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Riederer EA, Moënne-Loccoz P, Valiyaveetil FI. Distinct roles of the Na + binding sites in the allosteric coupling mechanism of the glutamate transporter homolog, Glt Ph. Proc Natl Acad Sci U S A 2022; 119:e2121653119. [PMID: 35507872 PMCID: PMC9171649 DOI: 10.1073/pnas.2121653119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
Glutamate transporters carry out the concentrative uptake of glutamate by harnessing the ionic gradients present across cellular membranes. A central step in the transport mechanism is the coupled binding of Na+ and substrate. The sodium coupled Asp transporter, GltPh is an archaeal homolog of glutamate transporters that has been extensively used to probe the transport mechanism. Previous studies have shown that hairpin-2 (HP2) functions as the extracellular gate for the aspartate binding site and plays a key role in the coupled binding of sodium and aspartate to GltPh. The binding sites for three Na+ ions (Na1-3) have been identified in GltPh, but the specific roles of the individual Na+ sites in the binding process have not been elucidated. In this study, we developed assays to probe Na+ binding to the Na1 and Na3 sites and to monitor the conformational switch in the NMDGT motif. We used these assays along with a fluorescence assay to monitor HP2 movement and EPR spectroscopy to show that Na+ binding to the Na3 site is required for the NMDGT conformational switch while Na+ binding to the Na1 site is responsible for the partial opening of HP2. Complete opening of HP2 requires the conformational switch of the NMDGT motif and therefore Na+ binding to both the Na1 and the Na3 sites. Based on our studies, we also propose an alternate pathway for the coupled binding of Na+ and Asp.
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Affiliation(s)
- Erika A. Riederer
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239
| | - Francis I. Valiyaveetil
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239
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2
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Ahmed MS, Lauersen KJ, Ikram S, Li C. Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites. ACS Synth Biol 2021; 10:646-669. [PMID: 33751883 DOI: 10.1021/acssynbio.0c00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.
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Affiliation(s)
- Muhammad Saad Ahmed
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, The Mall, Rawalpindi 46000, Pakistan
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Sana Ikram
- Beijing Higher Institution Engineering Research Center for Food Additives and Ingredients, Beijing Technology & Business University (BTBU), Beijing 100048, P. R. China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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3
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Alleva C, Kovalev K, Astashkin R, Berndt MI, Baeken C, Balandin T, Gordeliy V, Fahlke C, Machtens JP. Na +-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters. SCIENCE ADVANCES 2020; 6:6/47/eaba9854. [PMID: 33208356 PMCID: PMC7673805 DOI: 10.1126/sciadv.aba9854] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 10/02/2020] [Indexed: 05/22/2023]
Abstract
Excitatory amino acid transporters (EAATs) harness [Na+], [K+], and [H+] gradients for fast and efficient glutamate removal from the synaptic cleft. Since each glutamate is cotransported with three Na+ ions, [Na+] gradients are the predominant driving force for glutamate uptake. We combined all-atom molecular dynamics simulations, fluorescence spectroscopy, and x-ray crystallography to study Na+:substrate coupling in the EAAT homolog GltPh A lipidic cubic phase x-ray crystal structure of wild-type, Na+-only bound GltPh at 2.5-Å resolution revealed the fully open, outward-facing state primed for subsequent substrate binding. Simulations and kinetic experiments established that only the binding of two Na+ ions to the Na1 and Na3 sites ensures complete HP2 gate opening via a conformational selection-like mechanism and enables high-affinity substrate binding via electrostatic attraction. The combination of Na+-stabilized gate opening and electrostatic coupling of aspartate to Na+ binding provides a constant Na+:substrate transport stoichiometry over a broad range of neurotransmitter concentrations.
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Affiliation(s)
- C Alleva
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
| | - K Kovalev
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - M I Berndt
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - V Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ch Fahlke
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - J-P Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
- Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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5
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Riederer EA, Focke PJ, Georgieva ER, Akyuz N, Matulef K, Borbat PP, Freed JH, Blanchard SC, Boudker O, Valiyaveetil FI. A facile approach for the in vitro assembly of multimeric membrane transport proteins. eLife 2018; 7:36478. [PMID: 29889023 PMCID: PMC6025958 DOI: 10.7554/elife.36478] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Membrane proteins such as ion channels and transporters are frequently homomeric. The homomeric nature raises important questions regarding coupling between subunits and complicates the application of techniques such as FRET or DEER spectroscopy. These challenges can be overcome if the subunits of a homomeric protein can be independently modified for functional or spectroscopic studies. Here, we describe a general approach for in vitro assembly that can be used for the generation of heteromeric variants of homomeric membrane proteins. We establish the approach using GltPh, a glutamate transporter homolog that is trimeric in the native state. We use heteromeric GltPh transporters to directly demonstrate the lack of coupling in substrate binding and demonstrate how heteromeric transporters considerably simplify the application of DEER spectroscopy. Further, we demonstrate the general applicability of this approach by carrying out the in vitro assembly of VcINDY, a Na+-coupled succinate transporter and CLC-ec1, a Cl-/H+ antiporter.
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Affiliation(s)
- Erika A Riederer
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Paul J Focke
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Kimberly Matulef
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Olga Boudker
- Weill Cornell Medicine, New York, United States.,Howard Hughes Medical Institute, Maryland, United States
| | - Francis I Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
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6
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Scopelliti AJ, Font J, Vandenberg RJ, Boudker O, Ryan RM. Structural characterisation reveals insights into substrate recognition by the glutamine transporter ASCT2/SLC1A5. Nat Commun 2018; 9:38. [PMID: 29295993 PMCID: PMC5750217 DOI: 10.1038/s41467-017-02444-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022] Open
Abstract
Cancer cells undergo a shift in metabolism where they become reliant on nutrients such as the amino-acid glutamine. Glutamine enters the cell via the alanine/serine/cysteine transporter 2 (ASCT2) that is upregulated in several cancers to maintain an increased supply of this nutrient and are therefore an attractive target in cancer therapeutic development. ASCT2 belongs to the glutamate transporter (SLC1A) family but is the only transporter in this family able to transport glutamine. The structural basis for glutamine selectivity of ASCT2 is unknown. Here, we identify two amino-acid residues in the substrate-binding site that are responsible for conferring glutamine selectivity. We introduce corresponding mutations into a prokaryotic homologue of ASCT2 and solve four crystal structures, which reveal the structural basis for neutral amino acid and inhibitor binding in this family. This structural model of ASCT2 may provide a basis for future development of selective ASCT2 inhibitors to treat glutamine-dependent cancers. Cancer cells are reliant on nutrients such as glutamine, which enter the cell via the alanine/serine/cysteine transporter 2 (ASCT2). Here, authors use crystallography to show which amino-acid residues in the substrate-binding site are responsible for conferring glutamine selectivity to ASCT2.
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Affiliation(s)
- Amanda J Scopelliti
- Transporter Biology Group, Discipline of Pharmacology, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Josep Font
- Transporter Biology Group, Discipline of Pharmacology, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Robert J Vandenberg
- Transporter Biology Group, Discipline of Pharmacology, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Renae M Ryan
- Transporter Biology Group, Discipline of Pharmacology, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.
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7
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Focke PJ, Hein C, Hoffmann B, Matulef K, Bernhard F, Dötsch V, Valiyaveetil FI. Combining in Vitro Folding with Cell Free Protein Synthesis for Membrane Protein Expression. Biochemistry 2016; 55:4212-9. [PMID: 27384110 DOI: 10.1021/acs.biochem.6b00488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell free protein synthesis (CFPS) has emerged as a promising methodology for protein expression. While polypeptide production is very reliable and efficient using CFPS, the correct cotranslational folding of membrane proteins during CFPS is still a challenge. In this contribution, we describe a two-step protocol in which the integral membrane protein is initially expressed by CFPS as a precipitate followed by an in vitro folding procedure using lipid vesicles for converting the protein precipitate to the correctly folded protein. We demonstrate the feasibility of using this approach for the K(+) channels KcsA and MVP and the amino acid transporter LeuT. We determine the crystal structure of the KcsA channel obtained by CFPS and in vitro folding to show the structural similarity to the cellular expressed KcsA channel and to establish the feasibility of using this two-step approach for membrane protein production for structural studies. Our studies show that the correct folding of these membrane proteins with complex topologies can take place in vitro without the involvement of the cellular machinery for membrane protein biogenesis. This indicates that the folding instructions for these complex membrane proteins are contained entirely within the protein sequence.
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Affiliation(s)
- Paul J Focke
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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8
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Abstract
Interaction of multiple ligands with a protein or protein complex is a widespread phenomenon that allows for cooperativity. Here, we review the use of the Hill equation, which is commonly used to analyze binding or kinetic data, to analyze the kinetics of ion-coupled transporters and show how the mechanism of transport affects the Hill coefficient. Importantly, the Hill analysis of ion-coupled transporters can provide the exact number of transported co-ions, regardless of the extent of the cooperativity in ion binding.
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Affiliation(s)
- Juke S Lolkema
- Department of Molecular Microbiology and Department of Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Dirk-Jan Slotboom
- Department of Molecular Microbiology and Department of Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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9
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Hänelt I, Jensen S, Wunnicke D, Slotboom DJ. Low Affinity and Slow Na+ Binding Precedes High Affinity Aspartate Binding in the Secondary-active Transporter GltPh. J Biol Chem 2015; 290:15962-72. [PMID: 25922069 DOI: 10.1074/jbc.m115.656876] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/30/2022] Open
Abstract
GltPh from Pyrococcus horikoshii is a homotrimeric Na(+)-coupled aspartate transporter. It belongs to the widespread family of glutamate transporters, which also includes the mammalian excitatory amino acid transporters that take up the neurotransmitter glutamate. Each protomer in GltPh consists of a trimerization domain involved in subunit interactions and a transport domain containing the substrate binding site. Here, we have studied the dynamics of Na(+) and aspartate binding to GltPh. Tryptophan fluorescence measurements on the fully active single tryptophan mutant F273W revealed that Na(+) binds with low affinity to the apoprotein (Kd 120 mm), with a particularly low kon value (5.1 m(-1)s(-1)). At least two sodium ions bind before aspartate. The binding of Na(+) requires a very high activation energy (Ea 106.8 kJ mol(-1)) and consequently has a large Q10 value of 4.5, indicative of substantial conformational changes before or after the initial binding event. The apparent affinity for aspartate binding depended on the Na(+) concentration present. Binding of aspartate was not observed in the absence of Na(+), whereas in the presence of high Na(+) concentrations (above the Kd for Na(+)) the dissociation constants for aspartate were in the nanomolar range, and the aspartate binding was fast (kon of 1.4 × 10(5) m(-1)s(-1)), with low Ea and Q10 values (42.6 kJ mol(-1) and 1.8, respectively). We conclude that Na(+) binding is most likely the rate-limiting step for substrate binding.
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Affiliation(s)
- Inga Hänelt
- From the Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sonja Jensen
- From the Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dorith Wunnicke
- From the Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dirk Jan Slotboom
- From the Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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