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Jones DR, McLean R, Hobbs JK, Abbott DW. A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. J Struct Biol 2019; 207:279-286. [PMID: 31200020 DOI: 10.1016/j.jsb.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Yersinia enterocolitica is a pectinolytic zoonotic foodborne pathogen, the genome of which contains pectin-binding proteins and several different classes of pectinases, including polysaccharide lyases (PLs) and an exopolygalacturonase. These proteins operate within a coordinated pathway to completely saccharify homogalacturonan (HG). Polysaccharide lyase family 2 (PL2) is divided into two major subfamilies that are broadly-associated with contrasting 'endolytic' (PL2A) or 'exolytic' (PL2B) activities on HG. In the Y. enterocolitica genome, the PL2A gene is adjacent to an independent carbohydrate binding module from family 32 (YeCBM32), which possesses a N-terminal secretion tag and is known to specifically bind HG. Independent CBMs are rare in nature and, most commonly, are fused to enzymes in order to potentiate catalysis. The unconventional gene architecture of YePL2A and YeCBM32, therefore, may represent an ancestral relic of a fission event that decoupled PL2A from its cognate CBM. To provide further insight into the evolution of this pectinolytic locus and the molecular basis of HG depolymerisation within Y. enterocolitica, we have resurrected a YePL2A-YeCBM32 chimera and demonstrated that the extant PL2A digests HG more efficiently. In addition, we have engineered a tryptophan from the active site of the exolytic YePL2B into YePL2A (YePL2A-K291W) and demonstrated, using X-ray crystallography of substrate complexes, that it is a structural determinant of exo-activity within the PL2 family. In this manner, surrogate structural platforms may assist in the study of phylogenetic relationships informed by extant and resurrected sequences, and can be used to overcome challenging structural problems within carbohydrate active enzyme families.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
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Guo S, Langelaan DN, Phippen SW, Smith SP, Voets IK, Davies PL. Conserved structural features anchor biofilm-associated RTX-adhesins to the outer membrane of bacteria. FEBS J 2018; 285:1812-1826. [PMID: 29575515 DOI: 10.1111/febs.14441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/05/2018] [Accepted: 03/19/2018] [Indexed: 11/30/2022]
Abstract
Repeats-in-toxin (RTX) adhesins are present in many Gram-negative bacteria to facilitate biofilm formation. Previously, we reported that the 1.5-MDa RTX adhesin (MpIBP) from the Antarctic bacterium, Marinomonas primoryensis, is tethered to the bacterial cell surface via its N-terminal Region I (RI). Here, we show the detailed structural features of RI. It has an N-terminal periplasmic retention domain (RIN), a central domain (RIM) that can insert into the β-barrel of an outer-membrane pore protein during MpIBP secretion, and three extracellular domains at its C terminus (RIC) that transition the protein into the extender region (RII). RIN has a novel β-sandwich fold with a similar shape to βγ-crystallins and tryptophan RNA attenuation proteins. Because RIM undergoes fast and extensive degradation in vitro, its narrow cylindrical shape was rapidly measured by small-angle X-ray scattering before proteolysis could occur. The crystal structure of RIC comprises three tandem β-sandwich domains similar to those in RII, but increasing in their hydrophobicity with proximity to the outer membrane. In addition, the key Ca2+ ion that rigidifies the linkers between RII domains is not present between the first two of these RIC domains. This more flexible RI linker near the cell surface can act as a 'pivot' to help the 0.6-μm-long MpIBP sweep over larger volumes to find its binding partners. Since the physical features of RI are well conserved in the RTX adhesins of many Gram-negative bacteria, our detailed structural and bioinformatic analyses serve as a model for investigating the surface retention of biofilm-forming bacteria, including human pathogens.
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Affiliation(s)
- Shuaiqi Guo
- Protein Function Discovery Group, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada.,Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, the Netherlands.,Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, the Netherlands
| | - David N Langelaan
- Protein Function Discovery Group, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Sean W Phippen
- Protein Function Discovery Group, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Steven P Smith
- Protein Function Discovery Group, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Ilja K Voets
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, the Netherlands.,Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, the Netherlands
| | - Peter L Davies
- Protein Function Discovery Group, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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Guo S, Stevens CA, Vance TDR, Olijve LLC, Graham LA, Campbell RL, Yazdi SR, Escobedo C, Bar-Dolev M, Yashunsky V, Braslavsky I, Langelaan DN, Smith SP, Allingham JS, Voets IK, Davies PL. Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. SCIENCE ADVANCES 2017; 3:e1701440. [PMID: 28808685 PMCID: PMC5550230 DOI: 10.1126/sciadv.1701440] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-μm-long adhesin using a "dissect and build" structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like β-sandwich domains that rigidify on binding Ca2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several "repeats-in-toxin" motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.
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Affiliation(s)
- Shuaiqi Guo
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
- Laboratory of Macromolecular and Organic Chemistry of Department of Chemical Engineering and Chemistry, and Laboratory of Physical Chemistry of Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
| | - Corey A. Stevens
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tyler D. R. Vance
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Luuk L. C. Olijve
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
- Laboratory of Macromolecular and Organic Chemistry of Department of Chemical Engineering and Chemistry, and Laboratory of Physical Chemistry of Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
| | - Laurie A. Graham
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Robert L. Campbell
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Saeed R. Yazdi
- Faculty of Engineering and Applied Science and Department of Chemical Engineering, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Carlos Escobedo
- Faculty of Engineering and Applied Science and Department of Chemical Engineering, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Maya Bar-Dolev
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Victor Yashunsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - David N. Langelaan
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Steven P. Smith
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - John S. Allingham
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Ilja K. Voets
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
- Laboratory of Macromolecular and Organic Chemistry of Department of Chemical Engineering and Chemistry, and Laboratory of Physical Chemistry of Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands
| | - Peter L. Davies
- Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Corresponding author.
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Grondin JM, Duan D, Kirlin AC, Abe KT, Chitayat S, Spencer HL, Spencer C, Campigotto A, Houliston S, Arrowsmith CH, Allingham JS, Boraston AB, Smith SP. Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens. PLoS One 2017; 12:e0171606. [PMID: 28158290 PMCID: PMC5291390 DOI: 10.1371/journal.pone.0171606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/23/2017] [Indexed: 02/03/2023] Open
Abstract
Clostridium perfringens is a commensal member of the human gut microbiome and an opportunistic pathogen whose genome encodes a suite of putative large, multi-modular carbohydrate-active enzymes that appears to play a role in the interaction of the bacterium with mucin-based carbohydrates. Among the most complex of these is an enzyme that contains a presumed catalytic module belonging to glycoside hydrolase family 31 (GH31). This large enzyme, which based on its possession of a GH31 module is a predicted α-glucosidase, contains a variety of non-catalytic ancillary modules, including three CBM32 modules that to date have not been characterized. NMR-based experiments demonstrated a preference of each module for galacto-configured sugars, including the ability of all three CBM32s to recognize the common mucin monosaccharide GalNAc. X-ray crystal structures of the CpGH31 CBM32s, both in apo form and bound to GalNAc, revealed the finely-tuned molecular strategies employed by these sequentially variable CBM32s in coordinating a common ligand. The data highlight that sequence similarities to previously characterized CBMs alone are insufficient for identifying the molecular mechanism of ligand binding by individual CBMs. Furthermore, the overlapping ligand binding profiles of the three CBMs provide a fail-safe mechanism for the recognition of GalNAc among the dense eukaryotic carbohydrate networks of the colonic mucosa. These findings expand our understanding of ligand targeting by large, multi-modular carbohydrate-active enzymes, and offer unique insights into of the expanding ligand-binding preferences and binding site topologies observed in CBM32s.
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Affiliation(s)
- Julie M. Grondin
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Da Duan
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alyssa C. Kirlin
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Kento T. Abe
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Seth Chitayat
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Holly L. Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Craig Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alisha Campigotto
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John S. Allingham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Steven P. Smith
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
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Grondin JM, Chitayat S, Ficko-Blean E, Houliston S, Arrowsmith CH, Boraston AB, Smith SP. An Unusual Mode of Galactose Recognition by a Family 32 Carbohydrate-Binding Module. J Mol Biol 2014; 426:869-80. [DOI: 10.1016/j.jmb.2013.11.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/30/2013] [Accepted: 11/22/2013] [Indexed: 11/27/2022]
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