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Takeuchi K, Ueda T, Imai M, Fujisaki M, Shimura M, Tokunaga Y, Kofuku Y, Shimada I. Affinity-directed substrate/H +-antiport by a MATE transporter. Structure 2024; 32:1150-1164.e3. [PMID: 38815577 DOI: 10.1016/j.str.2024.05.004] [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: 11/06/2023] [Revised: 03/16/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
Multidrug and toxin extrusion (MATE) family transporters excrete toxic compounds coupled to Na+/H+ influx. Although structures of MATE transporters are available, the mechanism by which substrate export is coupled to ion influx remains unknown. To address this issue, we conducted a structural analysis of Pyrococcus furiosus MATE (PfMATE) using solution nuclear magnetic resonance (NMR). The NMR analysis, along with thorough substitutions of all non-exposed acidic residues, confirmed that PfMATE is under an equilibrium between inward-facing (IF) and outward-facing (OF) conformations, dictated by the Glu163 protonation. Importantly, we found that only the IF conformation exhibits a mid-μM affinity for substrate recognition. In contrast, the OF conformation exhibited only weak mM substrate affinity, suitable for releasing substrate to the extracellular side. These results indicate that PfMATE is an affinity-directed H+ antiporter where substrates selectively bind to the protonated IF conformation in the equilibrium, and subsequent proton release mechanistically ensures H+-coupled substrate excretion by the transporter.
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Affiliation(s)
- Koh Takeuchi
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan; Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan.
| | - Takumi Ueda
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Misaki Imai
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan; Research and Development Department, Japan Biological Informatics Consortium, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Miwa Fujisaki
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan; Research and Development Department, Japan Biological Informatics Consortium, Aomi 2-3-26, Koto-ku, Tokyo 135-0064, Japan
| | - Mie Shimura
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Yuji Tokunaga
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan; Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan
| | - Yutaka Kofuku
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan; Center for Biosystems Dynamics Research, RIKEN, Kanagawa 230-0045, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8528, Japan.
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Gheorghita AA, Wozniak DJ, Parsek MR, Howell PL. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS Microbiol Rev 2023; 47:fuad060. [PMID: 37884397 PMCID: PMC10644985 DOI: 10.1093/femsre/fuad060] [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: 04/21/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
The biofilm matrix is a fortress; sheltering bacteria in a protective and nourishing barrier that allows for growth and adaptation to various surroundings. A variety of different components are found within the matrix including water, lipids, proteins, extracellular DNA, RNA, membrane vesicles, phages, and exopolysaccharides. As part of its biofilm matrix, Pseudomonas aeruginosa is genetically capable of producing three chemically distinct exopolysaccharides - alginate, Pel, and Psl - each of which has a distinct role in biofilm formation and immune evasion during infection. The polymers are produced by highly conserved mechanisms of secretion, involving many proteins that span both the inner and outer bacterial membranes. Experimentally determined structures, predictive modelling of proteins whose structures are yet to be solved, and structural homology comparisons give us insight into the molecular mechanisms of these secretion systems, from polymer synthesis to modification and export. Here, we review recent advances that enhance our understanding of P. aeruginosa multiprotein exopolysaccharide biosynthetic complexes, and how the glycoside hydrolases/lyases within these systems have been commandeered for antimicrobial applications.
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Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, 776 Biomedical Research Tower, 460 W 12th Ave, Columbus, OH 43210, United States
- Department of Microbiology, The Ohio State University College, Biological Sciences Bldg, 105, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Health Sciences Bldg, 1705 NE Pacific St, Seattle, WA 98195-7735, United States
| | - P Lynne Howell
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
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3
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Jiang Y, Li Z. Identification and genomic analysis of Pseudosulfitobacter koreense sp. nov. isolated from toxin-producing dinoflagellate Alexandrium pacificum. Arch Microbiol 2023; 205:245. [PMID: 37209217 DOI: 10.1007/s00203-023-03583-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
The bacterial strain AP-MA-4T isolated from the marine dinoflagellate Alexandrium pacificum (KCTC AG60911), was subjected to a taxonomic analysis. Cells of strain AP-MA-4T were Gram-stain-negative, aerobic, rod-shaped, optimum growth at 20 °C, pH 7.0, in the presence of 5% (w/v) NaCl. Strain AP-MA-4T shared the highest 16S rRNA gene sequence similarity to Pseudosulfitobacter pseudonitzschiae DSM 26824T (98.5%), followed by Ascidiaceihabitans donghaensis RSS1-M3T (96.3%), Pseudoseohaeicola caenipelagi BS-W13T (95.7%), and Sulfitobacter pontiacus CHLG 10T (95.3%). Based on 16S rRNA phylogeny, strain AP-MA-4T is phylogenetically closely related to Pseudosulfitobacter pseudonitzschiae (type species of Pseudosulfitobacter) and could be distinguished from the type species based on their phenotypic properties. The genome length of strain AP-MA-4T was 3.48 Mbp with a 62.9% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain AP-MA-4 T and its closely related type strains were 72.2-83.3 and 18.2-27.6%, respectively. Summed feature 8 (C18:1ω7c and/or C18:1ω6c) was identified the major fatty acids (> 10%). Phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and phospholipid (PL) were demonstrated as the major polar lipids. The major respiratory quinone is ubiquinone-10 (Q-10). Based on genotypic and phenotypic features, strain AP-MA-4T (= KCTC 92289T = GDMCC 1.3585T) represents a new Pseudosulfitobacter species, in which the name Pseudosulfitobacter koreense sp. nov. is proposed.
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Affiliation(s)
- Yue Jiang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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4
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Dastvan R, Rasouli A, Dehghani-Ghahnaviyeh S, Gies S, Tajkhorshid E. Proton-driven alternating access in a spinster lipid transporter. Nat Commun 2022; 13:5161. [PMID: 36055994 PMCID: PMC9440201 DOI: 10.1038/s41467-022-32759-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange.
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Affiliation(s)
- Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha Gies
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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5
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Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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6
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The Poly-Glutamate Motif of GmMATE4 Regulates Its Isoflavone Transport Activity. MEMBRANES 2022; 12:membranes12020206. [PMID: 35207127 PMCID: PMC8880658 DOI: 10.3390/membranes12020206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023]
Abstract
Multidrug and toxic compound extrusion (MATE) transporters in eukaryotes have been characterized to be antiporters that mediate the transport of substrates in exchange for protons. In plants, alkaloids, phytohormones, ion chelators, and flavonoids have been reported to be the substrates of MATE transporters. Structural analyses have been conducted to dissect the functional significance of various motifs of MATE proteins. However, an understanding of the functions of the N- and C-termini has been inadequate. Here, by performing phylogenetic analyses and protein sequence alignment of 14 representative plant species, we identified a distinctive N-terminal poly-glutamate motif among a cluster of MATE proteins in soybean. Amongst them, GmMATE4 has the most consecutive glutamate residues at the N-terminus. A subcellular localization study showed that GmMATE4 was localized at the vacuolar membrane-like structure. Protein charge prediction showed that the mutation of the glutamate residues to alanine would reduce the negative charge at the N-terminus. Using yeast as the model, we showed that GmMATE4 mediated the transport of daidzein, genistein, glycitein, and glycitin. In addition, the glutamate-to-alanine mutation reduced the isoflavone transport capacity of GmMATE4. Altogether, we demonstrated GmMATE4 as an isoflavone transporter and the functional significance of the N-terminal poly-glutamate motif of GmMATE4 for regulating the isoflavone transport activity.
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7
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Claxton DP, Jagessar KL, Mchaourab HS. Principles of Alternating Access in Multidrug and Toxin Extrusion (MATE) Transporters. J Mol Biol 2021; 433:166959. [PMID: 33774036 DOI: 10.1016/j.jmb.2021.166959] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
The multidrug and toxin extrusion (MATE) transporters catalyze active efflux of a broad range of chemically- and structurally-diverse compounds including antimicrobials and chemotherapeutics, thus contributing to multidrug resistance in pathogenic bacteria and cancers. Multiple methodological approaches have been taken to investigate the structural basis of energy transduction and substrate translocation in MATE transporters. Crystal structures representing members from all three MATE subfamilies have been interpreted within the context of an alternating access mechanism that postulates occupation of distinct structural intermediates in a conformational cycle powered by electrochemical ion gradients. Here we review the structural biology of MATE transporters, integrating the crystallographic models with biophysical and computational studies to define the molecular determinants that shape the transport energy landscape. This holistic analysis highlights both shared and disparate structural and functional features within the MATE family, which underpin an emerging theme of mechanistic diversity within the framework of a conserved structural scaffold.
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Affiliation(s)
- Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Kevin L Jagessar
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA.
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Abstract
Drug transporters are integral membrane proteins that play a critical role in drug disposition by affecting absorption, distribution, and excretion. They translocate drugs, as well as endogenous molecules and toxins, across membranes using ATP hydrolysis, or ion/concentration gradients. In general, drug transporters are expressed ubiquitously, but they function in drug disposition by being concentrated in tissues such as the intestine, the kidneys, the liver, and the brain. Based on their primary sequence and their mechanism, transporters can be divided into the ATP-binding cassette (ABC), solute-linked carrier (SLC), and the solute carrier organic anion (SLCO) superfamilies. Many X-ray crystallography and cryo-electron microscopy (cryo-EM) structures have been solved in the ABC and SLC transporter superfamilies or of their bacterial homologs. The structures have provided valuable insight into the structural basis of transport. This chapter will provide particular focus on the promiscuous drug transporters because of their effect on drug disposition and the challenges associated with them.
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Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, Athens, GA, USA.
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Zhu X, Baranowski E, Dong Y, Li X, Hao Z, Zhao G, Zhang H, Lu D, A. Rasheed M, Chen Y, Hu C, Chen H, Sagné E, Citti C, Guo A. An emerging role for cyclic dinucleotide phosphodiesterase and nanoRNase activities in Mycoplasma bovis: Securing survival in cell culture. PLoS Pathog 2020; 16:e1008661. [PMID: 32598377 PMCID: PMC7373297 DOI: 10.1371/journal.ppat.1008661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
Mycoplasmas are host-restricted prokaryotes with a nearly minimal genome. To overcome their metabolic limitations, these wall-less bacteria establish intimate interactions with epithelial cells at mucosal surfaces. The alarming rate of antimicrobial resistance among pathogenic species is of particular concern in the medical and veterinary fields. Taking advantage of the reduced mycoplasma genome, random transposon mutagenesis was combined with high-throughput screening in order to identify key determinants of mycoplasma survival in the host-cell environment and potential targets for drug development. With the use of the ruminant pathogen Mycoplasma bovis as a model, three phosphodiesterases of the DHH superfamily were identified as essential for the proliferation of this species under cell culture conditions, while dispensable for axenic growth. Despite a similar domain architecture, recombinant Mbov_0327 and Mbov_0328 products displayed different substrate specificities. While rMbovP328 protein exhibited activity towards cyclic dinucleotides and nanoRNAs, rMbovP327 protein was only able to degrade nanoRNAs. The Mbov_0276 product was identified as a member of the membrane-associated GdpP family of phosphodiesterases that was found to participate in cyclic dinucleotide and nanoRNA degradation, an activity which might therefore be redundant in the genome-reduced M. bovis. Remarkably, all these enzymes were able to convert their substrates into mononucleotides, and medium supplementation with nucleoside monophosphates or nucleosides fully restored the capacity of a Mbov_0328/0327 knock-out mutant to grow under cell culture conditions. Since mycoplasmas are unable to synthesize DNA/RNA precursors de novo, cyclic dinucleotide and nanoRNA degradation are likely contributing to the survival of M. bovis by securing the recycling of purines and pyrimidines. These results point toward proteins of the DHH superfamily as promising targets for the development of new antimicrobials against multidrug-resistant pathogenic mycoplasma species.
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Affiliation(s)
- Xifang Zhu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | | | - Yaqi Dong
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xixi Li
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hui Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Doukun Lu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Muhammad A. Rasheed
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Eveline Sagné
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
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10
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Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter. Proc Natl Acad Sci U S A 2020; 117:4732-4740. [PMID: 32075917 DOI: 10.1073/pnas.1917139117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters are ubiquitous ion-coupled antiporters that extrude structurally and chemically dissimilar cytotoxic compounds and have been implicated in conferring multidrug resistance. Here, we integrate double electron-electron resonance (DEER) with functional assays and site-directed mutagenesis of conserved residues to illuminate principles of ligand-dependent alternating access of PfMATE, a proton-coupled MATE from the hyperthermophilic archaeon Pyrococcus furiosus Pairs of spin labels monitoring the two sides of the transporter reconstituted into nanodiscs reveal large-amplitude movement of helices that alter the orientation of a putative substrate binding cavity. We found that acidic pH favors formation of an inward-facing (IF) conformation, whereas elevated pH (>7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. The lipid-dependent PfMATE isomerization between OF and IF conformation is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access.
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11
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Krah A, Huber RG, Zachariae U, Bond PJ. On the ion coupling mechanism of the MATE transporter ClbM. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183137. [PMID: 31786188 DOI: 10.1016/j.bbamem.2019.183137] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/27/2019] [Accepted: 11/26/2019] [Indexed: 01/02/2023]
Abstract
Bacteria use a number of mechanisms to defend themselves from antimicrobial drugs. One important defense strategy is the ability to export drugs by multidrug transporters. One class of multidrug transporter, the so-called multidrug and toxic compound extrusion (MATE) transporters, extrude a variety of antibiotic compounds from the bacterial cytoplasm. These MATE transporters are driven by a Na+, H+, or combined Na+/H+ gradient, and act as antiporters to drive a conformational change in the transporter from the outward to the inward-facing conformation. In the inward-facing conformation, a chemical compound (drug) binds to the protein, resulting in a switch to the opposite conformation, thereby extruding the drug. Using molecular dynamics simulations, we now report the structural basis for Na+ and H+ binding in the dual ion coupled MATE transporter ClbM from Escherichia coli, which is connected to colibactin-induced genotoxicity, yielding novel insights into the ion/drug translocation mechanism of this bacterial transporter.
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Affiliation(s)
- Alexander Krah
- Korea Institute for Advanced Study, School of Computational Sciences, 85 Hoegiro, Dongdaemun-gu, Seoul 02455, Republic of Korea; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK; Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore 138671, Singapore.
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore 138671, Singapore
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Peter J Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Str., #07-01 Matrix, Singapore 138671, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
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12
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Draft Genome Sequence of Marinobacter sp. Strain LZ-6, Isolated from the Toxic Dinoflagellate Alexandrium catenella. Microbiol Resour Announc 2019; 8:8/37/e00795-19. [PMID: 31515344 PMCID: PMC6742795 DOI: 10.1128/mra.00795-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Here, we report the draft genome sequence of Marinobacter sp. strain LZ-6, isolated from the cell culture of a toxic marine dinoflagellate, Alexandrium catenella LZT09. A total of 4,405 predicted protein-coding genes were revealed, including those associated with initial biosynthesis of the key intermediate of paralytic shellfish poisoning toxins (PSTs), namely saxitoxin, and with toxic compound extrusion.
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