrolase on xyloglucan oligosaccharide degradation. Our findings shed light on the true role of LacA and the enzymatic coordination between β-galactosidase and other hydrolases on xyloglucan degradation.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masahiro Watanabe
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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12
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Matsuzawa T, Kameyama A, Yaoi K. A novel isoprimeverose-producing enzyme from Phaeoacremonium minimum is active with low concentrations of xyloglucan oligosaccharides. FEBS Open Bio 2018; 9:92-100. [PMID: 30652077 PMCID: PMC6325624 DOI: 10.1002/2211-5463.12549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 11/12/2022] Open
Abstract
Xyloglucan is one of the major polysaccharides found in the plant cell wall and seeds. Owing to its complex branched structure, several different hydrolases are required to degrade it. Isoprimeverose‐producing enzymes (IPase) are unique among the glycoside hydrolase 3 family in that they recognize and release a disaccharide from the nonreducing end of xyloglucan oligosaccharides. Only two IPases have been previously isolated and characterized. A novel IPase from Phaeoacremonium minimum (PmIPase) was expressed and characterized. The xylopyranosyl residue at the nonreducing end of xyloglucan oligosaccharides was essential for hydrolytic activity, and PmIPase was unable to hydrolyze cellobiose into d‐glucose. PmIPase had a Km for xyloglucan oligosaccharide substrate that was much lower than that of the reported IPase isolated from Aspergillus oryzae. This indicates that PmIPase was able to produce isoprimeverose efficiently from low concentrations of xyloglucan oligosaccharides. PmIPase also exhibited transglycosylation activity and was able to transfer isoprimeverose units to its substrates.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki Japan
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki Japan
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13
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Matsuzawa T, Watanabe M, Nakamichi Y, Fujimoto Z, Yaoi K. Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme. J Struct Biol 2018; 205:84-90. [PMID: 30445155 DOI: 10.1016/j.jsb.2018.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/30/2018] [Accepted: 11/12/2018] [Indexed: 11/26/2022]
Abstract
Isoprimeverose-producing enzymes (IPases) release isoprimeverose (α-d-xylopyranosyl-(1 → 6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. Aspergillus oryzae IPase (IpeA) is classified as a member of the glycoside hydrolase family 3 (GH3); however, it has unusual substrate specificity compared with other GH3 enzymes. Xylopyranosyl branching at the non-reducing ends of xyloglucan oligosaccharides is vital for IpeA activity. We solved the crystal structure of IpeA with isoprimeverose at 2.4 Å resolution, showing that the structure of IpeA formed a dimer and was composed of three domains: an N-terminal (β/α)8 TIM-barrel domain, α/β/α sandwich fold domain, and a C-terminal fibronectin-like domain. The catalytic TIM-barrel domain possessed a catalytic nucleophile (Asp300) and acid/base (Glu524) residues. Interestingly, we found that the cavity of the active site of IpeA was larger than that of other GH3 enzymes, and subsite -1' played an important role in its activity. The glucopyranosyl and xylopyranosyl residues of isoprimeverose were located at subsites -1 and -1', respectively. Gln58 and Tyr89 contributed to the interaction with the xylopyranosyl residue of isoprimeverose through hydrogen bonding and stacking effects, respectively. Our findings provide new insights into the substrate recognition of GH3 enzymes.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Masahiro Watanabe
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, HigashiHiroshima, Hiroshima 739-0046, Japan
| | - Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, HigashiHiroshima, Hiroshima 739-0046, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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14
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Gozu Y, Ishizaki Y, Hosoyama Y, Miyazaki T, Nishikawa A, Tonozuka T. A glycoside hydrolase family 31 dextranase with high transglucosylation activity from Flavobacterium johnsoniae. Biosci Biotechnol Biochem 2016; 80:1562-7. [DOI: 10.1080/09168451.2016.1182852] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Glycoside hydrolase family (GH) 31 enzymes exhibit various substrate specificities, although the majority of members are α-glucosidases. Here, we constructed a heterologous expression system of a GH31 enzyme, Fjoh_4430, from Flavobacterium johnsoniae NBRC 14942, using Escherichia coli, and characterized its enzymatic properties. The enzyme hydrolyzed dextran and pullulan to produce isomaltooligosaccharides and isopanose, respectively. When isomaltose was used as a substrate, the enzyme catalyzed disproportionation to form isomaltooligosaccharides. The enzyme also acted, albeit inefficiently, on p-nitrophenyl α-D-glucopyranoside, and p-nitrophenyl α-isomaltoside was the main product of the reaction. In contrast, Fjoh_4430 did not act on trehalose, kojibiose, nigerose, maltose, maltotriose, or soluble starch. The optimal pH and temperature were pH 6.0 and 60 °C, respectively. Our results indicate that Fjoh_4430 is a novel GH31 dextranase with high transglucosylation activity.
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Affiliation(s)
- Yoshifumi Gozu
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yuichi Ishizaki
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yuhei Hosoyama
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takatsugu Miyazaki
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
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15
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Tagami T, Miyano E, Sadahiro J, Okuyama M, Iwasaki T, Kimura A. Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1→6)-α-nigerosyl. J Biol Chem 2016; 291:16438-47. [PMID: 27302067 DOI: 10.1074/jbc.m116.727305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 11/06/2022] Open
Abstract
The actinobacterium Kribbella flavida NBRC 14399(T) produces cyclobis-(1→6)-α-nigerosyl (CNN), a cyclic glucotetraose with alternate α-(1→6)- and α-(1→3)-glucosidic linkages, from starch in the culture medium. We identified gene clusters associated with the production and intracellular catabolism of CNN in the K. flavida genome. One cluster encodes 6-α-glucosyltransferase and 3-α-isomaltosyltransferase, which are known to coproduce CNN from starch. The other cluster contains four genes annotated as a transcriptional regulator, sugar transporter, glycoside hydrolase family (GH) 31 protein (Kfla1895), and GH15 protein (Kfla1896). Kfla1895 hydrolyzed the α-(1→3)-glucosidic linkages of CNN and produced isomaltose via a possible linear tetrasaccharide. The initial rate of hydrolysis of CNN (11.6 s(-1)) was much higher than that of panose (0.242 s(-1)), and hydrolysis of isomaltotriose and nigerose was extremely low. Because Kfla1895 has a strong preference for the α-(1→3)-isomaltosyl moiety and effectively hydrolyzes the α-(1→3)-glucosidic linkage, it should be termed 1,3-α-isomaltosidase. Kfla1896 effectively hydrolyzed isomaltose with liberation of β-glucose, but displayed low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch, or dextran. The kcat/Km for isomaltose (4.81 ± 0.18 s(-1) mm(-1)) was 6.9- and 19-fold higher than those for panose and isomaltotriose, respectively. These results indicate that Kfla1896 is a new GH15 enzyme with high substrate specificity for isomaltose, suggesting the enzyme should be designated an isomaltose glucohydrolase. This is the first report to identify a starch-utilization pathway that proceeds via CNN.
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Affiliation(s)
- Takayoshi Tagami
- From the College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501 and
| | - Eri Miyano
- the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Juri Sadahiro
- the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masayuki Okuyama
- the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomohito Iwasaki
- From the College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501 and
| | - Atsuo Kimura
- the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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16
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Matsuzawa T, Kimura N, Suenaga H, Yaoi K. Screening, identification, and characterization of α-xylosidase from a soil metagenome. J Biosci Bioeng 2016; 122:393-9. [PMID: 27074950 DOI: 10.1016/j.jbiosc.2016.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/04/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
Abstract
A novel α-xylosidase, MeXyl31, was isolated and characterized from a soil metagenomic library. The amino acid sequence of MeXyl31 showed a slight homology with other characterized α-xylosidases. The optimal pH and temperature of recombinant MeXyl31 were pH 5.5 and 45°C, respectively. Recombinant MeXyl31 had a higher α-xylosidase activity toward pNP α-d-xylopyranoside than pNP α-d-glucopyranoside, isoprimeverose, and other xyloglucan oligosaccharides. The kcat/Km value toward pNP α-d-xylopyranoside was about 750-fold higher than that of isoprimeverose. MeXyl31 activity was strongly inactivated in the presence of zinc and copper ions. MeXyl31 is the first α-xylosidase isolated from the metagenome and, relative to other xyloglucan oligosaccharides, shows higher activity toward pNP α-d-xylopyranoside.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hikaru Suenaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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17
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Speciale G, Jin Y, Davies GJ, Williams SJ, Goddard-Borger ED. YihQ is a sulfoquinovosidase that cleaves sulfoquinovosyl diacylglyceride sulfolipids. Nat Chem Biol 2016; 12:215-7. [DOI: 10.1038/nchembio.2023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/31/2015] [Indexed: 11/09/2022]
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18
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Matsuzawa T, Mitsuishi Y, Kameyama A, Yaoi K. Identification of the Gene Encoding Isoprimeverose-producing Oligoxyloglucan Hydrolase in Aspergillus oryzae. J Biol Chem 2016; 291:5080-7. [PMID: 26755723 DOI: 10.1074/jbc.m115.701474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 11/06/2022] Open
Abstract
Aspergillus oryzae produces a unique β-glucosidase, isoprimeverose-producing oligoxyloglucan hydrolase (IPase), that recognizes and releases isoprimeverose (α-D-xylopyranose-(1 → 6)-D-glucopyranose) units from the non-reducing ends of oligoxyloglucans. A gene encoding A. oryzae IPase, termed ipeA, was identified and expressed in Pichia pastoris. With the exception of cellobiose, IpeA hydrolyzes a variety of oligoxyloglucans and is a member of the glycoside hydrolase family 3. Xylopyranosyl branching at the non-reducing ends was vital for IPase activity, and galactosylation at a α-1,6-linked xylopyranosyl side chain completely abolished IpeA activity. Hepta-oligoxyloglucan saccharide (Xyl3Glc4) substrate was preferred over tri- (Xyl1Glc2) and tetra- (Xyl2Glc2) oligoxyloglucan saccharides substrates. IpeA transferred isoprimeverose units to other saccharides, indicating transglycosylation activity. The ipeA gene was expressed in xylose and xyloglucan media and was strongly induced in the presence of xyloglucan endo-xyloglucanase-hydrolyzed products. This is the first study to report the identification of a gene encoding IPase in eukaryotes.
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Affiliation(s)
| | | | - Akihiko Kameyama
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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19
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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20
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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21
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Structural and biochemical characterization of novel bacterial α-galactosidases belonging to glycoside hydrolase family 31. Biochem J 2015; 469:145-58. [DOI: 10.1042/bj20150261] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/05/2015] [Indexed: 11/17/2022]
Abstract
We identified two bacterial enzymes as the first members that displayed α-galactosidase activity and the crystal structures provided insights into their novel substrate specificity. This is the first report of α-galactosidases which belong to the GH31 family.
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22
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Biochemical properties and substrate recognition mechanism of GH31 α-glucosidase from Bacillus sp. AHU 2001 with broad substrate specificity. Biochimie 2015; 108:140-8. [DOI: 10.1016/j.biochi.2014.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/11/2014] [Indexed: 11/19/2022]
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23
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Function and Structure Studies of GH Family 31 and 97 α-Glycosidases. Biosci Biotechnol Biochem 2014; 75:2269-77. [DOI: 10.1271/bbb.110610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Larsbrink J, Izumi A, Hemsworth GR, Davies GJ, Brumer H. Structural enzymology of Cellvibrio japonicus Agd31B protein reveals α-transglucosylase activity in glycoside hydrolase family 31. J Biol Chem 2012; 287:43288-99. [PMID: 23132856 PMCID: PMC3527916 DOI: 10.1074/jbc.m112.416511] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/05/2012] [Indexed: 01/06/2023] Open
Abstract
The metabolism of the storage polysaccharides glycogen and starch is of vital importance to organisms from all domains of life. In bacteria, utilization of these α-glucans requires the concerted action of a variety of enzymes, including glycoside hydrolases, glycoside phosphorylases, and transglycosylases. In particular, transglycosylases from glycoside hydrolase family 13 (GH13) and GH77 play well established roles in α-glucan side chain (de)branching, regulation of oligo- and polysaccharide chain length, and formation of cyclic dextrans. Here, we present the biochemical and tertiary structural characterization of a new type of bacterial 1,4-α-glucan 4-α-glucosyltransferase from GH31. Distinct from 1,4-α-glucan 6-α-glucosyltransferases (EC 2.4.1.24) and 4-α-glucanotransferases (EC 2.4.1.25), this enzyme strictly transferred one glucosyl residue from α(1→4)-glucans in disproportionation reactions. Substrate hydrolysis was undetectable for a series of malto-oligosaccharides except maltose for which transglycosylation nonetheless dominated across a range of substrate concentrations. Crystallographic analysis of the enzyme in free, acarbose-complexed, and trapped 5-fluoro-β-glucosyl-enzyme intermediate forms revealed extended substrate interactions across one negative and up to three positive subsites, thus providing structural rationalization for the unique, single monosaccharide transferase activity of the enzyme.
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Affiliation(s)
- Johan Larsbrink
- From the Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Atsushi Izumi
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Glyn R. Hemsworth
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom, and
| | - Harry Brumer
- From the Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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25
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Scott-Craig JS, Borrusch MS, Banerjee G, Harvey CM, Walton JD. Biochemical and molecular characterization of secreted α-xylosidase from Aspergillus niger. J Biol Chem 2011; 286:42848-54. [PMID: 22033931 PMCID: PMC3234869 DOI: 10.1074/jbc.m111.307397] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/26/2011] [Indexed: 11/06/2022] Open
Abstract
α-Linked xylose is a major component of xyloglucans in the cell walls of higher plants. An α-xylosidase (AxlA) was purified from a commercial enzyme preparation from Aspergillus niger, and the encoding gene was identified. The protein is a member of glycosyl hydrolase family 31. It was active on p-nitrophenyl-α-d-xyloside, isoprimeverose, xyloglucan heptasaccharide (XXXG), and tamarind xyloglucan. When expressed in Pichia pastoris, AxlA had activity comparable to the native enzyme on pNPαX and IP despite apparent hyperglycosylation. The pH optimum of AxlA was between 3.0 and 4.0. AxlA together with β-glucosidase depolymerized xyloglucan heptasaccharide. A combination of AxlA, β-glucosidase, xyloglucanase, and β-galactosidase in the optimal proportions of 51:5:19:25 or 59:5:11:25 could completely depolymerize tamarind XG to free Glc or Xyl, respectively. To the best of our knowledge, this is the first characterization of a secreted microbial α-xylosidase. Secreted α-xylosidases appear to be rare in nature, being absent from other tested commercial enzyme mixtures and from the genomes of most filamentous fungi.
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Affiliation(s)
- John S. Scott-Craig
- From the Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Melissa S. Borrusch
- From the Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Goutami Banerjee
- From the Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Christopher M. Harvey
- From the Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Jonathan D. Walton
- From the Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
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26
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Lochner A, Giannone RJ, Keller M, Antranikian G, Graham DE, Hettich RL. Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass. J Proteome Res 2011; 10:5302-14. [PMID: 21988591 DOI: 10.1021/pr200536j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometric analysis of Caldicellulosiruptor obsidiansis cultures grown on four different carbon sources identified 65% of the cells' predicted proteins in cell lysates and supernatants. Biological and technical replication together with sophisticated statistical analysis were used to reliably quantify protein abundances and their changes as a function of carbon source. Extracellular, multifunctional glycosidases were significantly more abundant on cellobiose than on the crystalline cellulose substrates Avicel and filter paper, indicating either disaccharide induction or constitutive protein expression. Highly abundant flagellar, chemotaxis, and pilus proteins were detected during growth on insoluble substrates, suggesting motility or specific substrate attachment. The highly abundant extracellular binding protein COB47_0549 together with the COB47_1616 ATPase might comprise the primary ABC-transport system for cellooligosaccharides, while COB47_0096 and COB47_0097 could facilitate monosaccharide uptake. Oligosaccharide degradation can occur either via extracellular hydrolysis by a GH1 β-glycosidase or by intracellular phosphorolysis using two GH94 enzymes. When C. obsidiansis was grown on switchgrass, the abundance of hemicellulases (including GH3, GH5, GH51, and GH67 enzymes) and certain sugar transporters increased significantly. Cultivation on biomass also caused a concerted increase in cytosolic enzymes for xylose and arabinose fermentation.
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Affiliation(s)
- Adriane Lochner
- Biosciences Division, BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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27
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The evolution of metabolic networks of E. coli. BMC SYSTEMS BIOLOGY 2011; 5:182. [PMID: 22044664 PMCID: PMC3229490 DOI: 10.1186/1752-0509-5-182] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/01/2011] [Indexed: 11/19/2022]
Abstract
Background Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts. Results We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All remaining orthologous groups were evaluated to see if new metabolic reactions could be added to generate a pangenome-scale metabolic model (iEco1712_pan). The pangenome model included reactions from a metabolic model update for E. coli K-12 MG1655 (iEco1339_MG1655) and enabled development of five additional strain-specific genome-scale metabolic models. These additional models include a second K-12 strain (iEco1335_W3110) and four pathogenic strains (two enterohemorrhagic E. coli O157:H7 and two uropathogens). When compared to the E. coli K-12 models, the metabolic models for the enterohemorrhagic (iEco1344_EDL933 and iEco1345_Sakai) and uropathogenic strains (iEco1288_CFT073 and iEco1301_UTI89) contained numerous lineage-specific gene and reaction differences. All six E. coli models were evaluated by comparing model predictions to carbon source utilization measurements under aerobic and anaerobic conditions, and to batch growth profiles in minimal media with 0.2% (w/v) glucose. An ancestral genome-scale metabolic model based on conserved ortholog groups in all 16 E. coli genomes was also constructed, reflecting the conserved ancestral core of E. coli metabolism (iEco1053_core). Comparative analysis of all six strain-specific E. coli models revealed that some of the pathogenic E. coli strains possess reactions in their metabolic networks enabling higher biomass yields on glucose. Finally the lineage-specific metabolic traits were compared to the ancestral core model predictions to derive new insight into the evolution of metabolism within this species. Conclusion Our findings demonstrate that a pangenome-scale metabolic model can be used to rapidly construct additional E. coli strain-specific models, and that quantitative models of different strains of E. coli can accurately predict strain-specific phenotypes. Such pangenome and strain-specific models can be further used to engineer metabolic phenotypes of interest, such as designing new industrial E. coli strains.
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28
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Structural and enzymatic characterization of a glycoside hydrolase family 31 α-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification. Biochem J 2011; 436:567-80. [DOI: 10.1042/bj20110299] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The desire for improved methods of biomass conversion into fuels and feedstocks has re-awakened interest in the enzymology of plant cell wall degradation. The complex polysaccharide xyloglucan is abundant in plant matter, where it may account for up to 20% of the total primary cell wall carbohydrates. Despite this, few studies have focused on xyloglucan saccharification, which requires a consortium of enzymes including endo-xyloglucanases, α-xylosidases, β-galactosidases and α-L-fucosidases, among others. In the present paper, we show the characterization of Xyl31A, a key α-xylosidase in xyloglucan utilization by the model Gram-negative soil saprophyte Cellvibrio japonicus. CjXyl31A exhibits high regiospecificity for the hydrolysis of XGOs (xylogluco-oligosaccharides), with a particular preference for longer substrates. Crystallographic structures of both the apo enzyme and the trapped covalent 5-fluoro-β-xylosyl-enzyme intermediate, together with docking studies with the XXXG heptasaccharide, revealed, for the first time in GH31 (glycoside hydrolase family 31), the importance of a PA14 domain insert in the recognition of longer oligosaccharides by extension of the active-site pocket. The observation that CjXyl31A was localized to the outer membrane provided support for a biological model of xyloglucan utilization by C. japonicus, in which XGOs generated by the action of a secreted endo-xyloglucanase are ultimately degraded in close proximity to the cell surface. Moreover, the present study diversifies the toolbox of glycosidases for the specific modification and saccharification of cell wall polymers for biotechnological applications.
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29
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Répérant M, Porcheron G, Rouquet G, Gilot P. The yicJI metabolic operon of Escherichia coli is involved in bacterial fitness. FEMS Microbiol Lett 2011; 319:180-6. [PMID: 21477255 DOI: 10.1111/j.1574-6968.2011.02281.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The yicJI operon of the common genetic backbone of Escherichia coli codes an α-xylosidase and a transporter of the galactosides--pentoses--hexuronides:cation symporter family. In the extraintestinal pathogenic E. coli strain BEN2908, a metabolic operon (frz) of seven genes is found downstream of the yicI gene. It was proved that frz promotes bacterial fitness under stressful conditions. During this work, we identified a motif containing a palindromic sequence in the promoter region of both the frz and the yicJI operons. We then showed that these two operons are cotranscribed, suggesting a functional relationship. The phenotypes of frz and yicJI deletion mutants were compared. Our results showed that although the yicJI operon is not essential for the life of E. coli, it is necessary for its fitness under all the growth conditions tested.
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Affiliation(s)
- Maryline Répérant
- Laboratoire de Pathogénie Bactérienne, Centre de Recherche de Tours, INRA, UR1282, Unité d'Infectiologie Animale et de Santé Publique, Nouzilly, France
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30
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Villarreal JM, Hernández-Lucas I, Gil F, Calderón IL, Calva E, Saavedra CP. cAMP receptor protein (CRP) positively regulates the yihU-yshA operon in Salmonella enterica serovar Typhi. MICROBIOLOGY-SGM 2010; 157:636-647. [PMID: 21148209 DOI: 10.1099/mic.0.046045-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is the aetiological agent of typhoid fever in humans. This bacterium is also able to persist in its host, causing a chronic disease by colonizing the spleen, liver and gallbladder, in the last of which the pathogen forms biofilms in order to survive the bile. Several genetic components, including the yihU-yshA genes, have been suggested to be involved in the survival of Salmonella in the gallbladder. In this work we describe how the yihU-yshA gene cluster forms a transcriptional unit regulated positively by the cAMP receptor global regulator CRP (cAMP receptor protein). The results obtained show that two CRP-binding sites on the regulatory region of the yihU-yshA operon are required to promote transcriptional activation. In this work we also demonstrate that the yihU-yshA transcriptional unit is carbon catabolite-repressed in Salmonella, indicating that it forms part of the CRP regulon in enteric bacteria.
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Affiliation(s)
- J M Villarreal
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - I Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - F Gil
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - I L Calderón
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - E Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - C P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
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31
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Kang MS, Okuyama M, Yaoi K, Mitsuishi Y, Kim YM, Mori H, Kimura A. Glycoside hydrolase family 31Escherichia coliα-xylosidase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701806348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Rouquet G, Porcheron G, Barra C, Répérant M, Chanteloup NK, Schouler C, Gilot P. A metabolic operon in extraintestinal pathogenic Escherichia coli promotes fitness under stressful conditions and invasion of eukaryotic cells. J Bacteriol 2009; 191:4427-40. [PMID: 19376853 PMCID: PMC2698472 DOI: 10.1128/jb.00103-09] [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: 01/26/2009] [Accepted: 04/14/2009] [Indexed: 11/20/2022] Open
Abstract
We identified a carbohydrate metabolic operon (frz) that is highly associated with extraintestinal pathogenic Escherichia coli (ExPEC) strains. The frz operon codes for three subunits of a phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) transporter of the fructose subfamily, for a transcriptional activator of PTSs of the MgA family, for two type II ketose-1,6-bisphosphate aldolases, for a sugar-specific kinase (repressor, open reading frame, kinase family [ROK]), and for a protein of the cupin superfamily. We proved that the frz operon promotes bacterial fitness under stressful conditions, such as oxygen restriction, late stationary phase of growth, or growth in serum or in the intestinal tract. Furthermore, we showed that frz is involved in adherence to and internalization in human type II pneumocytes, human enterocytes, and chicken liver cells by favoring the ON orientation of the fim operon promoter and thus acting on the expression of type 1 fimbriae, which are the major ExPEC adhesins. Both the PTS activator and the metabolic enzymes encoded by the frz operon are involved in these phenotypes.
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Affiliation(s)
- Géraldine Rouquet
- INRA, UR1282, Unité d'Infectiologie Animale et de Santé Publique, Laboratoire de Pathogénie Bactérienne, Centre de Recherche de Tours, Nouzilly, France
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33
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Crystal Structure of YihS in Complex with d-Mannose: Structural Annotation of Escherichia coli and Salmonella enterica yihS-encoded Proteins to an Aldose–Ketose Isomerase. J Mol Biol 2008; 377:1443-59. [DOI: 10.1016/j.jmb.2008.01.090] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/20/2022]
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34
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Kang MS, Okuyama M, Yaoi K, Mitsuishi Y, Kim YM, Mori H, Kim D, Kimura A. Aglycone specificity of Escherichia coliα-xylosidase investigated by transxylosylation. FEBS J 2007; 274:6074-84. [DOI: 10.1111/j.1742-4658.2007.06129.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Nakai H, Ito T, Hayashi M, Kamiya K, Yamamoto T, Matsubara K, Kim YM, Jintanart W, Okuyama M, Mori H, Chiba S, Sano Y, Kimura A. Multiple forms of α-glucosidase in rice seeds (Oryza sativa L., var Nipponbare). Biochimie 2007; 89:49-62. [PMID: 17056172 DOI: 10.1016/j.biochi.2006.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Accepted: 09/16/2006] [Indexed: 11/20/2022]
Abstract
Two isoforms of alpha-glucosidases (ONG2-I and ONG2-II) were purified from dry rice seeds (Oryza sativa L., var Nipponbare). Both ONG2-I and ONG2-II were the gene products of ONG2 mRNA expressed in ripening seeds. Each enzyme consisted of two components of 6kDa-peptide and 88kDa-peptide encoded by this order in ONG2 cDNA (ong2), and generated by post-translational proteolysis. The 88kDa-peptide of ONG2-II had 10 additional N-terminal amino acids compared with the 88kDa-peptide of ONG2-I. The peptides between 6kDa and 88kDa components (26 amino acids for ONG2-I and 16 for ONG2-II) were removed by post-translational proteolysis. Proteolysis induced changes in adsorption and degradation of insoluble starch granules. We also obtained three alpha-glucosidase cDNAs (ong1, ong3, and ong4) from ripening seeds. The ONG1, ONG2, and ONG4 genes were situated in distinct locus of rice genome. The transcripts encoding ONG2 and ONG3 were generated by alternative splicing. Members of alpha-glucosidase multigene family are differentially expressed during ripening and germinating stages in rice.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Electrophoresis, Polyacrylamide Gel
- Isoenzymes/genetics
- Isoenzymes/isolation & purification
- Isoenzymes/metabolism
- Molecular Sequence Data
- Multigene Family
- Oryza/enzymology
- Oryza/genetics
- Plant Proteins, Dietary/genetics
- Plant Proteins, Dietary/isolation & purification
- Plant Proteins, Dietary/metabolism
- Polymerase Chain Reaction
- Protein Processing, Post-Translational
- RNA, Messenger/analysis
- Seeds/enzymology
- Seeds/genetics
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Substrate Specificity
- alpha-Glucosidases/genetics
- alpha-Glucosidases/isolation & purification
- alpha-Glucosidases/metabolism
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Affiliation(s)
- Hiroyuki Nakai
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Sapporo 060-8589, Japan.
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36
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Gibson DL, White AP, Snyder SD, Martin S, Heiss C, Azadi P, Surette M, Kay WW. Salmonella produces an O-antigen capsule regulated by AgfD and important for environmental persistence. J Bacteriol 2006; 188:7722-30. [PMID: 17079680 PMCID: PMC1636306 DOI: 10.1128/jb.00809-06] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Accepted: 07/25/2006] [Indexed: 11/20/2022] Open
Abstract
In this study, we show that Salmonella produces an O-antigen capsule coregulated with the fimbria- and cellulose-associated extracellular matrix. Structural analysis of purified Salmonella extracellular polysaccharides yielded predominantly a repeating oligosaccharide unit similar to that of Salmonella enterica serovar Enteritidis lipopolysaccharide O antigen with some modifications. Putative carbohydrate transport and regulatory operons important for capsule assembly and translocation, designated yihU-yshA and yihVW, were identified by screening a random transposon library with immune serum generated to the capsule. The absence of capsule was confirmed by generating various isogenic Deltayih mutants, where yihQ and yihO were shown to be important in capsule assembly and translocation. Luciferase-based expression studies showed that AgfD regulates the yih operons in coordination with extracellular matrix genes coding for thin aggregative fimbriae and cellulose. Although the capsule did not appear to be important for multicellular behavior, we demonstrate that it was important for survival during desiccation stress. Since the yih genes are conserved in salmonellae and the O-antigen capsule was important for environmental persistence, the formation of this surface structure may represent a conserved survival strategy.
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Affiliation(s)
- D L Gibson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, V8W 3P6 British Columbia, Canada
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37
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Okuyama M, Kaneko A, Mori H, Chiba S, Kimura A. Structural elements to convert Escherichia coli alpha-xylosidase (YicI) into alpha-glucosidase. FEBS Lett 2006; 580:2707-11. [PMID: 16631751 DOI: 10.1016/j.febslet.2006.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 04/07/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
Escherichia coli YicI, a member of glycoside hydrolase family (GH) 31, is an alpha-xylosidase, although its amino-acid sequence displays approximately 30% identity with alpha-glucosidases. By comparing the amino-acid sequence of GH 31 enzymes and through structural comparison of the (beta/alpha)(8) barrels of GH 27 and GH 31 enzymes, the amino acids Phe277, Cys307, Phe308, Trp345, Lys414, and beta-->alpha loop 1 of (beta/alpha)(8) barrel of YicI have been identified as elements that might be important for YicI substrate specificity. In attempt to convert YicI into an alpha-glucosidase these elements have been targeted by site-directed mutagenesis. Two mutated YicI, short loop1-enzyme and C307I/F308D, showed higher alpha-glucosidase activity than wild-type YicI. C307I/F308D, which lost alpha-xylosidase activity, was converted into alpha-glucosidase.
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Affiliation(s)
- Masayuki Okuyama
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Sapporo 060-8589, Japan
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38
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Ernst HA, Lo Leggio L, Willemoës M, Leonard G, Blum P, Larsen S. Structure of the Sulfolobus solfataricus alpha-glucosidase: implications for domain conservation and substrate recognition in GH31. J Mol Biol 2006; 358:1106-24. [PMID: 16580018 DOI: 10.1016/j.jmb.2006.02.056] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 02/21/2006] [Accepted: 02/22/2006] [Indexed: 11/26/2022]
Abstract
The crystal structure of alpha-glucosidase MalA from Sulfolobus solfataricus has been determined at 2.5Angstrom resolution. It provides a structural model for enzymes representing the major specificity in glycoside hydrolase family 31 (GH31), including alpha-glucosidases from higher organisms, involved in glycogen degradation and glycoprotein processing. The structure of MalA shows clear differences from the only other structure known from GH31, alpha-xylosidase YicI. MalA and YicI share only 23% sequence identity. Although the two enzymes display a similar domain structure and both form hexamers, their structures differ significantly in quaternary organization: MalA is a dimer of trimers, YicI a trimer of dimers. MalA and YicI also differ in their substrate specificities, as shown by kinetic measurements on model chromogenic substrates. In addition, MalA has a clear preference for maltose (Glc-alpha1,4-Glc), whereas YicI prefers isoprimeverose (Xyl-alpha1,6-Glc). The structural origin of this difference occurs in the -1 subsite where MalA residues Asp251 and Trp284 could interact with OH6 of the substrate. The structure of MalA in complex with beta-octyl-glucopyranoside has been determined. It reveals Arg400, Asp87, Trp284, Met321 and Phe327 as invariant residues forming the +1 subsite in the GH31 alpha-glucosidases. Structural comparisons with other GH families suggest that the GH31 enzymes belong to clan GH-D.
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Affiliation(s)
- Heidi A Ernst
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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39
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Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NCJ, Withers SG. Expanding the Thioglycoligase Strategy to the Synthesis of α-Linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex. J Am Chem Soc 2006; 128:2202-3. [PMID: 16478160 DOI: 10.1021/ja057904a] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfataricus, catalyze thioglycoligase reactions using alpha-glycosyl fluorides and deoxythioglycosides as donors and acceptors, respectively, in yields up to 86%. In addition, we describe the Michaelis complex of YicI using one of the thioglycosides as a nonhydrolyzable substrate analogue and discuss the structural insights this yields into the specificity and mechanism of family 31 alpha-glycosidases and the molecular basis of an associated genetic disease.
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Affiliation(s)
- Young-Wan Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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40
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Naested H, Kramhøft B, Lok F, Bojsen K, Yu S, Svensson B. Production of enzymatically active recombinant full-length barley high pI alpha-glucosidase of glycoside family 31 by high cell-density fermentation of Pichia pastoris and affinity purification. Protein Expr Purif 2005; 46:56-63. [PMID: 16343940 DOI: 10.1016/j.pep.2005.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 09/30/2005] [Accepted: 10/05/2005] [Indexed: 12/01/2022]
Abstract
Recombinant barley high pI alpha-glucosidase was produced by high cell-density fermentation of Pichia pastoris expressing the cloned full-length gene. The gene was amplified from a genomic clone and exons (coding regions) were assembled by overlap PCR. The resulting cDNA was expressed under control of the alcohol oxidase 1 promoter using methanol induction of P. pastoris fermentation in a Biostat B 5 L reactor. Forty-two milligrams alpha-glucosidase was purified from 3.5 L culture in four steps applying an N-terminal hexa-histidine tag. The apparent molecular mass of the recombinant alpha-glucosidase was 100 kDa compared to 92 kDa of the native barley enzyme. The secreted recombinant enzyme was highly stabile during the 5-day fermentation and had significantly superior specific activity of the enzyme purified previously from barley malt. The kinetic parameters Km, Vmax, and kcat were determined to 1.7 mM, 139 nM x s(-1), and 85 s(-1) using maltose as substrate. This work presents the first production of fully active recombinant alpha-glucosidase of glycoside hydrolase family 31 from higher plants.
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Affiliation(s)
- Henrik Naested
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
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41
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Kitamura M, Ose T, Okuyama M, Watanabe H, Yao M, Mori H, Kimura A, Tanaka I. Crystallization and preliminary X-ray analysis of alpha-xylosidase from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:178-9. [PMID: 16510986 PMCID: PMC1952256 DOI: 10.1107/s1744309104033202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Accepted: 12/15/2004] [Indexed: 11/10/2022]
Abstract
Glycoside hydrolases have been implicated in many biological processes. To date, they have been classified into 93 glycoside hydrolase (GH) families based on amino-acid sequence similarity. alpha-Xylosidase from Escherichia coli belongs to GH family 31 and catalyzes the release of alpha-xylose from the non-reducing terminal side of alpha-xyloside. Single crystals of alpha-xylosidase have been grown by vapour diffusion at 293 K from 10%(w/v) PEG 20K, 2%(v/v) 2-propanol, 2%(v/v) glycerol and 0.1 M 2-morpholinoethanesulfonic acid pH 5.5. These crystals belong to space group P2(1)2(1)2(1) and X-ray diffraction data were collected to a resolution of 2.75 A. Crystals of selenomethionyl-substituted alpha-xylosidase were also obtained, which diffracted to at least 3.0 A. Based on the value of VM, the asymmetric unit in these crystals was assumed to contain six molecules.
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Affiliation(s)
- Momoyo Kitamura
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Toyoyuki Ose
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masayuki Okuyama
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiromi Watanabe
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Haruhide Mori
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Atsuo Kimura
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Isao Tanaka
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
- Correspondence e-mail:
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42
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Lovering AL, Lee SS, Kim YW, Withers SG, Strynadka NCJ. Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate. J Biol Chem 2004; 280:2105-15. [PMID: 15501829 DOI: 10.1074/jbc.m410468200] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have determined the first structure of a family 31 alpha-glycosidase, that of YicI from Escherichia coli, both free and trapped as a 5-fluoroxylopyranosyl-enzyme intermediate via reaction with 5-fluoro-alpha-D-xylopyranosyl fluoride. Our 2.2-A resolution structure shows an intimately associated hexamer with structural elements from several monomers converging at each of the six active sites. Our kinetic and mass spectrometry analyses verified several of the features observed in our structural data, including a covalent linkage from the carboxylate side chain of the identified nucleophile Asp(416) to C-1 of the sugar ring. Structure-based sequence comparison of YicI with the mammalian alpha-glucosidases lysosomal alpha-glucosidase and sucrase-isomaltase predicts a high level of structural similarity and provides a foundation for understanding the various mutations of these enzymes that elicit human disease.
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Affiliation(s)
- Andrew L Lovering
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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