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Sauer DB, Marden JJ, Sudar JC, Song J, Mulligan C, Wang DN. Structural basis of ion - substrate coupling in the Na +-dependent dicarboxylate transporter VcINDY. Nat Commun 2022; 13:2644. [PMID: 35551191 PMCID: PMC9098524 DOI: 10.1038/s41467-022-30406-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.
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Affiliation(s)
- David B Sauer
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer J Marden
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Joseph C Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Jinmei Song
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA.
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA.
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2
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Sauer DB, Wang B, Sudar JC, Song J, Marden J, Rice WJ, Wang DN. The ups and downs of elevator-type di-/tricarboxylate membrane transporters. FEBS J 2022; 289:1515-1523. [PMID: 34403567 PMCID: PMC9832446 DOI: 10.1111/febs.16158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/16/2021] [Indexed: 01/13/2023]
Abstract
The divalent anion sodium symporter (DASS) family contains both sodium-driven anion cotransporters and anion/anion exchangers. The family belongs to a broader ion transporter superfamily (ITS), which comprises 24 families of transporters, including those of AbgT antibiotic efflux transporters. The human proteins in the DASS family play major physiological roles and are drug targets. We recently determined multiple structures of the human sodium-dependent citrate transporter (NaCT) and the succinate/dicarboxylate transporter from Lactobacillus acidophilus (LaINDY). Structures of both proteins show high degrees of structural similarity to the previously determined VcINDY fold. Conservation between these DASS protein structures and those from the AbgT family indicates that the VcINDY fold represents the overall protein structure for the entire ITS. The new structures of NaCT and LaINDY are captured in the inward- or outward-facing conformations, respectively. The domain arrangements in these structures agree with a rigid body elevator-type transport mechanism for substrate translocation across the membrane. Two separate NaCT structures in complex with a substrate or an inhibitor allowed us to explain the inhibition mechanism and propose a detailed classification scheme for grouping disease-causing mutations in the human protein. Structural understanding of multiple kinetic states of DASS proteins is a first step toward the detailed characterization of their entire transport cycle.
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Affiliation(s)
- David B. Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph C. Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jennifer Marden
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - William J. Rice
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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3
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Yan H, Xu W, Zhang T, Feng L, Liu R, Wang L, Wu L, Zhang H, Zhang X, Li T, Peng Z, Jin C, Yu Y, Ping J, Ma M, He Z. Characterization of a novel arsenite long-distance transporter from arsenic hyperaccumulator fern Pteris vittata. THE NEW PHYTOLOGIST 2022; 233:2488-2502. [PMID: 35015902 DOI: 10.1111/nph.17962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Pteris vittata is an arsenic (As) hyperaccumulator that can accumulate several thousand mg As kg-1 DW in aboveground biomass. A key factor for its hyperaccumulation ability is its highly efficient As long-distance translocation system. However, the underlying molecular mechanisms remain unknown. We isolated PvAsE1 through the full-length cDNA over-expression library of P. vittata and characterized it through a yeast system, RNAi gametophytes and sporophytes, subcellular-location and in situ hybridization. Phylogenomic analysis was conducted to estimate the appearance time of PvAsE1. PvAsE1 was a plasma membrane-oriented arsenite (AsIII) effluxer. The silencing of PvAsE1 reduced AsIII long-distance translocation in P. vittata sporophytes. PvAsE1 was structurally similar to solute carrier (SLC)13 proteins. Its transcripts could be observed in parenchyma cells surrounding the xylem of roots. The appearance time was estimated at c. 52.7 Ma. PvAsE1 was a previously uncharacterized SLC13-like AsIII effluxer, which may contribute to AsIII long-distance translocation via xylem loading. PvAsE1 appeared late in fern evolution and might be an adaptive subject to the selection pressure at the Cretaceaou-Paleogene boundary. The identification of PvAsE1 provides clues for revealing the special As hyperaccumulation characteristics of P. vittata.
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Affiliation(s)
- Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenxiu Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tian Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Feng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ruoxi Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luyao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lulu Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Han Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohan Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhimei Peng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Jin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yijun Yu
- Zhejiang Station for Management of Arable Land Quality and Fertilizer, Hangzhou, 310020, China
| | - Junai Ping
- Sorghum Research Institute of Shanxi Agricultural University, Jinzhong, 030600, China
| | - Mi Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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4
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Thermostability-based binding assays reveal complex interplay of cation, substrate and lipid binding in the bacterial DASS transporter, VcINDY. Biochem J 2021; 478:3847-3867. [PMID: 34643224 PMCID: PMC8652582 DOI: 10.1042/bcj20210061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022]
Abstract
The divalent anion sodium symporter (DASS) family of transporters (SLC13 family in humans) are key regulators of metabolic homeostasis, disruption of which results in protection from diabetes and obesity, and inhibition of liver cancer cell proliferation. Thus, DASS transporter inhibitors are attractive targets in the treatment of chronic, age-related metabolic diseases. The characterisation of several DASS transporters has revealed variation in the substrate selectivity and flexibility in the coupling ion used to power transport. Here, using the model DASS co-transporter, VcINDY from Vibrio cholerae, we have examined the interplay of the three major interactions that occur during transport: the coupling ion, the substrate, and the lipid environment. Using a series of high-throughput thermostability-based interaction assays, we have shown that substrate binding is Na+-dependent; a requirement that is orchestrated through a combination of electrostatic attraction and Na+-induced priming of the binding site architecture. We have identified novel DASS ligands and revealed that ligand binding is dominated by the requirement of two carboxylate groups in the ligand that are precisely distanced to satisfy carboxylate interaction regions of the substrate-binding site. We have also identified a complex relationship between substrate and lipid interactions, which suggests a dynamic, regulatory role for lipids in VcINDY's transport cycle.
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5
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Soares-Silva I, Ribas D, Sousa-Silva M, Azevedo-Silva J, Rendulić T, Casal M. Membrane transporters in the bioproduction of organic acids: state of the art and future perspectives for industrial applications. FEMS Microbiol Lett 2021; 367:5873408. [PMID: 32681640 PMCID: PMC7419537 DOI: 10.1093/femsle/fnaa118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Organic acids such as monocarboxylic acids, dicarboxylic acids or even more complex molecules such as sugar acids, have displayed great applicability in the industry as these compounds are used as platform chemicals for polymer, food, agricultural and pharmaceutical sectors. Chemical synthesis of these compounds from petroleum derivatives is currently their major source of production. However, increasing environmental concerns have prompted the production of organic acids by microorganisms. The current trend is the exploitation of industrial biowastes to sustain microbial cell growth and valorize biomass conversion into organic acids. One of the major bottlenecks for the efficient and cost-effective bioproduction is the export of organic acids through the microbial plasma membrane. Membrane transporter proteins are crucial elements for the optimization of substrate import and final product export. Several transporters have been expressed in organic acid-producing species, resulting in increased final product titers in the extracellular medium and higher productivity levels. In this review, the state of the art of plasma membrane transport of organic acids is presented, along with the implications for industrial biotechnology.
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Affiliation(s)
- I Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - D Ribas
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - M Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - J Azevedo-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - T Rendulić
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - M Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
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6
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Buetti-Dinh A, Ruinelli M, Czerski D, Scapozza C, Martignier A, Roman S, Caminada A, Tonolla M. Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps. PLoS One 2021; 16:e0248877. [PMID: 33784327 PMCID: PMC8009434 DOI: 10.1371/journal.pone.0248877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/07/2021] [Indexed: 12/02/2022] Open
Abstract
The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.
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Affiliation(s)
- Antoine Buetti-Dinh
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (ABD); (MT)
| | - Michela Ruinelli
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Dorota Czerski
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Cristian Scapozza
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Agathe Martignier
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Annapaola Caminada
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (ABD); (MT)
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7
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Nakov T, Judy KJ, Downey KM, Ruck EC, Alverson AJ. Transcriptional Response of Osmolyte Synthetic Pathways and Membrane Transporters in a Euryhaline Diatom During Long-term Acclimation to a Salinity Gradient. JOURNAL OF PHYCOLOGY 2020; 56:1712-1728. [PMID: 32750159 DOI: 10.1111/jpy.13061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/10/2020] [Indexed: 05/15/2023]
Abstract
How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.
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Affiliation(s)
- Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
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8
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Jaramillo-Martinez V, Urbatsch IL, Ganapathy V. Functional Distinction between Human and Mouse Sodium-Coupled Citrate Transporters and Its Biologic Significance: An Attempt for Structural Basis Using a Homology Modeling Approach. Chem Rev 2020; 121:5359-5377. [PMID: 33040525 DOI: 10.1021/acs.chemrev.0c00529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NaCT (SLC13A5; mINDY), a sodium-coupled citrate transporter, is the mammalian ortholog of Drosophila INDY. Loss-of-function mutations in human NaCT cause severe complications with neonatal epilepsy and encephalopathy (EIEE25). Surprisingly, mice lacking this transporter do not have this detrimental brain phenotype. The marked differences in transport kinetics between mouse and human NaCTs provide at least a partial explanation for this conundrum, but a structural basis for the differences is lacking. Neither human nor mouse NaCT has been crystallized, and any information known on their structures is based entirely on what was inferred from the structure of VcINDY, a related transporter in bacteria. Here, we highlight the functional features of human and mouse NaCTs and provide a plausible molecular basis for the differences based on a full-length homology modeling approach. The transport characteristics of human NaCT markedly differ from those of VcINDY. Therefore, the modeling with VcINDY as the template is flawed, but this is the best available option at this time. With the newly deduced model, we determined the likely locations of the disease-causing mutations and propose a new classification for the mutations based on their location and potential impact on transport function. This new information should pave the way for future design and development of novel therapeutics to restore the lost function of the mutant transporters as a treatment strategy for patients with EIEE25.
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Affiliation(s)
- Valeria Jaramillo-Martinez
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research and Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research and Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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9
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Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife 2020; 9:e61350. [PMID: 32869741 PMCID: PMC7553777 DOI: 10.7554/elife.61350] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Jennifer J Marden
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolette Cocco
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
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10
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Structure and Mechanism of the Divalent Anion/Na⁺ Symporter. Int J Mol Sci 2019; 20:ijms20020440. [PMID: 30669552 PMCID: PMC6359215 DOI: 10.3390/ijms20020440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022] Open
Abstract
Integral membrane proteins of the divalent anion/Na⁺ symporter (DASS) family are conserved from bacteria to humans. DASS proteins typically mediate the coupled uptake of Na⁺ ions and dicarboxylate, tricarboxylate, or sulfate. Since the substrates for DASS include key intermediates and regulators of energy metabolism, alterations of DASS function profoundly affect fat storage, energy expenditure and life span. Furthermore, loss-of-function mutations in a human DASS have been associated with neonatal epileptic encephalopathy. More recently, human DASS has also been implicated in the development of liver cancers. Therefore, human DASS proteins are potentially promising pharmacological targets for battling obesity, diabetes, kidney stone, fatty liver, as well as other metabolic and neurological disorders. Despite its clinical relevance, the mechanism by which DASS proteins recognize and transport anionic substrates remains unclear. Recently, the crystal structures of a bacterial DASS and its humanized variant have been published. This article reviews the mechanistic implications of these structures and suggests future work to better understand how the function of DASS can be modulated for potential therapeutic benefit.
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11
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Forster IC. The molecular mechanism of SLC34 proteins: insights from two decades of transport assays and structure-function studies. Pflugers Arch 2018; 471:15-42. [PMID: 30244375 DOI: 10.1007/s00424-018-2207-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 01/08/2023]
Abstract
The expression cloning some 25 years ago of the first member of SLC34 solute carrier family, the renal sodium-coupled inorganic phosphate cotransporter (NaPi-IIa) from rat and human tissue, heralded a new era of research into renal phosphate handling by focussing on the carrier proteins that mediate phosphate transport. The cloning of NaPi-IIa was followed by that of the intestinal NaPi-IIb and renal NaPi-IIc isoforms. These three proteins constitute the main secondary-active Na+-driven pathways for apical entry of inorganic phosphate (Pi) across renal and intestinal epithelial, as well as other epithelial-like organs. The key role these proteins play in mammalian Pi homeostasis was revealed in the intervening decades by numerous in vitro and animal studies, including the development of knockout animals for each gene and the detection of naturally occurring mutations that can lead to Pi-handling dysfunction in humans. In addition to characterising their physiological regulation, research has also focused on understanding the underlying transport mechanism and identifying structure-function relationships. Over the past two decades, this research effort has used real-time electrophysiological and fluorometric assays together with novel computational biology strategies to develop a detailed, but still incomplete, understanding of the transport mechanism of SLC34 proteins at the molecular level. This review will focus on how our present understanding of their molecular mechanism has evolved in this period by highlighting the key experimental findings.
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Affiliation(s)
- Ian C Forster
- Ion Channels and Human Diseases Laboratory, Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, VIC, 3052, Australia.
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12
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Structure and function of the divalent anion/Na + symporter from Vibrio cholerae and a humanized variant. Nat Commun 2017; 8:15009. [PMID: 28436435 PMCID: PMC5413979 DOI: 10.1038/ncomms15009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/20/2017] [Indexed: 01/15/2023] Open
Abstract
Integral membrane proteins of the divalent anion/Na+ symporter (DASS) family translocate dicarboxylate, tricarboxylate or sulphate across cell membranes, typically by utilizing the preexisting Na+ gradient. The molecular determinants for substrate recognition by DASS remain obscure, largely owing to the absence of any substrate-bound DASS structure. Here we present 2.8-Å resolution X-ray structures of VcINDY, a DASS from Vibrio cholerae that catalyses the co-transport of Na+ and succinate. These structures portray the Na+-bound VcINDY in complexes with succinate and citrate, elucidating the binding sites for substrate and two Na+ ions. Furthermore, we report the structures of a humanized variant of VcINDY in complexes with succinate and citrate, which predict how a human citrate-transporting DASS may interact with its bound substrate. Our findings provide insights into metabolite transport by DASS, establishing a molecular basis for future studies on the regulation of this transport process. Divalent anion/Na+ symporter (DASS) transporters move intermediates of the Krebs cycle across the cell membrane. Here the authors present the substrate-bound structures of VcINDY, a DASS from Vibrio cholerae, which provide insights into the underlying transport mechanism.
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13
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Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME JOURNAL 2017; 11:1142-1157. [PMID: 28195581 PMCID: PMC5398378 DOI: 10.1038/ismej.2016.192] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1–2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Jasmin Schwarz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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14
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Mulligan C, Fitzgerald GA, Wang DN, Mindell JA. Functional characterization of a Na+-dependent dicarboxylate transporter from Vibrio cholerae. ACTA ACUST UNITED AC 2014; 143:745-59. [PMID: 24821967 PMCID: PMC4035743 DOI: 10.1085/jgp.201311141] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
VcINDY, a bacterial homolog of transporters implicated in lifespan in fruit flies and insulin resistance in mammals, is a high affinity, electrogenic, Na+-dependent dicarboxylate transporter. The SLC13 transporter family, whose members play key physiological roles in the regulation of fatty acid synthesis, adiposity, insulin resistance, and other processes, catalyzes the transport of Krebs cycle intermediates and sulfate across the plasma membrane of mammalian cells. SLC13 transporters are part of the divalent anion:Na+ symporter (DASS) family that includes several well-characterized bacterial members. Despite sharing significant sequence similarity, the functional characteristics of DASS family members differ with regard to their substrate and coupling ion dependence. The publication of a high resolution structure of dimer VcINDY, a bacterial DASS family member, provides crucial structural insight into this transporter family. However, marrying this structural insight to the current functional understanding of this family also demands a comprehensive analysis of the transporter’s functional properties. To this end, we purified VcINDY, reconstituted it into liposomes, and determined its basic functional characteristics. Our data demonstrate that VcINDY is a high affinity, Na+-dependent transporter with a preference for C4- and C5-dicarboxylates. Transport of the model substrate, succinate, is highly pH dependent, consistent with VcINDY strongly preferring the substrate’s dianionic form. VcINDY transport is electrogenic with succinate coupled to the transport of three or more Na+ ions. In contrast to succinate, citrate, bound in the VcINDY crystal structure (in an inward-facing conformation), seems to interact only weakly with the transporter in vitro. These transport properties together provide a functional framework for future experimental and computational examinations of the VcINDY transport mechanism.
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Affiliation(s)
- Christopher Mulligan
- Membrane Transport Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Gabriel A Fitzgerald
- Membrane Transport Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Da-Neng Wang
- The Helen L. and Martin Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, NY 10016 The Helen L. and Martin Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Joseph A Mindell
- Membrane Transport Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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15
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Sodium-coupled dicarboxylate and citrate transporters from the SLC13 family. Pflugers Arch 2013; 466:119-30. [PMID: 24114175 DOI: 10.1007/s00424-013-1369-y] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/19/2013] [Accepted: 09/23/2013] [Indexed: 12/30/2022]
Abstract
The SLC13 family in humans and other mammals consists of sodium-coupled transporters for anionic substrates: three transporters for dicarboxylates/citrate and two transporters for sulfate. This review will focus on the di- and tricarboxylate transporters: NaDC1 (SLC13A2), NaDC3 (SLC13A3), and NaCT (SLC13A5). The substrates of these transporters are metabolic intermediates of the citric acid cycle, including citrate, succinate, and α-ketoglutarate, which can exert signaling effects through specific receptors or can affect metabolic enzymes directly. The SLC13 transporters are important for regulating plasma, urinary and tissue levels of these metabolites. NaDC1, primarily found on the apical membranes of renal proximal tubule and small intestinal cells, is involved in regulating urinary levels of citrate and plays a role in kidney stone development. NaDC3 has a wider tissue distribution and high substrate affinity compared with NaDC1. NaDC3 participates in drug and xenobiotic excretion through interactions with organic anion transporters. NaCT is primarily a citrate transporter located in the liver and brain, and its activity may regulate metabolic processes. The recent crystal structure of the Vibrio cholerae homolog, VcINDY, provides a new framework for understanding the mechanism of transport in this family. This review summarizes current knowledge of the structure, function, and regulation of the di- and tricarboxylate transporters of the SLC13 family.
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16
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Pajor AM, Sun NN, Leung A. Functional characterization of SdcF from Bacillus licheniformis, a homolog of the SLC13 Na⁺/dicarboxylate transporters. J Membr Biol 2013; 246:705-15. [PMID: 23979173 DOI: 10.1007/s00232-013-9590-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/10/2013] [Indexed: 11/25/2022]
Abstract
The SdcF transporter from Bacillus licheniformis (gene BL02343) is a member of the divalent anion sodium symporter (DASS)/SLC13 family that includes Na⁺/dicarboxylate transporters from bacteria to humans. SdcF was functionally expressed in Escherichia coli (BL21) and assayed in right side out membrane vesicles. ScdF catalyzed the sodium-coupled transport of succinate and α-ketoglutarate. Succinate transport was strongly inhibited by malate, fumarate, tartrate, oxaloacetate and L-aspartate. Similar to the other DASS transporters, succinate transport by SdcF was inhibited by anthranilic acids, N-(p-amylcinnamoyl) anthranilic acid and flufenamate. SdcF transport was cation-dependent, with a K₀.₅ for sodium of ~1.5 mM and a K₀.₅ for Li⁺ of ~40 mM. Succinate transport kinetics by SdcF were sigmoidal, suggesting that SdcF may contain two cooperative substrate binding sites. The results support an ordered binding mechanism for SdcF in which sodium binds first and succinate binds last. We conclude that SdcF is a secondary active transporter for four- and five-carbon dicarboxylates that can use Na⁺ or Li⁺ as a driving cation.
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Affiliation(s)
- Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, 92093-0718, USA,
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17
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Pajor AM, Sun NN. Nonsteroidal anti-inflammatory drugs and other anthranilic acids inhibit the Na(+)/dicarboxylate symporter from Staphylococcus aureus. Biochemistry 2013; 52:2924-32. [PMID: 23566164 DOI: 10.1021/bi301611u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Na(+)/dicarboxylate symporter from Staphylococcus aureus, named SdcS, is a member of the divalent anion sodium symporter (DASS) family that also includes the mammalian SLC13 Na(+)/dicarboxylate cotransporters, NaDC1 and NaCT. The mammalian members of the family are sensitive to inhibition by anthranilic acid derivatives such as N-(p-amylcinnamoyl)anthranilic acid (ACA), which act as slow inhibitors. This study shows that SdcS is inhibited by ACA as well as the fenamate nonsteroidal anti-inflammatory drugs, flufenamate and niflumate. The inhibition was rapid and reversible. The IC(50) for ACA was approximately 55 μM. Succinate kinetics by SdcS were sigmoidal, with a K(0.5) of 9 μM and a Hill coefficient of 1.5. Addition of ACA decreased the V(max) and increased the Hill coefficient without affecting the K(0.5), consistent with its activity as a negative modulator of SdcS activity. ACA inhibition was not correlated with the K(0.5) for succinate in SdcS mutants, and ACA did not affect the reactivity of the N108C mutant to the cysteine reagent, MTSET. We conclude that ACA and other anthranilic acid derivatives are effective allosteric inhibitors of SdcS. Furthermore, the mechanism of inhibition appears to be distinct from the mechanism observed in human NaDC1.
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Affiliation(s)
- Ana M Pajor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California--San Diego, La Jolla, CA 92093-0718, USA
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18
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Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR. The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. BMC Genomics 2012; 13:690. [PMID: 23227809 PMCID: PMC3543383 DOI: 10.1186/1471-2164-13-690] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/22/2012] [Indexed: 11/24/2022] Open
Abstract
Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.
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Affiliation(s)
- Muktak Aklujkar
- University of Massachusetts Amherst, Amherst, MA 01003, USA.
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19
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Mancusso R, Gregorio GG, Liu Q, Wang DN. Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter. Nature 2012; 491:622-6. [PMID: 23086149 DOI: 10.1038/nature11542] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/30/2012] [Indexed: 01/01/2023]
Abstract
In human cells, cytosolic citrate is a chief precursor for the synthesis of fatty acids, triacylglycerols, cholesterol and low-density lipoprotein. Cytosolic citrate further regulates the energy balance of the cell by activating the fatty-acid-synthesis pathway while downregulating both the glycolysis and fatty-acid β-oxidation pathways. The rate of fatty-acid synthesis in liver and adipose cells, the two main tissue types for such synthesis, correlates directly with the concentration of citrate in the cytosol, with the cytosolic citrate concentration partially depending on direct import across the plasma membrane through the Na(+)-dependent citrate transporter (NaCT). Mutations of the homologous fly gene (Indy; I'm not dead yet) result in reduced fat storage through calorie restriction. More recently, Nact (also known as Slc13a5)-knockout mice have been found to have increased hepatic mitochondrial biogenesis, higher lipid oxidation and energy expenditure, and reduced lipogenesis, which taken together protect the mice from obesity and insulin resistance. To understand the transport mechanism of NaCT and INDY proteins, here we report the 3.2 Å crystal structure of a bacterial INDY homologue. One citrate molecule and one sodium ion are bound per protein, and their binding sites are defined by conserved amino acid motifs, forming the structural basis for understanding the specificity of the transporter. Comparison of the structures of the two symmetrical halves of the transporter suggests conformational changes that propel substrate translocation.
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Affiliation(s)
- Romina Mancusso
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA
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20
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Regulatory design in a simple system integrating membrane potential generation and metabolic ATP consumption. Robustness and the role of energy dissipating processes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1634-46. [PMID: 21945502 DOI: 10.1016/j.bbabio.2011.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/03/2011] [Accepted: 09/08/2011] [Indexed: 01/02/2023]
Abstract
Bacterial physiological responses integrate energy-coupling processes at the membrane level with metabolic energy demand. The regulatory design behind these responses remains largely unexplored. Propionigenium modestum is an adequate organism to study these responses because it presents the simplest scheme known integrating membrane potential generation and metabolic ATP consumption. A hypothetical sodium leak is added to the scheme as the sole regulatory site. Allosteric regulation is assumed to be absent. Information of the rate equations is not available. However, relevant features of the patterns of responses may be obtained using Metabolic Control Analysis (MCA) and Metabolic Control Design (MCD). With these tools, we show that membrane potential disturbances can be compensated by adjusting the leak flux, without significant perturbations of ATP consumption. Perturbations of membrane potential by ATP demand are inevitable and also require compensatory changes in the leak. Numerical simulations were performed with a kinetic model exhibiting the responses for small changes obtained with MCA and MCD. A modest leak (10% of input) was assumed for the reference state. We found that disturbances in membrane potential and ATP consumption, produced by environmental perturbations of the cation concentration, may be reverted to the reference state adjusting the leak. Leak changes can also compensate for undesirable effects on membrane potential produced by changes in nutrient availability or ATP demand, in a wide range of values. The system is highly robust to parameter fluctuations. The regulatory role of energy dissipating processes and the trade-off between energetic efficiency and regulatory capacity are discussed.
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21
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Fukui K, Koseki C, Yamamoto Y, Nakamura J, Sasahara A, Yuji R, Hashiguchi K, Usuda Y, Matsui K, Kojima H, Abe K. Identification of succinate exporter in Corynebacterium glutamicum and its physiological roles under anaerobic conditions. J Biotechnol 2011; 154:25-34. [PMID: 21420450 DOI: 10.1016/j.jbiotec.2011.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/06/2011] [Accepted: 03/14/2011] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum produces succinate from glucose via the reductive tricarboxylic acid cycle under microaerobic and anaerobic conditions. We identified a NCgl2130 gene of C. glutamicum as a novel succinate exporter that functions in succinate production, and designated sucE1. sucE1 expression levels were higher under microaerobic conditions than aerobic conditions, and overexpression or disruption of sucE1 respectively increased or decreased succinate productivity during fermentation. Under microaerobic conditions, the sucE1 disruptant sucE1Δ showed 30% less succinate productivity and a lower sugar-consumption rate than the parental strain. Under anaerobic conditions, succinate production by sucE1Δ ceased. The intracellular succinate and fructose-1,6-bisphosphate levels of sucE1Δ under microaerobic conditions were respectively 1.7-fold and 1.6-fold higher than those of the parental strain, suggesting that loss of SucE1 function caused a failure of succinate removal from the cells, leading to intracellular accumulation that inhibited upstream sugar metabolism. Homology and transmembrane helix searches identified SucE1 as a membrane protein belonging to the aspartate:alanine exchanger (AAE) family. Partially purified 6x-histidine-tagged SucE1 (SucE1-[His](6)) reconstituted in succinate-loaded liposomes clearly demonstrated counterflow and self-exchange activities for succinate. Together, these findings suggest that sucE1 encodes a novel succinate exporter that is induced under microaerobic conditions, and is important for succinate production under both microaerobic and anaerobic conditions.
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Affiliation(s)
- Keita Fukui
- Fermentation & Biotechnology Laboratories, Ajinomoto Co., Inc., Kawasaki-ku, Kanagawa, Japan. keita
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22
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Joshi AD, Pajor AM. Identification of conformationally sensitive amino acids in the Na(+)/dicarboxylate symporter (SdcS). Biochemistry 2009; 48:3017-24. [PMID: 19260674 DOI: 10.1021/bi8022625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Na(+)/dicarboxylate symporter (SdcS) from Staphylococcus aureus is a homologue of the mammalian Na(+)/dicarboxylate cotransporters (NaDC1) from the solute carrier 13 (SLC13) family. This study examined succinate transport by SdcS heterologously expressed in Escherichia coli, using right-side-out (RSO) and inside-out (ISO) membrane vesicles. The K(m) values for succinate in RSO and ISO vesicles were similar, approximately 30 microM. The single cysteine of SdcS was replaced to produce the cysteine-less transporter, C457S, which demonstrated functional characteristics similar to those of the wild type. Single-cysteine mutants were made in SdcS-C457S at positions that are functionally important in mammalian NaDC1. Mutant N108C of SdcS was sensitive to chemical labeling by MTSET {[2-(trimethylammonium)ethyl]methanethiosulfonate} from both the cytoplasmic and extracellular sides, depending on the conformational state of the transporter, suggesting that Asn-108 may be found in the translocation pore of the protein. Mutant D329C was sensitive to MTSET in the presence of Na(+) but only from the extracellular side. Finally, mutant L436C was insensitive to MTSET, although changes in its kinetic properties indicate that this residue may be important in substrate binding. In conclusion, this work identifies Asn-108 as a key residue in the translocation pathway of the protein, accessible in different states from both sides of the membrane. Functional characterization of SdcS should provide useful structural as well as functional details about mammalian transporters from the SLC13 family.
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Affiliation(s)
- Aditya D Joshi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
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23
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Strickler MA, Hall JA, Gaiko O, Pajor AM. Functional characterization of a Na(+)-coupled dicarboxylate transporter from Bacillus licheniformis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2489-96. [PMID: 19840771 DOI: 10.1016/j.bbamem.2009.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 09/02/2009] [Accepted: 10/12/2009] [Indexed: 10/20/2022]
Abstract
The Na(+)-coupled dicarboxylate transporter, SdcL, from Bacillus licheniformis is a member of the divalent anion/Na(+) symporter (DASS) family that includes the bacterial Na(+)/dicarboxylate cotransporter SdcS (from Staphyloccocus aureus) and the mammalian Na(+)/dicarboxylate cotransporters, NaDC1 and NaDC3. The transport properties of SdcL produced in Escherichia coli are similar to those of its prokaryotic and eukaryotic counterparts, involving the Na(+)-dependent transport of dicarboxylates such as succinate or malate across the cytoplasmic membrane with a K(m) of approximately 6 microM. SdcL may also transport aspartate, alpha-ketoglutarate and oxaloacetate with low affinity. The cotransport of Na(+) and dicarboxylate by SdcL has an apparent stoichiometry of 2:1, and a K(0.5) for Na(+) of 0.9 mM. Our findings represent the characterization of another prokaryotic protein of the DASS family with transport properties similar to its eukaryotic counterparts, but with a broader substrate specificity than other prokaryotic DASS family members. The broader range of substrates carried by SdcL may provide insight into domains of the protein that allow a more flexible or larger substrate binding pocket.
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Affiliation(s)
- Melodie A Strickler
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA 92093-0718, USA
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24
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Aliverdieva DA, Mamaev DV. Molecular characteristics of transporters of C4-dicarboxylates and mechanism of translocation. J EVOL BIOCHEM PHYS+ 2009. [DOI: 10.1134/s0022093009030016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Youn JW, Jolkver E, Krämer R, Marin K, Wendisch VF. Identification and characterization of the dicarboxylate uptake system DccT in Corynebacterium glutamicum. J Bacteriol 2008; 190:6458-66. [PMID: 18658264 PMCID: PMC2566012 DOI: 10.1128/jb.00780-08] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 07/21/2008] [Indexed: 11/20/2022] Open
Abstract
Many bacteria can utilize C(4)-carboxylates as carbon and energy sources. However, Corynebacterium glutamicum ATCC 13032 is not able to use tricarboxylic acid cycle intermediates such as succinate, fumarate, and l-malate as sole carbon sources. Upon prolonged incubation, spontaneous mutants which had gained the ability to grow on succinate, fumarate, and l-malate could be isolated. DNA microarray analysis showed higher mRNA levels of cg0277, which subsequently was named dccT, in the mutants than in the wild type, and transcriptional fusion analysis revealed that a point mutation in the promoter region of dccT was responsible for increased expression. The overexpression of dccT was sufficient to enable the C. glutamicum wild type to grow on succinate, fumarate, and l-malate as the sole carbon sources. Biochemical analyses revealed that DccT, which is a member of the divalent anion/Na(+) symporter family, catalyzes the effective uptake of dicarboxylates like succinate, fumarate, L-malate, and likely also oxaloacetate in a sodium-dependent manner.
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Affiliation(s)
- Jung-Won Youn
- Institute of Molecular Microbiology and Biotechnology, Westfalian Wilhelms University Muenster, Corrensstr. 3, D-48149 Muenster, Germany
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Identification of a gene encoding a transporter essential for utilization of C4 dicarboxylates in Corynebacterium glutamicum. Appl Environ Microbiol 2008; 74:5290-6. [PMID: 18586971 DOI: 10.1128/aem.00832-08] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Corynebacterium glutamicum R genome contains a total of eight genes encoding proteins with sequence similarity to C4-dicarboxylate transporters identified from other bacteria. Three of the genes encode proteins within the dicarboxylate/amino acid:cation symporter (DAACS) family, another three encode proteins within the tripartite ATP-independent periplasmic transporter family, and two encode proteins within the divalent anion:Na+ symporter (DASS) family. We observed that a mutant strain deficient in one of these genes, designated dcsT, of the DASS family did not aerobically grow on the C4 dicarboxylates succinate, fumarate, and malate as the sole carbon sources. Mutant strains deficient in each of the other seven genes grew as well as the wild-type strain under the same conditions, although one of these genes is a homologue of dctA of the DAACS family, involved in aerobic growth on C4 dicarboxylates in various bacteria. The utilization of C4 dicarboxylates was markedly enhanced by overexpression of the dcsT gene. We confirmed that the uptake of [13C]labeled succinate observed for the wild-type cells was hardly detected in the dcsT-deficient mutant but was markedly enhanced in a dcsT-overexpressing strain. These results suggested that in C. glutamicum, the uptake of C4 dicarboxylates for aerobic growth was mainly mediated by the DASS transporter encoded by dcsT. The expression level of the dcsT gene transiently increased in the early exponential phase during growth on nutrient-rich medium. This expression was enhanced by the addition of succinate in the mid-exponential phase and was repressed by the addition of glucose in the early exponential phase.
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Hall JA, Pajor AM. Functional reconstitution of SdcS, a Na+-coupled dicarboxylate carrier protein from Staphylococcus aureus. J Bacteriol 2006; 189:880-5. [PMID: 17114260 PMCID: PMC1797332 DOI: 10.1128/jb.01452-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In Staphylococcus aureus, the transport of dicarboxylates is mediated in part by the Na+-linked carrier protein SdcS. This transporter is a member of the divalent-anion/Na+ symporter (DASS) family, a group that includes the mammalian Na+/dicarboxylate cotransporters NaDC1 and NaDC3. In earlier work, we cloned and expressed SdcS in Escherichia coli and found it to have transport properties similar to those of its eukaryotic counterparts (J. A. Hall and A. M. Pajor, J. Bacteriol. 187:5189-5194, 2005). Here, we report the partial purification and subsequent reconstitution of functional SdcS into liposomes. These proteoliposomes exhibited succinate counterflow activity, as well as Na+ electrochemical-gradient-driven transport. Examination of substrate specificity indicated that the minimal requirement necessary for transport was a four-carbon terminal dicarboxylate backbone and that productive substrate-transporter interaction was sensitive to substitutions at the substrate C-2 and C-3 positions. Further analysis established that SdcS facilitates an electroneutral symport reaction having a 2:1 cation/dicarboxylate ratio. This study represents the first characterization of a reconstituted Na+-coupled DASS family member, thus providing an effective method to evaluate functional, as well as structural, aspects of DASS transporters in a system free of the complexities and constraints associated with native membrane environments.
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Affiliation(s)
- Jason A Hall
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0645, USA
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Pajor AM. Molecular properties of the SLC13 family of dicarboxylate and sulfate transporters. Pflugers Arch 2005; 451:597-605. [PMID: 16211368 PMCID: PMC1866268 DOI: 10.1007/s00424-005-1487-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 07/06/2005] [Indexed: 01/30/2023]
Abstract
The SLC13 gene family consists of five members in humans, with corresponding orthologs from different vertebrate species. All five genes code for sodium-coupled transporters that are found on the plasma membrane. Two of the transporters, NaS1 and NaS2, carry substrates such as sulfate, selenate and thiosulfate. The other members of the family (NaDC1, NaDC3, and NaCT) are transporters for di- and tri-carboxylates including succinate, citrate and alpha-ketoglutarate. The SLC13 transporters from vertebrates are electrogenic and they produce inward currents in the presence of sodium and substrate. Substrate-independent leak currents have also been described. Structure-function studies have identified the carboxy terminal half of these proteins as the most important for determining function. Transmembrane helices 9 and 10 may form part of the substrate permeation pathway and participate in conformational changes during the transport cycle. This review also discusses new members of the SLC13 superfamily that exhibit both sodium-dependent and sodium-independent transport mechanisms. The Indy protein from Drosophila, involved in determining lifespan, and the plant vacuolar malate transporter are both sodium-independent dicarboxylate transporters, possibly acting as exchangers. The purpose of this review is to provide an update on new advances in this gene family, particularly on structure-function studies and new members of the family.
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Affiliation(s)
- Ana M Pajor
- Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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