| 1. |
- Ejby, Morten, et al.
(author)
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An atp binding cassette transporter mediates the uptake of α-(1,6)-linked dietary oligosaccharides in bifidobacterium and correlates with competitive growth on these substrates
- 2016
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In: Journal of Biological Chemistry. - 0021-9258. ; 291:38, s. 20220-20231
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Journal article (peer-reviewed)abstract
- The molecular details and impact of oligosaccharide uptake by distinct human gut microbiota (HGM) are currently not well understood. Non-digestible dietary galacto- and gluco-α-(1,6)-oligosaccharides from legumes and starch, respectively, are preferentially fermented by mainly bifidobacteria and lactobacilli in the human gut. Here we show that the solute binding protein (BlG16BP) associated with an ATP binding cassette (ABC) transporter from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 binds α-(1,6)-linked glucosides and galactosides of varying size, linkage, and monosaccharide composition with preference for the trisaccharides raffinose and panose. This preference is also reflected in the α-(1,6)-galactoside uptake profile of the bacterium. Structures of BlG16BP in complex with raffinose and panose revealed the basis for the remarkable ligand binding plasticity of BlG16BP, which recognizes the nonreducing α-(1,6)-diglycoside in its ligands. BlG16BP homologues occur predominantly in bifidobacteria and a few Firmicutes but lack in other HGMs. Among seven bifidobacterial taxa, only those possessing this transporter displayed growth on α-(1,6)-glycosides. Competition assays revealed that the dominant HGM commensal Bacteroides ovatus was out-competed by B. animalis subsp. lactis Bl-04 in mixed cultures growing on raffinose, the preferred ligand for the BlG16BP. By comparison, B. ovatus mono-cultures grew very efficiently on this trisaccharide These findings suggest that the ABC-mediated uptake of raffinose provides an important competitive advantage, particularly against dominant Bacteroides that lack glycan-specific ABC-transporters. This novel insight highlights the role of glycan transport in defining the metabolic specialization of gut bacteria.
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| 2. |
- Ejby, Morten, et al.
(author)
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Structural basis for arabinoxylo-oligosaccharide capture by the probiotic Bifidobacterium animalis subsp lactis Bl-04
- 2013
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In: Molecular Microbiology. - : Wiley. - 1365-2958 .- 0950-382X. ; 90:5, s. 1100-1112
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Journal article (peer-reviewed)abstract
- Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo-oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactisBl-04. The binding protein BlAXBP, which is associated with an ATP-binding cassette (ABC) transporter that mediates the uptake of AXOS, displays an exceptionally broad specificity for arabinosyl-decorated and undecorated xylo-oligosaccharides, with preference for tri- and tetra-saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in two opposite orientations, which facilitates the optimization of interactions with the various ligands. Broad substrate specificity was further enhanced by a spacious binding pocket accommodating decorations at different mainchain positions and conformational flexibility of a lid-like loop. Phylogenetic and genetic analyses show that BlAXBP is highly conserved within Bifidobacterium, but is lacking in other gut microbiota members. These data indicate niche adaptation within Bifidobacterium and highlight the metabolic syntrophy (cross-feeding) among the gut microbiota.
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| 3. |
- Ejby, Morten, et al.
(author)
-
Structural basis for arabinoxylo-oligosaccharide capture by the probiotic Bifidobacterium animalis subsp lactis Bl-04
- 2012
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In: Journal of Psychopharmacology. - 1461-7285. ; 26:11, s. 1100-1112
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Journal article (peer-reviewed)abstract
- Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo-oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactisBl-04. The binding protein BlAXBP, which is associated with an ATP-binding cassette (ABC) transporter that mediates the uptake of AXOS, displays an exceptionally broad specificity for arabinosyl-decorated and undecorated xylo-oligosaccharides, with preference for tri- and tetra-saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in two opposite orientations, which facilitates the optimization of interactions with the various ligands. Broad substrate specificity was further enhanced by a spacious binding pocket accommodating decorations at different mainchain positions and conformational flexibility of a lid-like loop. Phylogenetic and genetic analyses show that BlAXBP is highly conserved within Bifidobacterium, but is lacking in other gut microbiota members. These data indicate niche adaptation within Bifidobacterium and highlight the metabolic syntrophy (cross-feeding) among the gut microbiota.
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| 4. |
- Logan, Derek, et al.
(author)
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Status of the crystallography beamlines at the MAX IV Laboratory
- 2015
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In: The European Physical Journal Plus. - : Springer Science and Business Media LLC. - 2190-5444. ; 130:3
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Research review (peer-reviewed)abstract
- The MAX IV Laboratory in Lund is currently operating two storage rings, the 1.5 GeV MAX II and the 700MeV MAX III, as well as constructing the new facility MAX IV, which will house a 1.5 GeV and a 3 GeV ring. At the MAX II synchrotron there are three hard X-ray beamlines at which crystallography can be performed: I711, I811 and I911. Beamline I711 is mainly used for powder diffraction. I811 is an EXAFS station at which surface XRD can also be carried out. I911 is a beamline with five experimental stations on a single superconducting wiggler source, of which two are currently used for macromolecular crystallography, namely the monochromatic station I911-2 and the tuneable station I911-3, which is equipped with a state-of-the-art goniometer and robotic sample changer. We will give an overview of the capabilities of these beamlines, focusing particularly on the macromolecular crystallography beamline I911 and some recent scientific highlights produced there. We will also give a brief overview of new beamlines for crystallography that are under construction or planned for the MAX IV facility.
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| 5. |
- Teze, David, et al.
(author)
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The catalytic acid-base in GH109 resides in a conserved GGHGG loop and allows for comparable α-retaining and β-inverting activity in an N-acetylgalactosaminidase from Akkermansia muciniphila
- 2019
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In: ChemRxiv. - : American Chemical Society (ACS).
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Other publication (other academic/artistic)abstract
- The study describes the first glycoside hydrolase that exhibits comparable levels of activity on α- and β-linked saccharide substrates. This enzyme, assigned into GH109, is encoded by the genome of the human gut symbiont Akkermansia muciniphila that is a model primary degrader of the heavily O-glycosylated mucin glycoprotein that coats the epithelial enterocytes.The elusive catalytic acid/base catalyst in GH109 enzymes is identified as a histidine that is presented by a flexible loop that positions it for catalysis on both α- and β-substrates. This dual activity may be an evolutionary adaptation to extend the range of substrates targeted by a single non-canonical NAD+-dependant GH.
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| 6. |
- Teze, David, et al.
(author)
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The Catalytic Acid-Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable α-Retaining and β-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia muciniphila
- 2020
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In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 10:6, s. 3809-3819
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Journal article (peer-reviewed)abstract
- Enzymes active on glycosidic bonds are defined according to the stereochemistry of both substrates and products of the reactions they catalyze. The CAZy classification further assigns these enzymes into sequence-based families sharing a common stereochemistry for substrates (either α- or β-) and products (i.e., inverting or retaining mechanism). Here we describe the N-acetylgalactosaminidases AmGH109A and AmGH109B (i.e., GH109: glycoside hydrolase family 109) from the human gut symbiont Akkermansia muciniphila. Notably, AmGH109A displays α-retaining and β-inverting N-acetylgalactosaminidase activities with comparable efficiencies on natural disaccharides. This dual specificity could provide an advantage in targeting a broader range of host-derived glycans. We rationalize this discovery through bioinformatics, structural, mutational, and computational studies, unveiling a histidine residing in a conserved GGHGG motif as the elusive catalytic acid-base of the GH109 family.
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| 7. |
- Thunnissen, Marjolein, et al.
(author)
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BioMAX: The Future Macromolecular Crystallography Beamline at MAX IV
- 2013
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In: 11th International Conference on Synchrotron Radiation Instrumentation (SRI 2012). - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 425
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Conference paper (peer-reviewed)abstract
- This paper describes the preliminary design of the BioMAX beamline at the 3 GeV ring of the MAX IV facility, focusing on the optics and x-ray beam performance. The MAX IV facility will include two storage rings with 1.5 GeV and 3.0 GeV electron energy and a linac serving both as injector for the two rings and feeding a short pulse facility. BioMAX is one of the first seven beamlines funded at the MAX IV facility. It is a multipurpose high-throughput beamline for macromolecular crystallography. The beamline aims to be robust and simple to operate with a beam benefiting from the properties of the MAX IV 3 GeV ring. However it does not aim at the smallest beam or crystal sizes since it is foreseen that it will be complemented with a microfocus beamline aiming at a beam size of 1 mu m. The beamline experiment setup will be highly automated, both in terms of sample handling hardware and data analysis, including feedback to the data collection. The BioMAX beamline is planned to be in operation in 2016.
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| 8. |
- Ursby, Thomas, et al.
(author)
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The macromolecular crystallography beamline I911-3 at the MAX IV laboratory.
- 2013
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In: Journal of Synchrotron Radiation. - 1600-5775. ; 20:Pt 4, s. 648-653
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Journal article (peer-reviewed)abstract
- The macromolecular crystallography beamline I911-3, part of the Cassiopeia/I911 suite of beamlines, is based on a superconducting wiggler at the MAX II ring of the MAX IV Laboratory in Lund, Sweden. The beamline is energy-tunable within a range between 6 and 18 keV. I911-3 opened for users in 2005. In 2010-2011 the experimental station was completely rebuilt and refurbished such that it has become a state-of-the-art experimental station with better possibilities for rapid throughput, crystal screening and work with smaller samples. This paper describes the complete I911-3 beamline and how it is embedded in the Cassiopeia suite of beamlines.
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