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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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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] [Key Words] [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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Trebesch N, Tajkhorshid E. Structure Reveals Homology in Elevator Transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544989. [PMID: 37398459 PMCID: PMC10312693 DOI: 10.1101/2023.06.14.544989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The elevator transport mechanism is one of the handful of canonical mechanisms by which transporters shuttle their substrates across the semi-permeable membranes that surround cells and organelles. Studies of molecular function are naturally guided by evolutionary context, but until now this context has been limited for elevator transporters because established evolutionary classification methods have organized them into several apparently unrelated families. Through comprehensive examination of the pertinent structures available in the Protein Data Bank, we show that 62 elevator transporters from 18 families share a conserved architecture in their transport domains consisting of 10 helices connected in 8 topologies. Through quantitative analysis of the structural similarity, structural complexity, and topologically-corrected sequence similarity among the transport domains, we provide compelling evidence that these elevator transporters are all homologous. Using our analysis, we have constructed a phylogenetic tree to enable quantification and visualization of the evolutionary relationships among elevator transporters and their families. We also report several examples of functional features that are shared by elevator transporters from different families. Our findings shed new light on the elevator transport mechanism and allow us to understand it in a far deeper and more nuanced manner.
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Affiliation(s)
- Noah Trebesch
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
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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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Nath S. The Need for Consistency with Physical Laws and Logic in Choosing Between Competing Molecular Mechanisms in Biological Processes: A Case Study in Modeling ATP Synthesis. FUNCTION (OXFORD, ENGLAND) 2022; 3:zqac054. [PMID: 36340246 PMCID: PMC9629475 DOI: 10.1093/function/zqac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Traditionally, proposed molecular mechanisms of fundamental biological processes have been tested against experiment. However, owing to a plethora of reasons-difficulty in designing, carrying out, and interpreting key experiments, use of different experimental models and systems, conduct of studies under widely varying experimental conditions, fineness in distinctions between competing mechanisms, complexity of the scientific issues, and the resistance of some scientists to discoveries that are contrary to popularly held beliefs-this has not solved the problem despite decades of work in the field/s. The author would like to prescribe an alternative way: that of testing competing models/mechanisms for their adherence to scientific laws and principles, and checking for errors in logic. Such tests are fairly commonly carried out in the mathematics, physics, and engineering literature. Further, reported experimental measurements should not be smaller than minimum detectable values for the measurement technique employed and should truly reflect function of the actual system without inapplicable extrapolation. Progress in the biological fields would be greatly accelerated, and considerable scientific acrimony avoided by adopting this approach. Some examples from the fundamental field of ATP synthesis in oxidative phosphorylation (OXPHOS) have been reviewed that also serve to illustrate the approach. The approach has never let the author down in his 35-yr-long experience on biological mechanisms. This change in thinking should lead to a considerable saving of both time and resources, help channel research efforts toward solution of the right problems, and hopefully provide new vistas to a younger generation of open-minded biological scientists.
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Affiliation(s)
- Sunil Nath
- Address correspondence to S.N. (e-mail: ; )
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