101
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Casal M, Queirós O, Talaia G, Ribas D, Paiva S. Carboxylic Acids Plasma Membrane Transporters in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:229-251. [PMID: 26721276 DOI: 10.1007/978-3-319-25304-6_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter covers the functionally characterized plasma membrane carboxylic acids transporters Jen1, Ady2, Fps1 and Pdr12 in the yeast Saccharomyces cerevisiae, addressing also their homologues in other microorganisms, as filamentous fungi and bacteria. Carboxylic acids can either be transported into the cells, to be used as nutrients, or extruded in response to acid stress conditions. The secondary active transporters Jen1 and Ady2 can mediate the uptake of the anionic form of these substrates by a H(+)-symport mechanism. The undissociated form of carboxylic acids is lipid-soluble, crossing the plasma membrane by simple diffusion. Furthermore, acetic acid can also be transported by facilitated diffusion via Fps1 channel. At the cytoplasmic physiological pH, the anionic form of the acid prevails and it can be exported by the Pdr12 pump. This review will highlight the mechanisms involving carboxylic acids transporters, and the way they operate according to the yeast cell response to environmental changes, as carbon source availability, extracellular pH and acid stress conditions.
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Affiliation(s)
- Margarida Casal
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Odília Queirós
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra, 1317, 4585-116, Gandra, PRD, Portugal
| | - Gabriel Talaia
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - David Ribas
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sandra Paiva
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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102
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Jørgensen ME, Olsen CE, Geiger D, Mirza O, Halkier BA, Nour-Eldin HH. A Functional EXXEK Motif is Essential for Proton Coupling and Active Glucosinolate Transport by NPF2.11. PLANT & CELL PHYSIOLOGY 2015; 56:2340-50. [PMID: 26443378 PMCID: PMC4675897 DOI: 10.1093/pcp/pcv145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/24/2015] [Indexed: 05/02/2023]
Abstract
The proton-dependent oligopeptide transporter (POT/PTR) family shares a highly conserved E1X1X2E2RFXYY (E1X1X2E2R) motif across all kingdoms of life. This motif is suggested to have a role in proton coupling and active transport in bacterial homologs. For the plant POT/PTR family, also known as the NRT1/PTR family (NPF), little is known about the role of the E1X1X2E2R motif. Moreover, nothing is known about the role of the X1 and X2 residues within the E1X1X2E2R motif. We used NPF2.11-a proton-coupled glucosinolate (GLS) symporter from Arabidopsis thaliana-to investigate the role of the E1X1X2E2K motif variant in a plant NPF transporter. Using liquid chromatography-mass spectrometry (LC-MS)-based uptake assays and two-electrode voltage clamp (TEVC) electrophysiology, we demonstrate an essential role for the E1X1X2E2K motif for accumulation of substrate by NPF2.11. Our data suggest that the highly conserved E1, E2 and K residues are involved in translocation of protons, as has been proposed for the E1X1X2E2R motif in bacteria. Furthermore, we show that the two residues X1 and X2 in the E1X1X2E2[K/R] motif are conserved as uncharged amino acids in POT/PTRs from bacteria to mammals and that introducing a positive or negative charge in either position hampers the ability to overaccumulate substrate relative to the assay medium. We hypothesize that introducing a charge at X1 and X2 interferes with the function of the conserved glutamate and lysine residues of the E1X1X2E2K motif and affects the mechanism behind proton coupling.
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Affiliation(s)
- Morten Egevang Jørgensen
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Carl Erik Olsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Dietmar Geiger
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
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103
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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.
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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
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104
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Nomura N, Verdon G, Kang HJ, Shimamura T, Nomura Y, Sonoda Y, Hussien SA, Qureshi AA, Coincon M, Sato Y, Abe H, Nakada-Nakura Y, Hino T, Arakawa T, Kusano-Arai O, Iwanari H, Murata T, Kobayashi T, Hamakubo T, Kasahara M, Iwata S, Drew D. Structure and mechanism of the mammalian fructose transporter GLUT5. Nature 2015; 526:397-401. [PMID: 26416735 PMCID: PMC4618315 DOI: 10.1038/nature14909] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/14/2015] [Indexed: 02/02/2023]
Abstract
The altered activity of the fructose transporter GLUT5, an isoform of the facilitated-diffusion glucose transporter family, has been linked to disorders such as type 2 diabetes and obesity. GLUT5 is also overexpressed in certain tumor cells and inhibitors are potential drugs for these conditions. Here, we describe the crystal structure of GLUT5 from Rattus norvegicus and Bos taurus in open outward- and open inward-facing conformations, respectively. GLUT5 has a major facilitator superfamily fold like other homologous monosaccharide transporters. Based on a comparison of the inward-facing structures of GLUT5 and human GLUT1, a ubiquitous glucose transporter, we show that a single point mutation is enough to switch the substrate binding preference of GLUT5 from fructose to glucose. A comparison of the substrate-free structures of GLUT5 with occluded substrate-bound structures of XylE suggests that, besides global rocker-switch like re-orientation of the bundles, local asymmetric rearrangements of C-terminal bundle helices TMs 7 and 10 underlie a “gated-pore” transport mechanism in such monosaccharide transporters.
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Affiliation(s)
- Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Grégory Verdon
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Hae Joo Kang
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yayoi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yo Sonoda
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K
| | - Saba Abdul Hussien
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Aziz Abdul Qureshi
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mathieu Coincon
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Yumi Sato
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitomi Abe
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoya Hino
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takatoshi Arakawa
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Osamu Kusano-Arai
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroko Iwanari
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Murata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takao Hamakubo
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Michihiro Kasahara
- Laboratory of Biophysics, School of Medicine, Teikyo University, Hachioji, Tokyo 192-0395, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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105
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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.
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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
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106
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Beale JH, Parker JL, Samsudin F, Barrett AL, Senan A, Bird LE, Scott D, Owens RJ, Sansom MSP, Tucker SJ, Meredith D, Fowler PW, Newstead S. Crystal Structures of the Extracellular Domain from PepT1 and PepT2 Provide Novel Insights into Mammalian Peptide Transport. Structure 2015; 23:1889-1899. [PMID: 26320580 PMCID: PMC4597091 DOI: 10.1016/j.str.2015.07.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/22/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022]
Abstract
Mammals obtain nitrogen via the uptake of di- and tri-peptides in the gastrointestinal tract through the action of PepT1 and PepT2, which are members of the POT family of proton-coupled oligopeptide transporters. PepT1 and PepT2 also play an important role in drug transport in the human body. Recent crystal structures of bacterial homologs revealed a conserved peptide-binding site and mechanism of transport. However, a key structural difference exists between bacterial and mammalian homologs with only the latter containing a large extracellular domain, the function of which is currently unknown. Here, we present the crystal structure of the extracellular domain from both PepT1 and PepT2 that reveal two immunoglobulin-like folds connected in tandem, providing structural insight into mammalian peptide transport. Functional and biophysical studies demonstrate that these domains interact with the intestinal protease trypsin, suggesting a role in clustering proteolytic activity to the site of peptide transport in eukaryotic cells. Crystal structure of the extracellular domains of PepT1 and PepT2 Modular architecture for a mammalian MFS transporter Extracellular domains contain immunoglobulin-like fold and interact with trypsin
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Affiliation(s)
- John H Beale
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Firdaus Samsudin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anne L Barrett
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Anish Senan
- Department of Biological Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Louise E Bird
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; OPPF-UK, Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - David Scott
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, UK; ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, UK; School of Biosciences, School of Biosciences, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Raymond J Owens
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; OPPF-UK, Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Membrane Transport, University of Oxford OX1 3PU, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK; OXION Initiative in Ion Channels and Membrane Transport, University of Oxford OX1 3PU, UK
| | - David Meredith
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Philip W Fowler
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; OXION Initiative in Ion Channels and Membrane Transport, University of Oxford OX1 3PU, UK.
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107
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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.
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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.
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108
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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).
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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.
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109
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Abstract
Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.
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Affiliation(s)
- Yigong Shi
- Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
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110
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Madej MG. Comparative Sequence-Function Analysis of the Major Facilitator Superfamily: The "Mix-and-Match" Method. Methods Enzymol 2015; 557:521-49. [PMID: 25950980 DOI: 10.1016/bs.mie.2014.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is a diverse group of secondary transporters with members found in all kingdoms of life. The paradigm for MFS is the lactose permease (LacY) of Escherichia coli, which has been the test bed for the development of many methods applied for the analysis of transport proteins. X-ray structures of an inward-facing conformation and the most recent structure of an almost occluded conformation confirm many conclusions from previous studies. One fundamentally important problem for understanding the mechanism of secondary active transport is the identification and physical localization of residues involved in substrate and H(+) binding. This information is exceptionally difficult to obtain with the MFS because of the broad sequence diversity among the members. The increasing number of solved MFS structures has led to the recognition of a common feature: inverted structure-repeat, formed by fused triple-helix domains with opposite orientation in the membrane. The presented method here exploits this feature to predict functionally homologous positions of known relevant positions in LacY. The triple-helix motifs are aligned in combinatorial fashion so as to detect substrate and H(+)-binding sites in symporters that transport substrates, ranging from simple ions like phosphate to more complex disaccharides.
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Affiliation(s)
- M Gregor Madej
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
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111
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Västermark Å, Driker A, Li J, Saier MH. Conserved movement of TMS11 between occluded conformations of LacY and XylE of the major facilitator superfamily suggests a similar hinge-like mechanism. Proteins 2015; 83:735-45. [PMID: 25586173 DOI: 10.1002/prot.24755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 12/11/2022]
Abstract
The Δ-distance maps can detect local remodeling that is difficult to accurately determine using superimpositions. Transmembrane segments (TMSs) 11 in both LacY and XylE of the major facilitator superfamily uniquely contribute the greatest amount of mobile surface area in the outward-occluded state and undergo analogous movements. The intracellular part of TMS11 moves away from the C-terminal domain and into the substrate cavity during the conformational change from the outward-occluded to the inward-occluded state. A difference was noted between LacY and XylE when they assumed the inward open state after releasing a substrate to the inside in which TMS11 of LacY moved further into the substrate release space, whereas in XylE, TMS11 slightly retracted into the C-terminal domain. Independent movement of the N-terminal half of TMS11 suggests that it is flexible in the middle. Repeat-swapped homology modeling was used to discover that a loop connecting TMSs 10 and 11 in LacY probably moves during the transition between the unavailable outward-open state and the outward-occluded state. TMSs 11 and the other elements displaying a notable domain-independent movement colocalize with the interdomain linker, suggesting that these elements could drive the alternating access movement between the domain halves. Preliminary evidence indicates that analogous movements occur in other members of the major facilitator superfamily.
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Affiliation(s)
- Åke Västermark
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, 92093-0116
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112
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Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, Forrest LR, Newstead S. Gating topology of the proton-coupled oligopeptide symporters. Structure 2015; 23:290-301. [PMID: 25651061 PMCID: PMC4321885 DOI: 10.1016/j.str.2014.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/10/2023]
Abstract
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | | | - Sebastian Radestock
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia M Dijkman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Jane Kwok
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lucy R Forrest
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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113
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Yaffe D, Vergara-Jaque A, Shuster Y, Listov D, Meena S, Singh SK, Forrest LR, Schuldiner S. Functionally important carboxyls in a bacterial homologue of the vesicular monoamine transporter (VMAT). J Biol Chem 2014; 289:34229-40. [PMID: 25336661 PMCID: PMC4256354 DOI: 10.1074/jbc.m114.607366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/30/2014] [Indexed: 11/06/2022] Open
Abstract
Transporters essential for neurotransmission in mammalian organisms and bacterial multidrug transporters involved in antibiotic resistance are evolutionarily related. To understand in more detail the evolutionary aspects of the transformation of a bacterial multidrug transporter to a mammalian neurotransporter and to learn about mechanisms in a milieu amenable for structural and biochemical studies, we identified, cloned, and partially characterized bacterial homologues of the rat vesicular monoamine transporter (rVMAT2). We performed preliminary biochemical characterization of one of them, Brevibacillus brevis monoamine transporter (BbMAT), from the bacterium B. brevis. BbMAT shares substrates with rVMAT2 and transports them in exchange with >1H(+), like the mammalian transporter. Here we present a homology model of BbMAT that has the standard major facilitator superfamily fold; that is, with two domains of six transmembrane helices each, related by 2-fold pseudosymmetry whose axis runs normal to the membrane and between the two halves. The model predicts that four carboxyl residues, a histidine, and an arginine are located in the transmembrane segments. We show here that two of the carboxyls are conserved, equivalent to the corresponding ones in rVMAT2, and are essential for H(+)-coupled transport. We conclude that BbMAT provides an excellent experimental paradigm for the study of its mammalian counterparts and bacterial multidrug transporters.
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Affiliation(s)
- Dana Yaffe
- From the Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, 91904 Jerusalem, Israel
| | - Ariela Vergara-Jaque
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20852, and
| | - Yonatan Shuster
- From the Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, 91904 Jerusalem, Israel
| | - Dina Listov
- From the Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, 91904 Jerusalem, Israel
| | - Sitaram Meena
- the Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Satinder K Singh
- the Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Lucy R Forrest
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Bethesda, Maryland 20852, and
| | - Shimon Schuldiner
- From the Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, 91904 Jerusalem, Israel,
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114
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Iyalomhe O, Herrick DZ, Cafiso DS, Maloney PC. Closure of the cytoplasmic gate formed by TM5 and TM11 during transport in the oxalate/formate exchanger from Oxalobacter formigenes. Biochemistry 2014; 53:7735-44. [PMID: 25409483 PMCID: PMC4270380 DOI: 10.1021/bi5012173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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OxlT, the oxalate/formate exchanger
of Oxalobacter
formigenes, is a member of the major facilitator superfamily
of transporters. In the present work, substrate (oxalate) was found
to enhance the reactivity of the cysteine mutant S336C on the cytoplasmic
end of helix 11 to methanethiosulfonate ethyl carboxylate. In addition,
S336C is found to spontaneously cross-link to S143C in TM5 in either
native or reconstituted membranes under conditions that support transport.
Continuous wave EPR measurements are consistent with this result and
indicate that positions 143 and 336 are in close proximity in the
presence of substrate. These two residues are localized within helix
interacting GxxxG-like motifs (G140LASG144 and
S336DIFG340) at the cytoplasmic poles of TM5
and TM11. Pulse EPR measurements were used to determine distances
and distance distributions across the cytoplasmic or periplasmic ends
of OxlT and were compared with the predictions of an inside-open homology
model. The data indicate that a significant population of transporter
is in an outside-open configuration in the presence of substrate;
however, each end of the transporter exhibits significant conformational
heterogeneity, where both inside-open and outside-open configurations
are present. These data indicate that TM5 and TM11, which form part
of the transport pathway, transiently close during transport and that
there is a conformational equilibrium between inside-open and outside-open
states of OxlT in the presence of substrate.
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Affiliation(s)
- Osigbemhe Iyalomhe
- Department of Physiology, The Johns Hopkins University, School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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115
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Parker JL, Mindell JA, Newstead S. Thermodynamic evidence for a dual transport mechanism in a POT peptide transporter. eLife 2014; 3. [PMID: 25457052 PMCID: PMC4271188 DOI: 10.7554/elife.04273] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/01/2014] [Indexed: 01/30/2023] Open
Abstract
Peptide transport plays an important role in cellular homeostasis as a key route for nitrogen acquisition in mammalian cells. PepT1 and PepT2, the mammalian proton coupled peptide transporters (POTs), function to assimilate and retain diet-derived peptides and play important roles in drug pharmacokinetics. A key characteristic of the POT family is the mechanism of peptide selectivity, with members able to recognise and transport >8000 different peptides. In this study, we present thermodynamic evidence that in the bacterial POT family transporter PepTSt, from Streptococcus thermophilus, at least two alternative transport mechanisms operate to move peptides into the cell. Whilst tri-peptides are transported with a proton:peptide stoichiometry of 3:1, di-peptides are co-transported with either 4 or 5 protons. This is the first thermodynamic study of proton:peptide stoichiometry in the POT family and reveals that secondary active transporters can evolve different coupling mechanisms to accommodate and transport chemically and physically diverse ligands across the membrane.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joseph A Mindell
- Membrane Transport Biophysics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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116
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Jensen JM, Aduri NG, Prabhala BK, Jahnsen R, Franzyk H, Mirza O. Critical role of a conserved transmembrane lysine in substrate recognition by the proton-coupled oligopeptide transporter YjdL. Int J Biochem Cell Biol 2014; 55:311-7. [PMID: 25261786 DOI: 10.1016/j.biocel.2014.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022]
Abstract
Proton-coupled oligopeptide transporters (POTs) utilize an electrochemical proton gradient to accumulate peptides in the cytoplasm. Changing the highly conserved active-site Lys117 in the Escherichia coli POT YjdL to glutamine resulted in loss of ligand affinity as well as inability to distinguish between a dipeptide ligand and the corresponding dipeptide amide. The radically changed pH(Bulk) profiles of Lys117Gln and Lys117Arg mutants indicate an important role of Lys117 in facilitating protonation of the transporter; a notion that is supported by the close proximity of Lys117 to the conserved ExxERFxYY POT motif previously shown to be involved in proton translocation. These results point toward a novel dual role of Lys117 in direct or indirect interaction with both proton and peptide.
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Affiliation(s)
- Johanne M Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Jahnsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Franzyk
- 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.
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117
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Function, Structure, and Evolution of the Major Facilitator Superfamily: The LacY Manifesto. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/523591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The major facilitator superfamily (MFS) is a diverse group of secondary transporters with members found in all kingdoms of life. A paradigm for MFS is the lactose permease (LacY) of Escherichia coli, which couples the stoichiometric translocation of a galactopyranoside and an H+ across the cytoplasmic membrane. LacY has been the test bed for the development of many methods applied for the analysis of transport proteins. X-ray structures of an inward-facing conformation and the most recent structure of an almost occluded conformation confirm many conclusions from previous studies. Although structure models are critical, they are insufficient to explain the catalysis of transport. The clues to understanding transport are based on the principles of enzyme kinetics. Secondary transport is a dynamic process—static snapshots of X-ray crystallography describe it only partially. However, without structural information, the underlying chemistry is virtually impossible to conclude. A large body of biochemical/biophysical data derived from systematic studies of site-directed mutants in LacY suggests residues critically involved in the catalysis, and a working model for the symport mechanism that involves alternating access of the binding site is presented. The general concepts derived from the bacterial LacY are examined for their relevance to other MFS transporters.
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118
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The Structure and Function of OxlT, the Oxalate Transporter of Oxalobacter formigenes. J Membr Biol 2014; 248:641-50. [DOI: 10.1007/s00232-014-9728-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/05/2014] [Indexed: 01/01/2023]
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119
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Functional implications and ubiquitin-dependent degradation of the peptide transporter Ptr2 in Saccharomyces cerevisiae. EUKARYOTIC CELL 2014; 13:1380-92. [PMID: 25172766 DOI: 10.1128/ec.00094-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The peptide transporter Ptr2 plays a central role in di- or tripeptide import in Saccharomyces cerevisiae. Although PTR2 transcription has been extensively analyzed in terms of upregulation by the Ubr1-Cup9 circuit, the structural and functional information for this transporter is limited. Here we identified 14 amino acid residues required for peptide import through Ptr2 based on the crystallographic information of Streptococcus thermophilus peptide transporter PepTst and based on the conservation of primary sequences among the proton-dependent oligopeptide transporters (POTs). Expression of Ptr2 carrying one of the 14 mutations of which the corresponding residues of PepTst are involved in peptide recognition, salt bridge interaction, or peptide translocation failed to enable ptr2Δtrp1 cell growth in alanyl-tryptophan (Ala-Trp) medium. We observed that Ptr2 underwent rapid degradation after cycloheximide treatment (half-life, approximately 1 h), and this degradation depended on Rsp5 ubiquitin ligase. The ubiquitination of Ptr2 most likely occurs at the N-terminal lysines 16, 27, and 34. Simultaneous substitution of arginine for the three lysines fully prevented Ptr2 degradation. Ptr2 mutants of the presumed peptide-binding site (E92Q, R93K, K205R, W362L, and E480D) exhibited severe defects in peptide import and were subjected to Rsp5-dependent degradation when cells were moved to Ala-Trp medium, whereas, similar to what occurs in the wild-type Ptr2, mutant proteins of the intracellular gate were upregulated. These results suggest that Ptr2 undergoes quality control and the defects in peptide binding and the concomitant conformational change render Ptr2 subject to efficient ubiquitination and subsequent degradation.
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120
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Cunningham P, Naftalin RJ. Reptation-induced coalescence of tunnels and cavities in Escherichia Coli XylE transporter conformers accounts for facilitated diffusion. J Membr Biol 2014; 247:1161-79. [PMID: 25163893 PMCID: PMC4207944 DOI: 10.1007/s00232-014-9711-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Abstract
Structural changes and xylose docking to eight conformers of Escherichia Coli XylE, a xylose transporter similar to mammalian passive glucose transporters GLUTs, have been examined. Xylose docks to inward and outward facing conformers at a high affinity central site (Ki 4–20 µM), previously identified by crystallography and additionally consistently docks to lower affinity sites in the external and internal vestibules (Ki 12–50 µM). All these sites lie within intramolecular tunnels and cavities. Several local regions in the central transmembrane zone have large positional divergences of both skeleton carbon Cα positions and side chains. One such in TM 10 is the destabilizing sequence G388-P389-V390-C391 with an average RMSD (4.5 ± 0.4 Å). Interchange between conformer poses results in coalescence of tunnels with adjacent cavities, thereby producing a transitory channel spanning the entire transporter. A fully open channel exists in one inward-facing apo-conformer, (PDB 4ja4c) as demonstrated by several different tunnel-finding algorithms. The conformer interchanges produce a gated network within a branched central channel that permits staged ligand diffusion across the transporter during the open gate periods. Simulation of this model demonstrates that small-scale conformational changes required for sequentially opening gate with frequencies in the ns-μs time domain accommodate diffusive ligand flow between adjacent sites with association–dissociation rates in the μs-ms domain without imposing delays. This current model helps to unify the apparently opposing concepts of alternate access and multisite models of ligand transport.
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Affiliation(s)
- Philip Cunningham
- Department of Bioinformatics, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
| | - Richard J. Naftalin
- Department of Physiology, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
- BHF Centre of Research Excellence, School of Medicine, King’s College London, Waterloo Campus, Franklin–Wilkins Building, London, SE1 9NH UK
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121
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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]
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122
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Wisedchaisri G, Park MS, Iadanza MG, Zheng H, Gonen T. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE. Nat Commun 2014; 5:4521. [PMID: 25088546 PMCID: PMC4137407 DOI: 10.1038/ncomms5521] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/25/2014] [Indexed: 01/19/2023] Open
Abstract
The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. Glucose transporters are a medically important class of membrane proteins often deregulated in diseases such as Type 2 diabetes. Here, Wisedchaisri et al. report the crystal structure of XylE in an inward-facing open conformation to provide a general mechanism of substrate transport for the sugar porter family of proteins.
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Affiliation(s)
- Goragot Wisedchaisri
- 1] Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA [2]
| | - Min-Sun Park
- 1] Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA [2]
| | - Matthew G Iadanza
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Hongjin Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
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123
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Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2. Nat Struct Mol Biol 2014; 21:728-31. [PMID: 25064511 DOI: 10.1038/nsmb.2860] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/20/2014] [Indexed: 01/24/2023]
Abstract
Peptide transporters of the PepT family have key roles in the transport of di- and tripeptides across membranes as well as in the absorption of orally administered drugs in the small intestine. We have determined structures of a PepT transporter from Shewanella oneidensis (PepT(So2)) in complex with three different peptides. The peptides bind in a large cavity lined by residues that are highly conserved in human PepT1 and PepT2. The bound peptides adopt extended conformations with their N termini clamped into a conserved polar pocket. A positively charged patch allows differential interactions with the C-terminal carboxylates of di- and tripeptides. Here we identify three pockets for peptide side chain interactions, and our binding studies define differential roles of these pockets for the recognition of different subtypes of peptide side chains.
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124
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Zhao Y, Mao G, Liu M, Zhang L, Wang X, Zhang XC. Crystal structure of the E. coli peptide transporter YbgH. Structure 2014; 22:1152-1160. [PMID: 25066136 DOI: 10.1016/j.str.2014.06.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/27/2014] [Accepted: 06/03/2014] [Indexed: 11/28/2022]
Abstract
E. coli YbgH belongs to the family of proton-dependent oligopeptide transporters (POTs), a subfamily of the major facilitator superfamily (MFS) of secondary active transporters. Like other MFS transporters, POT proteins switch between two major conformations during substrate transport. Apart from possessing a canonical 12-helix, two-domain transmembrane (TM) core, prokaryotic POT proteins usually have two TM helices inserted between the two domains. Here we determined the crystal structure of YbgH in its inward-facing conformation. Our structure-based functional studies investigated the roles of both the POT signature motif 2 and the inserted interdomain TM helix pair in the stabilization and regulation of the major conformational change in MFS/POT transporters. Furthermore, of all the proton-titratable amino acid residues, Glu21 is the only conserved one (among POTs) located in the central cavity and is critical for in vivo transport. Together, our results support the notion that MFS symporters utilize a transport mechanism based on substrate-protonation coupling.
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Affiliation(s)
- Yan Zhao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; National Laboratory of Macromolecules, National Center of Protein Science Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Guotao Mao
- 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
| | - Min Liu
- 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
| | - Laixing Zhang
- 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
| | - 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.
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125
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Hinchliffe P, Greene NP, Paterson NG, Crow A, Hughes C, Koronakis V. Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump. FEBS Lett 2014; 588:3147-53. [PMID: 24996185 PMCID: PMC4158417 DOI: 10.1016/j.febslet.2014.06.055] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 10/28/2022]
Abstract
Periplasmic adaptor proteins are key components of bacterial tripartite efflux pumps. The 2.85 Å resolution structure of an MFS (major facilitator superfamily) pump adaptor, Aquifex aeolicus EmrA, shows linearly arranged α-helical coiled-coil, lipoyl, and β-barrel domains, but lacks the fourth membrane-proximal domain shown in other pumps to interact with the inner membrane transporter. The adaptor α-hairpin, which binds outer membrane TolC, is exceptionally long at 127 Å, and the β-barrel contains a conserved disordered loop. The structure extends the view of adaptors as flexible, modular components that mediate diverse pump assembly, and suggests that in MFS tripartite pumps a hexamer of adaptors could provide a periplasmic seal.
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Affiliation(s)
- Philip Hinchliffe
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Nicholas P Greene
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Neil G Paterson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Allister Crow
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Colin Hughes
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Vassilis Koronakis
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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126
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Lyons JA, Parker JL, Solcan N, Brinth A, Li D, Shah STA, Caffrey M, Newstead S. Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters. EMBO Rep 2014; 15:886-93. [PMID: 24916388 PMCID: PMC4149780 DOI: 10.15252/embr.201338403] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An enigma in the field of peptide transport is the structural basis for ligand promiscuity, as exemplified by PepT1, the mammalian plasma membrane peptide transporter. Here, we present crystal structures of di- and tripeptide-bound complexes of a bacterial homologue of PepT1, which reveal at least two mechanisms for peptide recognition that operate within a single, centrally located binding site. The dipeptide was orientated laterally in the binding site, whereas the tripeptide revealed an alternative vertical binding mode. The co-crystal structures combined with functional studies reveal that biochemically distinct peptide-binding sites likely operate within the POT/PTR family of proton-coupled symporters and suggest that transport promiscuity has arisen in part through the ability of the binding site to accommodate peptides in multiple orientations for transport.
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Affiliation(s)
- Joseph A Lyons
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alette Brinth
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Dianfan Li
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Syed T A Shah
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, Dublin, Ireland
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
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127
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Shibuya S, Ozawa Y, Toda T, Watanabe K, Tometsuka C, Ogura T, Koyama YI, Shimizu T. Collagen peptide and vitamin C additively attenuate age-related skin atrophy in Sod1-deficient mice. Biosci Biotechnol Biochem 2014; 78:1212-20. [PMID: 25229861 DOI: 10.1080/09168451.2014.915728] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Age-related skin thinning is correlated with a decrease in the content of collagen in the skin. Accumulating evidence suggests that collagen peptide (CP) and vitamin C (VC) transcriptionally upregulate type I collagen in vivo. However, the additive effects of CP and VC on age-related skin changes remain unclear. We herein demonstrate that CP and a VC derivative additively corrected age-related skin thinning via reduced oxidative damage in superoxide dismutase 1 (Sod1)-deficient mice. Co-treatment with these compounds significantly normalized the altered gene expression of Col1a1, Has2, and Ci1, a proton-coupled oligopeptide transporter, in Sod1(-/-) skin. The in vitro analyses further revealed that collagen oligopeptide, a digestive product of ingested CP, significantly promoted the bioactivity of the VC derivative with respect to the migration and proliferation of Sod1(-/-) fibroblasts. These findings suggest that combined treatment with CP and VC is effective in cases of age-related skin pathology.
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Affiliation(s)
- Shuichi Shibuya
- a Department of Advanced Aging Medicine , Chiba University Graduate School of Medicine , Chiba , Japan
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128
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Newstead S. Molecular insights into proton coupled peptide transport in the PTR family of oligopeptide transporters. Biochim Biophys Acta Gen Subj 2014; 1850:488-99. [PMID: 24859687 PMCID: PMC4331665 DOI: 10.1016/j.bbagen.2014.05.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 12/15/2022]
Abstract
Background Cellular uptake of small peptides is an important physiological process mediated by the PTR family of proton-coupled peptide transporters. In bacteria peptides can be used as a source of amino acids and nitrogen. Similarly in humans peptide transport is the principle route for the uptake and retention of dietary protein in the form of short di- and tri-peptides for cellular metabolism. Scope of the review Recent crystal structures of bacterial PTR family transporters, combined with biochemical studies of transport have revealed key molecular details underpinning ligand promiscuity and the mechanism of proton-coupled transport within the family. Major conclusions Pairs of salt bridge interactions between transmembrane helices work in tandem to orchestrate alternating access transport within the PTR family. Key roles for residues conserved between bacterial and eukaryotic homologues suggest a conserved mechanism of peptide recognition and transport that in some cases has been subtly modified in individual species. General significance Physiological studies on PepT1 and PepT2, the mammalian members of this family, have identified these transporters as being responsible for the uptake of many pharmaceutically important drug molecules, including antibiotics and antiviral medications and demonstrated their promiscuity can be used for improving the oral bioavailability of poorly absorbed compounds. The insights gained from recent structural studies combined with previous physiological and biochemical analyses are rapidly advancing our understanding of this medically important transporter superfamily. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins. Crystal structures of PTR family transporters Identification of mechanistically important salt bridge interactions. Conservation of key functional residues between bacterial and mammalian homologues. High resolution structural information on peptide binding.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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129
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Analysing the substrate multispecificity of a proton-coupled oligopeptide transporter using a dipeptide library. Nat Commun 2014; 4:2502. [PMID: 24060756 PMCID: PMC3791473 DOI: 10.1038/ncomms3502] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/23/2013] [Indexed: 01/26/2023] Open
Abstract
Peptide uptake systems that involve members of the proton-coupled oligopeptide transporter (POT) family are conserved across all organisms. POT proteins have characteristic substrate multispecificity, with which one transporter can recognize as many as 8,400 types of di/tripeptides and certain peptide-like drugs. Here we characterize the substrate multispecificity of Ptr2p, a major peptide transporter of Saccharomyces cerevisiae, using a dipeptide library. The affinities (Ki) of di/tripeptides toward Ptr2p show a wide distribution range from 48 mM to 0.020 mM. This substrate multispecificity indicates that POT family members have an important role in the preferential uptake of vital amino acids. In addition, we successfully establish high performance ligand affinity prediction models (97% accuracy) using our comprehensive dipeptide screening data in conjunction with simple property indices for describing ligand molecules. Our results provide an important clue to the development of highly absorbable peptides and their derivatives including peptide-like drugs. Proton-coupled oligopeptide transporters (POTs) can recognize and mediate the uptake of up to 8,400 di/tripeptides or peptide-like drugs. Ito et al. comprehensively map the substrate specificity of the yeast POT Ptr2p, and use this information to construct models for the prediction of ligand affinity.
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130
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Stelzl LS, Fowler PW, Sansom MS, Beckstein O. Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol 2014; 426:735-51. [PMID: 24513108 PMCID: PMC3905165 DOI: 10.1016/j.jmb.2013.10.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 12/29/2022]
Abstract
The major facilitator superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling molecular dynamics method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free-energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepTSo, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin–spin distance measurements that have been interpreted to show occluded conformations. During the simulations, a salt bridge that has been postulated to be involved in driving the conformational transition formed. Our results argue against a simple rigid-body domain motion as implied by a strict “rocker-switch mechanism” and instead hint at an intricate coupling between two flexible gates. The transport mechanism of LacY is hypothesized to involve an intermediate “occluded” state. Such a state is observed in computer simulations of the conformational transitions. Simulation data are validated with experimental double electron–electron spin resonance measurements. The structural gating elements of LacY are identified. Occluded LacY is similar to known occluded structures of homologous proteins.
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Affiliation(s)
- Lukas S. Stelzl
- 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
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author Department of Physics, Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287-1504, USA.
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131
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Ho CH, Frommer WB. Fluorescent sensors for activity and regulation of the nitrate transceptor CHL1/NRT1.1 and oligopeptide transporters. eLife 2014; 3:e01917. [PMID: 24623305 PMCID: PMC3950950 DOI: 10.7554/elife.01917] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To monitor nitrate and peptide transport activity in vivo, we converted the dual-affinity nitrate transceptor CHL1/NRT1.1/NPF6.3 and four related oligopeptide transporters PTR1, 2, 4, and 5 into fluorescence activity sensors (NiTrac1, PepTrac). Substrate addition to yeast expressing transporter fusions with yellow fluorescent protein and mCerulean triggered substrate-dependent donor quenching or resonance energy transfer. Fluorescence changes were nitrate/peptide-specific, respectively. Like CHL1, NiTrac1 had biphasic kinetics. Mutation of T101A eliminated high-affinity transport and blocked the fluorescence response to low nitrate. NiTrac was used for characterizing side chains considered important for substrate interaction, proton coupling, and regulation. We observed a striking correlation between transport activity and sensor output. Coexpression of NiTrac with known calcineurin-like proteins (CBL1, 9; CIPK23) and candidates identified in an interactome screen (CBL1, KT2, WNKinase 8) blocked NiTrac1 responses, demonstrating the suitability for in vivo analysis of activity and regulation. The new technology is applicable in plant and medical research. DOI:http://dx.doi.org/10.7554/eLife.01917.001 About 1% of global energy output is used to produce nitrogen-enriched fertiliser to improve crop yields, but much of this energy is wasted because plants absorb only a fraction of the nitrogen that is applied as fertiliser. Even worse, the excess nitrogen leaches into water sources, poisoning the environment and causing health problems. However, to date, most efforts to increase the efficiency of nitrogen uptake in plants have been unsuccessful. The key to improving the uptake efficiency of a nutrient is to identify obstacles in its journey from the soil to cells inside the plant. The first obstacle that nitrate ions encounter is the membrane of the cells on the surface of the roots of the plant. Many researchers believe that it would be possible to increase the amount of nitrogen absorbed by the plant if more was known about the ways that plants control how nitrate ions and other chemicals enter cells. The cell membrane contains gated pores called transporters that allow particular molecules to pass through it. Although the transporters responsible for the uptake of nitrate ions, peptides, and ammonium ions (the main nitrogen compounds that plants acquire) have been identified, current experimental techniques cannot determine when and where a specific transporter is active within a living plant. This makes it difficult to know where to target modifications and to determine how effective they have been at each step. The nitrate transporter also acts as an antenna that measures nitrate concentration to ensure it is used optimally in the plant, but current techniques cannot show how this actually works. Now, Ho and Frommer have exploited the fact that a transporter changes shape as it does its job to create sensors that can track the movement of nitrate and peptides through the cell membrane. By using fluorescent proteins to monitor how the shape of the transporter changes, Ho and Frommer were able to measure how structural mutations and regulatory proteins influenced the movement of nitrate and peptides through the membrane. For efficiency, all of this work was performed in yeast cells. The next goal is to use the technique in plants to uncover how they adjust to changes in nutrient levels in the soil. DOI:http://dx.doi.org/10.7554/eLife.01917.002
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Affiliation(s)
- Cheng-Hsun Ho
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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132
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Crystal structure of the plant dual-affinity nitrate transporter NRT1.1. Nature 2014; 507:73-7. [PMID: 24572362 PMCID: PMC3968801 DOI: 10.1038/nature13074] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/23/2014] [Indexed: 01/24/2023]
Abstract
Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter, which can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr101. Yet how this posttranslational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 indeed dimerizes in the cell membrane and the phosphomimetic mutation of Thr101 converts the protein into a monophasic high affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.
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133
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Parker JL, Newstead S. Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1. Nature 2014; 507:68-72. [PMID: 24572366 PMCID: PMC3982047 DOI: 10.1038/nature13116] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/31/2014] [Indexed: 12/11/2022]
Abstract
The NRT1/PTR family of proton-coupled transporters are responsible for nitrogen assimilation in eukaryotes and bacteria through the uptake of peptides. However, in the majority of plant species members of this family have evolved to transport nitrate as well as additional secondary metabolites and hormones. In response to falling nitrate levels, NRT1.1 is phosphorylated on an intracellular threonine that switches the transporter from a low to high affinity state. Here we present both the apo and nitrate bound crystal structures of Arabidopsis thaliana NRT1.1, which together with in vitro binding and transport data identify a key role for His356 in nitrate binding. Our data support a model whereby phosphorylation increases structural flexibility and in turn the rate of transport. Comparison with peptide transporters further reveals how the NRT1/PTR family has evolved to recognize diverse nitrogenous ligands, whilst maintaining elements of a conserved coupling mechanism within this superfamily of nutrient transporters.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Simon Newstead
- 1] Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK [2] Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK
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134
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Harris NJ, Findlay HE, Simms J, Liu X, Booth PJ. Relative domain folding and stability of a membrane transport protein. J Mol Biol 2014; 426:1812-25. [PMID: 24530957 DOI: 10.1016/j.jmb.2014.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
There is a limited understanding of the folding of multidomain membrane proteins. Lactose permease (LacY) of Escherichia coli is an archetypal member of the major facilitator superfamily of membrane transport proteins, which contain two domains of six transmembrane helices each. We exploit chemical denaturation to determine the unfolding free energy of LacY and employ Trp residues as site-specific thermodynamic probes. Single Trp LacY mutants are created with the individual Trps situated at mirror image positions on the two LacY domains. The changes in Trp fluorescence induced by urea denaturation are used to construct denaturation curves from which unfolding free energies can be determined. The majority of the single Trp tracers report the same stability and an unfolding free energy of approximately +2 kcal mol(-1). There is one exception; the fluorescence of W33 at the cytoplasmic end of helix I on the N domain is unaffected by urea. In contrast, the equivalent position on the first helix, VII, of the C-terminal domain exhibits wild-type stability, with the single Trp tracer at position 243 on helix VII reporting an unfolding free energy of +2 kcal mol(-1). This indicates that the region of the N domain of LacY at position 33 on helix I has enhanced stability to urea, when compared the corresponding location at the start of the C domain. We also find evidence for a potential network of stabilising interactions across the domain interface, which reduces accessibility to the hydrophilic substrate binding pocket between the two domains.
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Affiliation(s)
- Nicola J Harris
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - John Simms
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Xia Liu
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Paula J Booth
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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135
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Abstract
The Major Facilitator Superfamily (MFS) is a diverse group of secondary transporters with over 10,000 members, found in all kingdoms of life, including Homo sapiens. One objective of determining crystallographic models of the bacterial representatives is identification and physical localization of residues important for catalysis in transporters with medical relevance. The recently solved crystallographic models of the D-xylose permease XylE from Escherichia coli and GlcP from Staphylococcus epidermidus, homologs of the human D-glucose transporters, the GLUTs (SLC2), provide information about the structure of these transporters. The goal of this work is to examine general concepts derived from the bacterial XylE, GlcP, and other MFS transporters for their relevance to the GLUTs by comparing conservation of functionally critical residues. An energy landscape for symport and uniport is presented. Furthermore, the substrate selectivity of XylE is compared with GLUT1 and GLUT5, as well as a XylE mutant that transports D-glucose.
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136
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New insights into the substrate specificities of proton-coupled oligopeptide transporters from E. coli by a pH sensitive assay. FEBS Lett 2014; 588:560-5. [PMID: 24440353 DOI: 10.1016/j.febslet.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/31/2013] [Accepted: 01/03/2014] [Indexed: 11/23/2022]
Abstract
Proton-coupled oligopeptide transporters (POTs) are secondary active transporters that facilitate di- and tripeptide uptake by coupling it to an inward directed proton electrochemical gradient. Here the substrate specificities of Escherichia coli POTs YdgR, YhiP and YjdL were investigated by means of a label free transport assay using the hydrophilic pH sensitive dye pyranine and POT overexpressing E. coli cells. The results confirm and extend the functional knowledge on E. coli POTs. In contrast to previous assumptions, alanine and trialanine appears to be substrates of YjdL, albeit poor compared to dipeptides. Similarly tetraalanine apparently is a substrate of both YdgR and YhiP.
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137
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Perlin MH, Andrews J, San Toh S. Essential Letters in the Fungal Alphabet. ADVANCES IN GENETICS 2014; 85:201-53. [DOI: 10.1016/b978-0-12-800271-1.00004-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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138
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Cornier PG, Delpiccolo CML, Mascali FC, Boggián DB, Mata EG, Cárdenas MG, Blank VC, Roguin LP. In vitro anticancer activity and SAR studies of triazolyl aminoacyl(peptidyl) penicillins. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00332a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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139
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A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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140
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Léran S, Varala K, Boyer JC, Chiurazzi M, Crawford N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong JM, Halkier BA, Harris JM, Hedrich R, Limami AM, Rentsch D, Seo M, Tsay YF, Zhang M, Coruzzi G, Lacombe B. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. TRENDS IN PLANT SCIENCE 2014; 19:5-9. [PMID: 24055139 DOI: 10.1016/j.tplants.2013.08.008] [Citation(s) in RCA: 369] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/16/2013] [Accepted: 08/22/2013] [Indexed: 05/18/2023]
Abstract
Members of the plant NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family display protein sequence homology with the SLC15/PepT/PTR/POT family of peptide transporters in animals. In comparison to their animal and bacterial counterparts, these plant proteins transport a wide variety of substrates: nitrate, peptides, amino acids, dicarboxylates, glucosinolates, IAA, and ABA. The phylogenetic relationship of the members of the NRT1/PTR family in 31 fully sequenced plant genomes allowed the identification of unambiguous clades, defining eight subfamilies. The phylogenetic tree was used to determine a unified nomenclature of this family named NPF, for NRT1/PTR FAMILY. We propose that the members should be named accordingly: NPFX.Y, where X denotes the subfamily and Y the individual member within the species.
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Affiliation(s)
- Sophie Léran
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Kranthi Varala
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Jean-Christophe Boyer
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Maurizio Chiurazzi
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nigel Crawford
- Section of Cell and Developmental Biology, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Françoise Daniel-Vedele
- INRA AgroParisTech, UMR1318 Institut Jean-Pierre Bourgin, RD10, 78026 Versailles Cedex, France
| | - Laure David
- INRA AgroParisTech, UMR1318 Institut Jean-Pierre Bourgin, RD10, 78026 Versailles Cedex, France
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Emilio Fernandez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa Baja E, Campus de Rabanales, E-14071, Córdoba, Spain
| | - Brian Forde
- Centre for Sustainable Agriculture, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Walter Gassmann
- Division of Plant Sciences, CS Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Dietmar Geiger
- Universität Würzburg, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Alain Gojon
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Ji-Ming Gong
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Barbara A Halkier
- DynaMo Centre of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jeanne M Harris
- Department of Plant Biology, 315 Jeffords Hall, 63 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA
| | - Rainer Hedrich
- Universität Würzburg, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Anis M Limami
- UMR 1345 Research Institute of Horticulture and Seeds (INRA, Agrocampus-Ouest, University of Angers), SFR 4207 Quasav, 2 Bd Lavoisier, 49045 Angers Cedex, France
| | - Doris Rentsch
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Mingyong Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gloria Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Benoît Lacombe
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France.
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141
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The Life and Times of Lac Permease: Crystals Ain’t Everything, but They Certainly Do Help. SPRINGER SERIES IN BIOPHYSICS 2014. [DOI: 10.1007/978-3-642-53839-1_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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142
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Functional Expression of Drug Transporters in Glial Cells. PHARMACOLOGY OF THE BLOOD BRAIN BARRIER: TARGETING CNS DISORDERS 2014; 71:45-111. [DOI: 10.1016/bs.apha.2014.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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143
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Hendus-Altenburger R, Kragelund BB, Pedersen SF. Structural dynamics and regulation of the mammalian SLC9A family of Na⁺/H⁺ exchangers. CURRENT TOPICS IN MEMBRANES 2014; 73:69-148. [PMID: 24745981 DOI: 10.1016/b978-0-12-800223-0.00002-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mammalian Na⁺/H⁺ exchangers of the SLC9A family are widely expressed and involved in numerous essential physiological processes. Their primary function is to mediate the 1:1 exchange of Na⁺ for H⁺ across the membrane in which they reside, and they play central roles in regulation of body, cellular, and organellar pH. Their function is tightly regulated through mechanisms involving interactions with multiple protein and lipid-binding partners, phosphorylations, and other posttranslational modifications. Biochemical and mutational analyses indicate that the SLC9As have a short intracellular N-terminus, 12 transmembrane (TM) helices necessary and sufficient for ion transport, and a C-terminal cytoplasmic tail region with essential regulatory roles. No high-resolution structures of the SLC9As exist; however, models based on crystal structures of the bacterial NhaAs support the 12 TM organization and suggest that TMIV and XI may form a central part of the ion-translocation pathway, whereas pH sensing may involve TMII, TMIX, and several intracellular loops. Similar to most ion transporters studied, SLC9As likely exist as coupled dimers in the membrane, and this appears to be important for the well-studied cooperativity of H⁺ binding. The aim of this work is to summarize and critically discuss the currently available evidence on the structural dynamics, regulation, and binding partner interactions of SLC9As, focusing in particular on the most widely studied isoform, SLC9A1/NHE1. Further, novel bioinformatic and structural analyses are provided that to some extent challenge the existing paradigm on how ions are transported by mammalian SLC9As.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Section for Cell and Developmental Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Stine Falsig Pedersen
- Section for Cell and Developmental Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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144
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Kottra G, Spanier B, Verri T, Daniel H. Peptide transporter isoforms are discriminated by the fluorophore-conjugated dipeptides β-Ala- and d-Ala-Lys-N-7-amino-4-methylcoumarin-3-acetic acid. Physiol Rep 2013; 1:e00165. [PMID: 24744852 PMCID: PMC3970736 DOI: 10.1002/phy2.165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/16/2013] [Accepted: 10/26/2013] [Indexed: 02/06/2023] Open
Abstract
Peptide transporters of the SLC15 family are classified by structure and function into PEPT1 (low‐affinity/high‐capacity) and PEPT2 (high‐affinity/low‐capacity) isoforms. Despite the differences in kinetics, both transporter isoforms are reckoned to transport essentially all possible di‐ and tripeptides. We here report that the fluorophore‐conjugated dipeptide derivatives β‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (β‐AK‐AMCA) and d‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (d‐AK‐AMCA) are transported by distinct PEPT isoforms in a species‐specific manner. Transport of the fluorophore peptides was studied (1) in vitro after heterologous expression in Xenopus oocytes of PEPT1 and PEPT2 isoforms from different vertebrate species and of PEPT1 and PEPT2 transporters from Caenorhabditis elegans by using electrophysiological and fluorescence methods and (2) in vivo in C. elegans by using fluorescence methods. Our results indicate that both substrates are transported by the vertebrate “renal‐type” and the C. elegans “intestinal‐type” peptide transporter only. A systematic analysis among species finds four predicted amino acid residues along the sequence that may account for the substrate uptake differences observed between the vertebrate PEPT1/nematode PEPT2 and the vertebrate PEPT2/nematode PEPT1 subtype. This selectivity on basis of isoforms and species may be helpful in better defining the structure–function determinants of the proteins of the SLC15 family. Peptide transporters of the SLC15 family can be classified by structure and function into the PEPT1 (low‐affinity/high‐capacity) and PEPT2 (high‐affinity/low‐capacity) phenotype. We found that the fluorophore‐conjugated dipeptide derivatives β‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (β‐AK‐AMCA) and d‐Ala‐Lys‐N‐7‐amino‐4‐methylcoumarin‐3‐acetic acid (d‐AK‐AMCA) are transported only by distinct PEPT isoforms in a species‐specific manner. This selectivity on basis of isoforms and species should be helpful in further defining the substrate‐binding domain of peptide transporters.
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Affiliation(s)
- Gabor Kottra
- ZIEL Research Center of Nutrition and Food Sciences, Abteilung Biochemie, Technische Universität München, Gregor-Mendel-Str. 2, Freising, D-85350, Germany
| | - Britta Spanier
- ZIEL Research Center of Nutrition and Food Sciences, Abteilung Biochemie, Technische Universität München, Gregor-Mendel-Str. 2, Freising, D-85350, Germany
| | - Tiziano Verri
- Laboratory of General Physiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, Lecce, I-73100, Italy
| | - Hannelore Daniel
- ZIEL Research Center of Nutrition and Food Sciences, Abteilung Biochemie, Technische Universität München, Gregor-Mendel-Str. 2, Freising, D-85350, Germany
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145
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Abstract
One fundamentally important problem for understanding the mechanism of coupling between substrate and H(+) translocation with secondary active transport proteins is the identification and physical localization of residues involved in substrate and H(+) binding. This information is exceptionally difficult to obtain with the Major Facilitator Superfamily (MFS) because of the broad sequence diversity of the members. The MFS is the largest and most diverse group of transporters, many of which are clinically important, and includes members from all kingdoms of life. A wide range of substrates is transported, in many instances against a concentration gradient by transduction of the energy stored in an H(+) electrochemical gradient using symport mechanisms, which are discussed herein. Crystallographic structures of MFS members indicate that a deep central hydrophilic cavity surrounded by 12 mostly irregular transmembrane helices represents a common structural feature. An inverted triple-helix structural symmetry motif within the N- and C-terminal six-helix bundles suggests that the proteins may have arisen by intragenic multiplication. In the work presented here, the triple-helix motifs are aligned in combinatorial fashion so as to detect functionally homologous positions with known atomic structures of MFS members. Substrate and H(+)-binding sites in symporters that transport substrates, ranging from simple ions like phosphate to more complex peptides or disaccharides, are found to be in similar locations. It also appears likely that there is a homologous ordered kinetic mechanism for the H(+)-coupled MFS symporters.
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146
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Duddempudi PK, Goyal R, Date SS, Jansen M. Delineating the extracellular water-accessible surface of the proton-coupled folate transporter. PLoS One 2013; 8:e78301. [PMID: 24205192 PMCID: PMC3799626 DOI: 10.1371/journal.pone.0078301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
The proton-coupled folate transporter (PCFT) was recently identified as the major uptake route for dietary folates in humans. The three-dimensional structure of PCFT and its detailed interplay with function remain to be determined. We screened the water-accessible extracellular surface of HsPCFT using the substituted-cysteine accessibility method, to investigate the boundaries between the water-accessible surface and inaccessible buried protein segments. Single-cysteines, engineered individually at 40 positions in a functional cysteine-less HsPCFT background construct, were probed for plasma-membrane expression in Xenopus oocytes with a bilayer-impermeant primary-amine-reactive biotinylating agent (sulfosuccinimidyl 6-(biotinamido) hexanoate), and additionally for water-accessibility of the respective engineered cysteine with the sulfhydryl-selective biotinylating agent 2-((biotinoyl)amino)ethyl methanethiosulfonate. The ratio between Cys-selective over amine-selective labeling was further used to evaluate three-dimensional models of HsPCFT generated by homology / threading modeling. The closest homologues of HsPCFT with a known experimentally-determined three-dimensional structure are all members of one of the largest membrane protein super-families, the major facilitator superfamily (MFS). The low sequence identity - 14% or less – between HsPCFT and these templates necessitates experiment-based evaluation and model refinement of homology / threading models. With the present set of single-cysteine accessibilities, the models based on GlpT and PepTSt are most promising for further refinement.
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Affiliation(s)
- Phaneendra Kumar Duddempudi
- Department of Pharmacology and Neuroscience, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raman Goyal
- Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Swapneeta Sanjay Date
- Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Michaela Jansen
- Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- * E-mail:
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147
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Yeast nutrient transceptors provide novel insight in the functionality of membrane transporters. Curr Genet 2013; 59:197-206. [PMID: 24114446 PMCID: PMC3824880 DOI: 10.1007/s00294-013-0413-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/17/2013] [Accepted: 09/30/2013] [Indexed: 11/21/2022]
Abstract
In the yeast Saccharomyces cerevisiae several nutrient transporters have been identified that possess an additional function as nutrient receptor. These transporters are induced when yeast cells are starved for their substrate, which triggers entry into stationary phase and acquirement of a low protein kinase A (PKA) phenotype. Re-addition of the lacking nutrient triggers exit from stationary phase and sudden activation of the PKA pathway, the latter being mediated by the nutrient transceptors. At the same time, the transceptors are ubiquitinated, endocytosed and sorted to the vacuole for breakdown. Investigation of the signaling function of the transceptors has provided a new read-out and new tools for gaining insight into the functionality of transporters. Identification of amino acid residues that bind co-transported ions in symporters has been challenging because the inactivation of transport by site-directed mutagenesis is not conclusive with respect to the cause of the inactivation. The discovery of nontransported agonists of the signaling function in transceptors has shown that transport is not required for signaling. Inactivation of transport with maintenance of signaling in transceptors supports that a true proton-binding residue was mutagenised. Determining the relationship between transport and induction of endocytosis has also been challenging, since inactivation of transport by mutagenesis easily causes loss of all affinity for the substrate. The use of analogues with different combinations of transport and signaling capacities has revealed that transport, ubiquitination and endocytosis can be uncoupled in several unexpected ways. The results obtained are consistent with transporters undergoing multiple substrate-induced conformational changes, which allow interaction with different accessory proteins to trigger specific downstream events.
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148
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Peptide transporter DtpA has two alternate conformations, one of which is promoted by inhibitor binding. Proc Natl Acad Sci U S A 2013; 110:E3978-86. [PMID: 24082128 DOI: 10.1073/pnas.1312959110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Peptide transporters (PTRs) of the large PTR family facilitate the uptake of di- and tripeptides to provide cells with amino acids for protein synthesis and for metabolic intermediates. Although several PTRs have been structurally and functionally characterized, how drugs modulate peptide transport remains unclear. To obtain insight into this mechanism, we characterize inhibitor binding to the Escherichia coli PTR dipeptide and tripeptide permease A (DtpA), which shows substrate specificities similar to its human homolog hPEPT1. After demonstrating that Lys[Z-NO2]-Val, the strongest inhibitor of hPEPT1, also acts as a high-affinity inhibitor for DtpA, we used single-molecule force spectroscopy to localize the structural segments stabilizing the peptide transporter and investigated which of these structural segments change stability upon inhibitor binding. This characterization was done with DtpA embedded in the lipid membrane and exposed to physiologically relevant conditions. In the unbound state, DtpA adopts two main alternate conformations in which transmembrane α-helix (TMH) 2 is either stabilized (in ∼43% of DtpA molecules) or not (in ∼57% of DtpA molecules). The two conformations are understood to represent the inward- and outward-facing conformational states of the transporter. With increasing inhibitor concentration, the conformation characterized by a stabilized TMH 2 becomes increasingly prevalent, reaching ∼92% at saturation. Our measurements further suggest that Lys[Z-NO2]-Val interacts with discrete residues in TMH 2 that are important for ligand binding and substrate affinity. These interactions in turn stabilize TMH 2, thereby promoting the inhibited conformation of DtpA.
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149
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Brandsch M. Drug transport via the intestinal peptide transporter PepT1. Curr Opin Pharmacol 2013; 13:881-7. [PMID: 24007794 DOI: 10.1016/j.coph.2013.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 01/12/2023]
Abstract
The focus of this review is on the pharmaceutical relevance of the intestinal peptide transporter PepT1. The review is limited to the progress made in the field over the past two years. Much of this progress is being driven by the prevailing view that PepT1 can be used for drug delivery purposes. Studies have indeed shown that several drugs, prodrugs and drug candidates gain entry into the systemic circulation via PepT1. Very recent examples are prodrugs of zanamivir, oseltamivir and didanosine.
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Affiliation(s)
- Matthias Brandsch
- Biozentrum of the Martin-Luther-University Halle-Wittenberg, D-06120 Halle, Germany.
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150
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Romano A, Barca A, Storelli C, Verri T. Teleost fish models in membrane transport research: the PEPT1(SLC15A1) H+-oligopeptide transporter as a case study. J Physiol 2013; 592:881-97. [PMID: 23981715 DOI: 10.1113/jphysiol.2013.259622] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human genes for passive, ion-coupled transporters and exchangers are included in the so-called solute carrier (SLC) gene series, to date consisting of 52 families and 398 genes. Teleost fish genes for SLC proteins have also been described in the last two decades, and catalogued in preliminary SLC-like form in 50 families and at least 338 genes after systematic GenBank database mining (December 2010-March 2011). When the kinetic properties of the expressed proteins are studied in detail, teleost fish SLC transporters always reveal extraordinary 'molecular diversity' with respect to the mammalian counterparts, which reflects peculiar adaptation of the protein to the physiology of the species and/or to the environment where the species lives. In the case of the H+ -oligopeptide transporter PEPT1(SLC15A1), comparative analysis of diverse teleost fish orthologs has shown that the protein may exhibit very eccentric properties in terms of pH dependence (e.g., the adaptation of zebrafish PEPT1 to alkaline pH), temperature dependence (e.g., the adaptation of icefish PEPT1 to sub-zero temperatures) and/or substrate specificity (e.g., the species-specificity of PEPT1 for the uptake of l-lysine-containing peptides). The revelation of such peculiarities is providing new contributions to the discussion on PEPT1 in both basic (e.g., molecular structure-function analyses) and applied research (e.g., optimizing diets to enhance growth of commercially valuable fish).
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Affiliation(s)
- Alessandro Romano
- Laboratory of General Physiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy.
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