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Işık EB, Serçinoğlu O. Unraveling the ligand specificity and promiscuity of the Staphylococcus aureus NorA efflux pump: a computational study. J Biomol Struct Dyn 2024:1-12. [PMID: 38497784 DOI: 10.1080/07391102.2024.2326670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
Staphylococcus aureus, a gram-positive bacterial pathogen, develops antibiotic resistance partly through enhanced activity of transmembrane multi-drug efflux pump proteins like NorA. Being a prominent member of the Major Facilitator Superfamily (MFS), NorA transports various small molecules including hydrophilic fluoroquinolone antibiotics across the cell membrane. Intriguingly, NorA is inhibited by a structurally diverse set of small molecule inhibitors as well, indicating a highly promiscuous ligand/inhibitor recognition. Our study aims to elucidate the structural facets of this promiscuity. Known NorA inhibitors were grouped into five clusters based on chemical class and docked into ligand binding pockets on NorA conformations generated via molecular dynamics simulations. We discovered that several key residues, such as I23, E222, and F303, are involved in inhibitor binding. Additionally, residues I244, T223, F303, and F140 were identified as prominent in interactions with specific ligand clusters. Our findings suggest that NorA's substrate binding site, encompassing residues aiding ligand recognition based on chemical nature, facilitates the recognition of chemically diverse ligands. This insight into NorA's structural promiscuity in ligand recognition not only enhances understanding of antibiotic resistance mechanisms in S. aureus but also sets the stage for the development of more effective efflux pump inhibitors, vital for combating multidrug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Esra Büşra Işık
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, Türkiye
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakıf University, Beykoz, Istanbul, Türkiye
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, Türkiye
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2
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Varela MF, Ortiz-Alegria A, Lekshmi M, Stephen J, Kumar S. Functional Roles of the Conserved Amino Acid Sequence Motif C, the Antiporter Motif, in Membrane Transporters of the Major Facilitator Superfamily. Biology (Basel) 2023; 12:1336. [PMID: 37887046 PMCID: PMC10604125 DOI: 10.3390/biology12101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The biological membrane surrounding all living cells forms a hydrophobic barrier to the passage of biologically important molecules. Integral membrane proteins called transporters circumvent the cellular barrier and transport molecules across the cell membrane. These molecular transporters enable the uptake and exit of molecules for cell growth and homeostasis. One important collection of related transporters is the major facilitator superfamily (MFS). This large group of proteins harbors passive and secondary active transporters. The transporters of the MFS consist of uniporters, symporters, and antiporters, which share similarities in structures, predicted mechanism of transport, and highly conserved amino acid sequence motifs. In particular, the antiporter motif, called motif C, is found primarily in antiporters of the MFS. The antiporter motif's molecular elements mediate conformational changes and other molecular physiological roles during substrate transport across the membrane. This review article traces the history of the antiporter motif. It summarizes the physiological evidence reported that supports these biological roles.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Anely Ortiz-Alegria
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
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3
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Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C. Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Cell Rep 2023; 42:112831. [PMID: 37467108 DOI: 10.1016/j.celrep.2023.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.
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Affiliation(s)
- Vadim Kotov
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Maxime Killer
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Hamburg, Germany
| | - Katharina E J Jungnickel
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jian Lei
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany; State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, People's Republic of China
| | - Giada Finocchio
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Josi Steinke
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Kim Bartels
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Jan Strauss
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - Florine Dupeux
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Irina Cornaciu
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - José A Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs CS 90181, 38042 Grenoble Cedex 9, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Christian Löw
- Center for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany; European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607 Hamburg, Germany.
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4
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Chen H, Ahmed S, Zhao H, Elghobashi-Meinhardt N, Dai Y, Kim JH, McDonald JG, Li X, Lee CH. Structural and functional insights into Spns2-mediated transport of sphingosine-1-phosphate. Cell 2023; 186:2644-2655.e16. [PMID: 37224812 PMCID: PMC10330195 DOI: 10.1016/j.cell.2023.04.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/23/2023] [Accepted: 04/19/2023] [Indexed: 05/26/2023]
Abstract
Sphingosine-1-phosphate (S1P) is an important signaling sphingolipid that regulates the immune system, angiogenesis, auditory function, and epithelial and endothelial barrier integrity. Spinster homolog 2 (Spns2) is an S1P transporter that exports S1P to initiate lipid signaling cascades. Modulating Spns2 activity can be beneficial in treatments of cancer, inflammation, and immune diseases. However, the transport mechanism of Spns2 and its inhibition remain unclear. Here, we present six cryo-EM structures of human Spns2 in lipid nanodiscs, including two functionally relevant intermediate conformations that link the inward- and outward-facing states, to reveal the structural basis of the S1P transport cycle. Functional analyses suggest that Spns2 exports S1P via facilitated diffusion, a mechanism distinct from other MFS lipid transporters. Finally, we show that the Spns2 inhibitor 16d attenuates the transport activity by locking Spns2 in the inward-facing state. Our work sheds light on Spns2-mediated S1P transport and aids the development of advanced Spns2 inhibitors.
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Affiliation(s)
- Hongwen Chen
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shahbaz Ahmed
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongtu Zhao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Yaxin Dai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jae Hun Kim
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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5
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Varela MF, Stephen J, Bharti D, Lekshmi M, Kumar S. Inhibition of Multidrug Efflux Pumps Belonging to the Major Facilitator Superfamily in Bacterial Pathogens. Biomedicines 2023; 11:1448. [PMID: 37239119 PMCID: PMC10216197 DOI: 10.3390/biomedicines11051448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Bacterial pathogens resistant to multiple structurally distinct antimicrobial agents are causative agents of infectious disease, and they thus constitute a serious concern for public health. Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily constitute central resistance systems in bacterial pathogens. This review article addresses the recent efforts to modulate these antimicrobial efflux transporters from a molecular perspective. Such investigations can potentially restore the clinical efficacy of infectious disease chemotherapy.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM 88130, USA
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Deeksha Bharti
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
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6
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Gharabli H, Rafiq M, Iqbal A, Yan R, Aduri NG, Sharma N, Prabhala BK, Mirza O. Functional Characterization of the Putative POT from Clostridium perfringens. Biology (Basel) 2023; 12:biology12050651. [PMID: 37237465 DOI: 10.3390/biology12050651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Proton-coupled oligopeptide transporters (POTs) are a fundamental part of the cellular transport machinery that provides plants, bacteria, and mammals with nutrition in the form of short peptides. However, POTs are not restricted to peptide transport; mammalian POTs have especially been in focus due to their ability to transport several peptidomimetics in the small intestine. Herein, we studied a POT from Clostridium perfringens (CPEPOT), which unexpectedly exhibited atypical characteristics. First, very little uptake of a fluorescently labelled peptide β-Ala-Lys-AMCA, an otherwise good substrate of several other bacterial POTs, was observed. Secondly, in the presence of a competitor peptide, enhanced uptake of β-Ala-Lys-AMCA was observed due to trans-stimulation. This effect was also observed even in the absence of a proton electrochemical gradient, suggesting that β-Ala-Lys-AMCA uptake mediated by CPEPOT is likely through the substrate-concentration-driving exchange mechanism, unlike any other functionally characterized bacterial POTs.
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Affiliation(s)
- Hani Gharabli
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anna Iqbal
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ruyu Yan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Nanda G Aduri
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Neha Sharma
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bala K Prabhala
- Department of Physics, Chemistry and Pharmacy, Faculty of Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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7
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Stephen J, Salam F, Lekshmi M, Kumar SH, Varela MF. The Major Facilitator Superfamily and Antimicrobial Resistance Efflux Pumps of the ESKAPEE Pathogen Staphylococcus aureus. Antibiotics (Basel) 2023; 12:antibiotics12020343. [PMID: 36830254 PMCID: PMC9952236 DOI: 10.3390/antibiotics12020343] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The ESKAPEE bacterial pathogen Staphylococcus aureus has posed a serious public health concern for centuries. Throughout its evolutionary course, S. aureus has developed strains with resistance to antimicrobial agents. The bacterial pathogen has acquired multidrug resistance, causing, in many cases, untreatable infectious diseases and raising serious public safety and healthcare concerns. Amongst the various mechanisms for antimicrobial resistance, integral membrane proteins that serve as secondary active transporters from the major facilitator superfamily constitute a chief system of multidrug resistance. These MFS transporters actively export structurally different antimicrobial agents from the cells of S. aureus. This review article discusses the S. aureus-specific MFS multidrug efflux pump systems from a molecular mechanistic perspective, paying particular attention to structure-function relationships, modulation of antimicrobial resistance mediated by MFS drug efflux pumps, and direction for future investigation.
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Affiliation(s)
- Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Fathima Salam
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Sanath H. Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
- Correspondence: ; Tel.: +1-575-562-2464
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Li Y, Ge X. Molecular Dynamics Investigation of MFS Efflux Pump MdfA Reveals an Intermediate State between Its Inward and Outward Conformations. Int J Mol Sci 2022; 24:ijms24010356. [PMID: 36613823 PMCID: PMC9820426 DOI: 10.3390/ijms24010356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Multidrug resistance poses a major challenge to antibiotic therapy. A principal cause of antibiotic resistance is through active export by efflux pumps embedded in the bacterial membrane. Major facilitator superfamily (MFS) efflux pumps constitute a major group of transporters, which are often related to quinolone resistance in clinical settings. Although a rocker-switch model is proposed for description of their conformational transitions, detailed changes in this process remain poorly understood. Here we used MdfA from E. coli as a representative MFS efflux pump to investigate factors that can affect its conformational transition in silico. Molecular dynamics (MD) simulations of MdfA's inward and outward conformations revealed an intermediate state between these two conformations. By comparison of the subtle differences between the intermediate state and the average state, we indicated that conformational transition from outward to inward was initiated by protonation of the periplasmic side. Subsequently, hydrophilic interaction of the periplasmic side with water was promoted and the regional structure of helix 1 was altered to favor this process. As the hydrophobic interaction between MdfA and membrane was also increased, energy was concentrated and stored for the opposite transition. In parallel, salt bridges at the cytoplasmic side were altered to lower probabilities to facilitate the entrance of substrate. In summary, we described the total and local changes during MdfA's conformational transition, providing insights for the development of potential inhibitors.
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Affiliation(s)
| | - Xizhen Ge
- Correspondence: ; Tel.: +86-10-5207-2337
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Yao J, Bai J, Liu S, Fu J, Zhang Y, Luo T, Ren H, Wang R, Zhao Y. Editing of a Novel Cd Uptake-Related Gene CUP1 Contributes to Reducing Cd Accumulations in Arabidopsis thaliana and Brassica napus. Cells 2022; 11. [PMID: 36497146 DOI: 10.3390/cells11233888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Brassica napus is a Cd hyperaccumulator, which is a serious threat to food and fodder safety. However, no related studies on developing Cd-safe B. napus have been reported yet. Here, we screened out a novel Cd uptake-related gene, AtCUP1, from the major facilitator superfamily in Arabidopsis thaliana. The mutation of AtCUP1 decreased Cd accumulation, both in roots and shoots of A. thaliana. Furthermore, the disruption of the AtCUP1 gene by the CRISPR/Cas9 system significantly reduced Cd accumulation in A. thaliana. Interestingly, the disruption of the BnCUP1 gene, an orthologous gene of AtCUP1, by the CRISPR/Cas9 system also diminished Cd accumulation in both roots and shoots of B. napus based on the hydroponics assay. Furthermore, for the field experiment, the Cd accumulations of BnCUP1-edited lines were reduced by 52% in roots and 77% in shoots compared to that of wild-type (WT) lines, and the biomass and yield of BnCUP1-edited lines increased by 42% and 47% of that of WT, respectively. Noteworthily, agronomic characteristics of B. napus were not apparently affected by BnCUP1-editing. Thus, BnCUP1-edited lines are excellent non-transgenic germplasm resources for reducing Cd accumulation without a distinct compromise in yield, which could be applied to agricultural production in Cd-contaminated soils.
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Diao J, Li S, Ma L, Zhang P, Bai J, Wang J, Ma X, Ma W. Genome-Wide Analysis of Major Facilitator Superfamily and Its Expression in Response of Poplar to Fusarium oxysporum. Front Genet 2021; 12:769888. [PMID: 34745233 PMCID: PMC8567078 DOI: 10.3389/fgene.2021.769888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
The major facilitator superfamily (MFS) is one of the largest known membrane transporter families. MFSs are involved in many essential functions, but studies on the MFS family in poplar have not yet been reported. Here, we identified 41 MFS genes from Populus trichocarpa (PtrMFSs). We built a phylogenetic tree, which clearly divided members of PtrMFS into six groups with specific gene structures and protein motifs/domains. The promoter regions contain various cis-acting elements involved in stress and hormone responsiveness. Genes derived from segmental duplication events are unevenly distributed in 17 poplar chromosomes. Collinearity analysis showed that PtrMFS genes are conserved and homologous to corresponding genes from four other species. Transcriptome data indicated that 40 poplar MFS genes were differentially expressed when treated with Fusarium oxysporum. Co-expression networks and gene function annotations of MFS genes showed that MFS genes tightly co-regulated and closely related in function of transmembrane transport. Taken together, we systematically analyzed structure and function of genes and proteins in the PtrMFS family. Evidence indicated that poplar MFS genes play key roles in plant development and response to a biological stressor.
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Affiliation(s)
- Jian Diao
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Shuxuan Li
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ling Ma
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ping Zhang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Jianyang Bai
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Jiaqi Wang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqian Ma
- Institute of Forest Protection, Heilongjiang Academy of Forestry, Harbin, China
| | - Wei Ma
- College of Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
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11
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Liu N, Wang Q, He C, An B. CgMFS1, a Major Facilitator Superfamily Transporter, Is Required for Sugar Transport, Oxidative Stress Resistance, and Pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis. Curr Issues Mol Biol 2021; 43:1548-57. [PMID: 34698108 DOI: 10.3390/cimb43030109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/03/2022] Open
Abstract
Colletotrichum gloeosporioides is the main causal agent of anthracnose in various plant species. Determining the molecular mechanisms underlying the pathogenicity and fungicide resistance of C. gloeosporioides could help build new strategies for disease control. The major facilitator superfamily (MFS) has multiple roles in the transport of a diverse range of substrates. In the present study, an MFS protein CgMFS1 was characterized in C. gloeosporioides. This protein contains seven transmembrane domains, and its predicted 3D structure is highly similar to the reported hexose transporters. To investigate the biological functions of CgMFS1, the gene knock-out mutant ΔCgMFS1 was constructed. A colony growth assay showed that the mutant was remarkably decreased in vegetative growth in minimal medium supplemented with monosaccharides and oligosaccharides as the sole carbon sources, whereas it showed a similar growth rate and colony morphology as wild types when using soluble starch as the carbon source. A stress assay revealed that CgMFS1 is involved in oxidative stress but not in the fungicide resistance of C. gloeosporioides. Furthermore, its pathogenicity was significantly impaired in the mutant, although its appressorium formation was not affected. Our results demonstrate that CgMFS1 is required for sugar transport, resistance to oxidative stress, and the pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis.
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12
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Singh G, Akhter Y. Molecular insights into the differential efflux mechanism of Rv1634 protein, a multidrug transporter of major facilitator superfamily in Mycobacterium tuberculosis. Proteins 2021; 90:566-578. [PMID: 34601761 DOI: 10.1002/prot.26253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 11/08/2022]
Abstract
Currently, multidrug-resistant tuberculosis (MDR-TB) is a public health crisis and a major health security threat globally. In Mycobacterium tuberculosis (Mtb), major facilitator superfamily (MFS) is the largest group of secondary active transporters. Along with the transport of their natural substrates, MFS proteins were involved in a drug efflux mechanism that ultimately lead to resistance against available anti-TB drugs in Mtb. In the present study, the three-dimensional structure model of an MFS protein, Rv1634, a probable multidrug transporter from Mtb, was generated using homology modeling. The protein structure model was found in inward-open conformation having 14 transmembrane helices. In addition, a central transport channel was deduced across the protein, and a single binding pocket was identified halfway through the central cavity by structural alignment with the homologous protein structures. Further, Rv1634 protein was studied based on the differential structural behavior of apo and ligand-bound forms. All the protein systems were inserted into a phospholipid bilayer to characterize the conformational dynamics of the protein using molecular dynamics (MD) simulations. Detailed analysis of the MD trajectories showed the diverse substrate specificity of the binding pocket for the antibiotics that caused differential movement in the ciprofloxacin and norfloxacin, to which Mtb strains have now become resistant. The expulsion of the drugs outside the bacterial cell occurs through the alternating-access mechanism of N and C-terminal domains, which is intriguing and essential to the understanding the drug resistance mechanism in pathogenic bacteria.
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Affiliation(s)
- Garima Singh
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
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13
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Pasqua M, Bonaccorsi di Patti MC, Fanelli G, Utsumi R, Eguchi Y, Trirocco R, Prosseda G, Grossi M, Colonna B. Host - Bacterial Pathogen Communication: The Wily Role of the Multidrug Efflux Pumps of the MFS Family. Front Mol Biosci 2021; 8:723274. [PMID: 34381818 PMCID: PMC8350985 DOI: 10.3389/fmolb.2021.723274] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022] Open
Abstract
Bacterial pathogens are able to survive within diverse habitats. The dynamic adaptation to the surroundings depends on their ability to sense environmental variations and to respond in an appropriate manner. This involves, among others, the activation of various cell-to-cell communication strategies. The capability of the bacterial cells to rapidly and co-ordinately set up an interplay with the host cells and/or with other bacteria facilitates their survival in the new niche. Efflux pumps are ubiquitous transmembrane transporters, able to extrude a large set of different molecules. They are strongly implicated in antibiotic resistance since they are able to efficiently expel most of the clinically relevant antibiotics from the bacterial cytoplasm. Besides antibiotic resistance, multidrug efflux pumps take part in several important processes of bacterial cell physiology, including cell to cell communication, and contribute to increase the virulence potential of several bacterial pathogens. Here, we focus on the structural and functional role of multidrug efflux pumps belonging to the Major Facilitator Superfamily (MFS), the largest family of transporters, highlighting their involvement in the colonization of host cells, in virulence and in biofilm formation. We will offer an overview on how MFS multidrug transporters contribute to bacterial survival, adaptation and pathogenicity through the export of diverse molecules. This will be done by presenting the functions of several relevant MFS multidrug efflux pumps in human life-threatening bacterial pathogens as Staphylococcus aureus, Listeria monocytogenes, Klebsiella pneumoniae, Shigella/E. coli, Acinetobacter baumannii.
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Affiliation(s)
- Martina Pasqua
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | | | - Giulia Fanelli
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Ryutaro Utsumi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
| | - Yoko Eguchi
- Department of Science and Technology on Food Safety, Kindai University, Kinokawa, Japan
| | - Rita Trirocco
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Milena Grossi
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Bianca Colonna
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
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14
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Kloehn J, Lunghi M, Varesio E, Dubois D, Soldati-Favre D. Untargeted Metabolomics Uncovers the Essential Lysine Transporter in Toxoplasma gondii. Metabolites 2021; 11:metabo11080476. [PMID: 34436417 PMCID: PMC8399914 DOI: 10.3390/metabo11080476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022] Open
Abstract
Apicomplexan parasites are responsible for devastating diseases, including malaria, toxoplasmosis, and cryptosporidiosis. Current treatments are limited by emerging resistance to, as well as the high cost and toxicity of existing drugs. As obligate intracellular parasites, apicomplexans rely on the uptake of many essential metabolites from their host. Toxoplasma gondii, the causative agent of toxoplasmosis, is auxotrophic for several metabolites, including sugars (e.g., myo-inositol), amino acids (e.g., tyrosine), lipidic compounds and lipid precursors (cholesterol, choline), vitamins, cofactors (thiamine) and others. To date, only few apicomplexan metabolite transporters have been characterized and assigned a substrate. Here, we set out to investigate whether untargeted metabolomics can be used to identify the substrate of an uncharacterized transporter. Based on existing genome- and proteome-wide datasets, we have identified an essential plasma membrane transporter of the major facilitator superfamily in T. gondii-previously termed TgApiAT6-1. Using an inducible system based on RNA degradation, TgApiAT6-1 was depleted, and the mutant parasite's metabolome was compared to that of non-depleted parasites. The most significantly reduced metabolite in parasites depleted in TgApiAT6-1 was identified as the amino acid lysine, for which T. gondii is predicted to be auxotrophic. Using stable isotope-labeled amino acids, we confirmed that TgApiAT6-1 is required for efficient lysine uptake. Our findings highlight untargeted metabolomics as a powerful tool to identify the substrate of orphan transporters.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
- Correspondence: (J.K.); (D.S.-F.); Tel.: +41-22-379-57-16 (J.K.); +41-22-379-56-72 (D.S.-F.)
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
| | - Emmanuel Varesio
- Institute of Pharmaceutical Sciences of Western Switzerland, School of Pharmaceutical Sciences, Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, 1211 Geneva, Switzerland;
| | - David Dubois
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
- Correspondence: (J.K.); (D.S.-F.); Tel.: +41-22-379-57-16 (J.K.); +41-22-379-56-72 (D.S.-F.)
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15
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Liu Y, Li C, Gupta M, Verma N, Johri AK, Stroud RM, Voth GA. Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT. Proc Natl Acad Sci U S A 2021; 118:e2101932118. [PMID: 34135124 DOI: 10.1073/pnas.2101932118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphate is an indispensable metabolite in a wide variety of cells and is involved in nucleotide and lipid synthesis, signaling, and chemical energy storage. Proton-coupled phosphate transporters within the major facilitator family are crucial for phosphate uptake in plants and fungi. Similar proton-coupled phosphate transporters have been found in different protozoan parasites that cause human diseases, in breast cancer cells with elevated phosphate demand, in osteoclast-like cells during bone reabsorption, and in human intestinal Caco2BBE cells for phosphate homeostasis. However, the mechanism of proton-driven phosphate transport remains unclear. Here, we demonstrate in a eukaryotic, high-affinity phosphate transporter from Piriformospora indica (PiPT) that deprotonation of aspartate 324 (D324) triggers phosphate release. Quantum mechanics/molecular mechanics molecular dynamics simulations combined with free energy sampling have been employed here to identify the proton transport pathways from D324 upon the transition from the occluded structure to the inward open structure and phosphate release. The computational insights so gained are then corroborated by studies of D45N and D45E amino acid substitutions via mutagenesis experiments. Our findings confirm the function of the structurally predicted cytosolic proton exit tunnel and suggest insights into the role of the titratable phosphate substrate.
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16
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Donzella L, Varela JA, Sousa MJ, Morrissey JP. Identification of novel pentose transporters in Kluyveromyces marxianus using a new screening platform. FEMS Yeast Res 2021; 21:6247623. [PMID: 33890624 PMCID: PMC8110514 DOI: 10.1093/femsyr/foab026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/21/2021] [Indexed: 11/29/2022] Open
Abstract
The capacity of yeasts to assimilate xylose or arabinose is strongly dependent on plasma membrane transport proteins. Because pentoses comprise a substantial proportion of available sugars in lignocellulosic hydrolysates, their utilisation is centrally important for the development of second generation biorefineries. Relatively few native pentose transporters have been studied and there is intense interest in expanding the repertoire. To aid the identification of novel transporters, we developed a screening platform in the native pentose-utilising yeast Kluyveromyces marxianus. This involved the targeted deletion of twelve transporters of the major facilitator superfamily (MFS) and application of a synthetic biology pipeline for rapid testing of candidate pentose transporters. Using this K. marxianus ΔPT platform, we identified several K. marxianus putative xylose or arabinose transporter proteins that recovered a null strain's ability to growth on these pentoses. Four proteins of the HGT-family were able to support growth in media with high or low concentrations of either xylose or arabinose, while six HXT-like proteins displayed growth only at high xylose concentrations, indicating solely low affinity transport activity. The study offers new insights into the evolution of sugar transporters in yeast and expands the set of native pentose transporters for future functional and biotechnological studies.
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Affiliation(s)
- Lorena Donzella
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland.,Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, R. da Universidade, Braga 4710-057, Portugal
| | - Javier A Varela
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland
| | - Maria João Sousa
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, R. da Universidade, Braga 4710-057, Portugal
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland
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17
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Ceder MM, Aggarwal T, Hosseini K, Maturi V, Patil S, Perland E, Williams MJ, Fredriksson R. CG4928 Is Vital for Renal Function in Fruit Flies and Membrane Potential in Cells: A First In-Depth Characterization of the Putative Solute Carrier UNC93A. Front Cell Dev Biol 2020; 8:580291. [PMID: 33163493 PMCID: PMC7591606 DOI: 10.3389/fcell.2020.580291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/16/2020] [Indexed: 01/23/2023] Open
Abstract
The number of transporter proteins that are not fully characterized is immense. Here, we used Drosophila melanogaster and human cell lines to perform a first in-depth characterization of CG4928, an ortholog to the human UNC93A, of which little is known. Solute carriers regulate and maintain biochemical pathways important for the body, and malfunctioning transport is associated with multiple diseases. Based on phylogenetic analysis, CG4928 is closely related to human UNC93A and has a secondary and a tertiary protein structure and folding similar to major facilitator superfamily transporters. Ubiquitous knockdown of CG4928 causes flies to have a reduced secretion rate from the Malpighian tubules; altering potassium content in the body and in the Malpighian tubules, homologous to the renal system; and results in the development of edema. The edema could be rescued by using amiloride, a common diuretic, and by maintaining the flies on ion-free diets. CG4928-overexpressing cells did not facilitate the transport of sugars and amino acids; however, proximity ligation assay revealed that CG4928 co-localized with TASK1 channels. Overexpression of CG4928 resulted in induced apoptosis and cytotoxicity, which could be restored when cells were kept in high-sodium media. Furthermore, the basal membrane potential was observed to be disrupted. Taken together, the results indicate that CG4928 is of importance for generating the cellular membrane potential by an unknown manner. However, we speculate that it most likely acts as a regulator or transporter of potassium flows over the membrane.
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Affiliation(s)
- Mikaela M Ceder
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Tanya Aggarwal
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Kimia Hosseini
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Varun Maturi
- Department of Pharmacy, Drug Delivery, Uppsala University, Uppsala, Sweden
| | - Sourabh Patil
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Emelie Perland
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
| | - Michael J Williams
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Biosciences, Molecular Neuropharmacology, Uppsala University, Uppsala, Sweden
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18
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Tortosa V, Bonaccorsi di Patti MC, Iacovelli F, Pasquadibisceglie A, Falconi M, Musci G, Polticelli F. Dynamical Behavior of the Human Ferroportin Homologue from Bdellovibrio bacteriovorus: Insight into the Ligand Recognition Mechanism. Int J Mol Sci 2020; 21:E6785. [PMID: 32947891 PMCID: PMC7555787 DOI: 10.3390/ijms21186785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023] Open
Abstract
Members of the major facilitator superfamily of transporters (MFS) play an essential role in many physiological processes such as development, neurotransmission, and signaling. Aberrant functions of MFS proteins are associated with several diseases, including cancer, schizophrenia, epilepsy, amyotrophic lateral sclerosis and Alzheimer's disease. MFS transporters are also involved in multidrug resistance in bacteria and fungi. The structures of most MFS members, especially those of members with significant physiological relevance, are yet to be solved. The lack of structural and functional information impedes our detailed understanding, and thus the pharmacological targeting, of these transporters. To improve our knowledge on the mechanistic principles governing the function of MSF members, molecular dynamics (MD) simulations were performed on the inward-facing and outward-facing crystal structures of the human ferroportin homologue from the Gram-negative bacterium Bdellovibrio bacteriovorus (BdFpn). Several simulations with an excess of iron ions were also performed to explore the relationship between the protein's dynamics and the ligand recognition mechanism. The results reinforce the existence of the alternating-access mechanism already described for other MFS members. In addition, the reorganization of salt bridges, some of which are conserved in several MFS members, appears to be a key molecular event facilitating the conformational change of the transporter.
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Affiliation(s)
- Valentina Tortosa
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (A.P.)
| | | | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (F.I.); (M.F.)
| | | | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (F.I.); (M.F.)
| | - Giovanni Musci
- Department Biosciences and Territory, University of Molise, 86090 Pesche, Italy;
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (V.T.); (A.P.)
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
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19
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Seica AFS, Iancu CV, Pfeilschifter B, Madej MG, Choe JY, Hellwig P. Asp 22 drives the protonation state of the Staphylococcus epidermidis glucose/H + symporter. J Biol Chem 2020; 295:15253-15261. [PMID: 32859752 DOI: 10.1074/jbc.ra120.014069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/26/2020] [Indexed: 12/24/2022] Open
Abstract
The Staphylococcus epidermidis glucose/H+ symporter (GlcPSe) is a membrane transporter highly specific for glucose and a homolog of the human glucose transporters (GLUT, SLC2 family). Most GLUTs and their bacterial counterparts differ in the transport mechanism, adopting uniport and sugar/H+ symport, respectively. Unlike other bacterial GLUT homologs (for example, XylE), GlcPSe has a loose H+/sugar coupling. Asp22 is part of the proton-binding site of GlcPSe and crucial for the glucose/H+ co-transport mechanism. To determine how pH variations affect the proton site and the transporter, we performed surface-enhanced IR absorption spectroscopy on the immobilized GlcPSe We found that Asp22 has a pKa of 8.5 ± 0.1, a value consistent with that determined previously for glucose transport, confirming the central role of this residue for the transport mechanism of GlcPSe A neutral replacement of the negatively charged Asp22 led to positive charge displacements over the entire pH range, suggesting that the polarity change of the WT reflects the protonation state of Asp22 We expected that the substitution of the residue Ile105 for a serine, located within hydrogen-bonding distance to Asp22, would change the microenvironment, but the pKa of Asp22 corresponded to that of the WT. A167E mutation, selected in analogy to the XylE, introduced an additional protonatable site and perturbed the protonation state of Asp22, with the latter now exhibiting a pKa of 6.4. These studies confirm that Asp22 is the proton-binding residue in GlcPSe and show that charged residues in its vicinity affect the pKa of glucose/H+ symport.
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Affiliation(s)
- Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France
| | - Cristina V Iancu
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA
| | - Benedikt Pfeilschifter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Regensburg, Germany
| | - M Gregor Madej
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Regensburg, Germany
| | - Jun-Yong Choe
- Department of Chemistry, East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA; Department of Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, USA.
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, Strasbourg, France
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20
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Ceder MM, Lekholm E, Klaesson A, Tripathi R, Schweizer N, Weldai L, Patil S, Fredriksson R. Glucose Availability Alters Gene and Protein Expression of Several Newly Classified and Putative Solute Carriers in Mice Cortex Cell Culture and D. melanogaster. Front Cell Dev Biol 2020; 8:579. [PMID: 32733888 PMCID: PMC7358622 DOI: 10.3389/fcell.2020.00579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Many newly identified solute carriers (SLCs) and putative transporters have the possibility to be intricately involved in glucose metabolism. Here we show that many transporters of this type display a high degree of regulation at both mRNA and protein level following no or low glucose availability in mouse cortex cultures. We show that this is also the case in Drosophila melanogaster subjected to starvation or diets with different sugar content. Interestingly, re-introduction of glucose to media, or refeeding flies, normalized the gene expression of a number of the targets, indicating a fast and highly dynamic control. Our findings demonstrate high conservation of these transporters and how dependent both cell cultures and organisms are on gene and protein regulation during metabolic fluctuations. Several transporter genes were regulated simultaneously maybe to initiate alternative metabolic pathways as a response to low glucose levels, both in the cell cultures and in D. melanogaster. Our results display that newly identified SLCs of Major Facilitator Superfamily type, as well as the putative transporters included in our study, are regulated by glucose availability and could be involved in several cellular aspects dependent of glucose and/or its metabolites. Recently, a correlation between dysregulation of glucose in the central nervous system and numerous diseases such as obesity, type 2 diabetes mellitus as well as neurological disease such as Alzheimer’s and Parkinson’s diseases indicate a complex regulation and fine tuning of glucose levels in the brain. The fact that almost one third of transporters and transporter-related proteins remain orphans with unknown or contradictive substrate profile, location and function, pinpoint the need for further research about them to fully understand their mechanistic role and their impact on cellular metabolism.
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Affiliation(s)
- Mikaela M Ceder
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Emilia Lekholm
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Axel Klaesson
- Pharmaceutical Cell Biology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Rekha Tripathi
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Nadine Schweizer
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Lydia Weldai
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Sourabh Patil
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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21
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Kathare PK, Dharmasiri S, Vincill ED, Routray P, Ahmad I, Roberts DM, Dharmasiri N. Arabidopsis PIC30 encodes a major facilitator superfamily transporter responsible for the uptake of picolinate herbicides. Plant J 2020; 102:18-33. [PMID: 31710151 DOI: 10.1111/tpj.14608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Picloram is an auxinic herbicide that is widely used for controlling broad leaf weeds. However, its mechanism of transport into plants is poorly understood. In a genetic screen for picloram resistance, we identified three Arabidopsis mutant alleles of PIC30 (PICLORAM RESISTANT30) that are specifically resistant to picolinates, but not to other auxins. PIC30 is a previously uncharacterized gene that encodes a major facilitator superfamily (MFS) transporter. Similar to most members of MFS, PIC30 contains 12 putative transmembrane domains, and PIC30-GFP fusion protein selectively localizes to the plasma membrane. In planta transport assays demonstrate that PIC30 specifically transports picloram, but not indole-3-acetic acid (IAA). Functional analysis of Xenopus laevis oocytes injected with PIC30 cRNA demonstrated PIC30 mediated transport of picloram and several anions, including nitrate and chloride. Consistent with these roles of PIC30, three allelic pic30 mutants are selectively insensitive to picolinate herbicides, while pic30-3 is also defective in chlorate (analogue of nitrate) transport and also shows reduced uptake of 15NO3- . Overexpression of PIC30 fully complements both picloram and chlorate insensitive phenotypes of pic30-3. Despite the continued use of picloram as an herbicide, a transporter for picloram was not known until now. This work provides insight into the mechanisms of plant resistance to picolinate herbicides and also shed light on the possible endogenous function of PIC30 protein.
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Affiliation(s)
- Praveen K Kathare
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA
| | - Sunethra Dharmasiri
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666
| | - Eric D Vincill
- Department of Biochemistry, and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Pratyush Routray
- Department of Biochemistry, and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Idrees Ahmad
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666
| | - Daniel M Roberts
- Department of Biochemistry, and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Nihal Dharmasiri
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666
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22
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Jiang Y, Shen Y, Gu L, Wang Z, Su N, Niu K, Guo W, Hou S, Bao X, Tian C, Fang X. Identification and Characterization of an Efficient d-Xylose Transporter in Saccharomyces cerevisiae. J Agric Food Chem 2020; 68:2702-2710. [PMID: 32054270 DOI: 10.1021/acs.jafc.9b07113] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
d-Xylose is the most abundant hemicellulosic monomer on earth, but wild-type Saccharomyces cerevisiae has very limited d-xylose uptake capacity. We conducted bioprospecting for new sugar transporters from the d-xylose-consuming filamentous fungus Trichoderma reesei and identified three candidates belonging to the major facilitator superfamily. When they were expressed in yeast and assayed for d-xylose uptake, one of them, Xltr1p, had d-xylose transport activity that was more efficient than that of Gal2p, an endogenous yeast transporter. Site-directed mutagenesis was used to examine the functional contributions of 13 amino acid residues for the uptake of d-xylose, and these experiments identified particular amino acids that function distinctly in d-xylose vs glucose transport (e.g., F300). Excitingly, the yeast strain expressing the N326FXltr1p variant was able to carry a "high efficiency" transport for d-xylose but was nearly unable to utilize glucose; in contrast, the strain with the F300AXltr1p variant grew on glucose but lost d-xylose transport activity.
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Affiliation(s)
- Yi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- College of Bioengineering, Qilu University of Technology, Jinan 250100, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhenzhen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ning Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Shaoli Hou
- Yantai Huakangrongzan Biotechnology Co., Ltd, Yantai 264006, China
| | - Xiaoming Bao
- College of Bioengineering, Qilu University of Technology, Jinan 250100, China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- National Glycoengineering Research Center, Shandong University, Qingdao, Shandong 266237, China
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Kumar S, Lekshmi M, Parvathi A, Ojha M, Wenzel N, Varela MF. Functional and Structural Roles of the Major Facilitator Superfamily Bacterial Multidrug Efflux Pumps. Microorganisms 2020; 8:E266. [PMID: 32079127 DOI: 10.3390/microorganisms8020266] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogenic microorganisms that are multidrug-resistant can pose severe clinical and public health concerns. In particular, bacterial multidrug efflux transporters of the major facilitator superfamily constitute a notable group of drug resistance mechanisms primarily because multidrug-resistant pathogens can become refractory to antimicrobial agents, thus resulting in potentially untreatable bacterial infections. The major facilitator superfamily is composed of thousands of solute transporters that are related in terms of their phylogenetic relationships, primary amino acid sequences, two- and three-dimensional structures, modes of energization (passive and secondary active), and in their mechanisms of solute and ion translocation across the membrane. The major facilitator superfamily is also composed of numerous families and sub-families of homologous transporters that are conserved across all living taxa, from bacteria to humans. Members of this superfamily share several classes of highly conserved amino acid sequence motifs that play essential mechanistic roles during transport. The structural and functional importance of multidrug efflux pumps that belong to the major facilitator family and that are harbored by Gram-negative and -positive bacterial pathogens are considered here.
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24
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Massa López D, Thelen M, Stahl F, Thiel C, Linhorst A, Sylvester M, Hermanns-Borgmeyer I, Lüllmann-Rauch R, Eskild W, Saftig P, Damme M. The lysosomal transporter MFSD1 is essential for liver homeostasis and critically depends on its accessory subunit GLMP. eLife 2019; 8:50025. [PMID: 31661432 PMCID: PMC6819133 DOI: 10.7554/elife.50025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022] Open
Abstract
Lysosomes are major sites for intracellular, acidic hydrolase-mediated proteolysis and cellular degradation. The export of low-molecular-weight catabolic end-products is facilitated by polytopic transmembrane proteins mediating secondary active or passive transport. A number of these lysosomal transporters, however, remain enigmatic. We present a detailed analysis of MFSD1, a hitherto uncharacterized lysosomal family member of the major facilitator superfamily. MFSD1 is not N-glycosylated. It contains a dileucine-based sorting motif needed for its transport to lysosomes. Mfsd1 knockout mice develop splenomegaly and severe liver disease. Proteomics of isolated lysosomes from Mfsd1 knockout mice revealed GLMP as a critical accessory subunit for MFSD1. MFSD1 and GLMP physically interact. GLMP is essential for the maintenance of normal levels of MFSD1 in lysosomes and vice versa. Glmp knockout mice mimic the phenotype of Mfsd1 knockout mice. Our data reveal a tightly linked MFSD1/GLMP lysosomal membrane protein transporter complex. Lysosomes are specialized, enclosed compartments within cells with harsh chemical conditions where enzymes break down large molecules into smaller component parts. The products of these reactions are then transported out of the lysosome by transporter proteins so that they can be used to build new molecules that the cell needs. Despite their importance, only a few lysosomal transporters have been thoroughly studied. A protein called MFSD1 had previously been identified as a potential lysosomal transporter, but its precise role has not been described. Now, Massa López et al. have characterized the role of MFSD1, by genetically modifying mice so they could no longer make the transporter. These mice developed severe liver damage. In particular, a specific type of cell that is important for lining blood vessels in the liver, seemed to be lost in these mice. Older MFSD1 deficient mice also had more tumors in their livers compared to normal mice. Massa López et al. next examined what happened to other lysosomal proteins in the MFSD1 deficient mice, and found that these mice had strikingly low levels of a protein called GLMP. To better understand the relationship between GLMP and MFSD1, another strain of genetically modified mice was analyzed, this time missing GLMP. Mice without GLMP were found to have very similar liver problems to those observed in the mice lacking MFSD1. Moreover, the GLMP deficient mice had low levels of the MFSD1 protein. Further experiments demonstrated that MFSD1 and GLMP physically interact with each other: GLMP seemed to protect MFSD1 from being degraded in the harsh internal environment of the lysosome. Thus both GLMP and MFSD1 were needed to form a stable lysosomal transporter. Characterizing MFSD1 is important for scientists attempting to understand how the lysosomal membrane and transporters work. Moreover, these findings may shed light on how defects in lysosomal transporters contribute to metabolic disease.
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Affiliation(s)
- David Massa López
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Melanie Thelen
- Institute for Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, Germany
| | - Felix Stahl
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department of Pediatrics I, University of Heidelberg, Heidelberg, Germany
| | - Arne Linhorst
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Marc Sylvester
- Institute for Biochemistry and Molecular Biology, Rheinische-Friedrich-Wilhelms-University, Bonn, Germany
| | - Irm Hermanns-Borgmeyer
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Winnie Eskild
- Department of Bioscience, University of Oslo, Oslo, Norway
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Markus Damme
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
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25
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Sarikhani MR, Malboobi MA, Aliasgharzad N, Greiner R. Identification of two novel bacterial phosphatase-encoding genes in Pseudomonas putida strain P13. J Appl Microbiol 2019; 127:1113-1124. [PMID: 31287935 DOI: 10.1111/jam.14376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/23/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
AIMS Isolation and identification of genes encoding putative phosphatases from Pseudomonas putida strain P13 DSM 23335. METHODS AND RESULTS By functional screening of a P. putida P13 genomic library, a number of Pho+ clones were identified. Two genes were identified that encoded proteins exhibiting both phytase and sugar phosphatase activities. The proteins were 249 and 462 amino acids, with molecular masses of 26 and 50 kDa respectively. Sequence alignments revealed no significant similarities to representatives of known phosphatase or phytase gene families. However, the genes were found to have a high similarity to members of the major facilitator superfamily (MFS). Both genes were overexpressed in Escherichia coli and the corresponding partially purified recombinant enzymes were found to have significant phytate-dephosphorylating activity. The protein designated P. putida phytase 1 (Ppp1) displayed the highest activity among potential substrates studied on Na phytate, whereas Ppp2 more likely represents a sugar phosphatase than a phytase. The optimal conditions for phytate dephosphorylation were determined as 60°C and pH 4·5 (Ppp1) or pH 5·0 (Ppp2). CONCLUSIONS Two novel bacterial phosphatase-encoding genes, named ppp1 and ppp2, were isolated from P. putida P13 DSM 23335 by a functional screening procedure. SIGNIFICANCE AND IMPACT OF THE STUDY Phosphatase-encoding genes are of great importance for industrial applications, particularly in agriculture. The identified phosphatase genes represent a new class of acid phosphatases.
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Affiliation(s)
- M R Sarikhani
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - M A Malboobi
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - N Aliasgharzad
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - R Greiner
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
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26
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Nagamura R, Fukuda M, Kawamoto A, Matoba K, Dohmae N, Ishitani R, Takagi J, Nureki O. Structural basis for oligomerization of the prokaryotic peptide transporter PepT So2. Acta Crystallogr F Struct Biol Commun 2019; 75:348-358. [PMID: 31045564 PMCID: PMC6497099 DOI: 10.1107/s2053230x19003546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022]
Abstract
Using cryo-EM and X-ray crystallography, the atomic resolution structure of the tetrameric form of the proton-dependent oligopeptide transporter PepTSo2 was determined and the novel oligomerization mechanism was revealed. Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. The human POTs PepT1 and PepT2 are also involved in the absorption of various orally ingested drugs. Previously reported structures revealed that the bacterial POTs possess 14 helices, of which H1–H6 and H7–H12 constitute the typical MFS fold and the residual two helices are involved in the cytoplasmic linker. PepTSo2 from Shewanella oneidensis is a unique POT which reportedly assembles as a 200 kDa tetramer. Although the previously reported structures suggested the importance of H12 for tetramer formation, the structural basis for the PepTSo2-specific oligomerization remains unclear owing to the lack of a high-resolution tetrameric structure. In this study, the expression and purification conditions for tetrameric PepTSo2 were optimized. A single-particle cryo-EM analysis revealed the tetrameric structure of PepTSo2 incorporated into Salipro nanoparticles at 4.1 Å resolution. Furthermore, a combination of lipidic cubic phase (LCP) crystallization and an automated data-processing system for multiple microcrystals enabled crystal structures of PepTSo2 to be determined at resolutions of 3.5 and 3.9 Å. The present structures in a lipid bilayer revealed the detailed mechanism for the tetrameric assembly of PepTSo2, in which a characteristic extracellular loop (ECL) interacts with two asparagine residues on H12 which were reported to be important for tetramerization and plays an essential role in oligomeric assembly. This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins.
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Affiliation(s)
- Reina Nagamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kyoko Matoba
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naoshi Dohmae
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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27
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Valoskova K, Biebl J, Roblek M, Emtenani S, Gyoergy A, Misova M, Ratheesh A, Reis-Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife 2019; 8:e41801. [PMID: 30910009 PMCID: PMC6435326 DOI: 10.7554/elife.41801] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva's vertebrate ortholog, MFSD1, rescues the minerva mutant's migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.
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Affiliation(s)
| | - Julia Biebl
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Marko Roblek
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Shamsi Emtenani
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Attila Gyoergy
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Michaela Misova
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Aparna Ratheesh
- Institute of Science and Technology AustriaKlosterneuburgAustria
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical SchoolUniversity of WarwickCoventryUnited Kingdom
| | | | | | - Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Daria E Siekhaus
- Institute of Science and Technology AustriaKlosterneuburgAustria
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28
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Willson BJ, Dalzell L, Chapman LNM, Thomas GH. Enhanced functionalisation of major facilitator superfamily transporters via fusion of C-terminal protein domains is both extensive and varied in bacteria. Microbiology (Reading) 2019; 165:419-424. [PMID: 30657446 DOI: 10.1099/mic.0.000771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The evolution of gene fusions that result in covalently linked protein domains is widespread in bacteria, where spatially coupling domain functionalities can have functional advantages in vivo. Fusions to integral membrane proteins are less widely studied but could provide routes to enhance membrane function in synthetic biology. We studied the major facilitator superfamily (MFS), as the largest family of transporter proteins in bacteria, to examine the extent and nature of fusions to these proteins. A remarkably diverse variety of fusions are identified and the 8 most abundant examples are described, including additional enzymatic domains and a range of sensory and regulatory domains, many not previously described. Significantly, these fusions are found almost exclusively as C-terminal fusions, revealing that the usually cytoplasmic C-terminal end of MFS protein would the permissive end for engineering synthetic fusions to other cytoplasmic proteins.
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Affiliation(s)
- Benjamin J Willson
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Lindsey Dalzell
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Liam N M Chapman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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29
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Varela JA, Puricelli M, Montini N, Morrissey JP. Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus. Front Microbiol 2019; 9:3330. [PMID: 30687296 PMCID: PMC6335341 DOI: 10.3389/fmicb.2018.03330] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 11/24/2022] Open
Abstract
In yeasts, proteins of the Major Superfamily Transporter selectively bind and allow the uptake of sugars to permit growth on varied substrates. The genome of brewer’s yeast, Saccharomyces cerevisiae, encodes multiple hexose transporters (Hxt) to transport glucose and other MFS proteins for maltose, galactose, and other monomers. For sugar uptake, the dairy yeast, Kluyveromyces lactis, uses Rag1p for glucose, Hgt1 for glucose and galactose, and Lac12 for lactose. In the related industrial species Kluyveromyces marxianus, there are four genes encoding Lac12-like proteins but only one of them, Lac12, can transport lactose. In this study, which initiated with efforts to investigate possible functions encoded by the additional LAC12 genes in K. marxianus, a genome-wide survey of putative MFS sugar transporters was performed. Unexpectedly, it was found that the KHT and the HGT genes are present as tandem arrays of five to six copies, with the precise number varying between isolates. Heterologous expression of individual genes in S. cerevisiae and mutagenesis of single and multiple genes in K. marxianus was performed to establish possible substrates for these transporters. The focus was on the sugar galactose since it was already reported in K. lactis that this hexose was a substrate for both Lac12 and Hgt1. It emerged that three of the four copies of Lac12, four Hgt-like proteins and one Kht-like protein have some capacity to transport galactose when expressed in S. cerevisiae and inactivation of all eight genes was required to completely abolish galactose uptake in K. marxianus. Analysis of the amino acid sequence of all known yeast galactose transporters failed to identify common residues that explain the selectivity for galactose. Instead, the capacity to transport galactose has arisen three different times in K. marxianus via polymorphisms in proteins that are probably ancestral glucose transporters. Although, this is analogous to S. cerevisiae, in which Gal2 is related to glucose transporters, there are not conserved amino acid changes, either with Gal2, or among the K. marxianus galactose transporters. The data highlight how gene duplication and functional diversification has provided K. marxianus with versatile capacity to utilise sugars for growth.
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Affiliation(s)
- Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Martina Puricelli
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Noemi Montini
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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30
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Liao YY, Li JL, Pan RL, Chiou TJ. Structure-Function Analysis Reveals Amino Acid Residues of Arabidopsis Phosphate Transporter AtPHT1;1 Crucial for Its Activity. Front Plant Sci 2019; 10:1158. [PMID: 31608095 PMCID: PMC6761603 DOI: 10.3389/fpls.2019.01158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/26/2019] [Indexed: 05/05/2023]
Abstract
Phosphorus (P), an essential plant macronutrient, is acquired in the form of inorganic phosphate (Pi) by transporters located at the plasma membrane of root cells. To decipher the Pi transport mechanism, Arabidopsis thaliana Pi transporter 1;1 (AtPHT1;1), the most predominantly H+-coupled Pi co-transporter in the root, was selected for structure-function analysis. We first predicted its secondary and tertiary structures on the basis of the Piriformospora indica Pi transporter (PiPT) and identified 28 amino acid residues potentially engaged in the activity of AtPHT1;1. We then mutagenized these residues into alanine and expressed them in the yeast pam2 mutant defective in high-affinity Pi transporters and Arabidopsis pht1;1 mutant, respectively, for functional complementation validation. We further incorporated the functional characterization and structure analyses to propose a mechanistic model for the function of AtPHT1;1. We showed that D35, D38, R134, and D144, implicated in H+ transfer across the membrane, and Y312 and N421, involved in initial interaction and translocation of Pi, are all essential for its transport activity. When Pi enters the binding pocket, the two aromatic moieties of Y145 and F169 and the hydrogen bonds generated from Q172, W304, Y312, D308, and K449 can build a scaffold to stabilize the structure. Subsequent interaction between Pi and the positive residue of K449 facilitates its release. Furthermore, D38, D93, R134, D144, D212, R216, R233, D367, K373, and E504 may form internal electrostatic interactions for structure ensemble and adaptability. This study offers a comprehensive model for elucidating the transport mechanism of a plant Pi transporter.
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Affiliation(s)
- Ya-Yun Liao
- Department of Life Science, Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Jia-Ling Li
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Rong-Long Pan
- Department of Life Science, Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
- *Correspondence: Tzyy-Jen Chiou, ; Rong-Long Pan,
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- *Correspondence: Tzyy-Jen Chiou, ; Rong-Long Pan,
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31
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Lin Y, Deepak RNVK, Zheng JZ, Fan H, Zheng L. A dual substrate-accessing mechanism of a major facilitator superfamily protein facilitates lysophospholipid flipping across the cell membrane. J Biol Chem 2018; 293:19919-19931. [PMID: 30373772 DOI: 10.1074/jbc.ra118.005548] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/23/2018] [Indexed: 11/06/2022] Open
Abstract
Lysophospholipid transporter (LplT) is a member of the major facilitator superfamily present in many Gram-negative bacteria. LplT catalyzes flipping of lysophospholipids (LPLs) across the bacterial inner membrane, playing an important role in bacterial membrane homeostasis. We previously reported that LplT promotes both uptake of exogenous LPLs and intramembranous LPL flipping across the bilayer. To gain mechanistic insight into this dual LPL-flipping activity, here we implemented a combination of computational approaches and LPL transport analyses to study LPL binding of and translocation by LplT. Our results suggest that LplT translocates LPLs through an elongated cavity exhibiting an extremely asymmetric polarity. We found that two D(E)N motifs form a head group-binding site, in which the carboxylate group of Asp-30 is important for LPL head group recognition. Substitutions of residues in the head group-binding site disrupted both LPL uptake and flipping activities. However, alteration of hydrophobic residues on the interface between the N- and C-terminal domains impaired LPL flipping specifically, resulting in LPLs accumulation in the membrane, but LPL uptake remained active. These results suggest a dual substrate-accessing mechanism, in which LplT recruits LPLs to its substrate-binding site via two routes, either from its extracellular entry or through a membrane-embedded groove between transmembrane helices, and then moves them toward the inner membrane leaflet. This LPL-flipping mechanism is likely conserved in many bacterial species, and our findings illustrate how LplT adjusts the major facilitator superfamily translocation pathway to perform its versatile lipid homeostatic functions.
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Affiliation(s)
- Yibin Lin
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030
| | - R N V Krishna Deepak
- the Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671 Singapore, and
| | - Jonathan Zixiang Zheng
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030
| | - Hao Fan
- the Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671 Singapore, and .,the Department of Biological Sciences (DBS), National University of Singapore, 117558 Singapore, and Center for Computational Biology, DUKE-NUS Medical School, 169857 Singapore
| | - Lei Zheng
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, the University of Texas Health Science Center at Houston McGovern Medical School, Houston Texas 77030,
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32
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Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 2018; 210:219-234. [PMID: 30045857 PMCID: PMC6116967 DOI: 10.1534/genetics.118.301161] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/23/2018] [Indexed: 01/20/2023] Open
Abstract
Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.
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Affiliation(s)
- Douglas A Higgins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Megan K M Young
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Mary Tremaine
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Maria Sardi
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Jenna M Fletcher
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Margaret Agnew
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Lisa Liu
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Quinn Dickinson
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - David Peris
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Russell L Wrobel
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Chris Todd Hittinger
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Audrey P Gasch
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Steven W Singer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California 94720
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Robert Landick
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53726
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53726
| | - Michael P Thelen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Trey K Sato
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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33
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Abdel-Motaal H, Meng L, Zhang Z, Abdelazez AH, Shao L, Xu T, Meng F, Abozaed S, Zhang R, Jiang J. An Uncharacterized Major Facilitator Superfamily Transporter From Planococcus maritimus Exhibits Dual Functions as a Na +(Li +, K +)/H + Antiporter and a Multidrug Efflux Pump. Front Microbiol 2018; 9:1601. [PMID: 30061877 PMCID: PMC6055358 DOI: 10.3389/fmicb.2018.01601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 02/01/2023] Open
Abstract
Within major facilitator superfamily (MFS), up to 27 unknown major facilitator families and many members of 60 well-characterized families have been functionally unknown as yet, due to their sharing no or significantly low sequence identity with characterized MFS members. Here we present the first report on the characterization of one functionally unknown MFS transporter designated MdrP with the accession version No. ANU18183.1 from the slight halophile Planococcus maritimus DS 17275T. During the screening of Na+/H+ antiporter genes, we found at first that MdrP exhibits Na+(Li+, K+)/H+ antiport activity, and propose that it should represent a novel class of Na+(Li+, K+)/H+ antiporters. However, we speculate that MdrP may possess an additional protein function. The existence of the signature Motif A of drug/H+antiporter (DHA) family members and phylogenetic analysis suggest that MdrP may also function as a drug efflux pump, which was established by minimum inhibitory concentration tests and drug efflux activity assays. Taken together, this novel MFS transporter exhibits dual functions as a Na+(Li+, K+)/H+ antiporter and a multidrug efflux pump, which will be very helpful to not only positively contribute to the function prediction of uncharacterized MFS members especially DHA1 family ones, but also broaden the knowledge of Na+/H+ antiporters.
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Affiliation(s)
- Heba Abdel-Motaal
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China.,Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Lin Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Zhenglai Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Amro H Abdelazez
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Li Shao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Tong Xu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Fankui Meng
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Shaima Abozaed
- Department of Microbiology, Agriculture Research Center, Soils, Water, Environment and Microbiology Research Institute, Giza, Egypt
| | - Rui Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Juquan Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, and Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
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Perland E, Bagchi S, Klaesson A, Fredriksson R. Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression. Open Biol 2018; 7:rsob.170142. [PMID: 28878041 PMCID: PMC5627054 DOI: 10.1098/rsob.170142] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/31/2017] [Indexed: 12/21/2022] Open
Abstract
Solute carriers (SLCs) are vital as they are responsible for a major part of the molecular transport over lipid bilayers. At present, there are 430 identified SLCs, of which 28 are called atypical SLCs of major facilitator superfamily (MFS) type. These are MFSD1, 2A, 2B, 3, 4A, 4B, 5, 6, 6 L, 7, 8, 9, 10, 11, 12, 13A, 14A and 14B; SV2A, SV2B and SV2C; SVOP and SVOPL; SPNS1, SPNS2 and SPNS3; and UNC93A and UNC93B1. We studied their fundamental properties, and we also included CLN3, an atypical SLC not yet belonging to any protein family (Pfam) clan, because its involvement in the same neuronal degenerative disorders as MFSD8. With phylogenetic analyses and bioinformatic sequence comparisons, the proteins were divided into 15 families, denoted atypical MFS transporter families (AMTF1-15). Hidden Markov models were used to identify orthologues from human to Drosophila melanogaster and Caenorhabditis elegans Topology predictions revealed 12 transmembrane segments (for all except CLN3), corresponding to the common MFS structure. With single-cell RNA sequencing and in situ proximity ligation assay on brain cells, co-expressions of several atypical SLCs were identified. Finally, the transcription levels of all genes were analysed in the hypothalamic N25/2 cell line after complete amino acid starvation, showing altered expression levels for several atypical SLCs.
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Affiliation(s)
- Emelie Perland
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Sonchita Bagchi
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Axel Klaesson
- Pharmaceutical Cell Biology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Molecular Neuropharmacology, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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35
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Vu BG, Moye-Rowley WS. Construction and Use of a Recyclable Marker To Examine the Role of Major Facilitator Superfamily Protein Members in Candida glabrata Drug Resistance Phenotypes. mSphere 2018; 3:e00099-18. [PMID: 29600281 DOI: 10.1128/mSphere.00099-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 11/27/2022] Open
Abstract
Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins. Candida glabrata is the second most common species causing candidiasis. C. glabrata can also readily acquire resistance to azole drugs, complicating its treatment. Here we add to the collection of disruption markers to aid in genetic analysis of this yeast. This new construct is marked with a nourseothricin resistance cassette that produces an estrogen-activated form of Cre recombinase in a methionine-regulated manner. This allows eviction and reuse of this cassette in a facile manner. Using this new disruption marker, we have constructed a series of strains lacking different members of the major facilitator superfamily (MFS) of membrane transporter proteins. The presence of 15 MFS proteins that may contribute to drug resistance in C. glabrata placed a premium on development of a marker that could easily be reused to construct multiple gene-disrupted strains. Employing this recyclable marker, we found that loss of the MFS transporter-encoding gene FLR1 caused a dramatic increase in diamide resistance (as seen before), and deletion of two other MFS-encoding genes did not influence this phenotype. Interestingly, loss of FLR1 led to an increase in levels of oxidized glutathione, suggesting a possible molecular explanation for this enhanced oxidant sensitivity. We also found that while overproduction of the transcription factor Yap1 could suppress the fluconazole sensitivity caused by loss of the important ATP-binding cassette transporter protein Cdr1, this required the presence of FLR1. IMPORTANCE Export of drugs is a problem for chemotherapy of infectious organisms. A class of membrane proteins called the major facilitator superfamily contains a large number of proteins that often elevate drug resistance when overproduced but do not impact this phenotype when the gene is removed. We wondered if this absence of a phenotype for a disruption allele might be due to the redundancy of this group of membrane proteins. We describe the production of an easy-to-use recyclable marker cassette that will allow construction of strains lacking multiple members of the MFS family of transporter proteins.
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36
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Zomot E, Yardeni EH, Vargiu AV, Tam HK, Malloci G, Ramaswamy VK, Perach M, Ruggerone P, Pos KM, Bibi E. A New Critical Conformational Determinant of Multidrug Efflux by an MFS Transporter. J Mol Biol 2018. [PMID: 29530612 DOI: 10.1016/j.jmb.2018.02.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Secondary multidrug (Mdr) transporters utilize ion concentration gradients to actively remove antibiotics and other toxic compounds from cells. The model Mdr transporter MdfA from Escherichia coli exchanges dissimilar drugs for protons. The transporter should open at the cytoplasmic side to enable access of drugs into the Mdr recognition pocket. Here we show that the cytoplasmic rim around the Mdr recognition pocket represents a previously overlooked important regulatory determinant in MdfA. We demonstrate that increasing the positive charge of the electrically asymmetric rim dramatically inhibits MdfA activity and sometimes even leads to influx of planar, positively charged compounds, resulting in drug sensitivity. Our results suggest that unlike the mutants with the electrically modified rim, the membrane-embedded wild-type MdfA exhibits a significant probability of an inward-closed conformation, which is further increased by drug binding. Since MdfA binds drugs from its inward-facing environment, these results are intriguing and raise the possibility that the transporter has a sensitive, drug-induced conformational switch, which favors an inward-closed state.
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Affiliation(s)
- Elia Zomot
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eliane Hadas Yardeni
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Heng-Keat Tam
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | | | - Michal Perach
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Eitan Bibi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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Balzano PM, Cunningham AL, Grassel C, Barry EM. Deletion of the Major Facilitator Superfamily Transporter fptB Alters Host Cell Interactions and Attenuates Virulence of Type A Francisella tularensis. Infect Immun 2018; 86:e00832-17. [PMID: 29311235 DOI: 10.1128/IAI.00832-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022] Open
Abstract
Francisella tularensis is a Gram-negative, facultative, intracellular coccobacillus that can infect a wide variety of hosts. In humans, F. tularensis causes the zoonosis tularemia following insect bites, ingestion, inhalation, and the handling of infected animals. The fact that a very small inoculum delivered by the aerosol route can cause severe disease, coupled with the possibility of its use as an aerosolized bioweapon, has led to the classification of Francisella tularensis as a category A select agent and has renewed interest in the formulation of a vaccine. To this end, we engineered a type A strain SchuS4 derivative containing a targeted deletion of the major facilitator superfamily (MFS) transporter fptB. Based on the attenuating capacity of this deletion in the F. tularensis LVS background, we hypothesized that the deletion of this transporter would alter the intracellular replication and cytokine induction of the type A strain and attenuate virulence in the stringent C57BL/6J mouse model. Here we demonstrate that the deletion of fptB significantly alters the intracellular life cycle of F. tularensis, attenuating intracellular replication in both cell line-derived and primary macrophages and inducing a novel cytosolic escape delay. Additionally, we observed prominent differences in the in vitro cytokine profiles in human macrophage-like cells. The mutant was highly attenuated in the C57BL/6J mouse model and provided partial protection against virulent type A F. tularensis challenge. These results indicate a fundamental necessity for this nutrient transporter in the timely progression of F. tularensis through its replication cycle and in pathogenesis.
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38
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Martinez Molledo M, Quistgaard EM, Flayhan A, Pieprzyk J, Löw C. Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Structure 2018; 26:467-476.e4. [PMID: 29429879 DOI: 10.1016/j.str.2018.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/22/2017] [Accepted: 01/10/2018] [Indexed: 12/27/2022]
Abstract
Proton-dependent oligopeptide transporters (POTs) are important for uptake of dietary di- and tripeptides in many organisms, and in humans are also involved in drug absorption. These transporters accept a wide range of substrates, but the structural basis for how different peptide side chains are accommodated has so far remained obscure. Twenty-eight peptides were screened for binding to PepTSt from Streptococcus thermophilus, and structures were determined of PepTSt in complex with four physicochemically diverse dipeptides, which bind with millimolar affinity: Ala-Leu, Phe-Ala, Ala-Gln, and Asp-Glu. The structures show that PepTSt can adapt to different peptide side chains through movement of binding site residues and water molecules, and that a good fit can be further aided by adjustment of the position of the peptide itself. Finally, structures were also determined in complex with adventitiously bound HEPES, polyethylene glycol, and phosphate molecules, which further underline the adaptability of the binding site. Dipeptides can adapt their position to best fit the PepTSt binding site The PepTSt binding site can adapt its structure to best fit the dipeptides The water network in the PepTSt binding site can adapt to best fit the dipeptides Aromatic binding site residues play a role in conferring PepTSt multispecificity
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39
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Perez AM, Gomez MM, Kalvapalle P, O'Brien-Gilbert E, Bennett MR, Shamoo Y. Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer. Mol Syst Biol 2017; 13:964. [PMID: 29273640 PMCID: PMC5740499 DOI: 10.15252/msb.20177635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection. Here, we present a physiological model that uses cellular fitness as a proxy to predict the biochemical properties of the MFS tetracycline efflux pump, TetB, and a family of single amino acid variants. We determined two lumped biochemical parameters roughly describing Km and Vmax for TetB and variants. Including in vivo protein levels into our model allowed for more specified prediction of pump parameters relating to substrate binding affinity and pumping efficiency for TetB and variants. We further demonstrated the general utility of our model by solely using fitness to assay a library of tet(B) variants and estimate their biochemical properties.
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Affiliation(s)
- Anisha M Perez
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Marcella M Gomez
- Department of Applied Mathematics & Statistics, University of California, Santa Cruz, CA, USA
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | | | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, TX, USA
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40
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Parker JL, Li C, Brinth A, Wang Z, Vogeley L, Solcan N, Ledderboge-Vucinic G, Swanson JMJ, Caffrey M, Voth GA, Newstead S. Proton movement and coupling in the POT family of peptide transporters. Proc Natl Acad Sci U S A 2017; 114:13182-7. [PMID: 29180426 DOI: 10.1073/pnas.1710727114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate.
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41
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Forget SM, McVey J, Vining LC, Jakeman DL. Streptomyces venezuelae ISP5230 Maintains Excretion of Jadomycin upon Disruption of the MFS Transporter JadL Located within the Natural Product Biosynthetic Gene Cluster. Front Microbiol 2017; 8:432. [PMID: 28377749 PMCID: PMC5359229 DOI: 10.3389/fmicb.2017.00432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/01/2017] [Indexed: 11/19/2022] Open
Abstract
JadL was identified as a Major Facilitator Superfamily (MFS) transporter (T.C. 2.A.1) through sequence homology. The protein is encoded by jadL, situated within the jadomycin biosynthetic gene cluster. JadL has, therefore, been assigned a putative role in host defense by exporting its probable substrates, the jadomycins, a family of secondary metabolites produced by Streptomyces venezuelae ISP5230. Herein, we evaluate this assumption through the construction and analysis of a jadL disrupted mutant, S. venezuelae VS678 (ΔjadL::aac(3)IV). Quantitative determination of jadomycin production with the jadL disrupted mutant did not show a significant decrease in production in comparison to the wildtype strain, as determined by HPLC and by tandem mass spectrometry. These results suggest that efflux of jadomycin occurs upon disruption of jadL, or that JadL is not involved in jadomycin efflux. Potentially, other transporters within S. venezuelae ISP5230 may adopt this role upon inactivation of JadL to export jadomycins.
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Affiliation(s)
| | - Jennifer McVey
- Department of Biology, Dalhousie University Halifax, NS, Canada
| | - Leo C Vining
- Department of Biology, Dalhousie University Halifax, NS, Canada
| | - David L Jakeman
- Department of Chemistry, Dalhousie UniversityHalifax, NS, Canada; College of Pharmacy, Dalhousie UniversityHalifax, NS, Canada
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42
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Nieves-Morión M, Lechno-Yossef S, López-Igual R, Frías JE, Mariscal V, Nürnberg DJ, Mullineaux CW, Wolk CP, Flores E. Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120. J Bacteriol 2017; 199:e00876-16. [PMID: 28096449 DOI: 10.1128/JB.00876-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 12/26/2022] Open
Abstract
When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO2 through oxygenic photosynthesis and heterocysts that are specialized in N2 fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of Anabaena mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of Anabaena was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in Anabaena, glucoside transporters influence the structure and function of septal junctions.IMPORTANCE Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO2 and N2 These organisms grow as filaments that fix these gases specifically in vegetative cells and heterocysts, respectively. For the filaments to grow, these types of cells exchange nutrients, including sucrose, which serves as a source of reducing power and of carbon skeletons for the heterocysts. Movement of sucrose between cells in the filament takes place through septal junctions and has been traced with a fluorescent sucrose analog, esculin, that can be taken up by the cells. Here, we identified α-glucoside transporters of Anabaena that mediate uptake of esculin and, notably, influence septal structure and the function of septal junctions.
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Perland E, Fredriksson R. Classification Systems of Secondary Active Transporters. Trends Pharmacol Sci 2016; 38:305-315. [PMID: 27939446 DOI: 10.1016/j.tips.2016.11.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 01/01/2023]
Abstract
Membrane-bound solute carrier (SLC) transporter proteins are vital to the human body, as they sustain homeostasis by moving soluble molecule as nutrients, drugs, and waste across lipid membranes. Of the 430 identified secondary active transporters in humans, 30% are still orphans, and systematic research has been requested to elaborate on their possible involvement in diseases and their potential as drug targets. To enable this, the various classification systems in use must be understood and used correctly. In this review, we describe how various classification systems for human SLCs are constructed, and how they overlap and differ. To facilitate communication between researchers and to avoid ambiguities, everyone must clearly state which classification system they are referring to when writing scientific articles.
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Affiliation(s)
- Emelie Perland
- Department of Pharmaceutical Bioscience, Molecular Neuropharmacology, Uppsala University, Uppsala SE 7512, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Bioscience, Molecular Neuropharmacology, Uppsala University, Uppsala SE 7512, Sweden.
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44
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Affiliation(s)
- Anke Reinders
- Department of Plant Biology, University of Minnesota, 140 Gortner Labs, 1479 Gortner Ave., St Paul, MN 55108, USA
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45
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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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46
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Abstract
Nitrate ([Formula: see text]) is one of the most important sources of mineral nitrogen, which also serves as a key signaling molecule for plant growth and development. To cope with nitrate fluctuation in soil that varies by up to four orders of magnitude, plants have evolved high- and low-affinity nitrate transporter systems, consisting of distinct families of transporters. Interestingly, the first cloned nitrate transporter in Arabidopsis, NRT1.1 functions as a dual-affinity transporter, which can change its affinity for nitrate in response to substrate availability. Phosphorylation of a threonine residue, Thr101, switches NRT1.1 from low- to high-affinity state. Recent structural studies have unveiled that the unmodified NRT1.1 transporter works as homodimers with Thr101 located in close proximity to the dimer interface. Modification on the Thr101 residue is shown to not only decouple the dimer configuration, but also increase structural flexibility, thereby, altering the substrate affinity of NRT1.1. The structure of NRT1.1 helps establish a novel paradigm in which protein oligomerzation and posttranslational modification can synergistically expand the functional capacity of the major facilitator superfamily (MFS) transporters.
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Affiliation(s)
- Ji Sun
- Department of Pharmacology, University of Washington Seattle, WA, USA
| | - Ning Zheng
- Department of Pharmacology, University of WashingtonSeattle, WA, USA; Howard Hughes Medical Institute, University of WashingtonSeattle, WA, USA
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47
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Kumar H, Finer-Moore JS, Kaback HR, Stroud RM. Structure of LacY with an α-substituted galactoside: Connecting the binding site to the protonation site. Proc Natl Acad Sci U S A 2015; 112:9004-9. [PMID: 26157133 PMCID: PMC4517220 DOI: 10.1073/pnas.1509854112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The X-ray crystal structure of a conformationally constrained mutant of the Escherichia coli lactose permease (the LacY double-Trp mutant Gly-46→Trp/Gly-262→Trp) with bound p-nitrophenyl-α-d-galactopyranoside (α-NPG), a high-affinity lactose analog, is described. With the exception of Glu-126 (helix IV), side chains Trp-151 (helix V), Glu-269 (helix VIII), Arg-144 (helix V), His-322 (helix X), and Asn-272 (helix VIII) interact directly with the galactopyranosyl ring of α-NPG to provide specificity, as indicated by biochemical studies and shown directly by X-ray crystallography. In contrast, Phe-20, Met-23, and Phe-27 (helix I) are within van der Waals distance of the benzyl moiety of the analog and thereby increase binding affinity nonspecifically. Thus, the specificity of LacY for sugar is determined solely by side-chain interactions with the galactopyranosyl ring, whereas affinity is increased by nonspecific hydrophobic interactions with the anomeric substituent.
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Affiliation(s)
- Hemant Kumar
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Janet S Finer-Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, CA 90095
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
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48
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Fischer J, Kleinau G, Müller A, Kühnen P, Zwanziger D, Kinne A, Rehders M, Moeller LC, Führer D, Grüters A, Krude H, Brix K, Biebermann H. Modulation of monocarboxylate transporter 8 oligomerization by specific pathogenic mutations. J Mol Endocrinol 2015; 54:39-50. [PMID: 25527620 DOI: 10.1530/jme-14-0272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The monocarboxylate transporter 8 (MCT8) is a member of the major facilitator superfamily (MFS). These membrane-spanning proteins facilitate translocation of a variety of substrates, MCT8 specifically transports iodothyronines. Mutations in MCT8 are the underlying cause of severe X-linked psychomotor retardation. At the molecular level, such mutations led to deficiencies in substrate translocation due to reduced cell-surface expression, impaired substrate binding, or decreased substrate translocation capabilities. However, the causal relationships between genotypes, molecular features of mutated MCT8, and patient characteristics have not yet been comprehensively deciphered. We investigated the relationship between pathogenic mutants of MCT8 and their capacity to form dimers (presumably oligomeric structures) as a potential regulatory parameter of the transport function of MCT8. Fourteen pathogenic variants of MCT8 were investigated in vitro with respect to their capacity to form oligomers. Particular mutations close to the substrate translocation channel (S194F, A224T, L434W, and R445C) were found to inhibit dimerization of MCT8. This finding is in contrast to those for other transporters or transmembrane proteins, in which substitutions predominantly at the outer-surface inhibit oligomerization. Moreover, specific mutations of MCT8 located in transmembrane helix 2 (del230F, V235M, and ins236V) increased the capacity of MCT8 variants to dimerize. We analyzed the localization of MCT8 dimers in a cellular context, demonstrating differences in MCT8 dimer formation and distribution. In summary, our results add a new link between the functions (substrate transport) and protein organization (dimerization) of MCT8, and might be of relevance for other members of the MFS. Finally, the findings are discussed in relationship to functional data combined with structural-mechanistical insights into MCT8.
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Affiliation(s)
- Jana Fischer
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Gunnar Kleinau
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Anne Müller
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Peter Kühnen
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Denise Zwanziger
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Anita Kinne
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Maren Rehders
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Lars C Moeller
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Dagmar Führer
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Annette Grüters
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Heiko Krude
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Klaudia Brix
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
| | - Heike Biebermann
- Institut für Experimentelle Pädiatrische EndokrinologieCharité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, GermanyLeibniz-Institut für Molekulare PharmakologieBerlin, GermanyUniversitätsklinikum EssenKlinik für Endokrinologie und Stoffwechselerkrankungen, Essen, GermanyJacobs University BremenBremen, Germany
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49
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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 Cell Mol Biol 2015; 10:131-140. [PMID: 27065631 PMCID: PMC4822553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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Yan N. Structural Biology of the Major Facilitator Superfamily Transporters. Annu Rev Biophys 2015. [PMID: 26098515 DOI: 10.1146/annurev-biophys-060414-0-33901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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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