101
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Gill SS, Gill R, Trivedi DK, Anjum NA, Sharma KK, Ansari MW, Ansari AA, Johri AK, Prasad R, Pereira E, Varma A, Tuteja N. Piriformospora indica: Potential and Significance in Plant Stress Tolerance. Front Microbiol 2016; 7:332. [PMID: 27047458 PMCID: PMC4801890 DOI: 10.3389/fmicb.2016.00332] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/03/2016] [Indexed: 11/17/2022] Open
Abstract
Owing to its exceptional ability to efficiently promote plant growth, protection and stress tolerance, a mycorrhiza like endophytic Agaricomycetes fungus Piriformospora indica has received a great attention over the last few decades. P. indica is an axenically cultiviable fungus which exhibits its versatility for colonizing/hosting a broad range of plant species through directly manipulating plant hormone-signaling pathway during the course of mutualism. P. indica-root colonization leads to a better plant performance in all respect, including enhanced root proliferation by indole-3-acetic acid production which in turn results into better nutrient-acquisition and subsequently to improved crop growth and productivity. Additionally, P. indica can induce both local and systemic resistance to fungal and viral plant diseases through signal transduction. P. indica-mediated stimulation in antioxidant defense system components and expressing stress-related genes can confer crop/plant stress tolerance. Therefore, P. indica can biotize micropropagated plantlets and also help these plants to overcome transplantation shock. Nevertheless, it can also be involved in a more complex symbiotic relationship, such as tripartite symbiosis and can enhance population dynamic of plant growth promoting rhizobacteria. In brief, P. indica can be utilized as a plant promoter, bio-fertilizer, bioprotector, bioregulator, and biotization agent. The outcome of the recent literature appraised herein will help us to understand the physiological and molecular bases of mechanisms underlying P. indica-crop plant mutual relationship. Together, the discussion will be functional to comprehend the usefulness of crop plant-P. indica association in both achieving new insights into crop protection/improvement as well as in sustainable agriculture production.
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Affiliation(s)
- Sarvajeet S Gill
- Stress Physiology and Molecular Biology Laboratory, Centre for Biotechnology, Maharshi Dayanand University Rohtak, India
| | - Ritu Gill
- Stress Physiology and Molecular Biology Laboratory, Centre for Biotechnology, Maharshi Dayanand University Rohtak, India
| | - Dipesh K Trivedi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Naser A Anjum
- Centre for Environmental and Marine Studies and Department of Chemistry, University of Aveiro Aveiro, Portugal
| | - Krishna K Sharma
- Department of Microbiology, Maharshi Dayanand University Rohtak, India
| | - Mohammed W Ansari
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Abid A Ansari
- Department of Biology, University of Tabuk Tabuk, Saudi Arabia
| | - Atul K Johri
- School of Life Sciences, Jawaharlal Nehru University New Delhi, India
| | - Ram Prasad
- Amity Institute of Microbial Technology, Amity University Noida, India
| | - Eduarda Pereira
- Centre for Environmental and Marine Studies and Department of Chemistry, University of Aveiro Aveiro, Portugal
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University Noida, India
| | - Narendra Tuteja
- Amity Institute of Microbial Technology, Amity University Noida, India
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102
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A phosphotyrosine switch regulates organic cation transporters. Nat Commun 2016; 7:10880. [PMID: 26979622 PMCID: PMC4799362 DOI: 10.1038/ncomms10880] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/28/2016] [Indexed: 12/21/2022] Open
Abstract
Membrane transporters are key determinants of therapeutic outcomes. They regulate systemic and cellular drug levels influencing efficacy as well as toxicities. Here we report a unique phosphorylation-dependent interaction between drug transporters and tyrosine kinase inhibitors (TKIs), which has uncovered widespread phosphotyrosine-mediated regulation of drug transporters. We initially found that organic cation transporters (OCTs), uptake carriers of metformin and oxaliplatin, were inhibited by several clinically used TKIs. Mechanistic studies showed that these TKIs inhibit the Src family kinase Yes1, which was found to be essential for OCT2 tyrosine phosphorylation and function. Yes1 inhibition in vivo diminished OCT2 activity, significantly mitigating oxaliplatin-induced acute sensory neuropathy. Along with OCT2, other SLC-family drug transporters are potentially part of an extensive 'transporter-phosphoproteome' with unique susceptibility to TKIs. On the basis of these findings we propose that TKIs, an important and rapidly expanding class of therapeutics, can functionally modulate pharmacologically important proteins by inhibiting protein kinases essential for their post-translational regulation.
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103
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Frigeni M, Iacobazzi F, Yin X, Longo N. Wide tolerance to amino acids substitutions in the OCTN1 ergothioneine transporter. Biochim Biophys Acta Gen Subj 2016; 1860:1334-42. [PMID: 26994919 DOI: 10.1016/j.bbagen.2016.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/24/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Organic cation transporters transfer solutes with a positive charge across the plasma membrane. The novel organic cation transporter 1 (OCTN1) and 2 (OCTN2) transport ergothioneine and carnitine, respectively. Mutations in the SLC22A5 gene encoding OCTN2 cause primary carnitine deficiency, a recessive disorders resulting in low carnitine levels and defective fatty acid oxidation. Variations in the SLC22A4 gene encoding OCTN1 are associated with rheumatoid arthritis and Crohn disease. METHODS Here we evaluate the functional properties of the OCTN1 transporter using chimeric transporters constructed by fusing different portion of the OCTN1 and OCTN2 cDNAs. Their relative abundance and subcellular distribution was evaluated through western blot analysis and confocal microscopy. RESULTS Substitutions of the C-terminal portion of OCTN1 with the correspondent residues of OCTN2 generated chimeric OCTN transporters more active than wild-type OCTN1 in transporting ergothioneine. Additional single amino acid substitutions introduced in chimeric OCTN transporters further increased ergothioneine transport activity. Kinetic analysis indicated that increased transport activity was due to an increased V(max), with modest changes in K(m) toward ergothioneine. CONCLUSIONS Our results indicate that the OCTN1 transporter is tolerant to extensive amino acid substitutions. This is in sharp contrast to the OCTN2 carnitine transporter that has been selected for high functional activity through evolution, with almost all substitutions reducing carnitine transport activity. GENERAL SIGNIFICANCE The widespread tolerance of OCTN1 to amino acid substitutions suggests that the corresponding SLC22A4 gene may have derived from a recent duplication of the SLC22A5 gene and might not yet have a defined physiological role.
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Affiliation(s)
- Marta Frigeni
- Division of Medical Genetics, Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, UT 84108, United States
| | - Francesco Iacobazzi
- Division of Medical Genetics, Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, UT 84108, United States; Department of Basic Medical Sciences, University of Bari, Policlinico, I-70124 Bari, Italy
| | - Xue Yin
- Division of Medical Genetics, Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, UT 84108, United States
| | - Nicola Longo
- Division of Medical Genetics, Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, UT 84108, United States.
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104
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Gu M, Chen A, Sun S, Xu G. Complex Regulation of Plant Phosphate Transporters and the Gap between Molecular Mechanisms and Practical Application: What Is Missing? MOLECULAR PLANT 2016; 9:396-416. [PMID: 26714050 DOI: 10.1016/j.molp.2015.12.012] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/18/2015] [Accepted: 12/11/2015] [Indexed: 05/18/2023]
Abstract
It has been almost 25 years since the first report of the gene encoding a high-affinity phosphate transporter (PT), PHO84, in yeast. Since then, an increasing number of yeast PHO84 homologs as well as other genes encoding proteins with phosphate (Pi) transport activities have been identified and functionally characterized in diverse plant species. Great progress has been made also in deciphering the molecular mechanism underlying the regulation of the abundance and/or activity of these genes and their products. The regulatory genes affect plant Pi homeostasis commonly through direct or indirect regulation of the abundance of PTs at different levels. However, little has been achieved in the use of PTs for developing genetically modified crops with high phosphorus use efficiency (PUE). This might be a consequence of overemphasizing Pi uptake from the rhizosphere and lack of knowledge about the roles of PTs in Pi transport and recycling within the plant that are required to optimize PUE. Here, we mainly focused on the genes encoding proteins with Pi transport activities and the emerging understanding of their regulation at the transcriptional, post-transcriptional, translational, and post-translational levels. In addition, we propose potential strategies for effective use of PTs in improving plant growth and development.
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Affiliation(s)
- Mian Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Aiqun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China.
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105
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Date SS, Chen CYC, Chen Y, Jansen M. Experimentally optimized threading structures of the proton-coupled folate transporter. FEBS Open Bio 2016; 6:216-30. [PMID: 27047750 PMCID: PMC4794783 DOI: 10.1002/2211-5463.12041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/13/2016] [Accepted: 01/29/2016] [Indexed: 12/18/2022] Open
Abstract
The proton‐coupled folate transporter (PCFT, SLC46A1) transports folic acid across the plasma membrane, together with an excess of protons such that the net charge translocation is positive. We developed 3D structural models of PCFT threaded onto the X‐ray structures of major facilitator superfamily (MFS) members that were identified as close structural homologues. The model of PCFT threaded onto the glycerol‐3‐phosphate transporter (GlpT) structure is consistent with detailed accessibility studies in the absence of extracellular substrate and at pH 7.4 presented here, and additionally with a multitude of other mutagenesis and functional studies. Characteristic MFS structural features are preserved in this PCFT model, such as 12 transmembrane helices divided into two pseudosymmetric bundles, and a high density of positive charges on the periphery of the cytoplasmic site that allow interactions with negatively charged lipid head‐groups. Under the experimental conditions, PCFT predominantly samples the resting state, which in this case is inward‐open. Several positions lining the substrate cavity have been identified. Motif A, a helix‐turn‐helix motif that is a hallmark of MFS transporters between transmembrane segments II and III is oriented appropriately to interact with residues from transmembrane segments IV as well as XI upon conformational transition to the outward‐open state. A charge‐relay system between three charged residues as well as apposing glycines in two α‐helices, both contributed to by motif A, become engaged when PCFT is modeled on the outward‐open state of a putative proton‐driven transporter (YajR).
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Affiliation(s)
- Swapneeta S Date
- Department of Cell Physiology and Molecular Biophysics School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Cheng-Yen Charles Chen
- Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Medical Student Summer Research Program School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Yidong Chen
- Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Medical Student Summer Research Program School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA; Center for Membrane Protein Research School of Medicine Texas Tech University Health Sciences Center Lubbock TX USA
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106
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Zhao R, Najmi M, Fiser A, Goldman ID. Identification of an Extracellular Gate for the Proton-coupled Folate Transporter (PCFT-SLC46A1) by Cysteine Cross-linking. J Biol Chem 2016; 291:8162-72. [PMID: 26884338 DOI: 10.1074/jbc.m115.693929] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 01/04/2023] Open
Abstract
The proton-coupled folate transporter (PCFT, SLC46A1) is required for intestinal folate absorption and folate homeostasis in humans. A homology model of PCFT, based upon theEscherichia coliglycerol 3-phosphate transporter structure, predicted that PCFT transmembrane domains (TMDs) 1, 2, 7, and 11 form an extracellular gate in the inward-open conformation. To assess this model, five residues (Gln(45)-TMD1, Asn(90)-TMD2, Leu(290)-TMD7, Ser(407)-TMD11 and Asn(411)-TMD11) in the predicted gate were substituted with Cys to generate single and nine double mutants. Transport function of the mutants was assayed in transient transfectants by measurement of [(3)H]substrate influx as was accessibility of the Cys residues to biotinylation. Pairs of Cys residues were assessed for spontaneous formation of a disulfide bond, induction of a disulfide bond by oxidization with dichloro(1,10-phenanthroline)copper (II) (CuPh), or the formation of a Cd(2+)complex. The data were consistent with the formation of a spontaneous disulfide bond between the N90C/S407C pair and a CuPh- and Cd(2+)-induced disulfide bond and complex, respectively, for the Q45C/L290C and L290C/N411C pairs. The decrease in activity induced by cross-linkage of the Cys residue pairs was due to a decrease in the influxVmaxconsistent with restriction in the mobility of the transporter. The presence of folate substrate decreased the CuPh-induced inhibition of transport. Hence, the data support the glycerol 3-phosphate transporter-based homology model of PCFT and the presence of an extracellular gate formed by TMDs 1, 2, 7, and 11.
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Affiliation(s)
- Rongbao Zhao
- From the Departments of Molecular Pharmacology, Medicine
| | - Mitra Najmi
- From the Departments of Molecular Pharmacology
| | - Andras Fiser
- Biochemistry, and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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107
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Lin S, Litaker RW, Sunda WG. Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton. JOURNAL OF PHYCOLOGY 2016; 52:10-36. [PMID: 26987085 DOI: 10.1111/jpy.12365] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/26/2015] [Indexed: 05/24/2023]
Abstract
Phosphorus (P) is an essential nutrient for marine phytoplankton and indeed all life forms. Current data show that P availability is growth-limiting in certain marine systems and can impact algal species composition. Available P occurs in marine waters as dissolved inorganic phosphate (primarily orthophosphate [Pi]) or as a myriad of dissolved organic phosphorus (DOP) compounds. Despite numerous studies on P physiology and ecology and increasing research on genomics in marine phytoplankton, there have been few attempts to synthesize information from these different disciplines. This paper is aimed to integrate the physiological and molecular information on the acquisition, utilization, and storage of P in marine phytoplankton and the strategies used by these organisms to acclimate and adapt to variations in P availability. Where applicable, we attempt to identify gaps in our current knowledge that warrant further research and examine possible metabolic pathways that might occur in phytoplankton from well-studied bacterial models. Physical and chemical limitations governing cellular P uptake are explored along with physiological and molecular mechanisms to adapt and acclimate to temporally and spatially varying P nutrient regimes. Topics covered include cellular Pi uptake and feedback regulation of uptake systems, enzymatic utilization of DOP, P acquisition by phagotrophy, P-limitation of phytoplankton growth in oceanic and coastal waters, and the role of P-limitation in regulating cell size and toxin levels in phytoplankton. Finally, we examine the role of P and other nutrients in the transition of phytoplankton communities from early succession species (diatoms) to late succession ones (e.g., dinoflagellates and haptophytes).
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Richard Wayne Litaker
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Fisheries and Habitat Research, Beaufort, North Carolina, 28516, USA
| | - William G Sunda
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Fisheries and Habitat Research, Beaufort, North Carolina, 28516, USA
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108
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Understanding transport by the major facilitator superfamily (MFS): structures pave the way. Nat Rev Mol Cell Biol 2016; 17:123-32. [PMID: 26758938 DOI: 10.1038/nrm.2015.25] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the major facilitator superfamily (MFS) of transport proteins are essential for the movement of a wide range of substrates across biomembranes. As this transport requires a series of conformational changes, structures of MFS transporters captured in different conformational states are needed to decipher the transport mechanism. Recently, a large number of MFS transporter structures have been determined, which has provided us with an unprecedented opportunity to understand general aspects of the transport mechanism. We propose an updated model for the conformational cycle of MFS transporters, the 'clamp-and-switch model', and discuss the role of so-called 'gating residues' and the substrate in modulating these conformational changes.
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109
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Abstract
The ancient and ubiquitous major facilitator superfamily (MFS) represents the largest secondary transporter family and plays a crucial role in a multitude of physiological processes. MFS proteins transport a broad spectrum of ions and solutes across membranes via facilitated diffusion, symport, or antiport. In recent years, remarkable advances in understanding the structural biology of the MFS transporters have been made. This article reviews the history, classification, and general features of the MFS proteins; summarizes recent structural progress with a focus on the sugar porter family transporters exemplified by GLUT1; and discusses the molecular mechanisms of substrate binding, alternating access, and cotransport coupling.
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Affiliation(s)
- Nieng Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China;
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110
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Samyn DR, Persson BL. Inorganic Phosphate and Sulfate Transport in S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:253-269. [PMID: 26721277 DOI: 10.1007/978-3-319-25304-6_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inorganic ions such as phosphate and sulfate are essential macronutrients required for a broad spectrum of cellular functions and their regulation. In a constantly fluctuating environment microorganisms have for their survival developed specific nutrient sensing and transport systems ensuring that the cellular nutrient needs are met. This chapter focuses on the S. cerevisiae plasma membrane localized transporters, of which some are strongly induced under conditions of nutrient scarcity and facilitate the active uptake of inorganic phosphate and sulfate. Recent advances in studying the properties of the high-affinity phosphate and sulfate transporters by means of site-directed mutagenesis have provided further insight into the molecular mechanisms contributing to substrate selectivity and transporter functionality of this important class of membrane transporters.
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Affiliation(s)
- D R Samyn
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden.
| | - B L Persson
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden
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111
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Bakshi M, Vahabi K, Bhattacharya S, Sherameti I, Varma A, Yeh KW, Baldwin I, Johri AK, Oelmüller R. WRKY6 restricts Piriformospora indica-stimulated and phosphate-induced root development in Arabidopsis. BMC PLANT BIOLOGY 2015; 15:305. [PMID: 26718529 PMCID: PMC4697310 DOI: 10.1186/s12870-015-0673-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/03/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND Arabidopsis root growth is stimulated by Piriformospora indica, phosphate limitation and inactivation of the WRKY6 transcription factor. Combinations of these factors induce unexpected alterations in root and shoot growth, root architecture and root gene expression profiles. RESULTS The results demonstrate that P. indica promotes phosphate uptake and root development under Pi limitation in wrky6 mutant. This is associated with the stimulation of PHOSPHATE1 expression and ethylene production. Expression profiles from the roots of wrky6 seedlings identified genes involved in hormone metabolism, transport, meristem, cell and plastid proliferation, and growth regulation. 25 miRNAs were also up-regulated in these roots. We generated and discuss here a list of common genes which are regulated in growing roots and which are common to all three growth stimuli investigated in this study. CONCLUSION Since root development of wrky6 plants exposed to P. indica under phosphate limitation is strongly promoted, we propose that common genes which respond to all three growth stimuli are central for the control of root growth and architecture. They can be tested for optimizing root growth in model and agricultural plants.
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Affiliation(s)
- Madhunita Bakshi
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Khabat Vahabi
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Samik Bhattacharya
- Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Irena Sherameti
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
| | - Ajit Varma
- Amity Institute of Microbial Technology, AUUP, Noida, India.
| | - Kai-Wun Yeh
- Institute of Plant Biology, Taiwan National University, Taipei, Taiwan.
| | - Ian Baldwin
- Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Straße 8, D-07745, Jena, Germany.
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ralf Oelmüller
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburgerstr. 159, D-07743, Jena, Germany.
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112
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Johri AK, Oelmüller R, Dua M, Yadav V, Kumar M, Tuteja N, Varma A, Bonfante P, Persson BL, Stroud RM. Fungal association and utilization of phosphate by plants: success, limitations, and future prospects. Front Microbiol 2015; 6:984. [PMID: 26528243 PMCID: PMC4608361 DOI: 10.3389/fmicb.2015.00984] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/03/2015] [Indexed: 11/29/2022] Open
Abstract
Phosphorus (P) is a major macronutrient for plant health and development. The available form of P is generally low in the rhizosphere even in fertile soils. A major proportion of applied phosphate (Pi) fertilizers in the soil become fixed into insoluble, unavailable forms, which restricts crop production throughout the world. Roots possess two distinct modes of P uptake from the soil, direct and indirect uptake. The direct uptake of P is facilitated by the plant's own Pi transporters while indirect uptake occurs via mycorrhizal symbiosis, where the host plant obtains P primarily from the fungal partner, while the fungus benefits from plant-derived reduced carbon. So far, only one Pi transporter has been characterized from the mycorrhizal fungus Glomus versiforme. As arbuscular mycorrhizal fungi cannot be cultured axenically, their Pi transporter network is difficult to exploite for large scale sustainable agriculture. Alternatively, the root-colonizing endophytic fungus Piriformospora indica can grow axenically and provides strong growth-promoting activity during its symbiosis with a broad spectrum of plants. P. indica contains a high affinity Pi transporter (PiPT) involved in improving Pi nutrition levels in the host plant under P limiting conditions. As P. indica can be manipulated genetically, it opens new vistas to be used in P deficient fields.
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Affiliation(s)
- Atul K. Johri
- School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Ralf Oelmüller
- Institute of Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Vikas Yadav
- School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Manoj Kumar
- School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Center for Genetic Engineering and BiotechnologyNew Delhi, India
- Institute of Microbial Technology, Amity UniversityNoida, India
| | - Ajit Varma
- Institute of Microbial Technology, Amity UniversityNoida, India
| | - Paola Bonfante
- Department of Biology, University of TorinoTorino, Italy
| | - Bengt L. Persson
- Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus UniversityKalmar, Sweden
| | - Robert M. Stroud
- Department of Biophysics and Biochemistry, University of California at San Francisco, San FranciscoCA, USA
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113
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Taniguchi R, Kato HE, Font J, Deshpande CN, Wada M, Ito K, Ishitani R, Jormakka M, Nureki O. Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin. Nat Commun 2015; 6:8545. [PMID: 26461048 PMCID: PMC4633820 DOI: 10.1038/ncomms9545] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/03/2015] [Indexed: 12/21/2022] Open
Abstract
In vertebrates, the iron exporter ferroportin releases Fe2+ from cells into plasma, thereby maintaining iron homeostasis. The transport activity of ferroportin is suppressed by the peptide hormone hepcidin, which exhibits upregulated expression in chronic inflammation, causing iron-restrictive anaemia. However, due to the lack of structural information about ferroportin, the mechanisms of its iron transport and hepcidin-mediated regulation remain largely elusive. Here we report the crystal structures of a putative bacterial homologue of ferroportin, BbFPN, in both the outward- and inward-facing states. Despite undetectable sequence similarity, BbFPN adopts the major facilitator superfamily fold. A comparison of the two structures reveals that BbFPN undergoes an intra-domain conformational rearrangement during the transport cycle. We identify a substrate metal-binding site, based on structural and mutational analyses. Furthermore, the BbFPN structures suggest that a predicted hepcidin-binding site of ferroportin is located within its central cavity. Thus, BbFPN may be a valuable structural model for iron homeostasis regulation by ferroportin. Iron export from vertebrate cells is mediated by ferroportin, which is suppressed by the peptide hormone hepcidin. Taniguchi et al. present crystal structures of a putative bacterial ferroportin homologue in both outward- and inward-facing states, providing insight into its transport mechanism.
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Affiliation(s)
- Reiya Taniguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hideaki E Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Josep Font
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chandrika N Deshpande
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Miki Wada
- Technical office, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Koichi Ito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Mika Jormakka
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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114
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Fontenot EB, Ditusa SF, Kato N, Olivier DM, Dale R, Lin WY, Chiou TJ, Macnaughtan MA, Smith AP. Increased phosphate transport of Arabidopsis thaliana Pht1;1 by site-directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions. PLANT, CELL & ENVIRONMENT 2015; 38:2012-22. [PMID: 25754174 DOI: 10.1111/pce.12522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/06/2015] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Members of the Pht1 family of plant phosphate (Pi) transporters play vital roles in Pi acquisition from soil and in planta Pi translocation to maintain optimal growth and development. The study of the specificities and biochemical properties of Pht1 transporters will contribute to improving the current understanding of plant phosphorus homeostasis and use-efficiency. In this study, we show through split in vivo interaction methods and in vitro analysis of microsomal root tissues that Arabidopsis thaliana Pht1;1 and Pht1;4 form homomeric and heteromeric complexes. Transient and heterologous expression of the Pht1;1 variants, Pht1;1(Y312D), Pht1;1(Y312A) and Pht1;1(Y312F), was used to analyse the role of a putative Pi binding residue (Tyr 312) in Pht1;1 transporter oligomerization and function. The homomeric interaction among Pht1;1 proteins was disrupted by mutation of Tyr 312 to Asp, but not to Ala or Phe. In addition, the Pht1;1(Y312D) variant conferred enhanced Pi transport when expressed in yeast cells. In contrast, mutation of Tyr 312 to Ala or Phe did not affect Pht1;1 transport kinetics. Our study demonstrates that modifications to the Pht1;1 higher-order structure affects Pi transport, suggesting that oligomerization may serve as a regulatory mechanism for modulating Pi uptake.
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Affiliation(s)
- Elena B Fontenot
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Sandra Feuer Ditusa
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Danielle M Olivier
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Renee Dale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Wei-Yi Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan, China
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan, China
| | - Megan A Macnaughtan
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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115
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Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ, Bill RM. The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 2015; 95:26-37. [PMID: 26431670 DOI: 10.1016/j.ymeth.2015.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies.
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Affiliation(s)
- Sarah J Routledge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lina Mikaliunaite
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Anjana Patel
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Michelle Clare
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie P Cartwright
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Zharain Bawa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Martin D B Wilks
- Smallpeice Enterprises Ltd, 27 Newbold Terrace East, Leamington Spa, Warwickshire CV32 4ES, UK
| | - Floren Low
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - David Hardy
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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116
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Zhang XC, Zhao Y, Heng J, Jiang D. Energy coupling mechanisms of MFS transporters. Protein Sci 2015; 24:1560-79. [PMID: 26234418 DOI: 10.1002/pro.2759] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 01/01/2023]
Abstract
Major facilitator superfamily (MFS) is a large class of secondary active transporters widely expressed across all life kingdoms. Although a common 12-transmembrane helix-bundle architecture is found in most MFS crystal structures available, a common mechanism of energy coupling remains to be elucidated. Here, we discuss several models for energy-coupling in the transport process of the transporters, largely based on currently available structures and the results of their biochemical analyses. Special attention is paid to the interaction between protonation and the negative-inside membrane potential. Also, functional roles of the conserved sequence motifs are discussed in the context of the 3D structures. We anticipate that in the near future, a unified picture of the functions of MFS transporters will emerge from the insights gained from studies of the common architectures and conserved motifs.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Jie Heng
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
| | - Daohua Jiang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 100101
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117
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Pu X, Lv X, Tan T, Fu F, Qin G, Lin H. Roles of mitochondrial energy dissipation systems in plant development and acclimation to stress. ANNALS OF BOTANY 2015; 116:583-600. [PMID: 25987710 PMCID: PMC4577992 DOI: 10.1093/aob/mcv063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/16/2015] [Accepted: 03/27/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants are sessile organisms that have the ability to integrate external cues into metabolic and developmental signals. The cues initiate specific signal cascades that can enhance the tolerance of plants to stress, and these mechanisms are crucial to the survival and fitness of plants. The adaption of plants to stresses is a complex process that involves decoding stress inputs as energy-deficiency signals. The process functions through vast metabolic and/or transcriptional reprogramming to re-establish the cellular energy balance. Members of the mitochondrial energy dissipation pathway (MEDP), alternative oxidases (AOXs) and uncoupling proteins (UCPs), act as energy mediators and might play crucial roles in the adaption of plants to stresses. However, their roles in plant growth and development have been relatively less explored. SCOPE This review summarizes current knowledge about the role of members of the MEDP in plant development as well as recent advances in identifying molecular components that regulate the expression of AOXs and UCPs. Highlighted in particular is a comparative analysis of the expression, regulation and stress responses between AOXs and UCPs when plants are exposed to stresses, and a possible signal cross-talk that orchestrates the MEDP, reactive oxygen species (ROS), calcium signalling and hormone signalling. CONCLUSIONS The MEDP might act as a cellular energy/metabolic mediator that integrates ROS signalling, energy signalling and hormone signalling with plant development and stress accumulation. However, the regulation of MEDP members is complex and occurs at transcriptional, translational, post-translational and metabolic levels. How this regulation is linked to actual fluxes through the AOX/UCP in vivo remains elusive.
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Affiliation(s)
- Xiaojun Pu
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xin Lv
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Tinghong Tan
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Faqiong Fu
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Gongwei Qin
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource & Eco-Environment and Plant Physiology Laboratory, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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118
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Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE. Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4. J Biol Chem 2015; 290:17796-17805. [PMID: 25971965 PMCID: PMC4505028 DOI: 10.1074/jbc.m114.617613] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 04/24/2015] [Indexed: 11/06/2022] Open
Abstract
Members of the Zrt and Irt protein (ZIP) family are a central participant in transition metal homeostasis as they function to increase the cytosolic concentration of zinc and/or iron. However, the lack of a crystal structure hinders elucidation of the molecular mechanism of ZIP proteins. Here, we employed GREMLIN, a co-evolution-based contact prediction approach in conjunction with the Rosetta structure prediction program to construct a structural model of the human (h) ZIP4 transporter. The predicted contact data are best fit by modeling hZIP4 as a dimer. Mutagenesis of residues that comprise a central putative hZIP4 transmembrane transition metal coordination site in the structural model alter the kinetics and specificity of hZIP4. Comparison of the hZIP4 dimer model to all known membrane protein structures identifies the 12-transmembrane monomeric Piriformospora indica phosphate transporter (PiPT), a member of the major facilitator superfamily (MFS), as a likely structural homolog.
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Affiliation(s)
- Sagar Antala
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Sergey Ovchinnikov
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195; Department of Biochemistry, University of Washington, Seattle, Washington 98195; Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Hetunandan Kamisetty
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195; Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195; Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Robert E Dempski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609.
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119
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Wright DJ, Tate CG. Isolation and characterisation of transport-defective substrate-binding mutants of the tetracycline antiporter TetA(B). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2261-70. [PMID: 26143388 PMCID: PMC4579554 DOI: 10.1016/j.bbamem.2015.06.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 11/20/2022]
Abstract
The tetracycline antiporter TetA(B) is a member of the Major Facilitator Superfamily which confers tetracycline resistance to cells by coupling the efflux of tetracycline to the influx of protons down their chemical potential gradient. Although it is a medically important transporter, its structure has yet to be determined. One possibility for why this has proven difficult is that the transporter may be conformationally heterogeneous in the purified state. To overcome this, we developed two strategies to rapidly identify TetA(B) mutants that were transport-defective and that could still bind tetracycline. Up to 9 amino acid residues could be deleted from the loop between transmembrane α-helices 6 and 7 with only a slight decrease in affinity of tetracycline binding as measured by isothermal titration calorimetry, although the mutant was transport-defective. Scanning mutagenesis where all the residues between 2 and 389 were mutated to either valine, alanine or glycine (VAG scan) identified 15 mutants that were significantly impaired in tetracycline transport. Of these mutants, 12 showed no evidence of tetracycline binding by isothermal titration calorimetry performed on the purified transporters. In contrast, the mutants G44V and G346V bound tetracycline 4–5 fold more weakly than TetA(B), with Kds of 28 μM and 36 μM, respectively, whereas the mutant R70G bound tetracycline 3-fold more strongly (Kd 2.1 μM). Systematic mutagenesis is thus an effective strategy for isolating transporter mutants that may be conformationally constrained and which represent attractive targets for crystallisation and structure determination. A rapid method was developed for the identification of transport-defective mutants of TetA(B). ITC was used to determine the affinity of tetracycline binding to the mutants. Fifteen transport-defective point mutations were identified. Three mutants bound tetracycline whereas the remainder did not The transport-defective mutants may facilitate crystallisation of TetA(B).
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Affiliation(s)
- David J Wright
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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120
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Bill RM, von der Haar T. Hijacked then lost in translation: the plight of the recombinant host cell in membrane protein structural biology projects. Curr Opin Struct Biol 2015; 32:147-55. [PMID: 26037971 PMCID: PMC4521084 DOI: 10.1016/j.sbi.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/10/2015] [Accepted: 04/10/2015] [Indexed: 11/13/2022]
Abstract
Membrane protein structural biologists need high-quality protein for crystallisation. Recombinant proteins are central to the structural biology supply chain. Understanding quality control in protein production is an emerging trend. The roles of translation and protein folding in the host cell are examined.
Membrane protein structural biology is critically dependent upon the supply of high-quality protein. Over the last few years, the value of crystallising biochemically characterised, recombinant targets that incorporate stabilising mutations has been established. Nonetheless, obtaining sufficient yields of many recombinant membrane proteins is still a major challenge. Solutions are now emerging based on an improved understanding of recombinant host cells; as a ‘cell factory’ each cell is tasked with managing limited resources to simultaneously balance its own growth demands with those imposed by an expression plasmid. This review examines emerging insights into the role of translation and protein folding in defining high-yielding recombinant membrane protein production in a range of host cells.
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Affiliation(s)
- Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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121
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Byrne B. Pichia pastoris as an expression host for membrane protein structural biology. Curr Opin Struct Biol 2015; 32:9-17. [DOI: 10.1016/j.sbi.2015.01.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/07/2015] [Accepted: 01/16/2015] [Indexed: 12/17/2022]
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122
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Baker A, Ceasar SA, Palmer AJ, Paterson JB, Qi W, Muench SP, Baldwin SA. Replace, reuse, recycle: improving the sustainable use of phosphorus by plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3523-40. [PMID: 25944926 DOI: 10.1093/jxb/erv210] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The 'phosphorus problem' has recently received strong interest with two distinct strands of importance. The first is that too much phosphorus (P) is entering into waste water, creating a significant economic and ecological problem. Secondly, while agricultural demand for phosphate fertilizer is increasing to maintain crop yields, rock phosphate reserves are rapidly declining. Unravelling the mechanisms by which plants sense, respond to, and acquire phosphate can address both problems, allowing the development of crop plants that are more efficient at acquiring and using limited amounts of phosphate while at the same time improving the potential of plants and other photosynthetic organisms for nutrient recapture and recycling from waste water. In this review, we attempt to synthesize these important but often disparate parts of the debate in a holistic fashion, since solutions to such a complex problem require integrated and multidisciplinary approaches that address both P supply and demand. Rapid progress has been made recently in our understanding of local and systemic signalling mechanisms for phosphate, and of expression and regulation of membrane proteins that take phosphate up from the environment and transport it within the plant. We discuss the current state of understanding of such mechanisms involved in sensing and responding to phosphate stress. We also discuss approaches to improve the P-use efficiency of crop plants and future direction for sustainable use of P, including use of photosynthetic organisms for recapture of P from waste waters.
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Affiliation(s)
- Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - S Antony Ceasar
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai 600034, India
| | - Antony J Palmer
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jaimie B Paterson
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK School of Civil Engineering, Faculty of Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Wanjun Qi
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen A Baldwin
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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123
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Stroud R. Wiggle Wiggle Not a Trickle: How do Membrane Transporters Work (to concentrate ions 1000 fold)? FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.362.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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124
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Madej MG. Comparative Sequence-Function Analysis of the Major Facilitator Superfamily: The "Mix-and-Match" Method. Methods Enzymol 2015; 557:521-49. [PMID: 25950980 DOI: 10.1016/bs.mie.2014.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is a diverse group of secondary transporters with members found in all kingdoms of life. The paradigm for MFS is the lactose permease (LacY) of Escherichia coli, which has been the test bed for the development of many methods applied for the analysis of transport proteins. X-ray structures of an inward-facing conformation and the most recent structure of an almost occluded conformation confirm many conclusions from previous studies. One fundamentally important problem for understanding the mechanism of secondary active transport is the identification and physical localization of residues involved in substrate and H(+) binding. This information is exceptionally difficult to obtain with the MFS because of the broad sequence diversity among the members. The increasing number of solved MFS structures has led to the recognition of a common feature: inverted structure-repeat, formed by fused triple-helix domains with opposite orientation in the membrane. The presented method here exploits this feature to predict functionally homologous positions of known relevant positions in LacY. The triple-helix motifs are aligned in combinatorial fashion so as to detect substrate and H(+)-binding sites in symporters that transport substrates, ranging from simple ions like phosphate to more complex disaccharides.
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Affiliation(s)
- M Gregor Madej
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
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125
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Purification of a Multidrug Resistance Transporter for Crystallization Studies. Antibiotics (Basel) 2015; 4:113-35. [PMID: 27025617 PMCID: PMC4790320 DOI: 10.3390/antibiotics4010113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 01/12/2023] Open
Abstract
Crystallization of integral membrane proteins is a challenging field and much effort has been invested in optimizing the overexpression and purification steps needed to obtain milligram amounts of pure, stable, monodisperse protein sample for crystallography studies. Our current work involves the structural and functional characterization of the Escherichia coli multidrug resistance transporter MdtM, a member of the major facilitator superfamily (MFS). Here we present a protocol for isolation of MdtM to increase yields of recombinant protein to the milligram quantities necessary for pursuit of structural studies using X-ray crystallography. Purification of MdtM was enhanced by introduction of an elongated His-tag, followed by identification and subsequent removal of chaperonin contamination. For crystallization trials of MdtM, detergent screening using size exclusion chromatography determined that decylmaltoside (DM) was the shortest-chain detergent that maintained the protein in a stable, monodispersed state. Crystallization trials of MdtM performed using the hanging-drop diffusion method with commercially available crystallization screens yielded 3D protein crystals under several different conditions. We contend that the purification protocol described here may be employed for production of high-quality protein of other multidrug efflux members of the MFS, a ubiquitous, physiologically and clinically important class of membrane transporters.
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126
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Kankipati HN, Rubio-Texeira M, Castermans D, Diallinas G, Thevelein JM. Sul1 and Sul2 sulfate transceptors signal to protein kinase A upon exit of sulfur starvation. J Biol Chem 2015; 290:10430-46. [PMID: 25724649 PMCID: PMC4400352 DOI: 10.1074/jbc.m114.629022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Indexed: 11/24/2022] Open
Abstract
Sulfate is an essential nutrient with pronounced regulatory effects on cellular metabolism and proliferation. Little is known, however, about how sulfate is sensed by cells. Sul1 and Sul2 are sulfate transporters in the yeast Saccharomyces cerevisiae, strongly induced upon sulfur starvation and endocytosed upon the addition of sulfate. We reveal Sul1,2-dependent activation of PKA targets upon sulfate-induced exit from growth arrest after sulfur starvation. We provide two major arguments in favor of Sul1 and Sul2 acting as transceptors for signaling to PKA. First, the sulfate analogue, d-glucosamine 2-sulfate, acted as a non-transported agonist of signaling by Sul1 and Sul2. Second, mutagenesis to Gln of putative H+-binding residues, Glu-427 in Sul1 or Glu-443 in Sul2, abolished transport without affecting signaling. Hence, Sul1,2 can function as pure sulfate sensors. Sul1E427Q and Sul2E443Q are also deficient in sulfate-induced endocytosis, which can therefore be uncoupled from signaling. Overall, our data suggest that transceptors can undergo independent conformational changes, each responsible for triggering different downstream processes. The Sul1 and Sul2 transceptors are the first identified plasma membrane sensors for extracellular sulfate. High affinity transporters induced upon starvation for their substrate may generally act as transceptors during exit from starvation.
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Affiliation(s)
- Harish Nag Kankipati
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Marta Rubio-Texeira
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Dries Castermans
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - George Diallinas
- the Faculty of Biology, University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - Johan M Thevelein
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
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127
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Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, Forrest LR, Newstead S. Gating topology of the proton-coupled oligopeptide symporters. Structure 2015; 23:290-301. [PMID: 25651061 PMCID: PMC4321885 DOI: 10.1016/j.str.2014.12.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/10/2023]
Abstract
Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport.
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Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | | | - Sebastian Radestock
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Nicolae Solcan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia M Dijkman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Jane Kwok
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lucy R Forrest
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, Frankfurt am Main, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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128
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Andersen JL, He GX, Kakarla P, K C R, Kumar S, Lakra WS, Mukherjee MM, Ranaweera I, Shrestha U, Tran T, Varela MF. Multidrug efflux pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus bacterial food pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:1487-547. [PMID: 25635914 PMCID: PMC4344678 DOI: 10.3390/ijerph120201487] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/15/2015] [Indexed: 02/07/2023]
Abstract
Foodborne illnesses caused by bacterial microorganisms are common worldwide and constitute a serious public health concern. In particular, microorganisms belonging to the Enterobacteriaceae and Vibrionaceae families of Gram-negative bacteria, and to the Staphylococcus genus of Gram-positive bacteria are important causative agents of food poisoning and infection in the gastrointestinal tract of humans. Recently, variants of these bacteria have developed resistance to medically important chemotherapeutic agents. Multidrug resistant Escherichia coli, Salmonella enterica, Vibrio cholerae, Enterobacter spp., and Staphylococcus aureus are becoming increasingly recalcitrant to clinical treatment in human patients. Of the various bacterial resistance mechanisms against antimicrobial agents, multidrug efflux pumps comprise a major cause of multiple drug resistance. These multidrug efflux pump systems reside in the biological membrane of the bacteria and actively extrude antimicrobial agents from bacterial cells. This review article summarizes the evolution of these bacterial drug efflux pump systems from a molecular biological standpoint and provides a framework for future work aimed at reducing the conditions that foster dissemination of these multidrug resistant causative agents through human populations.
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Affiliation(s)
- Jody L Andersen
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Gui-Xin He
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Prathusha Kakarla
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ranjana K C
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Sanath Kumar
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Wazir Singh Lakra
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India.
| | - Mun Mun Mukherjee
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Indrika Ranaweera
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Ugina Shrestha
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
| | - Thuy Tran
- Department of Clinical Laboratory and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Manuel F Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA.
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129
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Beletskiy EV, Kass SR. Selective binding and extraction of aqueous dihydrogen phosphate solutions via three-armed thiourea receptors. Org Biomol Chem 2015; 13:9844-9. [DOI: 10.1039/c5ob01450f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A three-armed thiourea host that strongly and selectively binds H2PO4−and extracts HPO42−from water into chloroform.
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Affiliation(s)
| | - Steven R. Kass
- Department of Chemistry
- University of Minnesota
- Minneapolis, USA
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130
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Ranaweera I, Shrestha U, Ranjana K, Kakarla P, Willmon TM, Hernandez AJ, Mukherjee MM, Barr SR, Varela MF. Structural comparison of bacterial multidrug efflux pumps of the major facilitator superfamily. TRENDS IN CELL & MOLECULAR BIOLOGY 2015; 10:131-140. [PMID: 27065631 PMCID: PMC4822553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The biological membrane is an efficient barrier against water-soluble substances. Solute transporters circumvent this membrane barrier by transporting water-soluble solutes across the membrane to the other sides. These transport proteins are thus required for all living organisms. Microorganisms, such as bacteria, effectively exploit solute transporters to acquire useful nutrients for growth or to expel substances that are inhibitory to their growth. Overall, there are distinct types of related solute transporters that are grouped into families or superfamilies. Of these various transporters, the major facilitator superfamily (MFS) represents a very large and constantly growing group and are driven by solute- and ion-gradients, making them passive and secondary active transporters, respectively. Members of the major facilitator superfamily transport an extreme variety of structurally different substrates such as antimicrobial agents, amino acids, sugars, intermediary metabolites, ions, and other small molecules. Importantly, bacteria, especially pathogenic ones, have evolved multidrug efflux pumps which belong to the major facilitator superfamily. Furthermore, members of this important superfamily share similar primary sequences in the form of highly conserved sequence motifs that confer useful functional properties during transport. The transporters of the superfamily also share similarities in secondary structures, such as possessing 12- or 14-membrane spanning α-helices and the more recently described 3-helix structure repeat element, known as the MFS fold. The three-dimensional structures of bacterial multidrug efflux pumps have been determined for only a few members of the superfamily, all drug pumps of which are surprisingly from Escherichia coli. This review briefly summarizes the structural properties of the bacterial multidrug efflux pumps of the major facilitator superfamily in a comparative manner and provides future directions for study.
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Affiliation(s)
- Indrika Ranaweera
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - Ugina Shrestha
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - K.C. Ranjana
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - Prathusha Kakarla
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - T. Mark Willmon
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | | | - Mun Mun Mukherjee
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - Sharla R. Barr
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
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131
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Galluccio M, Pochini L, Peta V, Iannì M, Scalise M, Indiveri C. Functional and molecular effects of mercury compounds on the human OCTN1 cation transporter: C50 and C136 are the targets for potent inhibition. Toxicol Sci 2014; 144:105-13. [PMID: 25490951 DOI: 10.1093/toxsci/kfu259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The effect of mercury compounds has been tested on the organic cation transporter, hOCTN1. MeHg(+), Hg(2+), or Cd(2+) caused strong inhibition of transport. 1,4-Dithioerythritol (DTE), cysteine (Cys), and N-acetyl-l-cysteine reversed (NAC) the inhibition at different extents. 2-Aminoethyl methanethiosulfonate hydrobromide (MTSEA), a prototype SH reagent, exerted inhibition of transport similar to that observed for the mercurial agents. To investigate the mechanism of action of mercurials, mutants of hOCTN1 in which each of the Cys residues was substituted by Ala have been constructed, over-expressed in Escherichia coli, and purified. Tetraethylammonium chloride (TEA) uptake mediated by each mutant in proteoliposomes was comparable to that of wild type (WT). IC50 values of the WT and mutants for the mercury compounds were derived from dose-response analyses. The mutants C50A and C136A showed significant increase of IC50 indicating that the 2 Cys residues were involved in the interaction with the mercury compounds and inhibition of the transporter. The double mutant C50A/C136A was constructed; the lack of inhibition confirmed that the 2 Cys residues are the targets of mercury compounds. MTSEA showed similar behavior with respect to the mercurial reagents with the difference that increased IC50 was observed also in the C81A mutant. Similar results were obtained when transport was measured as acetylcholine uptake. Ethyl mercury (Thimerosal) inhibited hOCTN1 as well. C50A, C50A/C136A and, at very lower extent, C136A showed increased IC50 indicating that C50 was the major target of this mercury compound. The homology model of hOCTN1 was built using as template PiPT and validated by the experimental data on mutant proteins.
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Affiliation(s)
- Michele Galluccio
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Lorena Pochini
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Valentina Peta
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Maria Iannì
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, Via Bucci 4C, University of Calabria, 87036 Arcavacata di Rende, Italy
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132
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Iyalomhe O, Herrick DZ, Cafiso DS, Maloney PC. Closure of the cytoplasmic gate formed by TM5 and TM11 during transport in the oxalate/formate exchanger from Oxalobacter formigenes. Biochemistry 2014; 53:7735-44. [PMID: 25409483 PMCID: PMC4270380 DOI: 10.1021/bi5012173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
OxlT, the oxalate/formate exchanger
of Oxalobacter
formigenes, is a member of the major facilitator superfamily
of transporters. In the present work, substrate (oxalate) was found
to enhance the reactivity of the cysteine mutant S336C on the cytoplasmic
end of helix 11 to methanethiosulfonate ethyl carboxylate. In addition,
S336C is found to spontaneously cross-link to S143C in TM5 in either
native or reconstituted membranes under conditions that support transport.
Continuous wave EPR measurements are consistent with this result and
indicate that positions 143 and 336 are in close proximity in the
presence of substrate. These two residues are localized within helix
interacting GxxxG-like motifs (G140LASG144 and
S336DIFG340) at the cytoplasmic poles of TM5
and TM11. Pulse EPR measurements were used to determine distances
and distance distributions across the cytoplasmic or periplasmic ends
of OxlT and were compared with the predictions of an inside-open homology
model. The data indicate that a significant population of transporter
is in an outside-open configuration in the presence of substrate;
however, each end of the transporter exhibits significant conformational
heterogeneity, where both inside-open and outside-open configurations
are present. These data indicate that TM5 and TM11, which form part
of the transport pathway, transiently close during transport and that
there is a conformational equilibrium between inside-open and outside-open
states of OxlT in the presence of substrate.
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Affiliation(s)
- Osigbemhe Iyalomhe
- Department of Physiology, The Johns Hopkins University, School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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133
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Fenollar-Ferrer C, Patti M, Knöpfel T, Werner A, Forster IC, Forrest LR. Structural fold and binding sites of the human Na⁺-phosphate cotransporter NaPi-II. Biophys J 2014; 106:1268-79. [PMID: 24655502 DOI: 10.1016/j.bpj.2014.01.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 12/17/2022] Open
Abstract
Phosphate plays essential biological roles and its plasma level in humans requires tight control to avoid bone loss (insufficiency) or vascular calcification (excess). Intestinal absorption and renal reabsorption of phosphate are mediated by members of the SLC34 family of sodium-coupled transporters (NaPi-IIa,b,c) whose membrane expression is regulated by various hormones, circulating proteins, and phosphate itself. Consequently, NaPi-II proteins are also potentially important pharmaceutical targets for controlling phosphate levels. Their crucial role in Pi homeostasis is underscored by pathologies resulting from naturally occurring SLC34 mutations and SLC34 knockout animals. SLC34 isoforms have been extensively studied with respect to transport mechanism and structure-function relationships; however, the three-dimensional structure is unknown. All SLC34 transporters share a duplicated motif comprising a glutamine followed by a stretch of threonine or serine residues, suggesting the presence of structural repeats as found in other transporter families. Nevertheless, standard bioinformatic approaches fail to clearly identify a suitable template for molecular modeling. Here, we used hydrophobicity profiles and hidden Markov models to define a structural repeat common to all SLC34 isoforms. Similar approaches identify a relationship with the core regions in a crystal structure of Vibrio cholerae Na(+)-dicarboxylate transporter VcINDY, from which we generated a homology model of human NaPi-IIa. The aforementioned SLC34 motifs in each repeat localize to the center of the model, and were predicted to form Na(+) and Pi coordination sites. Functional relevance of key amino acids was confirmed by biochemical and electrophysiological analysis of expressed, mutated transporters. Moreover, the validity of the predicted architecture is corroborated by extensive published structure-function studies. The model provides key information for elucidating the transport mechanism and predicts candidate substrate binding sites.
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Affiliation(s)
- Cristina Fenollar-Ferrer
- Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Monica Patti
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Thomas Knöpfel
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Andreas Werner
- Epithelial Research Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Ian C Forster
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland.
| | - Lucy R Forrest
- Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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134
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Piriformospora indica improves micropropagation, growth and phytochemical content of Aloe vera L. plants. Symbiosis 2014. [DOI: 10.1007/s13199-014-0298-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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135
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A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters. Nat Struct Mol Biol 2014; 21:1006-12. [PMID: 25282149 DOI: 10.1038/nsmb.2894] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Neurotransmitter/sodium symporters (NSSs) terminate synaptic signal transmission by Na+-dependent reuptake of released neurotransmitters. Key conformational states have been reported for the bacterial homolog LeuT and an inhibitor-bound Drosophila dopamine transporter. However, a coherent mechanism of Na+-driven transport has not been described. Here, we present two crystal structures of MhsT, an NSS member from Bacillus halodurans, in occluded inward-facing states with bound Na+ ions and L-tryptophan, providing insight into the cytoplasmic release of Na+. The switch from outward- to inward-oriented states is centered on the partial unwinding of transmembrane helix 5, facilitated by a conserved GlyX9Pro motif that opens an intracellular pathway for water to access the Na2 site. We propose a mechanism, based on our structural and functional findings, in which solvation through the TM5 pathway facilitates Na+ release from Na2 and the transition to an inward-open state.
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136
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Function, Structure, and Evolution of the Major Facilitator Superfamily: The LacY Manifesto. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/523591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The major facilitator superfamily (MFS) is a diverse group of secondary transporters with members found in all kingdoms of life. A paradigm for MFS is the lactose permease (LacY) of Escherichia coli, which couples the stoichiometric translocation of a galactopyranoside and an H+ across the cytoplasmic membrane. LacY has been the test bed for the development of many methods applied for the analysis of transport proteins. X-ray structures of an inward-facing conformation and the most recent structure of an almost occluded conformation confirm many conclusions from previous studies. Although structure models are critical, they are insufficient to explain the catalysis of transport. The clues to understanding transport are based on the principles of enzyme kinetics. Secondary transport is a dynamic process—static snapshots of X-ray crystallography describe it only partially. However, without structural information, the underlying chemistry is virtually impossible to conclude. A large body of biochemical/biophysical data derived from systematic studies of site-directed mutants in LacY suggests residues critically involved in the catalysis, and a working model for the symport mechanism that involves alternating access of the binding site is presented. The general concepts derived from the bacterial LacY are examined for their relevance to other MFS transporters.
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137
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The Structure and Function of OxlT, the Oxalate Transporter of Oxalobacter formigenes. J Membr Biol 2014; 248:641-50. [DOI: 10.1007/s00232-014-9728-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/05/2014] [Indexed: 01/01/2023]
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138
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He Y, Wang K, Yan N. The recombinant expression systems for structure determination of eukaryotic membrane proteins. Protein Cell 2014; 5:658-72. [PMID: 25119489 PMCID: PMC4145085 DOI: 10.1007/s13238-014-0086-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic membrane proteins, many of which are key players in various biological processes, constitute more than half of the drug targets and represent important candidates for structural studies. In contrast to their physiological significance, only very limited number of eukaryotic membrane protein structures have been obtained due to the technical challenges in the generation of recombinant proteins. In this review, we examine the major recombinant expression systems for eukaryotic membrane proteins and compare their relative advantages and disadvantages. We also attempted to summarize the recent technical strategies in the advancement of eukaryotic membrane protein purification and crystallization.
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Affiliation(s)
- Yuan He
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua university, Beijing, 100084, China
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139
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Wisedchaisri G, Park MS, Iadanza MG, Zheng H, Gonen T. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE. Nat Commun 2014; 5:4521. [PMID: 25088546 PMCID: PMC4137407 DOI: 10.1038/ncomms5521] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/25/2014] [Indexed: 01/19/2023] Open
Abstract
The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. Glucose transporters are a medically important class of membrane proteins often deregulated in diseases such as Type 2 diabetes. Here, Wisedchaisri et al. report the crystal structure of XylE in an inward-facing open conformation to provide a general mechanism of substrate transport for the sugar porter family of proteins.
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Affiliation(s)
- Goragot Wisedchaisri
- 1] Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA [2]
| | - Min-Sun Park
- 1] Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA [2]
| | - Matthew G Iadanza
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Hongjin Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
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140
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Tomasiak TM, Pedersen BP, Chaudhary S, Rodriguez A, Colmanares YR, Roe-Zurz Z, Thamminana S, Tessema M, Stroud RM. General qPCR and Plate Reader Methods for Rapid Optimization of Membrane Protein Purification and Crystallization Using Thermostability Assays. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2014; 77:29.11.1-29.11.14. [PMID: 25081745 PMCID: PMC4672949 DOI: 10.1002/0471140864.ps2911s77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This unit describes rapid and generally applicable methods to identify conditions that stabilize membrane proteins using temperature-based denaturation measurements as a proxy for target time-dependent stability. Recent developments with thiol-reactive dyes sensitive to the unmasking of cysteine residues upon protein unfolding have allowed for routine application of thermostability assays to systematically evaluate the stability of membrane protein preparations after various purification procedures. Test conditions can include different lipid cocktails, lipid-detergent micelles, pH, salts, osmolytes, and potential active-site ligands. Identification and use of conditions that stabilize the structure have proven successful in enabling the structure determination of numerous families of membrane proteins that otherwise were intractable.
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Affiliation(s)
- Thomas M Tomasiak
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Bjørn P Pedersen
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Sarika Chaudhary
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Andrew Rodriguez
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Yaneth Robles Colmanares
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Zygy Roe-Zurz
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Sobha Thamminana
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Meseret Tessema
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California
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141
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Johnson ZL, Lee JH, Lee K, Lee M, Kwon DY, Hong J, Lee SY. Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters. eLife 2014; 3:e03604. [PMID: 25082345 PMCID: PMC4139061 DOI: 10.7554/elife.03604] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively. DOI:http://dx.doi.org/10.7554/eLife.03604.001 DNA molecules are made from four bases—often named ‘G’, ‘A’, ‘C’, and ‘T’—that are arranged along a backbone made of sugars and phosphate groups. Chemicals called nucleosides are essentially the same as these four building blocks of DNA (and other similar molecules) but without the phosphate groups. Proteins called nucleoside transporters are found in the membranes that surround cells and can pump nucleosides into the cell. These transporters also allow drugs that are made from modified nucleosides to enter cells; however, it was previously unclear how different transporters recognized and imported specific nucleosides. Like other proteins, nucleoside transporters are basically strings of amino acids that have folded into a specific three-dimensional shape. A protein's shape is often important for defining what that protein can do, as often other molecules must bind to proteins—much like a key fitting into a lock. Johnson et al. have now revealed the three-dimensional structure of one nucleoside transporter protein bound to different nucleosides and nucleoside-derived chemicals, including three anti-cancer drugs and one anti-viral drug. Some of these chemicals were shown to bind more strongly to the transporter protein than others, and examining the three-dimensional structures revealed that the different chemicals interacted with slightly different amino acids in the transporter protein. Johnson et al. then used this information to chemically modify an anticancer drug so that it is transported more easily into cells and is imported by only one of the subtypes of nucleoside transporters that are found in humans. This provides proof of principle that information about the structure and function of a transporter protein can help to redesign chemicals such that they can enter cells more efficiently, and to tailor them for transport by specific transporters. A similar approach may in the future allow researchers to design new nucleoside-derived drugs that are better at getting inside specific cells and, as such, provide effective treatments against cancers and viral infections. DOI:http://dx.doi.org/10.7554/eLife.03604.002
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Affiliation(s)
- Zachary Lee Johnson
- Department of Biochemistry, Duke University Medical Center, Durham, United States
| | - Jun-Ho Lee
- Department of Biochemistry, Duke University Medical Center, Durham, United States
| | - Kiyoun Lee
- Department of Chemistry, Duke University, Durham, United States
| | - Minhee Lee
- Department of Chemistry, Duke University, Durham, United States
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, United States
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, United States Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, United States
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142
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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143
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Sippel KH, Bacik J, Quiocho FA, Fisher SZ. Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station. Acta Crystallogr F Struct Biol Commun 2014; 70:819-22. [PMID: 24915101 PMCID: PMC4051545 DOI: 10.1107/s2053230x14009704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP-phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by accepting a phosphate hydrogen. PBP phosphate affinity is relatively consistent across a broad pH range, indicating the capacity to bind monobasic (H2PO4-) and dibasic (HPO4(2-)) phosphate; however, the mechanism by which it might accommodate the second hydrogen of monobasic phosphate is unclear. To answer this question, neutron diffraction studies were initiated. Large single crystals with a volume of 8 mm3 were grown and subjected to hydrogen/deuterium exchange. A 2.5 Å resolution data set was collected on the Protein Crystallography Station at the Los Alamos Neutron Science Center. Initial refinement of the neutron data shows significant nuclear density, and refinement is ongoing. This is the first report of a neutron study from this superfamily.
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Affiliation(s)
- K. H. Sippel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - J. Bacik
- Bioscience Division B-11, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - F. A. Quiocho
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - S. Z. Fisher
- Scientific Activities Division, European Spallation Source, 221 00 Lund, Sweden
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144
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Ilgü H, Jeckelmann JM, Gachet MS, Boggavarapu R, Ucurum Z, Gertsch J, Fotiadis D. Variation of the detergent-binding capacity and phospholipid content of membrane proteins when purified in different detergents. Biophys J 2014; 106:1660-70. [PMID: 24739165 PMCID: PMC4008799 DOI: 10.1016/j.bpj.2014.02.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 02/21/2014] [Accepted: 02/26/2014] [Indexed: 11/24/2022] Open
Abstract
Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches.
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Affiliation(s)
- Hüseyin Ilgü
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - María Salomé Gachet
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Rajendra Boggavarapu
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland.
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145
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Stelzl LS, Fowler PW, Sansom MS, Beckstein O. Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol 2014; 426:735-51. [PMID: 24513108 PMCID: PMC3905165 DOI: 10.1016/j.jmb.2013.10.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/17/2013] [Accepted: 10/18/2013] [Indexed: 12/29/2022]
Abstract
The major facilitator superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling molecular dynamics method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free-energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepTSo, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin–spin distance measurements that have been interpreted to show occluded conformations. During the simulations, a salt bridge that has been postulated to be involved in driving the conformational transition formed. Our results argue against a simple rigid-body domain motion as implied by a strict “rocker-switch mechanism” and instead hint at an intricate coupling between two flexible gates. The transport mechanism of LacY is hypothesized to involve an intermediate “occluded” state. Such a state is observed in computer simulations of the conformational transitions. Simulation data are validated with experimental double electron–electron spin resonance measurements. The structural gating elements of LacY are identified. Occluded LacY is similar to known occluded structures of homologous proteins.
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Affiliation(s)
- Lukas S. Stelzl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philip W. Fowler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S.P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author Department of Physics, Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287-1504, USA.
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146
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Molecular cloning and functional analysis of a H(+)-dependent phosphate transporter gene from the ectomycorrhizal fungus Boletus edulis in southwest China. Fungal Biol 2014; 118:453-61. [PMID: 24863474 DOI: 10.1016/j.funbio.2014.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 02/26/2014] [Accepted: 03/06/2014] [Indexed: 01/09/2023]
Abstract
Phosphate transporters (PTs), as entry points for phosphorus (P) in organisms, are involved in a number of P nutrition processes such as phosphate uptake, transport, and transfer. In the study, a PT gene 1632 bp long (named BePT) was cloned, identified, and functionally characterized from Boletus edulis. BePT was expected to encode a polypeptide with 543 amino acid residues. The BePT polypeptide belonged to the major facilitator superfamily and showed a high degree of sequence identity to the Pht1 family. A topology model revealed that BePT exhibited 12 transmembrane helices, divided into two halves, and connected by a large hydrophilic loop in the middle. A yeast mutant complementation analysis suggested that BePT was a functional PT which mediated orthophosphate uptake of yeast at micromolar concentrations. Green fluorescent protein-BePT fusion proteins expressed were extensively restricted to the plasma membrane in BePT transformed yeast, and its activity was dependent on electrochemical membrane potential. In vitro, quantitative PCR confirmed that the expression of BePT was significantly upregulated at lower phosphorus availability, which may enhance phosphate uptake and transport under phosphate starvation. Our results suggest that BePT plays a key role in phosphate acquisition in the ectomycorrhizal fungus B. edulis.
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147
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Crystal structure of the plant dual-affinity nitrate transporter NRT1.1. Nature 2014; 507:73-7. [PMID: 24572362 PMCID: PMC3968801 DOI: 10.1038/nature13074] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/23/2014] [Indexed: 01/24/2023]
Abstract
Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter, which can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr101. Yet how this posttranslational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 indeed dimerizes in the cell membrane and the phosphomimetic mutation of Thr101 converts the protein into a monophasic high affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.
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148
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Major Facilitator Superfamily (MFS) evolved without 3-transmembrane segment unit rearrangements. Proc Natl Acad Sci U S A 2014; 111:E1162-3. [PMID: 24567407 DOI: 10.1073/pnas.1400016111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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149
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Valdés R, Elferich J, Shinde U, Landfear SM. Identification of the intracellular gate for a member of the equilibrative nucleoside transporter (ENT) family. J Biol Chem 2014; 289:8799-809. [PMID: 24497645 DOI: 10.1074/jbc.m113.546960] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Equilibrative nucleoside transporters of the SLC29 family play important roles in many physiological and pharmacological processes, including import of drugs for treatment of cancer, AIDS, cardiovascular, and parasitic diseases. However, no crystal structure is available for any member of this family. In previous studies we generated a computational model of the Leishmania donovani nucleoside transporter 1.1 (LdNT1.1) that captured this permease in the outward-closed conformation, and we identified the extracellular gate. In the present study we have modeled the inward-closed conformation of LdNT1.1 using the crystal structure of the Escherichia coli fucose transporter FucP and have identified four transmembrane helices whose ends close to form a predicted intracellular gate. We have tested this prediction by site-directed mutagenesis of relevant helix residues and by cross-linking of introduced cysteine pairs. The results are consistent with the predictions of the computational model and suggest that a similarly constituted gate operates in other members of the equilibrative nucleoside transporter family.
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Affiliation(s)
- Raquel Valdés
- From the Departments of Molecular Microbiology and Immunology and
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150
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Abstract
The Major Facilitator Superfamily (MFS) is a diverse group of secondary transporters with over 10,000 members, found in all kingdoms of life, including Homo sapiens. One objective of determining crystallographic models of the bacterial representatives is identification and physical localization of residues important for catalysis in transporters with medical relevance. The recently solved crystallographic models of the D-xylose permease XylE from Escherichia coli and GlcP from Staphylococcus epidermidus, homologs of the human D-glucose transporters, the GLUTs (SLC2), provide information about the structure of these transporters. The goal of this work is to examine general concepts derived from the bacterial XylE, GlcP, and other MFS transporters for their relevance to the GLUTs by comparing conservation of functionally critical residues. An energy landscape for symport and uniport is presented. Furthermore, the substrate selectivity of XylE is compared with GLUT1 and GLUT5, as well as a XylE mutant that transports D-glucose.
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