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Lekshmi M, Ortiz-Alegria A, Kumar S, Varela MF. Major facilitator superfamily efflux pumps in human pathogens: Role in multidrug resistance and beyond. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100248. [PMID: 38974671 PMCID: PMC11225705 DOI: 10.1016/j.crmicr.2024.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
The major facilitator superfamily (MFS) of proteins constitutes a large group of related solute transporters found across all known living taxa of organisms. The transporters of the MFS contain an extremely diverse array of substrates, including ions, molecules of intermediary metabolism, and structurally different antimicrobial agents. First discovered over 30 years ago, the MFS represents an important collection of integral membrane transporters. Bacterial microorganisms expressing multidrug efflux pumps belonging to the MFS are considered serious pathogens, accounting for alarming morbidity and mortality numbers annually. This review article considers recent advances in the structure-function relationships, the transport mechanism, and modulation of MFS multidrug efflux pumps within the context of drug resistance mechanisms of bacterial pathogens of public health concerns.
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Affiliation(s)
- Manjusha Lekshmi
- QC Laboratory, Post Harvest Technology, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Anely Ortiz-Alegria
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, United States
| | - Sanath Kumar
- QC Laboratory, Post Harvest Technology, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, United States
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2
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Gao W, Li C, Wang F, Yang Y, Zhang L, Wang Z, Chen X, Tan M, Cao G, Zong G. An efflux pump in genomic island GI-M202a mediates the transfer of polymyxin B resistance in Pandoraea pnomenusa M202. Int Microbiol 2024; 27:277-290. [PMID: 37316617 PMCID: PMC10266961 DOI: 10.1007/s10123-023-00384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious infections. However, the risk of antimicrobial resistance and its spread to the environment should be brought to the forefront. METHODS Pandoraea pnomenusa M202 was isolated under selection with 8 mg/L polymyxin B from hospital sewage and then was sequenced by the PacBio RS II and Illumina HiSeq 4000 platforms. Mating experiments were performed to evaluate the transfer of the major facilitator superfamily (MFS) transporter in genomic islands (GIs) to Escherichia coli 25DN. The recombinant E. coli strain Mrc-3 harboring MFS transporter encoding gene FKQ53_RS21695 was also constructed. The influence of efflux pump inhibitors (EPIs) on MICs was determined. The mechanism of polymyxin B excretion mediated by FKQ53_RS21695 was investigated by Discovery Studio 2.0 based on homology modeling. RESULTS The MIC of polymyxin B for the multidrug-resistant bacterial strain P. pnomenusa M202, isolated from hospital sewage, was 96 mg/L. GI-M202a, harboring an MFS transporter-encoding gene and conjugative transfer protein-encoding genes of the type IV secretion system, was identified in P. pnomenusa M202. The mating experiment between M202 and E. coli 25DN reflected the transferability of polymyxin B resistance via GI-M202a. EPI and heterogeneous expression assays also suggested that the MFS transporter gene FKQ53_RS21695 in GI-M202a was responsible for polymyxin B resistance. Molecular docking revealed that the polymyxin B fatty acyl group inserts into the hydrophobic region of the transmembrane core with Pi-alkyl and unfavorable bump interactions, and then polymyxin B rotates around Tyr43 to externally display the peptide group during the efflux process, accompanied by an inward-to-outward conformational change in the MFS transporter. Additionally, verapamil and CCCP exhibited significant inhibition via competition for binding sites. CONCLUSIONS These findings demonstrated that GI-M202a along with the MFS transporter FKQ53_RS21695 in P. pnomenusa M202 could mediate the transmission of polymyxin B resistance.
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Affiliation(s)
- Wenhui Gao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Congcong Li
- Shandong Quancheng Test & Technology Limited Company, Ji'nan, 250101, China
| | - Fengtian Wang
- Jinan Municipal Minzu Hospital, Ji'nan, 250012, China
| | - Yilin Yang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Lu Zhang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Zhongxue Wang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Xi Chen
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Meixia Tan
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Guangxiang Cao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
| | - Gongli Zong
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
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Kalvaitienė G, Vaičiūtė D, Bučas M, Gyraitė G, Kataržytė M. Macrophytes and their wrack as a habitat for faecal indicator bacteria and Vibrio in coastal marine environments. MARINE POLLUTION BULLETIN 2023; 194:115325. [PMID: 37523954 DOI: 10.1016/j.marpolbul.2023.115325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
Waterborne pathogenic bacteria, including faecal indicator bacteria and potentially pathogenic Vibrio, are a global concern for diseases transmitted through water. A systematic review was conducted to analyse publications that investigated these bacteria in relation to macrophytes (seagrasses and macroalgae) in coastal marine environments. The highest quantities of FIB were found on brown algae and seagrasses, and the highest quantities of Vibrio bacteria were on red algae. The most extensively studied macrophyte group was brown algae, green algae were the least researched. Macrophyte wrack was found to favor the presence of FIB, but there is a lack of information about Vibrio quantities in this environment. To understand the role of Vibrio bacteria that are pathogenic to humans, molecular methods complementary to cultivation methods should be used. Further research is needed to understand the underlying mechanisms of FIB and potentially pathogenic Vibrio with macrophytes and their microbiome in the coastal marine environment.
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Affiliation(s)
- Greta Kalvaitienė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Diana Vaičiūtė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Martynas Bučas
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Greta Gyraitė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Marija Kataržytė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
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Lim Y, Seo JH, Giovannoni SJ, Kang I, Cho JC. Cultivation of marine bacteria of the SAR202 clade. Nat Commun 2023; 14:5098. [PMID: 37607927 PMCID: PMC10444878 DOI: 10.1038/s41467-023-40726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023] Open
Abstract
Bacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth's carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The growth of these strains is very slow (0.18-0.24 day-1) and is inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encode archaella (archaeal motility structures) and multiple sets of enzyme paralogs, including 80 genes coding for enolase superfamily enzymes and 44 genes encoding NAD(P)-dependent dehydrogenases. We propose that these enzyme paralogs participate in multiple parallel pathways for non-phosphorylative catabolism of sugars and sugar acids. Indeed, we demonstrate that SAR202 strains can utilize several substrates that are metabolized through the predicted pathways, such as sugars ʟ-fucose and ʟ-rhamnose, as well as their lactone and acid forms.
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Affiliation(s)
- Yeonjung Lim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea
| | - Ji-Hui Seo
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | | | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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Lehmann EF, Liziczai M, Drożdżyk K, Altermatt P, Langini C, Manolova V, Sundstrom H, Dürrenberger F, Dutzler R, Manatschal C. Structures of ferroportin in complex with its specific inhibitor vamifeport. eLife 2023; 12:e83053. [PMID: 36943194 PMCID: PMC10030120 DOI: 10.7554/elife.83053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
A central regulatory mechanism of iron homeostasis in humans involves ferroportin (FPN), the sole cellular iron exporter, and the peptide hormone hepcidin, which inhibits Fe2+ transport and induces internalization and degradation of FPN. Dysregulation of the FPN/hepcidin axis leads to diverse pathological conditions, and consequently, pharmacological compounds that inhibit FPN-mediated iron transport are of high clinical interest. Here, we describe the cryo-electron microscopy structures of human FPN in complex with synthetic nanobodies and vamifeport (VIT-2763), the first clinical-stage oral FPN inhibitor. Vamifeport competes with hepcidin for FPN binding and is currently in clinical development for β-thalassemia and sickle cell disease. The structures display two distinct conformations of FPN, representing outward-facing and occluded states of the transporter. The vamifeport site is located in the center of the protein, where the overlap with hepcidin interactions underlies the competitive relationship between the two molecules. The introduction of point mutations in the binding pocket of vamifeport reduces its affinity to FPN, emphasizing the relevance of the structural data. Together, our study reveals conformational rearrangements of FPN that are of potential relevance for transport, and it provides initial insight into the pharmacological targeting of this unique iron efflux transporter.
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Affiliation(s)
| | - Márton Liziczai
- Department of Biochemistry, University of ZurichZürichSwitzerland
| | | | | | - Cassiano Langini
- Department of Biochemistry, University of ZurichZürichSwitzerland
| | | | | | | | - Raimund Dutzler
- Department of Biochemistry, University of ZurichZürichSwitzerland
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Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
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7
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Tian W, Qin J, Lian C, Yao Q, Wang X. Identification of a major facilitator superfamily protein that is beneficial to L-lactic acid production by Bacillus coagulans at low pH. BMC Microbiol 2022; 22:310. [PMID: 36536285 PMCID: PMC9764580 DOI: 10.1186/s12866-022-02736-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Product inhibition is one of the major problems in lactic acid (LA) fermentation. Our previous study revealed that Bacillus coagulans 2-6 was an efficient producer of high-optical-purity L-LA. Its mutant strain B. coagulans Na-2 has better resistance to sodium lactate stress but the resistance mechanism has not been understood. RESULTS In this study, the whole-genome sequencing of B. coagulans Na-2 was performed and one mutant gene mfs coding for the major facilitator superfamily (MFS) protein was revealed by comparative genome analysis. Ten mutation sites were identified between the wild (MFS-2-6) and mutant (MFS-Na-2) proteins, among which T127A and N154T were predicted locating in the center of the transmembrane transport channel. The MFS-2-6 and MFS-Na-2 were expressed separately in a genetically operable strain, B. coagulans DSM1, using the genes' native promoter. The expression of the two MFS proteins had no effect and a negative effect on L-LA production when the pH was controlled at 6.0 and 7.0 by sodium hydroxide, respectively. However, 4.2 and 4.6-fold of L-LA concentrations were obtained at pH 5.0 by the strains expressing MFS-2-6 and MFS-Na-2 than that by the control strain, respectively. The intracellular pH values of the strains expressing MFS-2-6 and MFS-Na-2 were approximately 0.69 and 0.45 higher than that of the control strain during pH-controlled fermentation at 5.0. Results suggest that the expression of MFS-2-6 and MFS-Na-2 were both conducive to L-LA production at low pH, while the better performance of the latter was probably due to the more appropriate intracellular pH during the whole fermentation process. CONCLUSIONS The MFS protein identified here can improve the ability of B. coagulans to resist acidic environments and produce more L-LA at low pH. The MFS protein has an application potential in environment-friendly L-LA production.
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Affiliation(s)
- Wenzhe Tian
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China
| | - Jiayang Qin
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China.
| | - Congcong Lian
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China
| | - Qingshou Yao
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China
| | - Xiuwen Wang
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China
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Li Y, Ge X. Enhanced internal ionic interaction of MFS efflux pump MdfA contributes to its elevated antibiotic export. Phys Chem Chem Phys 2022; 25:788-795. [PMID: 36510750 DOI: 10.1039/d2cp05059e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Infections caused by Gram-negative pathogens are difficult to manage due to their antibiotic resistance. Efflux pumps, which transport intracellular toxins out of the cytoplasm, play an important role in the detoxification of bacteria when treated with antibiotics. The major facilitator superfamily (MFS) is a kind of widely distributed efflux pumps and can actively export clinically important antibiotics such as ciprofloxacin, while the role of internal ionic interactions in regulating drug export remains poorly understood. Herein we used a representative MFS efflux pump MdfA to investigate the impact of internal ionic interactions on the antibiotic resistance of E. coli. First, we identified the internal salt bridges of MdfA and searched their natural variants across all the sequenced E. coli isolates. By constructing these variants, we discovered that extending the salt bridge on the cytoplasmic side (E136D) conferred an elevated antibiotic resistance level of E. coli, and the level was further enhanced by combining it with an artificial mutation K346R. By analyzing the trajectories of MdfA's variants in molecular dynamics (MD) simulations, we revealed that ionic interaction strengths on the two sides were proportionally enhanced, while the protein flexibility was not affected. Moreover, enhanced interactions resulted in a larger surface for MdfA's protonation, suggesting a higher possibility for its activation. Collectively, our data revealed the importance of internal interactions on the drug export of MdfA, offering insights for the development of novel inhibitors against MFS efflux pumps.
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Affiliation(s)
- Ying Li
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
| | - Xizhen Ge
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
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9
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Structural basis of organic cation transporter-3 inhibition. Nat Commun 2022; 13:6714. [PMID: 36344565 PMCID: PMC9640557 DOI: 10.1038/s41467-022-34284-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Organic cation transporters (OCTs) facilitate the translocation of catecholamines, drugs and xenobiotics across the plasma membrane in various tissues throughout the human body. OCT3 plays a key role in low-affinity, high-capacity uptake of monoamines in most tissues including heart, brain and liver. Its deregulation plays a role in diseases. Despite its importance, the structural basis of OCT3 function and its inhibition has remained enigmatic. Here we describe the cryo-EM structure of human OCT3 at 3.2 Å resolution. Structures of OCT3 bound to two inhibitors, corticosterone and decynium-22, define the ligand binding pocket and reveal common features of major facilitator transporter inhibitors. In addition, we relate the functional characteristics of an extensive collection of previously uncharacterized human genetic variants to structural features, thereby providing a basis for understanding the impact of OCT3 polymorphisms.
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10
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Zhai G, Zhang Z, Dong C. Mutagenesis and functional analysis of SotB: A multidrug transporter of the major facilitator superfamily from Escherichia coli. Front Microbiol 2022; 13:1024639. [PMID: 36386622 PMCID: PMC9650428 DOI: 10.3389/fmicb.2022.1024639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 10/28/2023] Open
Abstract
Dysfunction of the major facilitator superfamily multidrug (MFS Mdr) transporters can lead to a variety of serious diseases in human. In bacteria, such membrane proteins are often associated with bacterial resistance. However, as one of the MFS Mdr transporters, the physiological function of SotB from Escherichia coli is poorly understood to date. To better understand the function and mechanism of SotB, a systematic study on this MFS Mdr transporter was carried out. In this study, SotB was found to directly efflux L-arabinose in E. coli by overexpressing sotB gene combined with cell based radiotracer uptake assay. Besides, the surface plasmon resonance (SPR) studies, the L-arabinose inhibition assays, together with precise molecular docking analysis, reveal the following: (i) the functional importance of E29 (protonation), H115/N343 (substrate recognition), and W119/S339 (substrate efflux) in the SotB mediated export of L-arabinose, and (ii) for the first time find that D-xylose, an isomer of L-arabinose, likely hinders the binding of L-arabinose with SotB as a competitive inhibitor. Finally, by analyzing the structure of SotB2 (shares 62.8% sequence similarity with SotB) predicted by AlphaFold 2, the different molecular mechanism of substrate recognition between SotB and SotB2 is explained. To our knowledge, this is the first systematic study of MFS Mdr transporter SotB. The structural information, together with the biochemical inspections in this study, provide a valuable framework for further deciphering the functional mechanisms of the physiologically important L-arabinose transporter SotB and its family.
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Affiliation(s)
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changjiang Dong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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11
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Jiang X. An overview of the Plasmodium falciparum hexose transporter and its therapeutic interventions. Proteins 2022; 90:1766-1778. [PMID: 35445447 PMCID: PMC9790349 DOI: 10.1002/prot.26351] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 12/30/2022]
Abstract
Despite intense elimination efforts, human malaria, caused by the infection of five Plasmodium species, remains the deadliest parasitic disease in the world. Even worse, with the emergence and spreading of the first-line drug-resistant Plasmodium parasites, therapeutic interventions based on novel plasmodial drug targets are more necessary than ever. Given that the blood-stage parasites primarily rely on glycolysis for their energy supply, blocking glucose uptake, the rate-limiting step of ATP generation, was considered a promising approach to kill these parasites. To achieve this goal, characterization of the plasmodial hexose transporter and development of selective inhibitors have been pursued for decades. Here, we review the identification and characterization of the Plasmodium falciparum hexose transporter (PfHT1) and summarize current advances in its inhibitor development.
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Affiliation(s)
- Xin Jiang
- School of Biotechnology and Biomolecular Sciencesthe University of New South WalesSydneyNew South Wales
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12
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Bazzone A, Tesmer L, Kurt D, Kaback HR, Fendler K, Madej MG. Investigation of sugar binding kinetics of the E. coli sugar/H + symporter XylE using solid supported membrane-based electrophysiology. J Biol Chem 2021; 298:101505. [PMID: 34929170 PMCID: PMC8784342 DOI: 10.1016/j.jbc.2021.101505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Bacterial transporters are difficult to study using conventional electrophysiology because of their low transport rates and the small size of bacterial cells. Here, we applied solid-supported membrane–based electrophysiology to derive kinetic parameters of sugar translocation by the Escherichia coli xylose permease (XylE), including functionally relevant mutants. Many aspects of the fucose permease (FucP) and lactose permease (LacY) have also been investigated, which allow for more comprehensive conclusions regarding the mechanism of sugar translocation by transporters of the major facilitator superfamily. In all three of these symporters, we observed sugar binding and transport in real time to determine KM, Vmax, KD, and kobs values for different sugar substrates. KD and kobs values were attainable because of a conserved sugar-induced electrogenic conformational transition within these transporters. We also analyzed interactions between the residues in the available X-ray sugar/H+ symporter structures obtained with different bound sugars. We found that different sugars induce different conformational states, possibly correlating with different charge displacements in the electrophysiological assay upon sugar binding. Finally, we found that mutations in XylE altered the kinetics of glucose binding and transport, as Q175 and L297 are necessary for uncoupling H+ and d-glucose translocation. Based on the rates for the electrogenic conformational transition upon sugar binding (>300 s−1) and for sugar translocation (2 s−1 − 30 s−1 for different substrates), we propose a multiple-step mechanism and postulate an energy profile for sugar translocation. We also suggest a mechanism by which d-glucose can act as an inhibitor for XylE.
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Affiliation(s)
- Andre Bazzone
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Laura Tesmer
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Derya Kurt
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - H Ronald Kaback
- University of California, Department of Physiology and Department of Microbiology, Immunology, Molecular Genetics, Molecular Biology Institute in Los Angeles CA, USA
| | - Klaus Fendler
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - M Gregor Madej
- Institute of Biophysics and Biophysical Chemistry, Department of Structural Biology, University of Regensburg, Universitätsstr. 31, 95053 Regensburg, Germany; Institute of Biophysics, Department of Structural Biology, Saarland University, Center of Human and Molecular Biology, Building 60, 66421 Homburg, Germany
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13
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Genetic and evolutionary characterization of the Major Facilitator Superfamily transporters of the antibacterial, Pantoea Natural Product 3. Res Microbiol 2021; 173:103899. [PMID: 34774705 DOI: 10.1016/j.resmic.2021.103899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022]
Abstract
Pantoea Natural Product 3 (PNP-3) is an antibiotic produced by Pantoea agglomerans that is effective against a broad range of multi-drug resistant bacteria. PNP-3 is encoded by a unique, eight-gene biosynthetic gene cluster composed of predicted enzymes (pnp3b, pnp3e-h), a regulator (pnp3d), and two Major Facilitator Superfamily transporters (pnp3a and pnp3c). To better characterize the role of the transporters, we generated pnp3a and pnp3c mutants and evaluated PNP-3 production. Disruption of pnp3a in Pantoea results in impaired growth and loss of antibiosis, suggesting a role in PNP-3 export and resistance. In contrast, pnp3c mutants display only reduced antibiotic production/export, suggesting a minor role for Pnp3c. Expression of pnp3a in susceptible Erwinia amylovora led to increased PNP-3 tolerance, while co-expression of pnp3a and pnp3e-h resulted in the production and export of PNP-3. Comparative genomic analyses identified pnp3a in 12 other Pantoea strains, eight of which carry a complete or nearly complete PNP-3 biosynthetic cluster. The four other Pantoea strains that carry pnp3a lack most of the PNP-3 cluster; however, they are PNP-3 tolerant. These results suggest Pnp3a plays an essential role in PNP-3 export and resistance in Pantoea.
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14
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Wan L, Zhu Y, Chen G, Luo G, Zhang W, Mu W. Efficient Production of 2'-Fucosyllactose from l-Fucose via Self-Assembling Multienzyme Complexes in Engineered Escherichia coli. ACS Synth Biol 2021; 10:2488-2498. [PMID: 34415729 DOI: 10.1021/acssynbio.1c00102] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2'-Fucosyllactose (2'-FL) has been widely used as a nutritional additive in infant formula due to its multifarious nutraceutical and pharmaceutical functions in neonate health. As such, it is essential to develop an efficient and extensive microbial fermentation platform to cater to the needs of the 2'-FL market. In this study, a spatial synthetic biology strategy was employed to promote 2'-FL biosynthesis in recombinant Escherichia coli. First, the salvage pathway for 2'-FL production from l-fucose and lactose was constructed by introducing a bifunctional enzyme l-fucokinase/GDP-l-fucose pyrophosphorylase (Fkp) derived from Bacteroides fragilis and an α-1,2-fucosyltransferase (FutC) derived from Helicobacter pylori into engineered E. coli BL21(DE3). Next, the endogenous genes involved in the degradation and shunting of the substrate and key intermediate were inactivated to improve the availability of precursors for 2'-FL biosynthesis. Moreover, to further improve the yield and titer of 2'-FL, a short peptide pair (RIAD-RIDD) was used to form self-assembling multienzyme complexes in vivo. The spatial localization of peptides and stoichiometry of enzyme assemblies were subsequently optimized to further improve 2'-FL production. Finally, cofactor regeneration was also considered to alleviate the potential cofactor deficiency and redox flux imbalance in the biocatalysis process. Fed-batch fermentation of the final WLS20 strain accumulated 30.5 g/L extracellular 2'-FL with the yield and productivity of 0.661 mol/mol fucose and 0.48 g/L/h, respectively. This research has demonstrated that the application of spatial synthetic biology and metabolic engineering strategies can dramatically enlarge the titer and yield of 2'-FL biosynthesis in engineered E. coli.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Geng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Guocong Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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15
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Console L, Tolomeo M, Cosco J, Massey K, Barile M, Indiveri C. Impact of natural mutations on the riboflavin transporter 2 and their relevance to human riboflavin transporter deficiency 2. IUBMB Life 2021; 74:618-628. [PMID: 34428344 DOI: 10.1002/iub.2541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/07/2021] [Accepted: 07/29/2021] [Indexed: 12/28/2022]
Abstract
Riboflavin transporter deficiency 2 (RTD2) is a rare neurological disorder caused by mutations in the Solute carrier family 52 member 2 (Slc52a2) gene encoding human riboflavin transporter 2 (RFVT2). This transporter is ubiquitously expressed and mediates tissue distribution of riboflavin, a water-soluble vitamin that, after conversion into FMN and FAD, plays pivotal roles in carbohydrate, protein, and lipid metabolism. The 3D structure of RFVT2 has been constructed by homology modeling using three different templates that are equilibrative nucleoside transporter 1 (ENT1), Fucose: proton symporter, and glucose transporter type 5 (GLUT5). The structure has been validated by several approaches. All known point mutations of RFVT2, associated with RTD2, have been localized in the protein 3D model. Six of these mutations have been introduced in the recombinant protein for functional characterization. The mutants W31S, S52F, S128L, L312P, C325G, and M423V have been expressed in E. coli, purified, and reconstituted into proteoliposomes for transport assay. All the mutants showed impairment of function. The Km for riboflavin of the mutants increased from about 3 to 9 times with respect to that of WT, whereas Vmax was only marginally affected. This agrees with the improved outcome of most RTD2 patients after administration of high doses of riboflavin.
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Affiliation(s)
- Lara Console
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Maria Tolomeo
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari, Bari, Italy
| | - Jessica Cosco
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | | | - Maria Barile
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari, Bari, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
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16
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Guan L, Hariharan P. X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB. Commun Biol 2021; 4:931. [PMID: 34341464 PMCID: PMC8329300 DOI: 10.1038/s42003-021-02462-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Major facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A. Guan and Hariharan report two crystal structures of melibiose transporter MelB in complex with substrate analogs, nitrophenyl-galactoside, and dodecyl-melibioside. Both structures revealed similar specific site for sugar recognition and resolved the cation-binding pocket, advancing the understanding of MelB and related transporters.
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Affiliation(s)
- Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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17
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Tuerkova A, Ungvári O, Laczkó-Rigó R, Mernyák E, Szakács G, Özvegy-Laczka C, Zdrazil B. Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides. J Chem Inf Model 2021; 61:3109-3127. [PMID: 34105971 PMCID: PMC8243326 DOI: 10.1021/acs.jcim.1c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Hepatic organic anion transporting polypeptides—OATP1B1,
OATP1B3, and OATP2B1—are expressed at the basolateral membrane
of hepatocytes, being responsible for the uptake of a wide range of
natural substrates and structurally unrelated pharmaceuticals. Impaired
function of hepatic OATPs has been linked to clinically relevant drug–drug
interactions leading to altered pharmacokinetics of administered drugs.
Therefore, understanding the commonalities and differences across
the three transporters represents useful knowledge to guide the drug
discovery process at an early stage. Unfortunately, such efforts remain
challenging because of the lack of experimentally resolved protein
structures for any member of the OATP family. In this study, we established
a rigorous computational protocol to generate and validate structural
models for hepatic OATPs. The multistep procedure is based on the
systematic exploration of available protein structures with shared
protein folding using normal-mode analysis, the calculation of multiple
template backbones from elastic network models, the utilization of
multiple template conformations to generate OATP structural models
with various degrees of conformational flexibility, and the prioritization
of models on the basis of enrichment docking. We employed the resulting
OATP models of OATP1B1, OATP1B3, and OATP2B1 to elucidate binding
modes of steroid analogs in the three transporters. Steroid conjugates
have been recognized as endogenous substrates of these transporters.
Thus, investigating this data set delivers insights into mechanisms
of substrate recognition. In silico predictions were complemented
with in vitro studies measuring the bioactivity of a compound set
on OATP expressing cell lines. Important structural determinants conferring
shared and distinct binding patterns of steroid analogs in the three
transporters have been identified. Overall, this comparative study
provides novel insights into hepatic OATP-ligand interactions and
selectivity. Furthermore, the integrative computational workflow for
structure-based modeling can be leveraged for other pharmaceutical
targets of interest.
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Affiliation(s)
- Alzbeta Tuerkova
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Althanstraße 14, A-1090 Vienna, Austria
| | - Orsolya Ungvári
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Réka Laczkó-Rigó
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Erzsébet Mernyák
- Department of Organic Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Gergely Szakács
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary.,Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Csilla Özvegy-Laczka
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Barbara Zdrazil
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Althanstraße 14, A-1090 Vienna, Austria
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18
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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19
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Abstract
Nucleosides play central roles in all facets of life, from metabolism to cellular signaling. Because of their physiochemical properties, nucleosides are lipid bilayer impermeable and thus rely on dedicated transport systems to cross biological membranes. In humans, two unrelated protein families mediate nucleoside membrane transport: the concentrative and equilibrative nucleoside transporter families. The objective of this review is to provide a broad outlook on the current status of nucleoside transport research. We will discuss the role played by nucleoside transporters in human health and disease, with emphasis placed on recent structural advancements that have revealed detailed molecular principles of these important cellular transport systems and exploitable pharmacological features.
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Affiliation(s)
- Nicholas J. Wright
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, North Carolina, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, North Carolina, 27710, USA
- Correspondence and requests for materials should be addressed to: S.-Y. Lee., , tel: 919-684-1005, fax: 919-684-8885
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20
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Eldakhakhny BM, Al Sadoun H, Choudhry H, Mobashir M. In-Silico Study of Immune System Associated Genes in Case of Type-2 Diabetes With Insulin Action and Resistance, and/or Obesity. Front Endocrinol (Lausanne) 2021; 12:641888. [PMID: 33927693 PMCID: PMC8078136 DOI: 10.3389/fendo.2021.641888] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
Type-2 diabetes and obesity are among the leading human diseases and highly complex in terms of diagnostic and therapeutic approaches and are among the most frequent and highly complex and heterogeneous in nature. Based on epidemiological evidence, it is known that the patients suffering from obesity are considered to be at a significantly higher risk of type-2 diabetes. There are several pieces of evidence that support the hypothesis that these diseases interlinked and obesity may aggravate the risk(s) of type-2 diabetes. Multi-level unwanted alterations such as (epi-) genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major sources that promote several complex diseases, and such a heterogeneous level of complexity is considered as a major barrier in the development of therapeutics. With so many known challenges, it is critical to understand the relationships and the shared causes between type-2 diabetes and obesity, and these are difficult to unravel and understand. For this purpose, we have selected publicly available datasets of gene expression for obesity and type-2 diabetes, have unraveled the genes and the pathways associated with the immune system, and have also focused on the T-cell signaling pathway and its components. We have applied a simplified computational approach to understanding differential gene expression and patterns and the enriched pathways for obesity and type-2 diabetes. Furthermore, we have also analyzed genes by using network-level understanding. In the analysis, we observe that there are fewer genes that are commonly differentially expressed while a comparatively higher number of pathways are shared between them. There are only 4 pathways that are associated with the immune system in case of obesity and 10 immune-associated pathways in case of type-2 diabetes, and, among them, only 2 pathways are commonly altered. Furthermore, we have presented SPNS1, PTPN6, CD247, FOS, and PIK3R5 as the overexpressed genes, which are the direct components of TCR signaling.
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Affiliation(s)
- Basmah Medhat Eldakhakhny
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hadeel Al Sadoun
- Stem Cell Unit, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Cancer and Mutagenesis Unit, Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
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21
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Feng J, Selvam B, Shukla D. How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK. Structure 2021; 29:922-933.e3. [PMID: 33836147 DOI: 10.1016/j.str.2021.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/07/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
Major facilitator superfamily (MFS) proteins operate via three different mechanisms: uniport, symport, and antiport. Despite extensive investigations, the molecular understanding of antiporters is less advanced than that of other transporters due to the complex coupling between two substrates and the lack of distinct structures. We employ extensive all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial NO3-/NO2- antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. Conformational transition occurs only in the presence of substrate, which weakens the electrostatic repulsion and stabilizes the transporter. Furthermore, we propose a state-dependent substrate exchange model, in which the relative spacing between the paired basic residues determines whether NO3- and NO2- bind simultaneously or sequentially. Overall, this work presents a general working model for the antiport mechanism within the MFS.
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Affiliation(s)
- Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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22
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Cryo-EM structures of Toll-like receptors in complex with UNC93B1. Nat Struct Mol Biol 2021; 28:173-180. [PMID: 33432245 DOI: 10.1038/s41594-020-00542-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/19/2020] [Indexed: 11/09/2022]
Abstract
Nucleic acid-sensing Toll-like receptors (TLRs) play a pivotal role in innate immunity by recognizing foreign DNA and RNA. Compartmentalization of these TLRs in the endosome limits their activation by self-derived nucleic acids and reduces the possibility of autoimmune reactions. Although chaperone Unc-93 homolog B1, TLR signaling regulator (UNC93B1) is indispensable for the trafficking of TLRs from the endoplasmic reticulum to the endosome, mechanisms of UNC93B1-mediated TLR regulation remain largely unknown. Here, we report two cryo-EM structures of human and mouse TLR3-UNC93B1 complexes and a human TLR7-UNC93B1 complex. UNC93B1 exhibits structural similarity to the major facilitator superfamily transporters. Both TLRs interact with the UNC93B1 amino-terminal six-helix bundle through their transmembrane and luminal juxtamembrane regions, but the complexes of TLR3 and TLR7 with UNC93B1 differ in their oligomerization state. The structural information provided here should aid in designing compounds to combat autoimmune diseases.
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23
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Focht D, Neumann C, Lyons J, Eguskiza Bilbao A, Blunck R, Malinauskaite L, Schwarz IO, Javitch JA, Quick M, Nissen P. A non-helical region in transmembrane helix 6 of hydrophobic amino acid transporter MhsT mediates substrate recognition. EMBO J 2021; 40:e105164. [PMID: 33155685 PMCID: PMC7780149 DOI: 10.15252/embj.2020105164] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
MhsT of Bacillus halodurans is a transporter of hydrophobic amino acids and a homologue of the eukaryotic SLC6 family of Na+ -dependent symporters for amino acids, neurotransmitters, osmolytes, or creatine. The broad range of transported amino acids by MhsT prompted the investigation of the substrate recognition mechanism. Here, we report six new substrate-bound structures of MhsT, which, in conjunction with functional studies, reveal how the flexibility of a Gly-Met-Gly (GMG) motif in the unwound region of transmembrane segment 6 (TM6) is central for the recognition of substrates of different size by tailoring the binding site shape and volume. MhsT mutants, harboring substitutions within the unwound GMG loop and substrate binding pocket that mimick the binding sites of eukaryotic SLC6A18/B0AT3 and SLC6A19/B0AT1 transporters of neutral amino acids, exhibited impaired transport of aromatic amino acids that require a large binding site volume. Conservation of a general (G/A/C)ΦG motif among eukaryotic members of SLC6 family suggests a role for this loop in a common mechanism for substrate recognition and translocation by SLC6 transporters of broad substrate specificity.
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Affiliation(s)
- Dorota Focht
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Caroline Neumann
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Joseph Lyons
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Ander Eguskiza Bilbao
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
| | - Rickard Blunck
- Department of PhysicsUniversité de MontréalMontréalQCCanada
| | - Lina Malinauskaite
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Ilona O Schwarz
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
| | - Jonathan A Javitch
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Center for Molecular RecognitionColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Department of PharmacologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNYUSA
| | - Matthias Quick
- Department of PsychiatryColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Center for Molecular RecognitionColumbia University Vagelos College of Physicians and SurgeonsNew YorkNYUSA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNYUSA
| | - Poul Nissen
- Department of Molecular Biology and GeneticsDanish Research Institute of Translational Neuroscience—DANDRITENordic‐EMBL Partnership for Molecular MedicineAarhus UniversityAarhus CDenmark
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24
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Zhao Z, Jiang Y, Li L, Chen Y, Li Y, Lan Q, Wu T, Lin C, Cao Y, Nandakumar KS, Zhou P, Tian Y, Pang J. Structural Insights into the Atomistic Mechanisms of Uric Acid Recognition and Translocation of Human Urate Anion Transporter 1. ACS OMEGA 2020; 5:33421-33432. [PMID: 33403304 PMCID: PMC7774290 DOI: 10.1021/acsomega.0c05360] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Background: Human urate transporter 1 (hURAT1) is the most pivotal therapeutic target for treating hyperuricemia. However, the molecular interactions between uric acid and URAT1 are still unknown due to lack of structural details. Methods: In the present study, several methods (homology modeling, sequence alignment, docking, and mutagenesis) were used to explain the atomistic mechanisms of uric acid transport of hURAT1. Results: Residues W357-F365 in the TMD7 and P484-R487 in the TMD11 present in the hURAT1 have unique roles in both binding to the uric acid and causing subsequent structural changes. These residues, located in the transport tunnel, were found to be related to the structural changes, as demonstrated by the reduced V max values and an unaltered expression of protein level. In addition, W357, G361, T363, F365, and R487 residues may confer high affinity for binding to uric acid. An outward-open homology model of hURAT1 revealed a crucial role for these two domains in the conformational changes of hURAT1. F241 and H245 in TMD5, and R477 and R487 in TMD11 may confer high affinity for uric acid, and as the docking analysis suggests, they may also enhance the affinity for the inhibitors. R477 relation to the structural changes was demonstrated by the V max values of the mutants and the contribution of positive charge to the uric acid selectivity. Conclusions: W357-F365 in TMD7, P484-R487 in TMD11, and residues F241, H245, and R477 were found to be critical for the translocation and recognition of uric acid.
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25
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Xiao Q, Sun B, Zhou Y, Wang C, Guo L, He J, Deng D. Visualizing the nonlinear changes of a drug-proton antiporter from inward-open to occluded state. Biochem Biophys Res Commun 2020; 534:272-278. [PMID: 33280821 DOI: 10.1016/j.bbrc.2020.11.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 11/24/2022]
Abstract
Drug-proton antiporters (DHA) play an important role in multi-drug resistance, utilizing the proton-motive force to drive the expulsion of toxic molecules, including antibiotics and drugs. DHA transporters belong to the major facilitator superfamily (MFS), members of which deliver substrates by utilizing the alternating access model of transport. However, the transport process is still elusive. Here, we report the structures of SotB, a member of DHA1 family (TCDB: 2.A.1.2) from Escherichia coli. Four crystal structures of SotB were captured in different conformations, including substrate-bound occluded, inward-facing, and inward-open states. Comparisons between the four structures reveal nonlinear rigid-body movements of alternating access during the state transition from inward-open to occluded conformation. This work not only reveals the conformational dynamics of SotB but also deepens our understanding of the alternating access mechanism of MFS transporters.
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Affiliation(s)
- Qingjie Xiao
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility Science Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Yanxia Zhou
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Chen Wang
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Li Guo
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianhua He
- Shanghai Synchrotron Radiation Facility Science Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Dong Deng
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
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26
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Xu C, Jia Q, Zhang L, Wang Z, Zhu S, Wang X, Liu Y, Li M, Zhang J, Wang X, Zhang J, Sun Q, Wang K, Zhu H, Duan L. Multiomics Study of Gut Bacteria and Host Metabolism in Irritable Bowel Syndrome and Depression Patients. Front Cell Infect Microbiol 2020; 10:580980. [PMID: 33194817 PMCID: PMC7658686 DOI: 10.3389/fcimb.2020.580980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Background and Aims Irritable bowel syndrome (IBS) and depression have high tendencies of comorbidity. In particular, diarrhea-predominant IBS (IBS-D) and depression exhibit similar fecal microbiota signatures, yet little is known about their pathogenic mechanism. Here, we propose that the differences in structure and composition of IBS-D and depression gut microbiota give rise to different downstream functions, which lead to distinct clinical phenotypes via host metabolism and further influence the interaction of brain–gut axis. Methods We performed multiomics study, including fecal metagenome-wide sequencing and serum metabolomics profiling in 65 individuals with IBS-D (n=22), depression (n=15), comorbid patients (n=13), and healthy controls (n=15). We analyzed functional genes contributed by the primary genus and evaluated their correlations with clinical indices and host metabolites. Results Metagenomic analysis revealed 26 clusters of orthologous groups of protein (COG) categories consisting of a total of 4,631 functional genes. Trehalose and maltose hydrolase (COG1554) and fucose permease (COG0738) were the most relevant and enriched functional genes in the IBS-D patients; urease accessory proteins UreE (COG2371) was that in the depression patients. Context based genome annotation suggest that an alteration of Escherichia coli and Enterobacter cloacae in IBS-D and depression respectively may be responsible for the enrichment described above. Correlation with host metabolites, such as maltotriose and isomaltose in carbohydrate metabolism and anandamide in neuroactive metabolism, drew further connections between these findings. Conclusions These changes led us to propose a connection between genomic signatures and clinical differences observed in IBS-D and depression. Our findings provide further insights into the involvement of gut microbiota in diseases related to brain–gut disorder.
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Affiliation(s)
- Congmin Xu
- Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peking University, Beijing, China
| | - Qiong Jia
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Lu Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Zhe Wang
- Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peking University, Beijing, China
| | - Shiwei Zhu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Xiaoqi Wang
- Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peking University, Beijing, China
| | - Yixuan Liu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Mo Li
- Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peking University, Beijing, China
| | - Jingjing Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Xiangqun Wang
- Department of Psychiatry, Institute of Mental Health, Peking University, Beijing, China
| | - Jindong Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Qinghua Sun
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Kun Wang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Huaiqiu Zhu
- Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peking University, Beijing, China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
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Abstract
The organic cation transporters (OCTs) OCT1, OCT2, OCT3, novel OCT (OCTN)1, OCTN2, multidrug and toxin exclusion (MATE)1, and MATE kidney-specific 2 are polyspecific transporters exhibiting broadly overlapping substrate selectivities. They transport organic cations, zwitterions, and some uncharged compounds and operate as facilitated diffusion systems and/or antiporters. OCTs are critically involved in intestinal absorption, hepatic uptake, and renal excretion of hydrophilic drugs. They modulate the distribution of endogenous compounds such as thiamine, L-carnitine, and neurotransmitters. Sites of expression and functions of OCTs have important impact on energy metabolism, pharmacokinetics, and toxicity of drugs, and on drug-drug interactions. In this work, an overview about the human OCTs is presented. Functional properties of human OCTs, including identified substrates and inhibitors of the individual transporters, are described. Sites of expression are compiled, and data on regulation of OCTs are presented. In addition, genetic variations of OCTs are listed, and data on their impact on transport, drug treatment, and diseases are reported. Moreover, recent data are summarized that indicate complex drug-drug interaction at OCTs, such as allosteric high-affinity inhibition of transport and substrate dependence of inhibitor efficacies. A hypothesis about the molecular mechanism of polyspecific substrate recognition by OCTs is presented that is based on functional studies and mutagenesis experiments in OCT1 and OCT2. This hypothesis provides a framework to imagine how observed complex drug-drug interactions at OCTs arise. Finally, preclinical in vitro tests that are performed by pharmaceutical companies to identify interaction of novel drugs with OCTs are discussed. Optimized experimental procedures are proposed that allow a gapless detection of inhibitory and transported drugs.
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Affiliation(s)
- Hermann Koepsell
- Institute of Anatomy and Cell Biology and Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, Würzburg, Germany
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28
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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] [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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29
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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] [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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30
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Groeneweg S, van Geest FS, Peeters RP, Heuer H, Visser WE. Thyroid Hormone Transporters. Endocr Rev 2020; 41:5637505. [PMID: 31754699 DOI: 10.1210/endrev/bnz008] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023]
Abstract
Thyroid hormone transporters at the plasma membrane govern intracellular bioavailability of thyroid hormone. Monocarboxylate transporter (MCT) 8 and MCT10, organic anion transporting polypeptide (OATP) 1C1, and SLC17A4 are currently known as transporters displaying the highest specificity toward thyroid hormones. Structure-function studies using homology modeling and mutational screens have led to better understanding of the molecular basis of thyroid hormone transport. Mutations in MCT8 and in OATP1C1 have been associated with clinical disorders. Different animal models have provided insight into the functional role of thyroid hormone transporters, in particular MCT8. Different treatment strategies for MCT8 deficiency have been explored, of which thyroid hormone analogue therapy is currently applied in patients. Future studies may reveal the identity of as-yet-undiscovered thyroid hormone transporters. Complementary studies employing animal and human models will provide further insight into the role of transporters in health and disease. (Endocrine Reviews 41: 1 - 55, 2020).
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Affiliation(s)
- Stefan Groeneweg
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ferdy S van Geest
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - W Edward Visser
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands Academic Center for Thyroid Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
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31
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Functional and Structural Roles of the Major Facilitator Superfamily Bacterial Multidrug Efflux Pumps. Microorganisms 2020; 8:microorganisms8020266. [PMID: 32079127 PMCID: PMC7074785 DOI: 10.3390/microorganisms8020266] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [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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32
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Bonetti S, Hirschi S, Bosshart PD. Expression, purification and crystallization of an SLC16 monocarboxylate transporter family homologue specific for l-lactate. Protein Expr Purif 2020; 165:105484. [DOI: 10.1016/j.pep.2019.105484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/01/2019] [Indexed: 02/06/2023]
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33
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The proton electrochemical gradient induces a kinetic asymmetry in the symport cycle of LacY. Proc Natl Acad Sci U S A 2019; 117:977-981. [PMID: 31889006 PMCID: PMC6969543 DOI: 10.1073/pnas.1916563117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protonation and deprotonation of Glu325 with a pKa of 10.5 is required for symport. Moreover, the H+ electrochemical gradient (∆μ∼H+) accelerates deprotonation on the intracellular side with a 50- to 100-fold decrease in the Km. To probe the pK on the cytoplasmic side of the membrane, rates of lactose/H+ efflux were determined from pH 5.0 to 9.0 without or with a membrane potential (ΔΨ, interior positive) in right-side-out membrane vesicles. WT lactose efflux has an apparent pK of ∼7.2 that is unaffected by ΔΨ, mutant E325A is defective, and pH or ΔΨ (interior positive) has no effect. The effect of ΔΨ (interior positive) on the Km for efflux with WT LacY is insignificant relative to the marked effect on influx. LacY catalyzes accumulation of galactosides against a concentration gradient by coupling galactoside and H+ transport (i.e., symport). While alternating access of sugar- and H+-binding sites to either side of the membrane is driven by binding and dissociation of sugar, the electrochemical H+ gradient (∆μ∼H+) functions kinetically by decreasing the Km for influx 50- to 100-fold with no change in Kd. The affinity of protonated LacY for sugar has an apparent pK (pKapp) of ∼10.5, due specifically to the pKa of Glu325, a residue that plays an irreplaceable role in coupling. In this study, rates of lactose/H+ efflux were measured from pH 5.0 to 9.0 in the absence or presence of a membrane potential (ΔΨ, interior positive), and the effect of the imposed ΔΨ on the kinetics of efflux was also studied in right-side-out membrane vesicles. The findings reveal that ∆μ∼H+ induces an asymmetry in the transport cycle based on the following observations: 1) the efflux rate of WT LacY exhibits a pKapp of ∼7.2 that is unaffected by the imposed ΔΨ; 2) ΔΨ increases the rate of efflux at all tested pH values, but enhancement is almost 2 orders of magnitude less than observed for influx; 3) mutant Glu325 ˗ Ala does little or no efflux in the absence or presence of ΔΨ, and ambient pH has no effect; and 4) the effect of ΔΨ (interior positive) on the Km for efflux is almost insignificant relative to the 50- to 100-fold decrease in the Km for influx driven by ΔΨ (interior negative).
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Batista MRB, Watts A, José Costa-Filho A. Exploring Conformational Transitions and Free-Energy Profiles of Proton-Coupled Oligopeptide Transporters. J Chem Theory Comput 2019; 15:6433-6443. [PMID: 31639304 DOI: 10.1021/acs.jctc.9b00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins involved in peptide uptake and transport belong to the proton-coupled oligopeptide transporter (POT) family. Crystal structures of POT family members reveal a common fold consisting of two domains of six transmembrane α helices that come together to form a "V" shaped transporter with a central substrate binding site. Proton-coupled oligopeptide transporters operate through an alternate access mechanism, where the membrane transporter undergoes global conformational changes, alternating between inward-facing (IF), outward-facing (OF), and occluded (OC) states. Conformational transitions are promoted by proton and ligand binding; however, due to the absence of crystallographic models of the outward-open state, the role of H+ and ligands is still not fully understood. To provide a comprehensive picture of the POT conformational equilibrium, conventional and enhanced sampling molecular dynamics simulations of PepTst in the presence or absence of ligand and protonation were performed. Free-energy profiles of the conformational variability of PepTst were obtained from microseconds of adaptive biasing force (ABF) simulations. Our results reveal that both proton and ligand significantly change the conformational free-energy landscape. In the absence of ligand and protonation, only transitions involving IF and OC states are allowed. After protonation of the residue Glu300, the wider free-energy well for Glu300 protonated PepTst indicates a greater conformational variability relative to the apo system, and OF conformations became accessible. For the Glu300 protonated Holo-PepTst, the presence of a second free-energy minimum suggests that OF conformations are not only accessible, but also stable. The differences in the free-energy profiles demonstrate that transitions toward outward-facing conformation occur only after protonation, which is likely the first step in the mechanism of peptide transport. Our extensive ABF simulations provide a fully atomic description of all states of the transport process, offering a model for the alternating access mechanism and how protonation and ligand control the conformational changes.
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Affiliation(s)
- Mariana R B Batista
- Ribeirão Preto School of Philosophy, Sciences and Letters , University of São Paulo , Ribeirao Preto , São Paulo 14040901 , Brazil
| | - Anthony Watts
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 2JD , United Kingdom
| | - Antonio José Costa-Filho
- Ribeirão Preto School of Philosophy, Sciences and Letters , University of São Paulo , Ribeirao Preto , São Paulo 14040901 , Brazil
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Wulff N, Ernst HA, Jørgensen ME, Lambertz S, Maierhofer T, Belew ZM, Crocoll C, Motawia MS, Geiger D, Jørgensen FS, Mirza O, Nour-Eldin HH. An Optimized Screen Reduces the Number of GA Transporters and Provides Insights Into Nitrate Transporter 1/Peptide Transporter Family Substrate Determinants. FRONTIERS IN PLANT SCIENCE 2019; 10:1106. [PMID: 31632416 PMCID: PMC6785635 DOI: 10.3389/fpls.2019.01106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/13/2019] [Indexed: 05/17/2023]
Abstract
Based on recent in vitro data, a relatively large number of the plant nitrate transporter 1/peptide transporter family (NPF) proteins have been suggested to function as gibberellic acid (GA) transporters. Most GA transporting NPF proteins also appear to transport other structurally unrelated phytohormones or metabolites. Several of the GAs used in previous in vitro assays are membrane permeable weak organic acids whose movement across membranes are influenced by the pH-sensitive ion-trap mechanism. Moreover, a large proportion of in vitro GA transport activities have been demonstrated indirectly via long-term yeast-based GA-dependent growth assays that are limited to detecting transport of bioactive GAs. Thus, there is a need for an optimized transport assay for identifying and characterizing GA transport. Here, we develop an improved transport assay in Xenopus laevis oocytes, wherein we directly measure movement of six different GAs across oocyte membranes over short time. We show that membrane permeability of GAs in oocytes can be predicted based on number of oxygen atoms and that several GAs do not diffuse over membranes regardless of changes in pH values. In addition, we show that small changes in internal cellular pH can result in strongly altered distribution of membrane permeable phytohormones. This prompts caution when interpreting heterologous transport activities. We use our transport assay to screen all Arabidopsis thaliana NPF proteins for transport activity towards six GAs (two membrane permeable and four non-permeable). The results presented here, significantly reduce the number of bona fide NPF GA transporters in Arabidopsis and narrow the activity to fewer subclades within the family. Furthermore, to gain first insight into the molecular determinants of substrate specificities toward organic molecules transported in the NPF, we charted all surface exposed amino acid residues in the substrate-binding cavity and correlated them to GA transport. This analysis suggests distinct residues within the substrate-binding cavity that are shared between GA transporting NPF proteins; the potential roles of these residues in determining substrate specificity are discussed.
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Affiliation(s)
- Nikolai Wulff
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Morten Egevang Jørgensen
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University Würzburg, Würzburg, Germany
- Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Sophie Lambertz
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tobias Maierhofer
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University Würzburg, Würzburg, Germany
| | - Zeinu Mussa Belew
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mohammed Saddik Motawia
- Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dietmar Geiger
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University Würzburg, Würzburg, Germany
| | | | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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36
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Zhang XC, Li B. Towards understanding the mechanisms of proton pumps in Complex-I of the respiratory chain. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-00094-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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37
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Zhou F, Yao D, Rao B, Zhang L, Nie W, Zou Y, Zhao J, Cao Y. Crystal structure of a bacterial homolog to human lysosomal transporter, spinster. Sci Bull (Beijing) 2019; 64:1310-1317. [PMID: 36659660 DOI: 10.1016/j.scib.2019.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 01/21/2023]
Abstract
Lysosomes break down various biomolecules and spinster is one of the major efflux carriers removing degradation products from lysosomal lumen to keep it in healthy size and proper function. Although it is well established that a dysfunctional spinster will cause enlarged lysosomes and in turn lead to developmental defects and abnormal behavior in animals, little was known about the transportation mechanism and substrate specificity of spinster. Here, we report a crystal structure of spinster homolog from Hyphomonas neptunium, HnSPNS, in its inward-facing conformation with and without substrate bound. HnSPNS is crystallized in a monomer and a substrate-binding cavity was formed in the center of its transmembrane helices. A blob of electron density corresponding to its substrate was found in the cavity near a conserved residue, R42, which is locked in position by the interactions with conserved residues E129 and R122. Our results suggest that human spinster serves as a transporter translocating negatively-charged lipophilic small molecules and E129 might serve as a switch to control the conformational change via its protonation-deprotonation cycle.
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Affiliation(s)
- Fu Zhou
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Deqiang Yao
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Bing Rao
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Li Zhang
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Wang Nie
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Zou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Yu Cao
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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38
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Kaback HR, Guan L. It takes two to tango: The dance of the permease. J Gen Physiol 2019; 151:878-886. [PMID: 31147449 PMCID: PMC6605686 DOI: 10.1085/jgp.201912377] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/14/2019] [Indexed: 11/20/2022] Open
Abstract
The lactose permease (LacY) of Escherichia coli is the prototype of the major facilitator superfamily, one of the largest families of membrane transport proteins. Structurally, two pseudo-symmetrical six-helix bundles surround a large internal aqueous cavity. Single binding sites for galactoside and H+ are positioned at the approximate center of LacY halfway through the membrane at the apex of the internal cavity. These features enable LacY to function by an alternating-access mechanism that can catalyze galactoside/H+ symport in either direction across the cytoplasmic membrane. The H+-binding site is fully protonated under physiological conditions, and subsequent sugar binding causes transition of the ternary complex to an occluded intermediate that can open to either side of the membrane. We review the structural and functional evidence that has provided new insight into the mechanism by which LacY achieves active transport against a concentration gradient.
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Affiliation(s)
- H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center of Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
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39
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Bosshart PD, Kalbermatter D, Bonetti S, Fotiadis D. Mechanistic basis of L-lactate transport in the SLC16 solute carrier family. Nat Commun 2019; 10:2649. [PMID: 31201333 PMCID: PMC6573034 DOI: 10.1038/s41467-019-10566-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/17/2019] [Indexed: 01/29/2023] Open
Abstract
In human and other mammalian cells, transport of L-lactate across plasma membranes is mainly catalyzed by monocarboxylate transporters (MCTs) of the SLC16 solute carrier family. MCTs play an important role in cancer metabolism and are promising targets for tumor treatment. Here, we report the crystal structures of an SLC16 family homologue with two different bound ligands at 2.54 and 2.69 Å resolution. The structures show the transporter in the pharmacologically relevant outward-open conformation. Structural information together with a detailed structure-based analysis of the transport function provide important insights into the molecular working mechanisms of ligand binding and L-lactate transport. The transport of L-lactate across plasma membranes is catalyzed by proton-driven monocarboxylate transporters (MCTs) of the SLC16 solute carrier family. Here, the authors present the crystal structures of a bacterial SLC16 homologue with the bound substrate L-lactate and ligand thiosalicylate both in an outward-open conformation and discuss the L-lactate transport mechanism.
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Affiliation(s)
- Patrick D Bosshart
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - Sara Bonetti
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland.
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40
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Yan H, Xu W, Xie J, Gao Y, Wu L, Sun L, Feng L, Chen X, Zhang T, Dai C, Li T, Lin X, Zhang Z, Wang X, Li F, Zhu X, Li J, Li Z, Chen C, Ma M, Zhang H, He Z. Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies. Nat Commun 2019; 10:2562. [PMID: 31189898 PMCID: PMC6561962 DOI: 10.1038/s41467-019-10544-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/14/2019] [Indexed: 01/06/2023] Open
Abstract
Cadmium (Cd) accumulation in rice grain poses a serious threat to human health. While several transport systems have been reported, the complexity of rice Cd transport and accumulation indicates the necessity of identifying additional genes, especially those that are responsible for Cd accumulation divergence between indica and japonica rice subspecies. Here, we show that a gene, OsCd1, belonging to the major facilitator superfamily is involved in root Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain Cd accumulation between indica and japonica. Near-isogenic line tests confirm that the indica variety carrying the japonica allele OsCd1V449 can reduce the grain Cd accumulation. Thus, the japonica allele OsCd1V449 may be useful for reducing grain Cd accumulation of indica rice cultivars through breeding. Grain of indica rice accumulates more toxic cadmium (Cd) than japonica, but the underlying genetic basis is unclear. Here, the authors show that natural variation of OsCd1 contributes to divergence in grain Cd accumulation and transferring japonica allele to indica rice leads to reduced Cd accumulation.
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Affiliation(s)
- Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenxiu Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jianyin Xie
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yiwei Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Lu Feng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xu Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changhua Dai
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuni Lin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zhanying Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xueqiang Wang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Fengmei Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Zhu
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Mi Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hongliang Zhang
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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41
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Jung S, Chin Y, Lee Y, Seo J. Enhanced production of 2’‐fucosyllactose from fucose by elimination of rhamnose isomerase and arabinose isomerase in engineeredEscherichia coli. Biotechnol Bioeng 2019; 116:2412-2417. [DOI: 10.1002/bit.27019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Sang‐Min Jung
- Department of Agricultural Biotechnology and Center for Food and BioconvergenceSeoul National UniversitySeoul Republic of Korea
| | - Young‐Wook Chin
- Research Group of Traditional FoodResearch Division of Strategic Food Technology, Korea Food Research InstituteWanju‐gun Jeollabuk‐do Republic of Korea
| | - Ye‐Gi Lee
- Department of Agricultural Biotechnology and Center for Food and BioconvergenceSeoul National UniversitySeoul Republic of Korea
| | - Jin‐Ho Seo
- Department of Agricultural Biotechnology and Center for Food and BioconvergenceSeoul National UniversitySeoul Republic of Korea
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42
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Micciche A, Rothrock MJ, Yang Y, Ricke SC. Essential Oils as an Intervention Strategy to Reduce Campylobacter in Poultry Production: A Review. Front Microbiol 2019; 10:1058. [PMID: 31139172 PMCID: PMC6527745 DOI: 10.3389/fmicb.2019.01058] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/26/2019] [Indexed: 12/19/2022] Open
Abstract
Campylobacter is a major foodborne pathogen and can be acquired through consumption of poultry products. With 1.3 million United States cases a year, the high prevalence of Campylobacter within the poultry gastrointestinal tract is a public health concern and thus a target for the development of intervention strategies. Increasing demand for antibiotic-free products has led to the promotion of various alternative pathogen control measures both at the farm and processing level. One such measure includes utilizing essential oils in both pre- and post-harvest settings. Essential oils are derived from plant-based extracts, and there are currently over 300 commercially available compounds. They have been proposed to control Campylobacter in the gastrointestinal tract of broilers. When used in concentrations low enough to not influence sensory characteristics, essential oils have also been proposed to decrease bacterial contamination of the poultry product during processing. This review explores the use of essential oils, particularly thymol, carvacrol, and cinnamaldehyde, and their role in reducing Campylobacter concentrations both pre- and post-harvest. This review also details the suggested mechanisms of action of essential oils on Campylobacter.
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Affiliation(s)
- Andrew Micciche
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Michael J. Rothrock
- United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
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43
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smFRET Probing Reveals Substrate-Dependent Conformational Dynamics of E. coli Multidrug MdfA. Biophys J 2019; 116:2296-2303. [PMID: 31146923 DOI: 10.1016/j.bpj.2019.04.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 11/21/2022] Open
Abstract
Bacterial multidrug-resistance transporters of the major facilitator superfamily are distinguished by their extraordinary ability to bind structurally diverse substrates, thus serving as a highly efficient tool to protect cells from multiple toxic substances present in their environment, including antibiotic drugs. However, details of the dynamic conformational changes of the transport cycle involved remain to be elucidated. Here, we used the single-molecule fluorescence resonance energy transfer technique to investigate the conformational behavior of the Escherichia coli multidrug transporter MdfA under conditions of different substrates, pH, and alkali metal ions. Our data show that different substrates exhibit distinct effects on both the conformational distribution and transition rate between two major conformations. Although the cationic substrate tetraphenylphosphonium favors the outward-facing conformation, it has less effect on the transition rate. In contrast, binding of the electroneutral substrate chloramphenicol tends to stabilize the inward-facing conformation and decreases the transition rate. Therefore, our study supports the notion that the MdfA transporter uses distinct mechanisms to transport electroneutral and cationic substrates.
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44
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Zhang XC, Li H. Interplay between the electrostatic membrane potential and conformational changes in membrane proteins. Protein Sci 2019; 28:502-512. [PMID: 30549351 DOI: 10.1002/pro.3563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022]
Abstract
Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge-carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hang Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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45
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Abstract
Transport of solutes across biological membranes is essential for cellular life. This process is mediated by membrane transport proteins which move nutrients, waste products, certain drugs and ions into and out of cells. Secondary active transporters couple the transport of substrates against their concentration gradients with the transport of other solutes down their concentration gradients. The alternating access model of membrane transporters and the coupling mechanism of secondary active transporters are introduced in this book chapter. Structural studies have identified typical protein folds for transporters that we exemplify by the major facilitator superfamily (MFS) and LeuT folds. Finally, substrate binding and substrate translocation of the transporters LacY of the MFS and AdiC of the amino acid-polyamine-organocation (APC) superfamily are described.
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Affiliation(s)
- Patrick D Bosshart
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
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46
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Trichez D, Knychala MM, Figueiredo CM, Alves SL, da Silva MA, Miletti LC, de Araujo PS, Stambuk BU. Key amino acid residues of the AGT1 permease required for maltotriose consumption and fermentation by Saccharomyces cerevisiae. J Appl Microbiol 2018; 126:580-594. [PMID: 30466168 DOI: 10.1111/jam.14161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 11/10/2018] [Indexed: 12/24/2022]
Abstract
AIMS The AGT1 gene encodes for a general α-glucoside-H+ symporter required for efficient maltotriose fermentation by Saccharomyces cerevisiae. In the present study, we analysed the involvement of four charged amino acid residues present in this transporter that are required for maltotriose consumption and fermentation by yeast cells. METHODS AND RESULTS By using a knowledge-driven approach based on charge, conservation, location, three-dimensional (3D) structural modelling and molecular docking analysis, we identified four amino acid residues (Glu-120, Asp-123, Glu-167 and Arg-504) in the AGT1 permease that could mediate substrate binding and translocation. Mutant permeases were generated by site-directed mutagenesis of these charged residues, and expressed in a yeast strain lacking this permease (agt1∆). While mutating the Arg-504 or Glu-120 residues into alanine totally abolished (R504A mutant) or greatly reduced (E120A mutant) maltotriose consumption by yeast cells, as well as impaired the active transport of several other α-glucosides, in the case of the Asp-123 and Glu-167 amino acids, it was necessary to mutate both residues (D123G/E167A mutant) in order to impair maltotriose consumption and fermentation. CONCLUSIONS Based on the results obtained with mutant proteins, molecular docking and the localization of amino acid residues, we propose a transport mechanism for the AGT1 permease. SIGNIFICANCE AND IMPACT OF THE STUDY Our results present new insights into the structural basis for active α-glucoside-H+ symport activity by yeast transporters, providing the molecular bases for improving the catalytic properties of this type of sugar transporters.
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Affiliation(s)
- D Trichez
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - M M Knychala
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - C M Figueiredo
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - S L Alves
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - M A da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - L C Miletti
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - P S de Araujo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - B U Stambuk
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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47
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Yang L, Yang L, Yu H, Liu L, Zhao X, Huang X. Conformational transitions of uracil transporter UraA from Escherichia coli: a molecular simulation study. J Biomol Struct Dyn 2018; 36:3398-3410. [DOI: 10.1080/07391102.2017.1388288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Liu Yang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Lianjuan Yang
- The Fungal Reference Laboratory of Shanghai Dermatology Hospital, Shanghai 200050, China
| | - Hui Yu
- Chemistry Teaching Center, College of Chemistry and Biology, Beihai University, Jilin 132013, People’s Republic of China
| | - Lu Liu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Xi Zhao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Xuri Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
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48
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Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Miyaji T, Omote H, Iwata S, Nomura N, Stubbs MT, Tanabe M. Outward open conformation of a Major Facilitator Superfamily multidrug/H + antiporter provides insights into switching mechanism. Nat Commun 2018; 9:4005. [PMID: 30275448 PMCID: PMC6167325 DOI: 10.1038/s41467-018-06306-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
Multidrug resistance (MDR) poses a major challenge to medicine. A principle cause of MDR is through active efflux by MDR transporters situated in the bacterial membrane. Here we present the crystal structure of the major facilitator superfamily (MFS) drug/H+ antiporter MdfA from Escherichia coli in an outward open conformation. Comparison with the inward facing (drug binding) state shows that, in addition to the expected change in relative orientations of the N- and C-terminal lobes of the antiporter, the conformation of TM5 is kinked and twisted. In vitro reconstitution experiments demonstrate the importance of selected residues for transport and molecular dynamics simulations are used to gain insights into antiporter switching. With the availability of structures of alternative conformational states, we anticipate that MdfA will serve as a model system for understanding drug efflux in MFS MDR antiporters. The multidrug resistance transporter mediated efflux of antibiotics from the bacterial cytoplasm represents a major challenge to medicine. Here authors solve the X-ray crystallographic structure of the drug/H+ antiporter MdfA from Escherichia coli and shed light on the conformational switching mechanism.
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Affiliation(s)
- Kumar Nagarathinam
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany.,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.,Institute of Virology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625, Hannover, Germany
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany
| | - Tohru Terada
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Narinobu Juge
- Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - Frank Jaenecke
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yunhon Hotta
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takaaki Miyaji
- Advanced Science Research Center, Okayama University, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - Hiroshi Omote
- Department of Membrane Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 1-1-1 Kita-ku, Tsushima-naka, Okayama, 700-8530, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.,RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Milton T Stubbs
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. .,Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120, Halle/Saale, Germany.
| | - Mikio Tanabe
- ZIK HALOmem, Kurt-Mothes-Straße 3, D-06120, Halle/Saale, Germany. .,Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
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49
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Selvam B, Mittal S, Shukla D. Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter. ACS CENTRAL SCIENCE 2018; 4:1146-1154. [PMID: 30276247 PMCID: PMC6161048 DOI: 10.1021/acscentsci.8b00330] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 05/21/2023]
Abstract
PepTSo is a proton-coupled bacterial symporter, from the major facilitator superfamily (MFS), which transports di-/tripeptide molecules. The recently obtained crystal structure of PepTSo provides an unprecedented opportunity to gain an understanding of functional insights of the substrate transport mechanism. Binding of the proton and peptide molecule induces conformational changes into occluded (OC) and outward-facing (OF) states, which we are able to characterize using molecular dynamics (MD) simulations. The structural knowledge of the OC and OF state is important to fully understand the major energy barrier associated with the transport cycle. In order to gain functional insight into the interstate dynamics, we performed extensive all atom MD simulations. The Markov state model was constructed to identify the free energy barriers between the states, and kinetic information on intermediate pathways was obtained using the transition pathway theory (TPT). TPT shows that the OF state is obtained by the movement of TM1 and TM7 at the extracellular side approximately 12-16 Å away from each other, and the inward movement of TM4 and TM10 at the intracellular halves to 3-4 Å characterizes the OC state. Helix distance distributions obtained from MD simulations were compared with experimental double electron-electron resonance spectroscopy and were found to be in excellent agreement with previous studies. We also predicted the optimal positions for placement of methane thiosulfonate spin label probes to capture the slowest protein dynamics. Our finding sheds light on the conformational cycle of this key membrane transporter and the functional relationships between the multiple intermediate states.
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Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
| | - Shriyaa Mittal
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative
Biology, and Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois, United States
- E-mail:
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Uptake dynamics in the Lactose permease (LacY) membrane protein transporter. Sci Rep 2018; 8:14324. [PMID: 30254312 PMCID: PMC6156506 DOI: 10.1038/s41598-018-32624-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 09/12/2018] [Indexed: 11/08/2022] Open
Abstract
The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 ± 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog β-D-galactopyranosyl-1-thio-β-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.
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