1
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Jiang W. Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics. J Chem Theory Comput 2024; 20:3085-3095. [PMID: 38568961 DOI: 10.1021/acs.jctc.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the λ-exchange of free energy perturbation (FEP). Two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/λ-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.
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Affiliation(s)
- Wei Jiang
- Computational Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, Illinois 60439, United States
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2
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Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries. Commun Biol 2024; 7:298. [PMID: 38461354 PMCID: PMC10925062 DOI: 10.1038/s42003-024-05910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024] Open
Abstract
Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict .
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Affiliation(s)
- Daniele Montepietra
- Department of Chemical, Life and Environmental Sustainability Sciences, University of Parma, Parma, 43125, Italy
- Istituto Nanoscienze - CNR-NANO, Center S3, via G. Campi 213/A, 41125, Modena, Italy
| | - Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - João M Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.
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3
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Currie MJ, Davies JS, Scalise M, Gulati A, Wright JD, Newton-Vesty MC, Abeysekera GS, Subramanian R, Wahlgren WY, Friemann R, Allison JR, Mace PD, Griffin MDW, Demeler B, Wakatsuki S, Drew D, Indiveri C, Dobson RCJ, North RA. Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter. eLife 2024; 12:RP92307. [PMID: 38349818 PMCID: PMC10942642 DOI: 10.7554/elife.92307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-electron microscopy (cryo-EM) structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the Haemophilus influenzae N-acetylneuraminate TRAP transporter (HiSiaQM) at 2.99 Å resolution (extending to 2.2 Å at the core), revealing new features. The improved resolution (the previous HiSiaQM structure is 4.7 Å resolution) permits accurate assignment of two Na+ sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the HiSiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity (KD) for the complex between the soluble HiSiaP protein and HiSiaQM is in the micromolar range and that a related SiaP can bind HiSiaQM. This work provides key data that enhances our understanding of the 'elevator-with-an-operator' mechanism of TRAP transporters.
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Affiliation(s)
- Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - James S Davies
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of CalabriaArcavacata di RendeItaly
| | - Ashutosh Gulati
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Joshua D Wright
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Gayan S Abeysekera
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Ramaswamy Subramanian
- Biological Sciences and Biomedical Engineering, Bindley Bioscience Center, Purdue University West LafayetteWest LafayetteUnited States
| | - Weixiao Y Wahlgren
- Department of Chemistry and Molecular Biology, Biochemistry and Structural Biology, University of GothenburgGothenburgSweden
| | - Rosmarie Friemann
- Centre for Antibiotic Resistance Research (CARe) at University of GothenburgGothenburgSweden
| | - Jane R Allison
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of AucklandAucklandNew Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of OtagoDunedinNew Zealand
| | - Michael DW Griffin
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of MontanaMissoulaUnited States
- Department of Chemistry and Biochemistry, University of LethbridgeLethbridgeCanada
| | - Soichi Wakatsuki
- Biological Sciences Division, SLAC National Accelerator LaboratoryMenlo ParkUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of CalabriaArcavacata di RendeItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Renwick CJ Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of CanterburyChristchurchNew Zealand
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
- School of Medical Sciences, Faculty of Medicine and Health, University of SydneySydneyAustralia
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4
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Davies JS, Currie MJ, Dobson RCJ, Horne CR, North RA. TRAPs: the 'elevator-with-an-operator' mechanism. Trends Biochem Sci 2024; 49:134-144. [PMID: 38102017 DOI: 10.1016/j.tibs.2023.11.006] [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: 09/01/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are nutrient-uptake systems found in bacteria and archaea. These evolutionary divergent transporter systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport. Here, we highlight breakthrough TRAP transporter structures and recent functional data that probe the mechanism of transport. Furthermore, we discuss recent structural and biophysical studies of the ion transporter superfamily (ITS) members and highlight mechanistic principles that are relevant for further exploration of the TRAP transporter system.
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Affiliation(s)
- James S Davies
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia.
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
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5
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Peter MF, Ruland JA, Kim Y, Hendricks P, Schneberger N, Siebrasse JP, Thomas GH, Kubitscheck U, Hagelueken G. Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP. Nat Commun 2024; 15:217. [PMID: 38191530 PMCID: PMC10774421 DOI: 10.1038/s41467-023-44327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
The tripartite ATP-independent periplasmic (TRAP) transporters use an extra cytoplasmic substrate binding protein (SBP) to transport a wide variety of substrates in bacteria and archaea. The SBP can adopt an open- or closed state depending on the presence of substrate. The two transmembrane domains of TRAP transporters form a monomeric elevator whose function is strictly dependent on the presence of a sodium ion gradient. Insights from experimental structures, structural predictions and molecular modeling have suggested a conformational coupling between the membrane elevator and the substrate binding protein. Here, we use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM from Haemophilus influenzae in different conformational states. The SBP, HiSiaP, is locked in its substrate-bound form and the transmembrane elevator, HiSiaQM, is locked in either its assumed inward- or outward-facing states. We characterize the disulfide-locked constructs and use single-molecule total internal reflection fluorescence (TIRF) microscopy to study their interactions. Our experiments demonstrate that the SBP and the transmembrane elevator are indeed conformationally coupled, meaning that the open and closed state of the SBP recognize specific conformational states of the transporter and vice versa.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Jan A Ruland
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Yeojin Kim
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Philipp Hendricks
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan Peter Siebrasse
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Ulrich Kubitscheck
- Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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6
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Roden A, Engelin MK, Pos KM, Geertsma ER. Membrane-anchored substrate binding proteins are deployed in secondary TAXI transporters. Biol Chem 2023:hsz-2022-0337. [PMID: 36916166 DOI: 10.1515/hsz-2022-0337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/10/2023] [Indexed: 03/16/2023]
Abstract
Substrate-binding proteins (SBPs) are part of solute transport systems and serve to increase substrate affinity and uptake rates. In contrast to primary transport systems, the mechanism of SBP-dependent secondary transport is not well understood. Functional studies have thus far focused on Na+-coupled Tripartite ATP-independent periplasmic (TRAP) transporters for sialic acid. Herein, we report the in vitro functional characterization of TAXIPm-PQM from the human pathogen Proteus mirabilis. TAXIPm-PQM belongs to a TRAP-subfamily using a different type of SBP, designated TRAP-associated extracytoplasmic immunogenic (TAXI) protein. TAXIPm-PQM catalyzes proton-dependent α-ketoglutarate symport and its SBP is an essential component of the transport mechanism. Importantly, TAXIPm-PQM represents the first functionally characterized SBP-dependent secondary transporter that does not rely on a soluble SBP, but uses a membrane-anchored SBP instead.
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Affiliation(s)
- Anja Roden
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Melanie K Engelin
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany
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7
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Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ. Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2023; 14:1120. [PMID: 36849793 PMCID: PMC9971032 DOI: 10.1038/s41467-023-36590-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na+ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Joshua D Wright
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Jack M Copping
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Daniela M Remus
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Ashutosh Gulati
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Dustin R Morado
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Gayan S Abeysekera
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Subramanian Ramaswamy
- Biological Sciences and Biomedical Engineering, Bindley Bioscience Center, Purdue University, 1203 W State St, West Lafayette, IN 47906, USA
| | - Rosmarie Friemann
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, S-40530, Gothenburg, Sweden
| | - Soichi Wakatsuki
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jane R Allison
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036, Arcavacata di Rende, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126, Bari, Italy
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.
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8
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Bell A, Severi E, Owen CD, Latousakis D, Juge N. Biochemical and structural basis of sialic acid utilization by gut microbes. J Biol Chem 2023; 299:102989. [PMID: 36758803 PMCID: PMC10017367 DOI: 10.1016/j.jbc.2023.102989] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The human gastrointestinal (GI) tract harbors diverse microbial communities collectively known as the gut microbiota that exert a profound impact on human health and disease. The repartition and availability of sialic acid derivatives in the gut have a significant impact on the modulation of gut microbes and host susceptibility to infection and inflammation. Although N-acetylneuraminic acid (Neu5Ac) is the main form of sialic acids in humans, the sialic acid family regroups more than 50 structurally and chemically distinct modified derivatives. In the GI tract, sialic acids are found in the terminal location of mucin glycan chains constituting the mucus layer and also come from human milk oligosaccharides in the infant gut or from meat-based foods in adults. The repartition of sialic acid in the GI tract influences the gut microbiota composition and pathogen colonization. In this review, we provide an update on the mechanisms underpinning sialic acid utilization by gut microbes, focusing on sialidases, transporters, and metabolic enzymes.
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Affiliation(s)
- Andrew Bell
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Emmanuele Severi
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Dimitrios Latousakis
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom.
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9
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Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525885. [PMID: 36789411 PMCID: PMC9928041 DOI: 10.1101/2023.01.27.525885] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Here, we introduce FRETpredict, a Python software program to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses an established Rotamer Library Approach to describe the FRET probes covalently bound to the protein. The software efficiently operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We demonstrate the performance and accuracy of the software for different types of systems: a relatively structured peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). We also describe a general approach to generate new rotamer libraries for FRET probes of interest. FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict.
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Affiliation(s)
- Daniele Montepietra
- Department of Physics, Computer Science and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A 41125 Modena, Italy
- Istituto Nanoscienze – CNR-NANO, Center S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - João M. Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Micha B. A. Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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10
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Peter MF, Ruland JA, Depping P, Schneberger N, Severi E, Moecking J, Gatterdam K, Tindall S, Durand A, Heinz V, Siebrasse JP, Koenig PA, Geyer M, Ziegler C, Kubitscheck U, Thomas GH, Hagelueken G. Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2022; 13:4471. [PMID: 35927235 PMCID: PMC9352664 DOI: 10.1038/s41467-022-31907-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are found widely in bacteria and archaea and consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains). HiSiaPQM and its homologs are TRAP transporters for sialic acid and are essential for host colonization by pathogenic bacteria. Here, we reconstitute HiSiaQM into lipid nanodiscs and use cryo-EM to reveal the structure of a TRAP transporter. It is composed of 16 transmembrane helices that are unexpectedly structurally related to multimeric elevator-type transporters. The idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. A model of the tripartite PQM complex is experimentally validated and reveals the coupling of the substrate-binding protein to the transporter domains. We use single-molecule total internal reflection fluorescence (TIRF) microscopy in solid-supported lipid bilayers and surface plasmon resonance to study the formation of the tripartite complex and to investigate the impact of interface mutants. Furthermore, we characterize high-affinity single variable domains on heavy chain (VHH) antibodies that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake, providing insight into how TRAP transporter function might be inhibited in vivo.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan A Ruland
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Peer Depping
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Aston Centre for Membrane Proteins and Lipids Research, Aston St., B4 7ET, Birmingham, UK
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Emmanuele Severi
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
- Biosciences Institute, Newcastle University, Newcastle, NE2 4HH, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sarah Tindall
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Alexandre Durand
- Institut de Génétique et de Biologie Molecule et Cellulaire, 1 Rue Laurent Fries, 67404, Illkirch Cedex, France
| | - Veronika Heinz
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Jan Peter Siebrasse
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Paul-Albert Koenig
- Core Facility Nanobodies, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Ulrich Kubitscheck
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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11
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Peter MF, Gebhardt C, Mächtel R, Muñoz GGM, Glaenzer J, Narducci A, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. Nat Commun 2022; 13:4396. [PMID: 35906222 PMCID: PMC9338047 DOI: 10.1038/s41467-022-31945-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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12
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Bisson C, Salmon RC, West L, Rafferty JB, Hitchcock A, Thomas GH, Kelly DJ. The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters. FEBS J 2021; 289:436-456. [PMID: 34375507 DOI: 10.1111/febs.16156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
The organic polymer lignin is a component of plant cell walls, which like (hemi)-cellulose is highly abundant in nature and relatively resistant to degradation. However, extracellular enzymes released by natural microbial consortia can cleave the β-aryl ether linkages in lignin, releasing monoaromatic phenylpropanoids that can be further catabolised by diverse species of bacteria. Biodegradation of lignin is therefore important in global carbon cycling, and its natural abundance also makes it an attractive biotechnological feedstock for the industrial production of commodity chemicals. Whilst the pathways for degradation of lignin-derived aromatics have been extensively characterised, much less is understood about how they are recognised and taken up from the environment. The purple phototrophic bacterium Rhodopseudomonas palustris can grow on a range of phenylpropanoid monomers and is a model organism for studying their uptake and breakdown. R. palustris encodes a tripartite ATP-independent periplasmic (TRAP) transporter (TarPQM) linked to genes encoding phenylpropanoid-degrading enzymes. The periplasmic solute-binding protein component of this transporter, TarP, has previously been shown to bind aromatic substrates. Here, we determine the high-resolution crystal structure of TarP from R. palustris as well as the structures of homologous proteins from the salt marsh bacterium Sagittula stellata and the halophile Chromohalobacter salexigens, which also grow on lignin-derived aromatics. In combination with tryptophan fluorescence ligand-binding assays, our ligand-bound co-crystal structures reveal the molecular basis for high-affinity recognition of phenylpropanoids by these TRAP transporters, which have potential for improving uptake of these compounds for biotechnological transformations of lignin.
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Affiliation(s)
- Claudine Bisson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
| | - Robert C Salmon
- Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
| | - Laura West
- Department of Biology, University of York, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
| | | | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
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13
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Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021; 8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
Multicomponent transporters are used by bacteria to transport a wide range of nutrients. These systems use a substrate-binding protein to bind the nutrient with high affinity and then deliver it to a membrane-bound transporter for uptake. Nutrient uptake pathways are linked to the colonisation potential and pathogenicity of bacteria in humans and may be candidates for antimicrobial targeting. Here we review current research into bacterial multicomponent transport systems, with an emphasis on the interaction at the membrane, as well as new perspectives on the role of lipids and higher oligomers in these complex systems.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joshua D Wright
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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14
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Severi E, Rudden M, Bell A, Palmer T, Juge N, Thomas GH. Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals. Microb Genom 2021; 7. [PMID: 34184979 PMCID: PMC8461474 DOI: 10.1099/mgen.0.000614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host-microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least eight times during the evolution of bacteria, from within four of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria, including Spirochaetes, Bacteroidetes, Planctomycetes and Verrucomicrobia, many of which are species that have not been previously recognized to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonization of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.
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Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, York, UK.,Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tracy Palmer
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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15
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Naz R, Okla MK, Fatima U, Mohsin M, Soufan WH, Alaraidh IA, Abdel-Maksoud MA, Ahmad A. Designing and Development of FRET-Based Nanosensor for Real Time Analysis of N-Acetyl-5-Neuraminic Acid in Living Cells. Front Nutr 2021; 8:621273. [PMID: 34136513 PMCID: PMC8200523 DOI: 10.3389/fnut.2021.621273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/28/2021] [Indexed: 12/22/2022] Open
Abstract
N-acetyl-5-neuraminic acid (NeuAc) plays crucial role in improving the growth, brain development, brain health maintenance, and immunity enhancement of infants. Commercially, it is used in the production of antiviral drugs, infant milk formulas, cosmetics, dietary supplements, and pharmaceutical products. Because of the rapidly increasing demand, metabolic engineering approach has attracted increasing attention for NeuAc biosynthesis. However, knowledge of metabolite flux in biosynthetic pathways is one of the major challenges in the practice of metabolic engineering. So, an understanding of the flux of NeuAc is needed to determine its cellular level at real time. The analysis of the flux can only be performed using a tool that has the capacity to measure metabolite level in cells without affecting other metabolic processes. A Fluorescence Resonance Energy Transfer (FRET)-based genetically-encoded nanosensor has been generated in this study to monitor the level of NeuAc in prokaryotic and eukaryotic cells. Sialic acid periplasmic binding protein (SiaP) from Haemophilus influenzae was exploited as a sensory element for the generation of nanosensor. The enhanced cyan fluorescent protein (ECFP) and Venus were used as Fluroscence Resonance Energy Transfer (FRET) pair. The nanosensor, which was termed fluorescent indicator protein for sialic acid (FLIP-SA), was successfully transformed into, and expressed in Escherichia coli BL21 (DE3) cells. The expressed protein of the nanosensor was isolated and purified. The purified nanosensor protein was characterized to assess the affinity, specificity, and stability in the pH range. The developed nanosensor exhibited FRET change after addition to NeuAc. The developed nanosensor was highly specific, exhibited pH stability, and detected NeuAc levels in the nanomolar to milimolar range. FLIP-SA was successfully introduced in bacterial and yeast cells and reported the real-time intracellular levels of NeuAc non-invasively. The FLIP-SA is an excellent tool for the metabolic flux analysis of the NeuAc biosynthetic pathway and, thus, may help unravel the regulatory mechanism of the metabolic pathway of NeuAc. Furthermore, FLIP-SA can be used for the high-throughput screening of E. coli mutant libraries for varied NeuAc production levels.
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Affiliation(s)
- Ruphi Naz
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Mohammad K Okla
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Urooj Fatima
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Walid H Soufan
- Department of Plant Production, Faculty of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim A Alaraidh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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16
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Kim KH. Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. J Comput Aided Mol Des 2021; 35:371-396. [PMID: 33712973 DOI: 10.1007/s10822-021-00377-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein-ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein-ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein-ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR.
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17
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Schäfer L, Meinert-Berning C, Kobus S, Höppner A, Smits SHJ, Steinbüchel A. Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T. FEBS J 2021; 288:4905-4917. [PMID: 33630388 DOI: 10.1111/febs.15789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/01/2022]
Abstract
Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7T , was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP-independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple sugar acid ligands. Protein crystals were obtained with bound d-xylonic acid, d-fuconic acid d-galactonic and d-gluconic acid, respectively. The protein shows the typical structure of an SBP of a tripartite ATP-independent periplasmic transporter consisting of two domains linked by a hinge and spanned by a long α-helix. By analysis of the structure, the substrate binding site of the protein was identified. The carboxylic group of the sugar acids interacts with Arg175, whereas the coordination of the hydroxylic groups at positions C2 and C3 is most probably realized by Arg154 and Asn151. Furthermore, it was observed that 2-keto-3-deoxy-d-gluconic acid is bound in protein crystals that were crystallized without the addition of any ligand, indicating that this molecule is prebound to the protein and is displaced by the other ligands if they are available. DATABASE: Structural data of CxaP complexes are available in the worldwide Protein Data Bank (https://www.rcsb.org) under the accession codes 7BBR (2-keto-3-deoxy-d-gluconic acid), 7BCR (d-galactonic acid), 7BCN (d-xylonic acid), 7BCO (d-fuconic acid) and 7BCP (d-gluconic acid).
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Affiliation(s)
- Lukas Schäfer
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Christina Meinert-Berning
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander Steinbüchel
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Peter MF, Gebhardt C, Glaenzer J, Schneberger N, de Boer M, Thomas GH, Cordes T, Hagelueken G. Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates. J Mol Biol 2021; 433:166756. [PMID: 33316271 DOI: 10.1016/j.jmb.2020.166756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
The pathogens Vibrio cholerae and Haemophilus influenzae use tripartite ATP-independent periplasmic transporters (TRAPs) to scavenge sialic acid from host tissues. They use it as a nutrient or to evade the innate immune system by sialylating surface lipopolysaccharides. An essential component of TRAP transporters is a periplasmic substrate binding protein (SBP). Without substrate, the SBP has been proposed to rest in an open-state, which is not recognised by the transporter. Substrate binding induces a conformational change of the SBP and it is thought that this closed state is recognised by the transporter, triggering substrate translocation. Here we use real time single molecule FRET experiments and crystallography to investigate the open- to closed-state transition of VcSiaP, the SBP of the sialic acid TRAP transporter from V. cholerae. We show that the conformational switching of VcSiaP is strictly substrate induced, confirming an important aspect of the proposed transport mechanism. Two new crystal structures of VcSiaP provide insights into the closing mechanism. While the first structure contains the natural ligand, sialic acid, the second structure contains an artificial peptide in the sialic acid binding site. Together, the two structures suggest that the ligand itself stabilises the closed state and that SBP closure is triggered by physically bridging the gap between the two lobes of the SBP. Finally, we demonstrate that the affinity for the artificial peptide substrate can be substantially increased by varying its amino acid sequence and by this, serve as a starting point for the development of peptide-based inhibitors of TRAP transporters.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany.
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19
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Arthisri AS, Sathiyamoorthy A, Meenakshi B, Chandran CR. Ratio of Salivary Sialic Acid to Fucose as Tumor Markers in Potentially Malignant Disorders and Oral Cancer. Contemp Clin Dent 2020; 11:131-135. [PMID: 33110325 PMCID: PMC7583536 DOI: 10.4103/ccd.ccd_336_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/21/2020] [Accepted: 06/07/2020] [Indexed: 12/02/2022] Open
Abstract
Background: Lack of noninvasive and economically feasible laboratory investigations in the early detection of cancer is a set-back in the prognosis of oral cancer (OC) patients. Aims: The aim of the study was to evaluate the ratio of sialic acid to fucose in salivary samples of OC and oral potentially malignant disorder (OPMD) patients. Materials and Methods: A total of 60 participants were selected and divided into three groups based on clinical and histopathological diagnosis: OC patients (n = 20), OPMD patients (n = 20), and healthy patients (n = 20). Unstimulated whole saliva of 1.5 ml was collected from the selected individuals for evaluating the salivary levels of sialic acid and fucose using the biochemical assay. Results: The difference in mean salivary sialic acid and fucose among the study groups was statistically significant (P = 0.001); one-way analysis of variance. The mean sialic acid to fucose ratio in the control group, OPMD group, and OC group were 0.34 mg/dl, 0.88 mg/dl, and 0.89 mg/dl, respectively. OC patients had significant elevation in the levels of salivary sialic acid, fucose, and their ratios (P = 0.001, P = 0.001, P = 0.003, respectively); Tukey's post hoc test. Conclusions: The ratio of salivary sialic acid to fucose is a predictable tumor marker for the diagnosis of OC. Further investigations are required to evaluate the influence of OC grading on this diagnostic marker.
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Affiliation(s)
- Anandhi Sekar Arthisri
- Department of Oral Medicine and Radiology, Ragas Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Asokan Sathiyamoorthy
- Department of Oral Medicine and Radiology, Tagore Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Bhagavatham Meenakshi
- Department of Biochemistry, Tagore Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Chitraa R Chandran
- Department of Periodontics, Tagore Dental College and Hospital, Chennai, Tamil Nadu, India
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20
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Cramer J, Jiang X, Schönemann W, Silbermann M, Zihlmann P, Siegrist S, Fiege B, Jakob RP, Rabbani S, Maier T, Ernst B. Enhancing the enthalpic contribution of hydrogen bonds by solvent shielding. RSC Chem Biol 2020; 1:281-287. [PMID: 34458766 PMCID: PMC8341794 DOI: 10.1039/d0cb00108b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
In biological systems, polar interactions are heavily burdened by high desolvation penalties resulting from strong solute-solvent interactions. As a consequence thereof, enthalpic contributions of hydrogen bonds to the free energy of binding are severely diminished. However, this effect is strongly attenuated for interactions within solvent-shielded areas of proteins. In microcalorimetric experiments, we show that the bacterial lectin FimH utilizes conformational adaptions to effectively shield its binding site from solvent. The transition into a lower dielectric environment results in an enthalpic benefit of approximately -13 kJ mol-1 for mannoside binding. However, this effect can be abrogated, if the hydrogen bond network within the binding site is disturbed by deoxygenation of the ligand. Conformational adaption leading to reduced local dielectric constants could represent a general mechanism for proteins to enable enthalpy-driven recognition of polar ligands.
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Affiliation(s)
- Jonathan Cramer
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Xiaohua Jiang
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Wojciech Schönemann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marleen Silbermann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Pascal Zihlmann
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Stefan Siegrist
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Brigitte Fiege
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman Peter Jakob
- Institute of Structural Biology, University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Said Rabbani
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Timm Maier
- Institute of Structural Biology, University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Bell A, Severi E, Lee M, Monaco S, Latousakis D, Angulo J, Thomas GH, Naismith JH, Juge N. Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J Biol Chem 2020; 295:13724-13736. [PMID: 32669363 PMCID: PMC7535918 DOI: 10.1074/jbc.ra120.014454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro-N-acetylneuraminic acid intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.
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Affiliation(s)
- Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Micah Lee
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dimitrios Latousakis
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-US), Sevilla, Spain
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.
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Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nat Microbiol 2019; 4:2393-2404. [PMID: 31636419 PMCID: PMC6881182 DOI: 10.1038/s41564-019-0590-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/12/2019] [Indexed: 12/26/2022]
Abstract
Sialic acid (Neu5Ac) is commonly found in terminal location of colonic mucins glycans where it is a much-coveted nutrient for gut bacteria including Ruminococcus gnavus. R. gnavus is part of the healthy gut microbiota in humans but shows a disproportionate representation in diseases. There is therefore a need in understanding the molecular mechanisms underpinning its adaptation to the gut. Previous in vitro work demonstrated that R. gnavus mucin glycan-foraging strategy is strain-dependent and associated with the expression of an intramolecular trans-sialidase releasing 2,7-anhydro-Neu5Ac instead of Neu5Ac from mucins. Here, we have unravelled the metabolism pathway of 2,7-anhydro-Neu5Ac in R. gnavus which is underpinned by the exquisite specificity of the sialic transporter for 2,7-anhydro-Neu5Ac, and by the action of an oxidoreductase converting 2,7-anhydro-Neu5Ac into Neu5Ac which then becomes substrate of a Neu5Ac-specific aldolase. Having generated a R. gnavus nan cluster deletion mutant that lost the ability to grow on sialylated substrates, we showed that in gnotobiotic mice colonised with R. gnavus wild-type and mutant strains, the fitness of the nan mutant was significantly impaired with a reduced ability to colonise the mucus layer. Overall, our study revealed a unique sialic acid pathway in bacteria, with significant implications for the spatial adaptation of mucin-foraging gut symbionts in health and disease.
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Darby JF, Hopkins AP, Shimizu S, Roberts SM, Brannigan JA, Turkenburg JP, Thomas GH, Hubbard RE, Fischer M. Water Networks Can Determine the Affinity of Ligand Binding to Proteins. J Am Chem Soc 2019; 141:15818-15826. [DOI: 10.1021/jacs.9b06275] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Adam P. Hopkins
- Demuris Ltd., The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne NE4 5BX, United Kingdom
| | | | | | | | | | | | - Roderick E. Hubbard
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, and Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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24
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Marinelli F, Fiorin G. Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements. Structure 2019; 27:359-370.e12. [PMID: 30528595 PMCID: PMC6860373 DOI: 10.1016/j.str.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/06/2018] [Accepted: 10/18/2018] [Indexed: 11/17/2022]
Abstract
Double electron-electron resonance (DEER) is a popular technique that exploits attached spin labels to probe the collective dynamics of biomolecules in a native environment. Like most spectroscopic approaches, DEER detects an ensemble of states accounting for biomolecular dynamics as well as the labels' intrinsic flexibility. Hence, the DEER data alone do not provide high-resolution structural information. To disentangle this variability, we introduce a minimally biased simulation method to sample a structural ensemble that reproduces multiple experimental signals within the uncertainty. In contrast to previous approaches, our method targets the raw data themselves, and thereby it brings forth an unbiased molecular interpretation of the experiments. After validation on the T4 lysozyme, we apply this technique to interpret recent DEER experiments on a membrane transporter binding protein (VcSiaP). The results highlight the large-scale conformational movement that occurs upon substrate binding and reveal that the unbound VcSiaP is more open in solution than the X-ray structure.
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Affiliation(s)
- Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA.
| | - Giacomo Fiorin
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
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25
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Gangi Setty T, Mowers JC, Hobbs AG, Maiya SP, Syed S, Munson RS, Apicella MA, Subramanian R. Molecular characterization of the interaction of sialic acid with the periplasmic binding protein from Haemophilus ducreyi. J Biol Chem 2018; 293:20073-20084. [PMID: 30315109 DOI: 10.1074/jbc.ra118.005151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/11/2018] [Indexed: 12/18/2022] Open
Abstract
The primary role of bacterial periplasmic binding proteins is sequestration of essential metabolites present at a low concentration in the periplasm and making them available for active transporters that transfer these ligands into the bacterial cell. The periplasmic binding proteins (SiaPs) from the tripartite ATP-independent periplasmic (TRAP) transport system that transports mammalian host-derived sialic acids have been well studied from different pathogenic bacteria, including Haemophilus influenzae, Fusobacterium nucleatum, Pasteurella multocida, and Vibrio cholerae SiaPs bind the sialic acid N-acetylneuraminic acid (Neu5Ac) with nanomolar affinity by forming electrostatic and hydrogen-bonding interactions. Here, we report the crystal structure of a periplasmic binding protein (SatA) of the ATP-binding cassette (ABC) transport system from the pathogenic bacterium Haemophilus ducreyi The structure of Hd-SatA in the native form and sialic acid-bound forms (with Neu5Ac and N-glycolylneuraminic acid (Neu5Gc)), determined to 2.2, 1.5, and 2.5 Å resolutions, respectively, revealed a ligand-binding site that is very different from those of the SiaPs of the TRAP transport system. A structural comparison along with thermodynamic studies suggested that similar affinities are achieved in the two classes of proteins through distinct mechanisms, one enthalpically driven and the other entropically driven. In summary, our structural and thermodynamic characterization of Hd-SatA reveals that it binds sialic acids with nanomolar affinity and that this binding is an entropically driven process. This information is important for future structure-based drug design against this pathogen and related bacteria.
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Affiliation(s)
- Thanuja Gangi Setty
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India,; the University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Jonathan C Mowers
- the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Aaron G Hobbs
- the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Shubha P Maiya
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India
| | - Sanaa Syed
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India
| | - Robert S Munson
- the Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210, and
| | - Michael A Apicella
- Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Ramaswamy Subramanian
- From the Institute for Stem Cell Biology and Regenerative Medicine, GKVK Post, Bangalore 560065, India,; the Departments of Biochemistry and Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.
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26
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Studying structure and function of membrane proteins with PELDOR/DEER spectroscopy – The crystallographers’ perspective. Methods 2018; 147:163-175. [DOI: 10.1016/j.ymeth.2018.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/20/2018] [Accepted: 03/01/2018] [Indexed: 12/16/2022] Open
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Substrate-bound outward-open structure of a Na +-coupled sialic acid symporter reveals a new Na + site. Nat Commun 2018; 9:1753. [PMID: 29717135 PMCID: PMC5931594 DOI: 10.1038/s41467-018-04045-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/28/2018] [Indexed: 01/03/2023] Open
Abstract
Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport.
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28
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Rosa LT, Bianconi ME, Thomas GH, Kelly DJ. Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity. Front Cell Infect Microbiol 2018; 8:33. [PMID: 29479520 PMCID: PMC5812351 DOI: 10.3389/fcimb.2018.00033] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/25/2018] [Indexed: 11/18/2022] Open
Abstract
The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of β-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the β-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport.
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Affiliation(s)
- Leonardo T Rosa
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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29
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Xu X, Tong T, Yang X, Pan Y, Lin L, Li C. Differences in survival, virulence and biofilm formation between sialidase-deficient and W83 wild-type Porphyromonas gingivalis strains under stressful environmental conditions. BMC Microbiol 2017; 17:178. [PMID: 28821225 PMCID: PMC5563019 DOI: 10.1186/s12866-017-1087-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/09/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis is a major causative pathogen of chronic periodontitis. Within the inflammatory microenvironment, there exists extreme pH values, elevated temperatures and oxidative stress. Pathogens adapt to these stressful environmental conditions by regulating the transcription of virulence genes, modifying themselves with macromolecules and by aggregating and entering into a biofilm growth phase. Our previous study showed that the P. gingivalis sialidase can help cells obtain sialic acid from the environment, which is used to modify macromolecules on the surface of P. gingivalis cells. In this study, we compared the survival, virulence factors and biofilm formation of a sialidase-deficient strain (ΔPG0352) and the wild-type P. gingivalis W83 strain under various pH values, temperatures and oxidative stress conditions to identify the roles of sialidase in the adaptation of P. gingivalis to stressful conditions. RESULTS Compared to the growth of the P. gingivalis W83 strain, the growth of the △PG0352 was more inhibited by oxidative stress (0.25 and 0.5 mM H2O2) and exhibited greater cell structure damage when treated with H2O2 as assessed by transmission electron microscopy. Both Lys-gingipain (Kgp) and Arg-gingipain (Rgp) activities were lower in the ΔPG0352 than those in the P. gingivalis W83 strain under all the assayed culture conditions. The lipopolysaccharide (LPS) activity of the W83 strain was higher than that of the ΔPG0352 under acidic conditions (pH 5.0), but no differences between the strains were observed under other conditions. Compared to the biofilms formed by P. gingivalis W83, those formed by the ΔPG0352 were decreased and discontinuous under acidic, alkaline and oxidative stress conditions. CONCLUSION Compared to the P. gingivalis W83 strain, the survival, virulence and biofilm formation of the ΔPG0352 were decreased under stressful environmental conditions.
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Affiliation(s)
- Xiaoyu Xu
- Department of Periodontics, School of Stomatology, China Medical University, No.117 Nanjing North Street, Heping District, Shenyang, Liaoning China
| | - Tong Tong
- Department of Periodontics, School of Stomatology, China Medical University, No.117 Nanjing North Street, Heping District, Shenyang, Liaoning China
- Department of Stomatology, Anshan Shuangshan Hospital, Anshan, Liaoning China
| | - Xue Yang
- Shenyang Medical College, Shenyang, Liaoning China
| | - Yaping Pan
- Department of Periodontics, School of Stomatology, China Medical University, No.117 Nanjing North Street, Heping District, Shenyang, Liaoning China
| | - Li Lin
- Department of Periodontics, School of Stomatology, China Medical University, No.117 Nanjing North Street, Heping District, Shenyang, Liaoning China
| | - Chen Li
- Department of Periodontics, School of Stomatology, China Medical University, No.117 Nanjing North Street, Heping District, Shenyang, Liaoning China
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30
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Sialic acid acquisition in bacteria-one substrate, many transporters. Biochem Soc Trans 2017; 44:760-5. [PMID: 27284039 DOI: 10.1042/bst20160056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/17/2022]
Abstract
The sialic acids are a family of 9-carbon sugar acids found predominantly on the cell-surface glycans of humans and other animals within the Deuterostomes and are also used in the biology of a wide range of bacteria that often live in association with these animals. For many bacteria sialic acids are simply a convenient source of food, whereas for some pathogens they are also used in immune evasion strategies. Many bacteria that use sialic acids derive them from the environment and so are dependent on sialic acid uptake. In this mini-review I will describe the discovery and characterization of bacterial sialic acids transporters, revealing that they have evolved multiple times across multiple diverse families of transporters, including the ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), major facilitator superfamily (MFS) and sodium solute symporter (SSS) transporter families. In addition there is evidence for protein-mediated transport of sialic acids across the outer membrane of Gram negative bacteria, which can be coupled to periplasmic processing of different sialic acids to the most common form, β-D-N-acetylneuraminic acid (Neu5Ac) that is most frequently taken up into the cell.
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31
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Glaenzer J, Peter MF, Thomas GH, Hagelueken G. PELDOR Spectroscopy Reveals Two Defined States of a Sialic Acid TRAP Transporter SBP in Solution. Biophys J 2017; 112:109-120. [PMID: 28076802 DOI: 10.1016/j.bpj.2016.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/29/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022] Open
Abstract
The tripartite ATP-independent periplasmic (TRAP) transporters are a widespread class of membrane transporters in bacteria and archaea. Typical substrates for TRAP transporters are organic acids including the sialic acid N-acetylneuraminic acid. The substrate binding proteins (SBP) of TRAP transporters are the best studied component and are responsible for initial high-affinity substrate binding. To better understand the dynamics of the ligand binding process, pulsed electron-electron double resonance (PELDOR, also known as DEER) spectroscopy was applied to study the conformational changes in the N-acetylneuraminic acid-specific SBP VcSiaP. The protein is the SBP of VcSiaPQM, a sialic acid TRAP transporter from Vibrio cholerae. Spin-labeled double-cysteine mutants of VcSiaP were analyzed in the substrate-bound and -free state and the measured distances were compared to available crystal structures. The data were compatible with two clear states only, which are consistent with the open and closed forms seen in TRAP SBP crystal structures. Substrate titration experiments demonstrated the transition of the population from one state to the other with no other observed forms. Mutants of key residues involved in ligand binding and/or proposed to be involved in domain closure were produced and the corresponding PELDOR experiments reveal important insights into the open-closed transition. The results are in excellent agreement with previous in vivo sialylation experiments. The structure of the spin-labeled Q54R1/L173R1 R125A mutant was solved at 2.1 Å resolution, revealing no significant changes in the protein structure. Thus, the loss of domain closure appears to be solely due to loss of binding. In conclusion, these data are consistent with TRAP SBPs undergoing a simple two-state transition from an open-unliganded to closed-liganded state during the transport cycle.
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Affiliation(s)
- Janin Glaenzer
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Martin F Peter
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | - Gregor Hagelueken
- Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany.
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Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase. Proc Natl Acad Sci U S A 2017; 114:7222-7227. [PMID: 28652365 DOI: 10.1073/pnas.1708217114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithm to reconstruct structural information from single-particle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.
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33
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Thomas GH. On the pull: periplasmic trapping of sugars before transport. Mol Microbiol 2017; 104:883-888. [PMID: 28407314 DOI: 10.1111/mmi.13691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2017] [Indexed: 11/28/2022]
Abstract
Bacteria have evolved many routes for taking up nutrients, demonstrating great versatility in the types and mechanism of uptake used in different physiological conditions. The discovery of a single transporter in the bacterium Advenella mimigardefordensis for the uptake of five different sugars, including L-glucose and D-xylose, is described in this issue (Meinert et al., ), providing yet another example of the surprising adaptability of bacterial transport strategies. The transporter identified is a tripartite ATP-independent (TRAP) transporter, not previously associated with sugar transport, and in fact does not transport the sugars directly at all, rather requiring them to be converted in the periplasm to their respective sugar acid forms before transport through what appears to be a novel general sugar acid transporter. In this commentary, I describe how this process is consistent with the known mechanisms of TRAP transporters and consider how the role of sugar oxidation, or oxidative fermentation, operates with multiple hexose and pentose sugars. Finally I suggest that the periplasmic conversion of nutrients acquired across the outer membrane, before transport across the inner membrane, could have potentially useful biological functions in Gram negative bacteria.
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Affiliation(s)
- Gavin H Thomas
- Department of Biology, Wentworth Way, University of York, York, UK, YO10 5DD
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Meinert C, Senger J, Witthohn M, Wübbeler JH, Steinbüchel A. Carbohydrate uptake in Advenella mimigardefordensis strain DPN7 T is mediated by periplasmic sugar oxidation and a TRAP-transport system. Mol Microbiol 2017; 104:916-930. [PMID: 28407382 DOI: 10.1111/mmi.13692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2017] [Indexed: 11/28/2022]
Abstract
In this study, we investigated an SBP (DctPAm ) of a tripartite ATP-independent periplasmic transport system (TRAP) in Advenella mimigardefordensis strain DPN7T . Deletion of dctPAm as well as of the two transmembrane compounds of the tripartite transporter, dctQ and dctM, impaired growth of A. mimigardefordensis strain DPN7T , if cultivated on mineral salt medium supplemented with d-glucose, d-galactose, l-arabinose, d-fucose, d-xylose or d-gluconic acid, respectively. The wild type phenotype was restored during complementation studies of A. mimigardefordensis ΔdctPAm using the broad host vector pBBR1MCS-5::dctPAm . Furthermore, an uptake assay with radiolabeled [14 C(U)]-d-glucose clearly showed that the deletion of dctPAm , dctQ and dctM, respectively, disabled the uptake of this aldoses in cells of either mutant strain. Determination of KD performing thermal shift assays showed a shift in the melting temperature of DctPAm in the presence of d-gluconic acid (KD 11.76 ± 1.3 µM) and the corresponding aldonic acids to the above-mentioned carbohydrates d-galactonate (KD 10.72 ± 1.4 µM), d-fuconic acid (KD 13.50 ± 1.6 µM) and d-xylonic acid (KD 8.44 ± 1.0 µM). The sugar (glucose) dehydrogenase activity (E.C.1.1.5.2) in the membrane fraction was shown for all relevant sugars, proving oxidation of the molecules in the periplasm, prior to transport.
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Affiliation(s)
- Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Jana Senger
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Marco Witthohn
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, D-48149, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Jeschke G. The Making and Breaking of a Substrate Trap. Biophys J 2017; 112:1-2. [DOI: 10.1016/j.bpj.2016.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022] Open
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Mitchell JA, Whitfield JH, Zhang WH, Henneberger C, Janovjak H, O’Mara ML, Jackson CJ. Rangefinder: A Semisynthetic FRET Sensor Design Algorithm. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Mitchell
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Jason H. Whitfield
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - William H. Zhang
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Christian Henneberger
- Institute
of Neurology, University College London, London, WC1E 6BT, United Kingdom
- German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
- Institute
of Cellular Neurosciences, University of Bonn, 53113 Bonn, Germany
| | - Harald Janovjak
- Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Megan L. O’Mara
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, 2601, Australia
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Involvement of Agrobacterium tumefaciens Galacturonate Tripartite ATP-Independent Periplasmic (TRAP) Transporter GaaPQM in Virulence Gene Expression. Appl Environ Microbiol 2015; 82:1136-1146. [PMID: 26637603 DOI: 10.1128/aem.02891-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/01/2015] [Indexed: 11/20/2022] Open
Abstract
Monosaccharides capable of serving as nutrients for the soil bacterium Agrobacterium tumefaciens are also inducers of the vir regulon present in the tumor-inducing (Ti) plasmid of this plant pathogen. One such monosaccharide is galacturonate, the predominant monomer of pectin found in plant cell walls. This ligand is recognized by the periplasmic sugar binding protein ChvE, which interacts with the VirA histidine kinase that controls vir gene expression. Although ChvE is also a member of the ChvE-MmsAB ABC transporter involved in the utilization of many neutral sugars, it is not involved in galacturonate utilization. In this study, a putative tripartite ATP-independent periplasmic (TRAP) transporter, GaaPQM, is shown to be essential for the utilization of galacturonic acid; we show that residue R169 in the predicted sugar binding site of the GaaP is required for activity. The gene upstream of gaaPQM (gaaR) encodes a member of the GntR family of regulators. GaaR is shown to repress the expression of gaaPQM, and the repression is relieved in the presence of the substrate for GaaPQM. Moreover, GaaR is shown to bind putative promoter regions in the sequences required for galacturonic acid utilization. Finally, A. tumefaciens strains carrying a deletion of gaaPQM are more sensitive to galacturonate as an inducer of vir gene expression, while the overexpression of gaaPQM results in strains being less sensitive to this vir inducer. This supports a model in which transporter activity is crucial in ensuring that vir gene expression occurs only at sites of high ligand concentration, such as those at a plant wound site.
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Fischer M, Hopkins AP, Severi E, Hawkhead J, Bawdon D, Watts AG, Hubbard RE, Thomas GH. Tripartite ATP-independent Periplasmic (TRAP) Transporters Use an Arginine-mediated Selectivity Filter for High Affinity Substrate Binding. J Biol Chem 2015; 290:27113-27123. [PMID: 26342690 PMCID: PMC4646407 DOI: 10.1074/jbc.m115.656603] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Indexed: 11/21/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are secondary transporters that have evolved an obligate dependence on a substrate-binding protein (SBP) to confer unidirectional transport. Different members of the DctP family of TRAP SBPs have binding sites that recognize a diverse range of organic acid ligands but appear to only share a common electrostatic interaction between a conserved arginine and a carboxylate group in the ligand. We investigated the significance of this interaction using the sialic acid-specific SBP, SiaP, from the Haemophilus influenzae virulence-related SiaPQM TRAP transporter. Using in vitro, in vivo, and structural methods applied to SiaP, we demonstrate that the coordination of the acidic ligand moiety of sialic acid by the conserved arginine (Arg-147) is essential for the function of the transporter as a high affinity scavenging system. However, at high substrate concentrations, the transporter can function in the absence of Arg-147 suggesting that this bi-molecular interaction is not involved in further stages of the transport cycle. As well as being required for high affinity binding, we also demonstrate that the Arg-147 is a strong selectivity filter for carboxylate-containing substrates in TRAP transporters by engineering the SBP to recognize a non-carboxylate-containing substrate, sialylamide, through water-mediated interactions. Together, these data provide biochemical and structural support that TRAP transporters function predominantly as high affinity transporters for carboxylate-containing substrates.
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Affiliation(s)
- Marcus Fischer
- York Structural Biology Laboratory, Departments of Chemistry, University of York, P. O. Box 373, York YO10 5YW
| | - Adam P Hopkins
- York Structural Biology Laboratory, Departments of Biology (Area 10), University of York, P. O. Box 373, York YO10 5YW
| | - Emmanuele Severi
- York Structural Biology Laboratory, Departments of Chemistry, University of York, P. O. Box 373, York YO10 5YW
| | - Judith Hawkhead
- York Structural Biology Laboratory, Departments of Biology (Area 10), University of York, P. O. Box 373, York YO10 5YW
| | - Daniel Bawdon
- York Structural Biology Laboratory, Departments of Biology (Area 10), University of York, P. O. Box 373, York YO10 5YW
| | - Andrew G Watts
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Roderick E Hubbard
- York Structural Biology Laboratory, Departments of Chemistry, University of York, P. O. Box 373, York YO10 5YW
| | - Gavin H Thomas
- York Structural Biology Laboratory, Departments of Biology (Area 10), University of York, P. O. Box 373, York YO10 5YW.
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Gangi Setty T, Cho C, Govindappa S, Apicella MA, Ramaswamy S. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1801-11. [PMID: 25004958 PMCID: PMC4089482 DOI: 10.1107/s139900471400830x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 04/12/2014] [Indexed: 11/10/2022]
Abstract
Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.
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Affiliation(s)
- Thanuja Gangi Setty
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065, India
| | - Christine Cho
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Sowmya Govindappa
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065, India
| | - Michael A. Apicella
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - S. Ramaswamy
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065, India
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Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species. Biochem J 2014; 458:499-511. [PMID: 24351045 PMCID: PMC3969230 DOI: 10.1042/bj20131415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many human-dwelling bacteria acquire sialic acid for growth or surface display. We identified previously a sialic acid utilization operon in Tannerella forsythia that includes a novel outer membrane sialic acid-transport system (NanOU), where NanO (neuraminate outer membrane permease) is a putative TonB-dependent receptor and NanU (extracellular neuraminate uptake protein) is a predicted SusD family protein. Using heterologous complementation of nanOU genes into an Escherichia coli strain devoid of outer membrane sialic acid permeases, we show that the nanOU system from the gut bacterium Bacteroides fragilis is functional and demonstrate its dependence on TonB for function. We also show that nanU is required for maximal function of the transport system and that it is expressed in a sialic acid-responsive manner. We also show its cellular localization to the outer membrane using fractionation and immunofluorescence experiments. Ligand-binding studies revealed high-affinity binding of sialic acid to NanU (Kd ~400 nM) from two Bacteroidetes species as well as binding of a range of sialic acid analogues. Determination of the crystal structure of NanU revealed a monomeric SusD-like structure containing a novel motif characterized by an extended kinked helix that might determine sugar-binding specificity. The results of the present study characterize the first bacterial extracellular sialic acid-binding protein and define a sialic acid-specific PUL (polysaccharide utilization locus).
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The sensor kinase DctS forms a tripartite sensor unit with DctB and DctA for sensing C4-dicarboxylates in Bacillus subtilis. J Bacteriol 2013; 196:1084-93. [PMID: 24375102 DOI: 10.1128/jb.01154-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The DctSR two-component system of Bacillus subtilis controls the expression of the aerobic C4-dicarboxylate transporter DctA. Deletion of DctA leads to an increased dctA expression. The inactivation of DctB, an extracellular binding protein, is known to inhibit the expression of dctA. Here, interaction between the sensor kinase DctS and the transporter DctA as well as the binding protein DctB was demonstrated in vivo using streptavidin (Strep) or His protein interaction experiments (mSPINE or mHPINE), and the data suggest that DctA and DctB act as cosensors for DctS. The interaction between DctS and DctB was also confirmed by the bacterial two-hybrid system (BACTH). In contrast, no indication was obtained for a direct interaction between the transporter DctA and the binding protein DctB. Activity levels of uptake of [(14)C]succinate by bacteria that expressed DctA from a plasmid were similar in the absence and the presence of DctB, demonstrating that the binding protein DctB is not required for transport. Thus, DctB is involved not in transport but in cosensing with DctS, highlighting DctB as the first example of a TRAP-type binding protein that acts as a cosensor. The simultaneous presence of DctS/DctB and DctS/DctA sensor pairs and the lack of direct interaction between the cosensors DctA and DctB indicate the formation of a tripartite complex via DctS. It is suggested that the DctS/DctA/DctB complex forms the functional unit for C4-dicarboxylate sensing in B. subtilis.
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Hopkins AP, Hawkhead JA, Thomas GH. Transport and catabolism of the sialic acids N-glycolylneuraminic acid and 3-keto-3-deoxy-D-glycero-D-galactonononic acid by Escherichia coli K-12. FEMS Microbiol Lett 2013; 347:14-22. [PMID: 23848303 DOI: 10.1111/1574-6968.12213] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/21/2013] [Accepted: 07/05/2013] [Indexed: 11/29/2022] Open
Abstract
Escherichia coli can transport and catabolize the common sialic acid, N-acetylneuraminic acid (Neu5Ac), as a sole source of carbon and nitrogen, which is an important mucus-derived carbon source in the mammalian gut. Herein we demonstrate that E. coli can also grow efficiently on the related sialic acids, N-glycolylneuraminic acid (Neu5Gc) and 3-keto-3-deoxy-D-glycero-D-galactonononic acid (KDN), which are transported via the sialic acid transporter NanT and catabolized using the sialic acid aldolase NanA. Catabolism of Neu5Gc uses the same pathway as Neu5Ac, likely producing glycolate instead and acetate during its breakdown and catabolism of KDN requires NanA activity, while other components of the Neu5Ac catabolism pathway are non-essential. We also demonstrate that these two sialic acids can support growth of an E. coli ∆nanT strain expressing sialic acid transporters from two bacterial pathogens, namely the tripartite ATP-independent periplasmic transporter SiaPQM from Haemophilus influenzae and the sodium solute symport transporter STM1128 from Salmonella enterica ssp. Typhimurium, suggesting that the ability to use Neu5Gc and KDN in addition to Neu5Ac is present in a number of human pathogens.
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Affiliation(s)
- Adam P Hopkins
- Department of Biology, University of York, Heslington, York, UK
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Murphy TF, Chonmaitree T, Barenkamp S, Kyd J, Nokso-Koivisto J, Patel JA, Heikkinen T, Yamanaka N, Ogra P, Swords WE, Sih T, Pettigrew MM. Panel 5: Microbiology and immunology panel. Otolaryngol Head Neck Surg 2013; 148:E64-89. [PMID: 23536533 DOI: 10.1177/0194599812459636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The objective is to perform a comprehensive review of the literature from January 2007 through June 2011 on the virology, bacteriology, and immunology related to otitis media. DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS Three subpanels with co-chairs comprising experts in the virology, bacteriology, and immunology of otitis media were formed. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a second draft was created. The entire panel met at the 10th International Symposium on Recent Advances in Otitis Media in June 2011 and discussed the review and refined the content further. A final draft was created, circulated, and approved by the panel. CONCLUSION Excellent progress has been made in the past 4 years in advancing an understanding of the microbiology and immunology of otitis media. Advances include laboratory-based basic studies, cell-based assays, work in animal models, and clinical studies. IMPLICATIONS FOR PRACTICE The advances of the past 4 years formed the basis of a series of short-term and long-term research goals in an effort to guide the field. Accomplishing these goals will provide opportunities for the development of novel interventions, including new ways to better treat and prevent otitis media.
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Affiliation(s)
- Timothy F Murphy
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, USA.
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Substrate-induced conformational changes in the S-component ThiT from an energy coupling factor transporter. Structure 2013; 21:861-7. [PMID: 23602660 DOI: 10.1016/j.str.2013.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/20/2013] [Accepted: 03/08/2013] [Indexed: 01/30/2023]
Abstract
Energy coupling factor (ECF) transporters are a recently discovered class of ABC transporters that mediate vitamin uptake in prokaryotes. Characteristic for ECF-type ABC transporters are small integral membrane proteins (S-components) that bind the transported substrates with high affinity. S-components associate with a second membrane protein (EcfT) and two peripheral ATPases to form a complete ATP-dependent transporter. Here, we have used EPR spectroscopy, stopped-flow fluorescence spectroscopy, and molecular dynamics simulations to determine the structural rearrangements that take place in the S-component ThiT from Lactococcus lactis upon binding of thiamin. Thiamin-induced conformational changes were confined to the long and partially membrane-embedded loop between transmembrane helices 1 and 2 that acts as a lid to occlude the binding site. The results indicate that solitary ThiT functions as a bona fide high-affinity substrate binding protein, which lacks a translocation pathway within the protein.
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Salmon RC, Cliff MJ, Rafferty JB, Kelly DJ. The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates. PLoS One 2013; 8:e59844. [PMID: 23555803 PMCID: PMC3610893 DOI: 10.1371/journal.pone.0059844] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791–1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with Kd values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782–1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar Kd values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.
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Affiliation(s)
- Robert C. Salmon
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - John B. Rafferty
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
- * E-mail: (JR); (DJK)
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
- * E-mail: (JR); (DJK)
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Bourdès A, Rudder S, East AK, Poole PS. Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols. PLoS One 2012; 7:e43578. [PMID: 23028462 PMCID: PMC3454389 DOI: 10.1371/journal.pone.0043578] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Förster resonance energy transfer (FRET) biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). To expand the number of available FRET biosensors we used the induction profile of the Sinorhizobium meliloti transportome to systematically screen for new FRET biosensors. METHODOLOGY/PRINCIPAL FINDINGS Two new vectors were developed for cloning genes for solute-binding proteins (SBPs) between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2) and red fluorescent protein (mKate2) FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, myo-inositol, L-rhamnose, L-fucose, β-diglucosides (cellobiose and gentiobiose), D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate). To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP) transport systems. CONCLUSIONS/SIGNIFICANCE FRET based on orange (mOrange2) and red fluorescent protein (mKate2) partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i) cyclic polyols, (ii) L-deoxy sugars, (iii) β-linked disaccharides and (iv) C4-dicarboxylates could be developed to study metabolism in vivo.
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Affiliation(s)
- Alexandre Bourdès
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Steven Rudder
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
- * E-mail:
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Chowdhury N, Norris J, McAlister E, Lau SYK, Thomas GH, Boyd EF. The VC1777-VC1779 proteins are members of a sialic acid-specific subfamily of TRAP transporters (SiaPQM) and constitute the sole route of sialic acid uptake in the human pathogen Vibrio cholerae. MICROBIOLOGY-SGM 2012; 158:2158-2167. [PMID: 22556361 DOI: 10.1099/mic.0.059659-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Sialic acids are nine-carbon amino sugars that are present on all mucous membranes and are often used by bacteria as nutrients. In pathogenic Vibrio the genes for sialic acid catabolism (SAC) are known to be important for host colonization, yet the route for sialic acid uptake is not proven. Vibrio cholerae contains a tripartite ATP-independent periplasmic (TRAP) transporter, SiaPQM (VC1777-VC1779), encoded by genes within the Vibrio pathogenicity island-2 (VPI-2), which are adjacent to the SAC genes nanA, nanE and nanK. We demonstrate a correlation of the occurrence of VPI-2 and the ability of Vibrio to grow on the common sialic acid N-acetylneuraminic acid (Neu5Ac), and that a V. cholerae N16961 mutant defective in vc1777, encoding the large membrane protein component of the TRAP transporter, SiaM, is unable to grow on Neu5Ac as the sole carbon source. Using the genome context and known structures of the SiaP protein component of the TRAP transporter, we define a subfamily of Neu5Ac-specific TRAP transporters, of which the vc1777-vc1779 genes are the only representatives in V. cholerae. A recent report has suggested that an entirely different TRAP transporter (VC1927-VC1929) is the Neu5Ac transporter in V. cholerae. Bioinformatics and genomic analysis suggest strongly that this is a C(4)-dicarboxylate-specific TRAP transporter, and indeed disruption of vc1929 results in a defect in growth on C(4)-dicarboxylates but not Neu5Ac. Together these data demonstrate unequivocally that the siaPQM-encoded TRAP transporter within VPI-2 is the sole sialic acid transporter in V. cholerae.
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Affiliation(s)
- Nityananda Chowdhury
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jessica Norris
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - Erin McAlister
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - S Y Kathy Lau
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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48
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Deka RK, Brautigam CA, Goldberg M, Schuck P, Tomchick DR, Norgard MV. Structural, bioinformatic, and in vivo analyses of two Treponema pallidum lipoproteins reveal a unique TRAP transporter. J Mol Biol 2012; 416:678-96. [PMID: 22306465 DOI: 10.1016/j.jmb.2012.01.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/15/2011] [Accepted: 01/11/2012] [Indexed: 01/22/2023]
Abstract
Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of "tetratricopeptide repeat" (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).
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Affiliation(s)
- Ranjit K Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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49
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Mulligan C, Leech AP, Kelly DJ, Thomas GH. The membrane proteins SiaQ and SiaM form an essential stoichiometric complex in the sialic acid tripartite ATP-independent periplasmic (TRAP) transporter SiaPQM (VC1777-1779) from Vibrio cholerae. J Biol Chem 2011; 287:3598-608. [PMID: 22167185 DOI: 10.1074/jbc.m111.281030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are widespread in bacteria but poorly characterized. They contain three subunits, a small membrane protein, a large membrane protein, and a substrate-binding protein (SBP). Although the function of the SBP is well established, the membrane components have only been studied in detail for the sialic acid TRAP transporter SiaPQM from Haemophilus influenzae, where the membrane proteins are genetically fused. Herein, we report the first in vitro characterization of a truly tripartite TRAP transporter, the SiaPQM system (VC1777-1779) from the human pathogen Vibrio cholerae. The active reconstituted transporter catalyzes unidirectional Na(+)-dependent sialic acid uptake having similar biochemical features to the orthologous system in H. influenzae. However, using this tripartite transporter, we demonstrate the tight association of the small, SiaQ, and large, SiaM, membrane proteins that form a 1:1 complex. Using reconstituted proteoliposomes containing particular combinations of the three subunits, we demonstrate biochemically that all three subunits are likely to be essential to form a functional TRAP transporter.
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Affiliation(s)
- Christopher Mulligan
- Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom
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50
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Thomas GH, Boyd EF. On sialic acid transport and utilization by Vibrio cholerae. Microbiology (Reading) 2011; 157:3253-3254. [DOI: 10.1099/mic.0.054692-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | - E. Fidelma Boyd
- Department of Biological Sciences, Wolf Hall, University of Delaware, Newark, DE 19716, USA
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