1
|
Selvam B, Chiang N, Shukla D. Energetics of substrate transport in proton-dependent oligopeptide transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592129. [PMID: 38746282 PMCID: PMC11092630 DOI: 10.1101/2024.05.01.592129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The PepT So transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepT So in different states, the molecular basis of peptide recognition and transport by PepT So is not fully elucidated. In this study, we employed molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepT So transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. Furthermore, we elucidated the proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepT So and identify critical residues that facilitate transport.
Collapse
|
2
|
Remm S, De Vecchis D, Schöppe J, Hutter CAJ, Gonda I, Hohl M, Newstead S, Schäfer LV, Seeger MA. Structural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410. Nat Commun 2023; 14:6449. [PMID: 37833269 PMCID: PMC10576003 DOI: 10.1038/s41467-023-42073-0] [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: 12/14/2022] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Mycobacterium tuberculosis is protected from antibiotic therapy by a multi-layered hydrophobic cell envelope. Major facilitator superfamily (MFS) transporter Rv1410 and the periplasmic lipoprotein LprG are involved in transport of triacylglycerides (TAGs) that seal the mycomembrane. Here, we report a 2.7 Å structure of a mycobacterial Rv1410 homologue, which adopts an outward-facing conformation and exhibits unusual transmembrane helix 11 and 12 extensions that protrude ~20 Å into the periplasm. A small, very hydrophobic cavity suitable for lipid transport is constricted by a functionally important ion-lock likely involved in proton coupling. Combining mutational analyses and MD simulations, we propose that TAGs are extracted from the core of the inner membrane into the central cavity via lateral clefts present in the inward-facing conformation. The functional role of the periplasmic helix extensions is to channel the extracted TAG into the lipid binding pocket of LprG.
Collapse
Affiliation(s)
- Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany
| | - Jendrik Schöppe
- Institute of Biochemistry, University of Zurich, Zürich, Switzerland
- Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Linkster Therapeutics, Zürich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland.
- National Center for Mycobacteria, Zurich, Switzerland.
| |
Collapse
|
3
|
Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C. Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Cell Rep 2023; 42:112831. [PMID: 37467108 DOI: 10.1016/j.celrep.2023.112831] [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: 02/15/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.
Collapse
Affiliation(s)
- Vadim Kotov
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Maxime Killer
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Hamburg, Germany
| | - Katharina E J Jungnickel
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jian Lei
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, People's Republic of China
| | - Giada Finocchio
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Josi Steinke
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Kim Bartels
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jan Strauss
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Florine Dupeux
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Irina Cornaciu
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - José A Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Christian Löw
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany.
| |
Collapse
|
4
|
Gharabli H, Rafiq M, Iqbal A, Yan R, Aduri NG, Sharma N, Prabhala BK, Mirza O. Functional Characterization of the Putative POT from Clostridium perfringens. BIOLOGY 2023; 12:biology12050651. [PMID: 37237465 DOI: 10.3390/biology12050651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Proton-coupled oligopeptide transporters (POTs) are a fundamental part of the cellular transport machinery that provides plants, bacteria, and mammals with nutrition in the form of short peptides. However, POTs are not restricted to peptide transport; mammalian POTs have especially been in focus due to their ability to transport several peptidomimetics in the small intestine. Herein, we studied a POT from Clostridium perfringens (CPEPOT), which unexpectedly exhibited atypical characteristics. First, very little uptake of a fluorescently labelled peptide β-Ala-Lys-AMCA, an otherwise good substrate of several other bacterial POTs, was observed. Secondly, in the presence of a competitor peptide, enhanced uptake of β-Ala-Lys-AMCA was observed due to trans-stimulation. This effect was also observed even in the absence of a proton electrochemical gradient, suggesting that β-Ala-Lys-AMCA uptake mediated by CPEPOT is likely through the substrate-concentration-driving exchange mechanism, unlike any other functionally characterized bacterial POTs.
Collapse
Affiliation(s)
- Hani Gharabli
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anna Iqbal
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ruyu Yan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Neha Sharma
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Physics, Chemistry and Pharmacy, Faculty of Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| |
Collapse
|
5
|
Killer M, Finocchio G, Mertens HDT, Svergun DI, Pardon E, Steyaert J, Löw C. Cryo-EM Structure of an Atypical Proton-Coupled Peptide Transporter: Di- and Tripeptide Permease C. Front Mol Biosci 2022; 9:917725. [PMID: 35898305 PMCID: PMC9309889 DOI: 10.3389/fmolb.2022.917725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the most promiscuous class of MFS transporters, with the potential to transport more than 8400 unique substrates. Over the past two decades, transport assays and biophysical studies have shown that various orthologues and paralogues display differences in substrate selectivity. The E. coli genome codes for four different POTs, known as Di- and tripeptide permeases A-D (DtpA-D). DtpC was shown previously to favor positively charged peptides as substrates. In this study, we describe, how we determined the structure of the 53 kDa DtpC by cryogenic electron microscopy (cryo-EM), and provide structural insights into the ligand specificity of this atypical POT. We collected and analyzed data on the transporter fused to split superfolder GFP (split sfGFP), in complex with a 52 kDa Pro-macrobody and with a 13 kDa nanobody. The latter sample was more stable, rigid and a significant fraction dimeric, allowing us to reconstruct a 3D volume of DtpC at a resolution of 2.7 Å. This work provides a molecular explanation for the selectivity of DtpC, and highlights the value of small and rigid fiducial markers such as nanobodies for structure determination of low molecular weight integral membrane proteins lacking soluble domains.
Collapse
Affiliation(s)
- Maxime Killer
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Giada Finocchio
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Haydyn D. T. Mertens
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Dmitri I. Svergun
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Molecular Biology Laboratory (EMBL), Hamburg Unit C/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- *Correspondence: Christian Löw,
| |
Collapse
|
6
|
Stauffer M, Jeckelmann JM, Ilgü H, Ucurum Z, Boggavarapu R, Fotiadis D. Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor. Commun Chem 2022; 5:23. [PMID: 36697632 PMCID: PMC9814568 DOI: 10.1038/s42004-022-00636-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/27/2022] [Indexed: 01/28/2023] Open
Abstract
Inhibitors for membrane transporters have been shown to be indispensable as drugs and tool compounds. The proton-dependent oligopeptide transporters PEPT1 and PEPT2 from the SLC15 family play important roles in human and mammalian physiology. With Lys[Z(NO2)]-Val (LZNV), a modified Lys-Val dipeptide, a potent transport inhibitor for PEPT1 and PEPT2 is available. Here we present the crystal structure of the peptide transporter YePEPT in complex with LZNV. The structure revealed the molecular interactions for inhibitor binding and a previously undescribed mostly hydrophobic pocket, the PZ pocket, involved in interaction with LZNV. Comparison with a here determined ligand-free structure of the transporter unveiled that the initially absent PZ pocket emerges through conformational changes upon inhibitor binding. The provided biochemical and structural information constitutes an important framework for the mechanistic understanding of inhibitor binding and action in proton-dependent oligopeptide transporters.
Collapse
Affiliation(s)
- Mirko Stauffer
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Jean-Marc Jeckelmann
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Hüseyin Ilgü
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Zöhre Ucurum
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Rajendra Boggavarapu
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland ,grid.67105.350000 0001 2164 3847Present Address: Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH USA
| | - Dimitrios Fotiadis
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| |
Collapse
|
7
|
Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D. Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. Int J Mol Sci 2022; 23:ijms23031595. [PMID: 35163519 PMCID: PMC8836200 DOI: 10.3390/ijms23031595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources.
Collapse
Affiliation(s)
- Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
| | - Christa Kanstrup
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Mariela González-Avendaño
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Ingo Dreyer
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Hussam Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 8900000, Chile
- Correspondence: ; Tel.: +56-(22)-3036667
| |
Collapse
|
8
|
Xiao Q, Chen Y, Liu C, Robson F, Roy S, Cheng X, Wen J, Mysore K, Miller AJ, Murray JD. MtNPF6.5 mediates chloride uptake and nitrate preference in Medicago roots. EMBO J 2021; 40:e106847. [PMID: 34523752 PMCID: PMC8561640 DOI: 10.15252/embj.2020106847] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/09/2022] Open
Abstract
The preference for nitrate over chloride through regulation of transporters is a fundamental feature of plant ion homeostasis. We show that Medicago truncatula MtNPF6.5, an ortholog of Arabidopsis thaliana AtNPF6.3/NRT1.1, can mediate nitrate and chloride uptake in Xenopus oocytes but is chloride selective and that its close homologue, MtNPF6.7, can transport nitrate and chloride but is nitrate selective. The MtNPF6.5 mutant showed greatly reduced chloride content relative to wild type, and MtNPF6.5 expression was repressed by high chloride, indicating a primary role for MtNPF6.5 in root chloride uptake. MtNPF6.5 and MtNPF6.7 were repressed and induced by nitrate, respectively, and these responses required the transcription factor MtNLP1. Moreover, loss of MtNLP1 prevented the rapid switch from chloride to nitrate as the main anion in nitrate-starved plants after nitrate provision, providing insight into the underlying mechanism for nitrate preference. Sequence analysis revealed three sub-types of AtNPF6.3 orthologs based on their predicted substrate-binding residues: A (chloride selective), B (nitrate selective), and C (legume specific). The absence of B-type AtNPF6.3 homologues in early diverged plant lineages suggests that they evolved from a chloride-selective MtNPF6.5-like protein.
Collapse
Affiliation(s)
- Qiying Xiao
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Centre for Excellence in Molecular Plant Sciences (CEMPS)Shanghai Institute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
| | - Yi Chen
- John Innes CentreNorwich Research Park, NorwichUK
| | - Cheng‐Wu Liu
- John Innes CentreNorwich Research Park, NorwichUK
- Present address:
School of Life SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Fran Robson
- John Innes CentreNorwich Research Park, NorwichUK
| | - Sonali Roy
- John Innes CentreNorwich Research Park, NorwichUK
- Noble Research InstituteArdmoreOKUSA
| | | | | | | | | | - Jeremy D Murray
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Centre for Excellence in Molecular Plant Sciences (CEMPS)Shanghai Institute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
- John Innes CentreNorwich Research Park, NorwichUK
| |
Collapse
|
9
|
Yu YC, Dickstein R, Longo A. Structural Modeling and in planta Complementation Studies Link Mutated Residues of the Medicago truncatula Nitrate Transporter NPF1.7 to Functionality in Root Nodules. FRONTIERS IN PLANT SCIENCE 2021; 12:685334. [PMID: 34276736 PMCID: PMC8282211 DOI: 10.3389/fpls.2021.685334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/17/2021] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation is a complex and regulated process that takes place in root nodules of legumes and allows legumes to grow in soils that lack nitrogen. Nitrogen is mostly acquired from the soil as nitrate and its level in the soil affects nodulation and nitrogen fixation. The mechanism(s) by which legumes modulate nitrate uptake to regulate nodule symbiosis remain unclear. In Medicago truncatula, the MtNPF1.7 transporter has been shown to control nodulation, symbiosis, and root architecture. MtNPF1.7 belongs to the nitrate/peptide transporter family and is a symporter with nitrate transport driven by proton(s). In this study we combined in silico structural predictions with in planta complementation of the severely defective mtnip-1 mutant plants to understand the role of a series of distinct amino acids in the transporter's function. Our results support hypotheses about the functional importance of the ExxE(R/K) motif including an essential role for the first glutamic acid of the motif in proton(s) and possibly substrate transport. Results reveal that Motif A, a motif conserved among major facilitator transport (MFS) proteins, is essential for function. We hypothesize that it participates in intradomain packing of transmembrane helices and stabilizing one conformation during transport. Our results also question the existence of a putative TMH4-TMH10 salt bridge. These results are discussed in the context of potential nutrient transport functions for MtNPF1.7. Our findings add to the knowledge of the mechanism of alternative conformational changes as well as symport transport in NPFs and enhance our knowledge of the mechanisms for nitrate signaling.
Collapse
|
10
|
Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
Collapse
Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| |
Collapse
|
11
|
Recent advances in understanding prodrug transport through the SLC15 family of proton-coupled transporters. Biochem Soc Trans 2021; 48:337-346. [PMID: 32219385 PMCID: PMC7200629 DOI: 10.1042/bst20180302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/15/2020] [Accepted: 03/04/2020] [Indexed: 12/28/2022]
Abstract
Solute carrier (SLC) transporters play important roles in regulating the movement of small molecules and ions across cellular membranes. In mammals, they play an important role in regulating the uptake of nutrients and vitamins from the diet, and in controlling the distribution of their metabolic intermediates within the cell. Several SLC families also play an important role in drug transport and strategies are being developed to hijack SLC transporters to control and regulate drug transport within the body. Through the addition of amino acid and peptide moieties several novel antiviral and anticancer agents have been developed that hijack the proton-coupled oligopeptide transporters, PepT1 (SCL15A1) and PepT2 (SLC15A2), for improved intestinal absorption and renal retention in the body. A major goal is to understand the rationale behind these successes and expand the library of prodrug molecules that utilise SLC transporters. Recent co-crystal structures of prokaryotic homologues of the human PepT1 and PepT2 transporters have shed important new insights into the mechanism of prodrug recognition. Here, I will review recent developments in our understanding of ligand recognition and binding promiscuity within the SLC15 family, and discuss current models for prodrug recognition.
Collapse
|
12
|
Prabhala BK, Rahman M, Nour-Eldin HH, Jørgensen FS, Mirza O. PTR2/POT/NPF transporters: what makes them tick? ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:219-240. [PMID: 33485485 DOI: 10.1016/bs.apcsb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PTR2/POT/NPF are a family of primarily proton coupled transporters that belong to the major facilitator super family and are found across most kingdoms of life. They are involved in uptake of nutrients, hormones, ions and several orally administered drug molecules. A wealth of structural and functional data is available for this family; the similarity between the protein structural features have been discussed and investigated in detail on several occasions, however there are no reports on the unification of substrate information. In order to fill this gap, we have collected information about substrates across the entire PTR2/POT/NPF family in order to provide key insights into what makes a molecule a substrate and whether there are common features among confirmed substrates. This review will be of particular interest for researchers in the field trying to probe the mechanisms responsible for the different selectivity of these transporters at a molecular resolution, and to design novel substrates.
Collapse
Affiliation(s)
- Bala K Prabhala
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Moazur Rahman
- School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan; Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Hussam H Nour-Eldin
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
13
|
Lasitza‐Male T, Bartels K, Jungwirth J, Wiggers F, Rosenblum G, Hofmann H, Löw C. Membrane Chemistry Tunes the Structure of a Peptide Transporter. Angew Chem Int Ed Engl 2020; 59:19121-19128. [PMID: 32744783 PMCID: PMC7590137 DOI: 10.1002/anie.202008226] [Citation(s) in RCA: 14] [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: 06/09/2020] [Indexed: 01/02/2023]
Abstract
Membrane proteins require lipid bilayers for function. While lipid compositions reach enormous complexities, high-resolution structures are usually obtained in artificial detergents. To understand whether and how lipids guide membrane protein function, we use single-molecule FRET to probe the dynamics of DtpA, a member of the proton-coupled oligopeptide transporter (POT) family, in various lipid environments. We show that detergents trap DtpA in a dynamic ensemble with cytoplasmic opening. Only reconstitutions in more native environments restore cooperativity, allowing an opening to the extracellular side and a sampling of all relevant states. Bilayer compositions tune the abundance of these states. A novel state with an extreme cytoplasmic opening is accessible in bilayers with anionic head groups. Hence, chemical diversity of membranes translates into structural diversity, with the current POT structures only sampling a portion of the full structural space.
Collapse
Affiliation(s)
- Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Jakub Jungwirth
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Felix Wiggers
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Gabriel Rosenblum
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
- Department of Medical Biochemistry and BiophysicsKarolinska Institutet17177StockholmSweden
| |
Collapse
|
14
|
Lasitza‐Male T, Bartels K, Jungwirth J, Wiggers F, Rosenblum G, Hofmann H, Löw C. Membrane Chemistry Tunes the Structure of a Peptide Transporter. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tanya Lasitza‐Male
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Kim Bartels
- Centre for Structural Systems Biology (CSSB) DESY and European Molecular Biology Laboratory Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Jakub Jungwirth
- Department of Chemical and Biological Physics Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Felix Wiggers
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Gabriel Rosenblum
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Hagen Hofmann
- Department of Structural Biology Weizmann Institute of Science Herzl St. 234 7610001 Rehovot Israel
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB) DESY and European Molecular Biology Laboratory Hamburg Notkestrasse 85 22607 Hamburg Germany
- Department of Medical Biochemistry and Biophysics Karolinska Institutet 17177 Stockholm Sweden
| |
Collapse
|
15
|
Johnson EO, Office E, Kawate T, Orzechowski M, Hung DT. Large-Scale Chemical-Genetic Strategy Enables the Design of Antimicrobial Combination Chemotherapy in Mycobacteria. ACS Infect Dis 2020; 6:56-63. [PMID: 31721551 PMCID: PMC6958538 DOI: 10.1021/acsinfecdis.9b00373] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets) for the discovery of new Mycobacterium tuberculosis inhibitors, which resulted in the identification of the small molecule BRD-8000, an inhibitor of a novel target, EfpA [ Johnson et al. ( 2019 ) Nature 517 , 72 ]. Leveraging the chemical genetic interaction profile of BRD-8000, we identified BRD-9327, another structurally distinct small molecule EfpA inhibitor. We show that the two compounds are synergistic and display collateral sensitivity because of their distinct modes of action and resistance mechanisms. High-level resistance to one increases the sensitivity to and reduces the emergence of resistance to the other. Thus, the combination of BRD-9327 and BRD-8000 represents a proof-of-concept for the novel strategy of leveraging chemical genetics in the design of antimicrobial combination chemotherapy in which mutual collateral sensitivity is exploited.
Collapse
Affiliation(s)
- Eachan O. Johnson
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Emma Office
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Tomohiko Kawate
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Marek Orzechowski
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| |
Collapse
|
16
|
Abstract
We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.
Collapse
|
17
|
Abstract
Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
Collapse
|
18
|
Nagamura R, Fukuda M, Kawamoto A, Matoba K, Dohmae N, Ishitani R, Takagi J, Nureki O. Structural basis for oligomerization of the prokaryotic peptide transporter PepT So2. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:348-358. [PMID: 31045564 PMCID: PMC6497099 DOI: 10.1107/s2053230x19003546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022]
Abstract
Using cryo-EM and X-ray crystallography, the atomic resolution structure of the tetrameric form of the proton-dependent oligopeptide transporter PepTSo2 was determined and the novel oligomerization mechanism was revealed. Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. The human POTs PepT1 and PepT2 are also involved in the absorption of various orally ingested drugs. Previously reported structures revealed that the bacterial POTs possess 14 helices, of which H1–H6 and H7–H12 constitute the typical MFS fold and the residual two helices are involved in the cytoplasmic linker. PepTSo2 from Shewanella oneidensis is a unique POT which reportedly assembles as a 200 kDa tetramer. Although the previously reported structures suggested the importance of H12 for tetramer formation, the structural basis for the PepTSo2-specific oligomerization remains unclear owing to the lack of a high-resolution tetrameric structure. In this study, the expression and purification conditions for tetrameric PepTSo2 were optimized. A single-particle cryo-EM analysis revealed the tetrameric structure of PepTSo2 incorporated into Salipro nanoparticles at 4.1 Å resolution. Furthermore, a combination of lipidic cubic phase (LCP) crystallization and an automated data-processing system for multiple microcrystals enabled crystal structures of PepTSo2 to be determined at resolutions of 3.5 and 3.9 Å. The present structures in a lipid bilayer revealed the detailed mechanism for the tetrameric assembly of PepTSo2, in which a characteristic extracellular loop (ECL) interacts with two asparagine residues on H12 which were reported to be important for tetramerization and plays an essential role in oligomeric assembly. This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins.
Collapse
Affiliation(s)
- Reina Nagamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kyoko Matoba
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naoshi Dohmae
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
19
|
Zhang XC, Li H. Interplay between the electrostatic membrane potential and conformational changes in membrane proteins. Protein Sci 2019; 28:502-512. [PMID: 30549351 DOI: 10.1002/pro.3563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022]
Abstract
Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge-carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.
Collapse
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
20
|
Abstract
Transport of solutes across biological membranes is essential for cellular life. This process is mediated by membrane transport proteins which move nutrients, waste products, certain drugs and ions into and out of cells. Secondary active transporters couple the transport of substrates against their concentration gradients with the transport of other solutes down their concentration gradients. The alternating access model of membrane transporters and the coupling mechanism of secondary active transporters are introduced in this book chapter. Structural studies have identified typical protein folds for transporters that we exemplify by the major facilitator superfamily (MFS) and LeuT folds. Finally, substrate binding and substrate translocation of the transporters LacY of the MFS and AdiC of the amino acid-polyamine-organocation (APC) superfamily are described.
Collapse
Affiliation(s)
- Patrick D Bosshart
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
| |
Collapse
|
21
|
Martinez Molledo M, Quistgaard EM, Löw C. Tripeptide binding in a proton-dependent oligopeptide transporter. FEBS Lett 2018; 592:3239-3247. [PMID: 30194725 PMCID: PMC6221056 DOI: 10.1002/1873-3468.13246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/30/2023]
Abstract
Proton-dependent oligopeptide transporters (POTs) are important for the uptake of di-/tripeptides in many organisms and for drug transport in humans. The binding mode of dipeptides has been well described. However, it is still debated how tripeptides are recognized. Here, we show that tripeptides of the sequence Phe-Ala-Xxx bind with similar affinities as dipeptides to the POT transporter from Streptococcus thermophilus (PepTS t ). We furthermore determined a 2.3-Å structure of PepTS t in complex with Phe-Ala-Gln. The phenylalanine and alanine residues of the peptide adopt the same positions as previously observed for the Phe-Ala dipeptide, while the glutamine side chain extends into a hitherto uncharacterized pocket. This pocket is adaptable in size and can likely accommodate a wide variety of peptide side chains.
Collapse
Affiliation(s)
- Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Esben M Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
22
|
Bai X, Moraes TF, Reithmeier RAF. Structural biology of solute carrier (SLC) membrane transport proteins. Mol Membr Biol 2018; 34:1-32. [PMID: 29651895 DOI: 10.1080/09687688.2018.1448123] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.
Collapse
Affiliation(s)
- Xiaoyun Bai
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | | |
Collapse
|
23
|
Medrano-Soto A, Moreno-Hagelsieb G, McLaughlin D, Ye ZS, Hendargo KJ, Saier MH. Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases. PLoS One 2018; 13:e0192851. [PMID: 29579047 PMCID: PMC5868767 DOI: 10.1371/journal.pone.0192851] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
Our laboratory has developed bioinformatic strategies for identifying distant phylogenetic relationships and characterizing families and superfamilies of transport proteins. Results using these tools suggest that the Anoctamin Superfamily of cation and anion channels, as well as lipid scramblases, includes three functionally characterized families: the Anoctamin (ANO), Transmembrane Channel (TMC) and Ca2+-permeable Stress-gated Cation Channel (CSC) families; as well as four families of functionally uncharacterized proteins, which we refer to as the Anoctamin-like (ANO-L), Transmembrane Channel-like (TMC-L), and CSC-like (CSC-L1 and CSC-L2) families. We have constructed protein clusters and trees showing the relative relationships among the seven families. Topological analyses suggest that the members of these families have essentially the same topologies. Comparative examination of these homologous families provides insight into possible mechanisms of action, indicates the currently recognized organismal distributions of these proteins, and suggests drug design potential for the disease-related channel proteins.
Collapse
Affiliation(s)
- Arturo Medrano-Soto
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | | | - Daniel McLaughlin
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Zachary S. Ye
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Kevin J. Hendargo
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
24
|
Spanier B, Rohm F. Proton Coupled Oligopeptide Transporter 1 (PepT1) Function, Regulation, and Influence on the Intestinal Homeostasis. Compr Physiol 2018; 8:843-869. [DOI: 10.1002/cphy.c170038] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
25
|
Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Structure 2018; 26:467-476.e4. [PMID: 29429879 PMCID: PMC5845931 DOI: 10.1016/j.str.2018.01.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/22/2017] [Accepted: 01/10/2018] [Indexed: 12/27/2022]
Abstract
Proton-dependent oligopeptide transporters (POTs) are important for uptake of dietary di- and tripeptides in many organisms, and in humans are also involved in drug absorption. These transporters accept a wide range of substrates, but the structural basis for how different peptide side chains are accommodated has so far remained obscure. Twenty-eight peptides were screened for binding to PepTSt from Streptococcus thermophilus, and structures were determined of PepTSt in complex with four physicochemically diverse dipeptides, which bind with millimolar affinity: Ala-Leu, Phe-Ala, Ala-Gln, and Asp-Glu. The structures show that PepTSt can adapt to different peptide side chains through movement of binding site residues and water molecules, and that a good fit can be further aided by adjustment of the position of the peptide itself. Finally, structures were also determined in complex with adventitiously bound HEPES, polyethylene glycol, and phosphate molecules, which further underline the adaptability of the binding site. Dipeptides can adapt their position to best fit the PepTSt binding site The PepTSt binding site can adapt its structure to best fit the dipeptides The water network in the PepTSt binding site can adapt to best fit the dipeptides Aromatic binding site residues play a role in conferring PepTSt multispecificity
Collapse
|
26
|
Longo A, Miles NW, Dickstein R. Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport. FRONTIERS IN PLANT SCIENCE 2018; 9:1668. [PMID: 30564251 PMCID: PMC6288477 DOI: 10.3389/fpls.2018.01668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/26/2018] [Indexed: 05/04/2023]
Abstract
Nitrogen is essential for all living species and may be taken up from the environment in different forms like nitrate or peptides. In plants, members of a transporter family named NPFs transport nitrate and peptides across biological membranes. NPFs are phylogenetically related to a family of peptide transporters (PTRs) or proton-coupled oligopeptide transporters (POTs) that are evolutionarily conserved in all organisms except in Archaea. POTs are present in low numbers in bacteria, algae and animals. NPFs have expanded in plants and evolved to transport a wide range of substrates including phytohormones and glucosinolates. Functional studies have shown that most NPFs, like POTs, operate as symporters with simultaneous inwardly directed movement of protons. Here we focus on four structural features of NPFs/POTs/PTRs that have been shown by structural and functional studies to be essential to proton-coupled symport transport. The first two features are implicated in proton binding and transport: a conserved motif named ExxER/K, located in the first transmembrane helix (TMH1) and a D/E residue in TMH7 that has been observed in some bacterial and algal transporters. The third and fourth features are two inter-helical salt bridges between residues on TMH1 and TMH7 or TMH4 and TMH10. To understand if the mechanism of transport is conserved in NPFs with the expansion to novel substrates, we collected NPFs sequences from 42 plant genomes. Sequence alignment revealed that the ExxER/K motif is not strictly conserved and its conservation level is different in the NPF subfamilies. The proton binding site on TMH7 is missing in all NPFs with the exception of two NPFs from moss. The two moss NPFs also have a positively charged amino acid on TMH1 that can form the salt bridge with the TMH7 negative residue. None of the other NPFs we examined harbor residues that can form the TMH1-TMH7 salt bridge. In contrast, the amino acids required to form the TMH4-TMH10 salt bridge are highly conserved in NPFs, with some exceptions. These results support the need for further biochemical and structural studies of individual NPFs for a better understanding of the transport mechanism in this family of transporters.
Collapse
Affiliation(s)
- Antonella Longo
- BioDiscovery Institute, University of North Texas, Denton, TX, United States
- Department of Biological Sciences, University of North Texas, Denton, TX, United States
- *Correspondence: Antonella Longo,
| | - Nicholas W. Miles
- BioDiscovery Institute, University of North Texas, Denton, TX, United States
- Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Rebecca Dickstein
- BioDiscovery Institute, University of North Texas, Denton, TX, United States
- Department of Biological Sciences, University of North Texas, Denton, TX, United States
| |
Collapse
|
27
|
Zhang XC, Liu M, Lu G, Heng J. Thermodynamic secrets of multidrug resistance: A new take on transport mechanisms of secondary active antiporters. Protein Sci 2017; 27:595-613. [PMID: 29193407 DOI: 10.1002/pro.3355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022]
Abstract
Multidrug resistance (MDR) presents a growing challenge to global public health. Drug extrusion transporters play a critical part in MDR; thus, their mechanisms of substrate recognition are being studied in great detail. In this work, we review common structural features of key transporters involved in MDR. Based on our membrane potential-driving hypothesis, we propose a general energy-coupling mechanism for secondary-active antiporters. This putative mechanism provides a common framework for understanding poly-specificity of most-if not all-MDR transporters.
Collapse
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangyuan Lu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Heng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| |
Collapse
|
28
|
Zhang XC, Liu M, Han L. Energy coupling mechanisms of AcrB-like RND transporters. BIOPHYSICS REPORTS 2017; 3:73-84. [PMID: 29238744 PMCID: PMC5719797 DOI: 10.1007/s41048-017-0042-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023] Open
Abstract
Prokaryotic AcrB-like proteins belong to a family of transporters of the RND superfamily, and as main contributing factor to multidrug resistance pose a tremendous threat to future human health. A unique feature of AcrB transporters is the presence of two separate domains responsible for carrying substrate and generating energy. Significant progress has been made in elucidating the three-dimensional structures of the homo-trimer complexes of AcrB-like transporters, and a three-step functional rotation was identified for this class of transporters. However, the detailed mechanisms for the transduction of the substrate binding signal, as well as the energy coupling processes between the functionally distinct domains remain to be established. Here, we propose a model for the interdomain communication in AcrB that explains how the substrate binding signal from the substrate-carrier domain triggers protonation in the transmembrane domain. Our model further provides a plausible mechanism that explains how protonation induces conformational changes in the substrate-carrier domain. We summarize the thermodynamic principles that govern the functional cycle of the AcrB trimer complex.
Collapse
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Min Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Han
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
29
|
Molecular mechanism of substrate recognition and transport by the AtSWEET13 sugar transporter. Proc Natl Acad Sci U S A 2017; 114:10089-10094. [PMID: 28878024 DOI: 10.1073/pnas.1709241114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sugar Will Eventually be Exported Transporters (SWEETs) are recently identified sugar transporters that can discriminate and transport di- or monosaccharides across a membrane following the concentration gradient. SWEETs play key roles in plant biological processes, such as pollen nutrition, nectar secretion, seed filling, and phloem loading. SWEET13 from Arabidopsis thaliana (AtSWEET13) is an important sucrose transporter in pollen development. Here, we report the 2.8-Å resolution crystal structure of AtSWEET13 in the inward-facing conformation with a substrate analog, 2'-deoxycytidine 5'-monophosphate, bound in the central cavity. In addition, based on the results of an in-cell transport activity assay and single-molecule Förster resonance energy transfer analysis, we suggest a mechanism for substrate selectivity based on the size of the substrate-binding pocket. Furthermore, AtSWEET13 appears to form a higher order structure presumably related to its function.
Collapse
|
30
|
Several hPepT1-transported drugs are substrates of the Escherichia coli proton-coupled oligopeptide transporter YdgR. Res Microbiol 2017; 168:443-449. [DOI: 10.1016/j.resmic.2017.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 11/23/2022]
|
31
|
Quistgaard EM, Martinez Molledo M, Löw C. Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121. PLoS One 2017; 12:e0173126. [PMID: 28264013 PMCID: PMC5338821 DOI: 10.1371/journal.pone.0173126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/15/2017] [Indexed: 12/03/2022] Open
Abstract
Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins.
Collapse
Affiliation(s)
- Esben M. Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
32
|
Harris NJ, Findlay HE, Sanders MR, Kedzierski M, Dos Santos Á, Booth PJ. Comparative stability of Major Facilitator Superfamily transport proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:655-663. [PMID: 28116476 PMCID: PMC5599477 DOI: 10.1007/s00249-017-1197-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 11/11/2022]
Abstract
Membrane transporters are a vital class of proteins for which there is little available structural and thermodynamic information. The Major Facilitator Superfamily (MFS) is a large group of transport proteins responsible for transporting a wide range of substrates in eukaryotes and prokaryotes. We have used far-UV circular dichroism (CD) to assess whether transporters from this superfamily have the same chemical and thermal stability. We have compared the stability of five different MFS transporters; PepTSo from Shewanella oneidensis and LacY, GalP, GlpT and XylE from Escherichia coli, as well as a known stable mutant of LacY, LacY-C154G. CD stability measurements revealed that these transporters fall into two broad categories. The ‘urea-sensitive’ category includes LacY-WT, GalP and GlpT, which each lose around a third of their secondary structure in 8 M urea and two-thirds in the harsher denaturant guanidine hydrochloride (GuHCl). The ‘urea-resistant’ category includes LacY-C154G, XylE and PepTSo. These resistant transporters lose very little secondary structure in 8 M urea, and LacY-C154G and PepTSo resist denaturation by GuHCl up to a concentration of 4 M. The stabilities of LacY, GlpT, XylE and PepTSo correlated with their crystal structure conformations, implying that a similar conformation is adopted in vitro. The ‘urea-sensitive’ transporters LacY and GlpT were crystallised inward-open states, while XylE and PepTSo were crystallised in occluded states. This study highlights the importance of studying a wide range of similar proteins, as a similar secondary structure and overall function does not necessarily confer the same stability in vitro.
Collapse
Affiliation(s)
- Nicola J Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK
| | - Heather E Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK
| | - Michael R Sanders
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK
| | - Mateusz Kedzierski
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK
| | - Ália Dos Santos
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, UK.
| |
Collapse
|
33
|
Newstead S. Recent advances in understanding proton coupled peptide transport via the POT family. Curr Opin Struct Biol 2016; 45:17-24. [PMID: 27865112 DOI: 10.1016/j.sbi.2016.10.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/22/2016] [Accepted: 10/26/2016] [Indexed: 10/20/2022]
Abstract
The POT family of membrane transporters use the inwardly directed proton electrochemical gradient to drive the uptake of essential nutrients into the cell. Originally discovered in bacteria, members of the family have been found in all kingdoms of life except the archaea. A remarkable feature of the family is their diverse substrate promiscuity. Whereas in mammals and bacteria they are predominantly di- and tri-peptide transporters, in plants the family has diverged to recognize nitrate, plant defence compounds and hormones. This promiscuity has led to the development of peptide-based pro-drugs that use PepT1 and PepT2, the mammalian homologues, to improve oral drug delivery. Recent crystal structures from bacterial and plant members of the family have revealed conserved features of the ligand-binding site and provided insights into post-translational regulation. Here I review the current understanding of transport, ligand promiscuity and regulation within the POT family.
Collapse
Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| |
Collapse
|
34
|
Affiliation(s)
- David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065;
| |
Collapse
|
35
|
Zhang XC, Han L. How does the chemical potential of the substrate drive a uniporter? Protein Sci 2016; 25:933-7. [PMID: 26807918 DOI: 10.1002/pro.2885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 01/17/2023]
Abstract
Uniporters are a large class of transporters mediating facilitated diffusion of substrates along the direction of the substrate concentration gradient. Recently, structures of several important uniporters have been reported; however, the precise mechanisms of uniporter function remain subject of debate. Here, we present a series of general thermodynamic descriptions of uniporters, aimed at understanding the structure-function relationship of uniporters, and in particular to reconcile biochemical phenomena of uniporters with our previously proposed thermodynamic model of general transporters.
Collapse
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Han
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
36
|
Samsudin F, Parker JL, Sansom MSP, Newstead S, Fowler PW. Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter. Cell Chem Biol 2016; 23:299-309. [PMID: 27028887 PMCID: PMC4760754 DOI: 10.1016/j.chembiol.2015.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/22/2015] [Accepted: 11/04/2015] [Indexed: 12/04/2022]
Abstract
Membrane transporters are critical modulators of drug pharmacokinetics, efficacy, and safety. One example is the proton-dependent oligopeptide transporter PepT1, also known as SLC15A1, which is responsible for the uptake of the β-lactam antibiotics and various peptide-based prodrugs. In this study, we modeled the binding of various peptides to a bacterial homolog, PepTSt, and evaluated a range of computational methods for predicting the free energy of binding. Our results show that a hybrid approach (endpoint methods to classify peptides into good and poor binders and a theoretically exact method for refinement) is able to accurately predict affinities, which we validated using proteoliposome transport assays. Applying the method to a homology model of PepT1 suggests that the approach requires a high-quality structure to be accurate. Our study provides a blueprint for extending these computational methodologies to other pharmaceutically important transporter families. A hierarchical computational approach determines ligand affinities to transporters Lysine-containing dipeptides proposed to bind vertically like a tripeptide Experimental structures are vital for the accurate prediction of affinities A model of prodrug interactions to human PepT1 is suggested
Collapse
Affiliation(s)
- Firdaus Samsudin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
37
|
Understanding transport by the major facilitator superfamily (MFS): structures pave the way. Nat Rev Mol Cell Biol 2016; 17:123-32. [PMID: 26758938 DOI: 10.1038/nrm.2015.25] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the major facilitator superfamily (MFS) of transport proteins are essential for the movement of a wide range of substrates across biomembranes. As this transport requires a series of conformational changes, structures of MFS transporters captured in different conformational states are needed to decipher the transport mechanism. Recently, a large number of MFS transporter structures have been determined, which has provided us with an unprecedented opportunity to understand general aspects of the transport mechanism. We propose an updated model for the conformational cycle of MFS transporters, the 'clamp-and-switch model', and discuss the role of so-called 'gating residues' and the substrate in modulating these conformational changes.
Collapse
|
38
|
Abstract
The ancient and ubiquitous major facilitator superfamily (MFS) represents the largest secondary transporter family and plays a crucial role in a multitude of physiological processes. MFS proteins transport a broad spectrum of ions and solutes across membranes via facilitated diffusion, symport, or antiport. In recent years, remarkable advances in understanding the structural biology of the MFS transporters have been made. This article reviews the history, classification, and general features of the MFS proteins; summarizes recent structural progress with a focus on the sugar porter family transporters exemplified by GLUT1; and discusses the molecular mechanisms of substrate binding, alternating access, and cotransport coupling.
Collapse
Affiliation(s)
- Nieng Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China;
| |
Collapse
|
39
|
Mousa JJ, Bruner SD. Structural and mechanistic diversity of multidrug transporters. Nat Prod Rep 2016; 33:1255-1267. [DOI: 10.1039/c6np00006a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The review article surveys recent structural and mechanistic advances in the field of multi-drug and natural product transporters.
Collapse
|
40
|
Aduri NG, Prabhala BK, Ernst HA, Jørgensen FS, Olsen L, Mirza O. Salt Bridge Swapping in the EXXERFXYY Motif of Proton-coupled Oligopeptide Transporters. J Biol Chem 2015; 290:29931-40. [PMID: 26483552 DOI: 10.1074/jbc.m115.675603] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 01/12/2023] Open
Abstract
Proton-coupled oligopeptide transporters (POTs) couple the inward transport of di- or tripeptides with an inwardly directed transport of protons. Evidence from several studies of different POTs has pointed toward involvement of a highly conserved sequence motif, E1XXE2RFXYY (from here on referred to as E1XXE2R), located on Helix I, in interactions with the proton. In this study, we investigated the intracellular substrate accumulation by motif variants with all possible combinations of glutamate residues changed to glutamine and arginine changed to a tyrosine, the latter being a natural variant found in the Escherichia coli POT YjdL. We found that YjdL motif variants with E1XXE2R, E1XXE2Y, E1XXQ2Y, or Q1XXE2Y were able to accumulate peptide, whereas those with E1XXQ2R, Q1XXE2R, or Q1XXQ2Y were unable to accumulate peptide, and Q1XXQ2R abolished uptake. These results suggest a mechanism that involves swapping of an intramotif salt bridge, i.e. R-E2 to R-E1, which is consistent with previous structural studies. Molecular dynamics simulations of the motif variants E1XXE2R and E1XXQ2R support this mechanism. The simulations showed that upon changing conformation arginine pushes Helix V, through interactions with the highly conserved FYING motif, further away from the central cavity in what could be a stabilization of an inward facing conformation. As E2 has been suggested to be the primary site for protonation, these novel findings show how protonation may drive conformational changes through interactions of two highly conserved motifs.
Collapse
Affiliation(s)
- Nanda G Aduri
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Heidi A Ernst
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Flemming S Jørgensen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Osman Mirza
- From the Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| |
Collapse
|
41
|
NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability. Proc Natl Acad Sci U S A 2015; 112:E5575-82. [PMID: 26417087 DOI: 10.1073/pnas.1510964112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Escherichia coli Na(+)/H(+) antiporter (Ec-NhaA) is the best-characterized of all pH-regulated Na(+)/H(+) exchangers that control cellular Na(+) and H(+) homeostasis. Ec-NhaA has 12 helices, 2 of which (VI and VII) are absent from other antiporters that share the Ec-NhaA structural fold. This α-hairpin is located in the dimer interface of the Ec-NhaA homodimer together with a β-sheet. Here we examine computationally and experimentally the role of the α-hairpin in the stability, dimerization, transport, and pH regulation of Ec-NhaA. Evolutionary analysis (ConSurf) indicates that the VI-VII helical hairpin is much less conserved than the remaining transmembrane region. Moreover, normal mode analysis also shows that intact NhaA and a variant, deleted of the α-hairpin, share similar dynamics, suggesting that the structure may be dispensable. Thus, two truncated Ec-NhaA mutants were constructed, one deleted of the α-hairpin and another also lacking the β-sheet. The mutants were studied at physiological pH in the membrane and in detergent micelles. The findings demonstrate that the truncated mutants retain significant activity and regulatory properties but are defective in the assembly/stability of the Ec-NhaA dimer.
Collapse
|
42
|
Zhang XC, Zhao Y, Heng J, Jiang D. Energy coupling mechanisms of MFS transporters. Protein Sci 2015; 24:1560-79. [PMID: 26234418 DOI: 10.1002/pro.2759] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 01/01/2023]
Abstract
Major facilitator superfamily (MFS) is a large class of secondary active transporters widely expressed across all life kingdoms. Although a common 12-transmembrane helix-bundle architecture is found in most MFS crystal structures available, a common mechanism of energy coupling remains to be elucidated. Here, we discuss several models for energy-coupling in the transport process of the transporters, largely based on currently available structures and the results of their biochemical analyses. Special attention is paid to the interaction between protonation and the negative-inside membrane potential. Also, functional roles of the conserved sequence motifs are discussed in the context of the 3D structures. We anticipate that in the near future, a unified picture of the functions of MFS transporters will emerge from the insights gained from studies of the common architectures and conserved motifs.
Collapse
Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Jie Heng
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Daohua Jiang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| |
Collapse
|
43
|
Boggavarapu R, Jeckelmann JM, Harder D, Ucurum Z, Fotiadis D. Role of electrostatic interactions for ligand recognition and specificity of peptide transporters. BMC Biol 2015; 13:58. [PMID: 26246134 PMCID: PMC4527243 DOI: 10.1186/s12915-015-0167-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background Peptide transporters are membrane proteins that mediate the cellular uptake of di- and tripeptides, and of peptidomimetic drugs such as β-lactam antibiotics, antiviral drugs and antineoplastic agents. In spite of their high physiological and pharmaceutical importance, the molecular recognition by these transporters of the amino acid side chains of short peptides and thus the mechanisms for substrate binding and specificity are far from being understood. Results The X-ray crystal structure of the peptide transporter YePEPT from the bacterium Yersinia enterocolitica together with functional studies have unveiled the molecular bases for recognition, binding and specificity of dipeptides with a charged amino acid residue at the N-terminal position. In wild-type YePEPT, the significant specificity for the dipeptides Asp-Ala and Glu-Ala is defined by electrostatic interaction between the in the structure identified positively charged Lys314 and the negatively charged amino acid side chain of these dipeptides. Mutagenesis of Lys314 into the negatively charged residue Glu allowed tuning of the substrate specificity of YePEPT for the positively charged dipeptide Lys-Ala. Importantly, molecular insights acquired from the prokaryotic peptide transporter YePEPT combined with mutagenesis and functional uptake studies with human PEPT1 expressed in Xenopus oocytes also allowed tuning of human PEPT1’s substrate specificity, thus improving our understanding of substrate recognition and specificity of this physiologically and pharmaceutically important peptide transporter. Conclusion This study provides the molecular bases for recognition, binding and specificity of peptide transporters for dipeptides with a charged amino acid residue at the N-terminal position. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0167-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rajendra Boggavarapu
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, CH-3012, Bern, Switzerland
| | - Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, CH-3012, Bern, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, CH-3012, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, CH-3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bühlstrasse 28, CH-3012, Bern, Switzerland.
| |
Collapse
|
44
|
Heng J, Zhao Y, Liu M, Liu Y, Fan J, Wang X, Zhao Y, Zhang XC. Substrate-bound structure of the E. coli multidrug resistance transporter MdfA. Cell Res 2015; 25:1060-73. [PMID: 26238402 DOI: 10.1038/cr.2015.94] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/02/2015] [Accepted: 05/07/2015] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance is a serious threat to public health. Proton motive force-driven antiporters from the major facilitator superfamily (MFS) constitute a major group of multidrug-resistance transporters. Currently, no reports on crystal structures of MFS antiporters in complex with their substrates exist. The E. coli MdfA transporter is a well-studied model system for biochemical analyses of multidrug-resistance MFS antiporters. Here, we report three crystal structures of MdfA-ligand complexes at resolutions up to 2.0 Å, all in the inward-facing conformation. The substrate-binding site sits proximal to the conserved acidic residue, D34. Our mutagenesis studies support the structural observations of the substrate-binding mode and the notion that D34 responds to substrate binding by adjusting its protonation status. Taken together, our data unveil the substrate-binding mode of MFS antiporters and suggest a mechanism of transport via this group of transporters.
Collapse
Affiliation(s)
- Jie Heng
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ming Liu
- College of Biotechnology, Tianjin University of Science and Technology, 29 13th Street, TEDA, Tianjin 300457, China
| | - Yue Liu
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Junping Fan
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xianping Wang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yongfang Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| |
Collapse
|
45
|
Wright DJ, Tate CG. Isolation and characterisation of transport-defective substrate-binding mutants of the tetracycline antiporter TetA(B). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2261-70. [PMID: 26143388 PMCID: PMC4579554 DOI: 10.1016/j.bbamem.2015.06.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 11/20/2022]
Abstract
The tetracycline antiporter TetA(B) is a member of the Major Facilitator Superfamily which confers tetracycline resistance to cells by coupling the efflux of tetracycline to the influx of protons down their chemical potential gradient. Although it is a medically important transporter, its structure has yet to be determined. One possibility for why this has proven difficult is that the transporter may be conformationally heterogeneous in the purified state. To overcome this, we developed two strategies to rapidly identify TetA(B) mutants that were transport-defective and that could still bind tetracycline. Up to 9 amino acid residues could be deleted from the loop between transmembrane α-helices 6 and 7 with only a slight decrease in affinity of tetracycline binding as measured by isothermal titration calorimetry, although the mutant was transport-defective. Scanning mutagenesis where all the residues between 2 and 389 were mutated to either valine, alanine or glycine (VAG scan) identified 15 mutants that were significantly impaired in tetracycline transport. Of these mutants, 12 showed no evidence of tetracycline binding by isothermal titration calorimetry performed on the purified transporters. In contrast, the mutants G44V and G346V bound tetracycline 4–5 fold more weakly than TetA(B), with Kds of 28 μM and 36 μM, respectively, whereas the mutant R70G bound tetracycline 3-fold more strongly (Kd 2.1 μM). Systematic mutagenesis is thus an effective strategy for isolating transporter mutants that may be conformationally constrained and which represent attractive targets for crystallisation and structure determination. A rapid method was developed for the identification of transport-defective mutants of TetA(B). ITC was used to determine the affinity of tetracycline binding to the mutants. Fifteen transport-defective point mutations were identified. Three mutants bound tetracycline whereas the remainder did not The transport-defective mutants may facilitate crystallisation of TetA(B).
Collapse
Affiliation(s)
- David J Wright
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
46
|
Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, Liang C, Liu L, Piao Z, Deng Q, Deng K, Xu C, Liang Y, Zhang L, Li L, Chu C. Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet 2015; 47:834-8. [PMID: 26053497 DOI: 10.1038/ng.3337] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/15/2015] [Indexed: 02/07/2023]
Abstract
Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.
Collapse
Affiliation(s)
- Bin Hu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shujun Ou
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hua Li
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ronghui Che
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhihua Zhang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuyang Chai
- College of Life Science, Capital Normal University, Beijing, China
| | - Hongru Wang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chengzhen Liang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Linchuan Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhongze Piao
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qiyun Deng
- China National Hybrid Rice Research and Development Center, Changsha, China
| | - Kun Deng
- School of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Chi Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Liang
- 1] State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhang
- School of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Legong Li
- College of Life Science, Capital Normal University, Beijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
47
|
Columbus L. Post-expression strategies for structural investigations of membrane proteins. Curr Opin Struct Biol 2015; 32:131-8. [PMID: 25951412 DOI: 10.1016/j.sbi.2015.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 01/26/2023]
Abstract
Currently, membrane proteins only comprise 1.5% of the protein data bank and, thus, still remain a challenge for structural biologists. Expression, stabilization in membrane mimics (e.g. detergent), heterogeneity (conformational and chemical), and crystallization in the presence of a membrane mimic are four major bottlenecks encountered. In response, several post-expression protein modifications have been utilized to facilitate structure determination of membrane proteins. This review highlights four approaches: limited proteolysis, deglycosylation, cysteine alkylation, and lysine methylation. Combined these approaches have facilitated the structure determination of more than 40 membrane proteins and, therefore, are a useful addition to the membrane protein structural biologist's toolkit.
Collapse
Affiliation(s)
- Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA 22902, United States.
| |
Collapse
|
48
|
Du D, van Veen HW, Luisi BF. Assembly and operation of bacterial tripartite multidrug efflux pumps. Trends Microbiol 2015; 23:311-9. [PMID: 25728476 DOI: 10.1016/j.tim.2015.01.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/13/2015] [Accepted: 01/22/2015] [Indexed: 01/21/2023]
Abstract
Microorganisms encode several classes of transmembrane pumps that can expel an enormous range of toxic substances, thereby improving their fitness in harsh environments and contributing to resistance against antimicrobial agents. In Gram-negative bacteria these pumps can take the form of tripartite assemblies that actively efflux drugs and other harmful compounds across the cell envelope. We describe recent structural and functional data that have provided insights into the transport mechanisms of these intricate molecular machines.
Collapse
Affiliation(s)
- Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| |
Collapse
|
49
|
Prabhala BK, Aduri NG, Hald H, Mirza O. Investigation of the Substrate Specificity of the Proton Coupled Peptide Transporter PepTSo from Shewanella oneidensis. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|