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Wiktorczyk-Kapischke N, Skowron K, Wałecka-Zacharska E. Genomic and pathogenicity islands of Listeria monocytogenes-overview of selected aspects. Front Mol Biosci 2023; 10:1161486. [PMID: 37388250 PMCID: PMC10300472 DOI: 10.3389/fmolb.2023.1161486] [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] [Received: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Listeria monocytogenes causes listeriosis, a disease characterized by a high mortality rate (up to 30%). Since the pathogen is highly tolerant to changing conditions (high and low temperature, wide pH range, low availability of nutrients), it is widespread in the environment, e.g., water, soil, or food. L. monocytogenes possess a number of genes that determine its high virulence potential, i.e., genes involved in the intracellular cycle (e.g., prfA, hly, plcA, plcB, inlA, inlB), response to stress conditions (e.g., sigB, gadA, caspD, clpB, lmo1138), biofilm formation (e.g., agr, luxS), or resistance to disinfectants (e.g., emrELm, bcrABC, mdrL). Some genes are organized into genomic and pathogenicity islands. The islands LIPI-1 and LIPI-3 contain genes related to the infectious life cycle and survival in the food processing environment, while LGI-1 and LGI-2 potentially ensure survival and durability in the production environment. Researchers constantly have been searching for new genes determining the virulence of L. monocytogenes. Understanding the virulence potential of L. monocytogenes is an important element of public health protection, as highly pathogenic strains may be associated with outbreaks and the severity of listeriosis. This review summarizes the selected aspects of L. monocytogenes genomic and pathogenicity islands, and the importance of whole genome sequencing for epidemiological purposes.
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Affiliation(s)
- Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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2
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Kumawat M, Nabi B, Daswani M, Viquar I, Pal N, Sharma P, Tiwari S, Sarma DK, Shubham S, Kumar M. Role of bacterial efflux pump proteins in antibiotic resistance across microbial species. Microb Pathog 2023:106182. [PMID: 37263448 DOI: 10.1016/j.micpath.2023.106182] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Efflux proteins are transporter molecules that actively pump out a variety of substrates, including antibiotics, from cells to the environment. They are found in both Gram-positive and Gram-negative bacteria and eukaryotic cells. Based on their protein sequence homology, energy source, and overall structure, efflux proteins can be divided into seven groups. Multidrug efflux pumps are transmembrane proteins produced by microbes to enhance their survival in harsh environments and contribute to antibiotic resistance. These pumps are present in all bacterial genomes studied, indicating their ancestral origins. Many bacterial genes encoding efflux pumps are involved in transport, a significant contributor to antibiotic resistance in microbes. Efflux pumps are widely implicated in the extrusion of clinically relevant antibiotics from cells to the extracellular environment and, as such, represent a significant challenge to antimicrobial therapy. This review aims to provide an overview of the structures and mechanisms of action, substrate profiles, regulation, and possible inhibition of clinically relevant efflux pumps. Additionally, recent advances in research and the pharmacological exploitation of efflux pump inhibitors as a promising intervention for combating drug resistance will be discussed.
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Affiliation(s)
- Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Muskan Daswani
- Department of Biotechnology, SantHirdaram Girls College, Bhopal, 462030, India
| | - Iqra Viquar
- Department of Biotechnology, SantHirdaram Girls College, Bhopal, 462030, India
| | - Namrata Pal
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Poonam Sharma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Shikha Tiwari
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Devojit Kumar Sarma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Swasti Shubham
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Manoj Kumar
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
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3
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Lewinson O, Orelle C, Seeger MA. Structures of ABC transporters: handle with care. FEBS Lett 2020; 594:3799-3814. [PMID: 33098660 PMCID: PMC7756565 DOI: 10.1002/1873-3468.13966] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
In the past two decades, the ATP‐binding cassette (ABC) transporters' field has undergone a structural revolution. The importance of structural biology to the development of the field of ABC transporters cannot be overstated, as the ensemble of structures not only revealed the architecture of ABC transporters but also shaped our mechanistic view of these remarkable molecular machines. Nevertheless, we advocate that the mechanistic interpretation of the structures is not trivial and should be carried out with prudence. Herein, we bring several examples of structures of ABC transporters that merit re‐interpretation via careful comparison to experimental data. We propose that it is of the upmost importance to place new structures within the context of the available experimental data.
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Affiliation(s)
- Oded Lewinson
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Cédric Orelle
- CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), University of Lyon, Lyon, France
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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4
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Colquhoun JM, Ha L, Beckley A, Meyers B, Flaherty DP, Dunman PM. Identification of Small Molecule Inhibitors of Staphylococcus aureus RnpA. Antibiotics (Basel) 2019; 8:antibiotics8020048. [PMID: 31035380 PMCID: PMC6627331 DOI: 10.3390/antibiotics8020048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus RnpA is thought to be a unique dual functional antimicrobial target that is required for two essential cellular processes, precursor tRNA processing and messenger RNA degradation. Herein, we used a previously described whole cell-based mupirocin synergy assay to screen members of a 53,000 compound small molecule diversity library and simultaneously enrich for agents with cellular RnpA inhibitory activity. A medicinal chemistry-based campaign was launched to generate a preliminary structure activity relationship and guide early optimization of two novel chemical classes of RnpA inhibitors identified, phenylcarbamoyl cyclic thiophene and piperidinecarboxamide. Representatives of each chemical class displayed potent anti-staphylococcal activity, limited the protein’s in vitro ptRNA processing and mRNA degradation activities, and exhibited favorable therapeutic indexes. The most potent piperidinecarboxamide RnpA inhibitor, JC2, displayed inhibition of cellular RnpA mRNA turnover, RnpA-depletion strain hypersusceptibility, and exhibited antimicrobial efficacy in a wax worm model of S. aureus infection. Taken together, these results establish that the whole cell screening assay used is amenable to identifying small molecule RnpA inhibitors within large chemical libraries and that the chemical classes identified here may represent progenitors of new classes of antimicrobials that target RnpA.
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Affiliation(s)
- Jennifer M Colquhoun
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Lisha Ha
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47906, USA.
| | - Andrew Beckley
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Brinkley Meyers
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47906, USA.
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47906, USA.
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47906, USA.
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine, Rochester, NY 14642, USA.
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5
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Xianwei T, Diannan L, Boxiong W. Substrate transport pathway inside outward open conformation of EmrD: a molecular dynamics simulation study. MOLECULAR BIOSYSTEMS 2017; 12:2634-41. [PMID: 27327574 DOI: 10.1039/c6mb00348f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EmrD transporter, which is a classical major facilitator superfamily (MFS) protein, can extrude a range of drug molecules out of E. coil. The drug molecules transport through the channel of MFS in an outward open state, an important issue in research about bacterial drug resistance, which however, is still unknown. In this paper, we construct a starting outward-open model of the EmrD transporter using a state transition method. The starting model is refined by a conventional molecular dynamics simulation. Locally enhanced sampling simulation (LES) is used to validate the outward-open model of EmrD. In the locally enhanced sampling simulation, ten substrates are placed along the channel of the outward-open EmrD, and these substrates are sampled in the outward-open center cavity. It is found that the translocation pathway of these substrates from the inside to the outside of the cell through the EmrD transporter is composed of two sub-pathways, one sub-pathway, including H2, H4, and H5, and another sub-pathway, including H8, H10, and H11. The results give us have a further insight to the ways of substrate translocation of an MFS protein. The model method is based on common features of an MFS protein, so this modeling method can be used to construct various MFS protein models which have a desired state with other conformations not known in the alternating-access mechanism.
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Affiliation(s)
- Tan Xianwei
- School of Life Sciences, Tsinghua University, Beijing, China.
| | - Lu Diannan
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Wang Boxiong
- Department of Precision Instrument, Tsinghua University, Beijing, China
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6
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Li JB, Tang S, Zheng JS, Tian CL, Liu L. Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins. Acc Chem Res 2017; 50:1143-1153. [PMID: 28374993 DOI: 10.1021/acs.accounts.7b00001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA. The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64-179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.
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Affiliation(s)
- Jia-Bin Li
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Ji-Shen Zheng
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Chang-Lin Tian
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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7
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Wozniak PP, Vriend G, Kotulska M. Correlated mutations select misfolded from properly folded proteins. Bioinformatics 2017; 33:1497-1504. [PMID: 28203707 DOI: 10.1093/bioinformatics/btx013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/11/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- P P Wozniak
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | - G Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M Kotulska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland
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8
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Zheng JS, He Y, Zuo C, Cai XY, Tang S, Wang ZA, Zhang LH, Tian CL, Liu L. Robust Chemical Synthesis of Membrane Proteins through a General Method of Removable Backbone Modification. J Am Chem Soc 2016; 138:3553-61. [PMID: 26943264 DOI: 10.1021/jacs.6b00515] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical protein synthesis can provide access to proteins with post-translational modifications or site-specific labelings. Although this technology is finding increasing applications in the studies of water-soluble globular proteins, chemical synthesis of membrane proteins remains elusive. In this report, a general and robust removable backbone modification (RBM) method is developed for the chemical synthesis of membrane proteins. This method uses an activated O-to-N acyl transfer auxiliary to install in the Fmoc solid-phase peptide synthesis process a RBM group with switchable reactivity toward trifluoroacetic acid. The method can be applied to versatile membrane proteins because the RBM group can be placed at any primary amino acid. With RBM, the membrane proteins and their segments behave almost as if they were water-soluble peptides and can be easily handled in the process of ligation, purification, and mass characterizations. After the full-length protein is assembled, the RBM group can be readily removed by trifluoroacetic acid. The efficiency and usefulness of the new method has been demonstrated by the successful synthesis of a two-transmembrane-domain protein (HCV p7 ion channel) with site-specific isotopic labeling and a four-transmembrane-domain protein (multidrug resistance transporter EmrE). This method enables practical synthesis of small- to medium-sized membrane proteins or membrane protein domains for biochemical and biophysical studies.
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Affiliation(s)
- Ji-Shen Zheng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Yao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chao Zuo
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiao-Ying Cai
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Zhipeng A Wang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Long-Hua Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, China
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9
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Boland C, Li D, Shah STA, Haberstock S, Dötsch V, Bernhard F, Caffrey M. Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination. Cell Mol Life Sci 2014; 71:4895-4910. [PMID: 25012698 DOI: 10.1007/s00018-014-1655-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 12/17/2022]
Abstract
Membrane proteins are key elements in cell physiology and drug targeting, but getting a high-resolution structure by crystallographic means is still enormously challenging. Novel strategies are in big demand to facilitate the structure determination process that will ultimately hasten the day when sequence information alone can provide a three-dimensional model. Cell-free or in vitro expression enables rapid access to large quantities of high-quality membrane proteins suitable for an array of applications. Despite its impressive efficiency, to date only two membrane proteins produced by the in vitro approach have yielded crystal structures. Here, we have analysed synergies of cell-free expression and crystallisation in lipid mesophases for generating an X-ray structure of the integral membrane enzyme diacylglycerol kinase to 2.28-Å resolution. The quality of cellular and cell-free-expressed kinase samples has been evaluated systematically by comparing (1) spectroscopic properties, (2) purity and oligomer formation, (3) lipid content and (4) functionality. DgkA is the first membrane enzyme crystallised based on cell-free expression. The study provides a basic standard for the crystallisation of cell-free-expressed membrane proteins and the methods detailed here should prove generally useful and contribute to accelerating the pace at which membrane protein structures are solved.
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Affiliation(s)
- Coilín Boland
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Syed Tasadaque Ali Shah
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Stefan Haberstock
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
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Sun J, Deng Z, Yan A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem Biophys Res Commun 2014; 453:254-67. [PMID: 24878531 DOI: 10.1016/j.bbrc.2014.05.090] [Citation(s) in RCA: 438] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
Abstract
Multidrug resistance (MDR) refers to the capability of bacterial pathogens to withstand lethal doses of structurally diverse drugs which are capable of eradicating non-resistant strains. MDR has been identified as a major threat to the public health of human being by the World Health Organization (WHO). Among the four general mechanisms that cause antibiotic resistance including target alteration, drug inactivation, decreased permeability and increased efflux, drug extrusion by the multidrug efflux pumps serves as an important mechanism of MDR. Efflux pumps not only can expel a broad range of antibiotics owing to their poly-substrate specificity, but also drive the acquisition of additional resistance mechanisms by lowering intracellular antibiotic concentration and promoting mutation accumulation. Over-expression of multidrug efflux pumps have been increasingly found to be associated with clinically relevant drug resistance. On the other hand, accumulating evidence has suggested that efflux pumps also have physiological functions in bacteria and their expression is subject tight regulation in response to various of environmental and physiological signals. A comprehensive understanding of the mechanisms of drug extrusion, and regulation and physiological functions of efflux pumps is essential for the development of anti-resistance interventions. In this review, we summarize the development of these research areas in the recent decades and present the pharmacological exploitation of efflux pump inhibitors as a promising anti-drug resistance intervention.
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Affiliation(s)
- Jingjing Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Ziqing Deng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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11
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Liguori L, Marques B, Villegas-Méndez A, Rothe R, Lenormand JL. Production of membrane proteins using cell–free expression systems. Expert Rev Proteomics 2014; 4:79-90. [PMID: 17288517 DOI: 10.1586/14789450.4.1.79] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Different overexpression systems are widely used in the laboratory to produce proteins in a reasonable amount for functional and structural studies. However, to optimize these systems without modifying the cellular functions of the living organism remains a challenging task. Cell-free expression systems have become a convenient method for the high-throughput expression of recombinant proteins, and great effort has been focused on generating high yields of proteins. Furthermore, these systems represent an attractive alternative for producing difficult-to-express proteins, such as membrane proteins. In this review, we highlight the recent improvements of these cell-free expression systems and their direct applications in the fields of membrane proteins production, protein therapy and modern proteomics.
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Affiliation(s)
- Lavinia Liguori
- University Joseph Fourier, HumProTher Laboratory, GREPI, CHU-Grenoble, 38043 Grenoble, France.
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12
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Schuldiner S. Undecided membrane proteins insert in random topologies. Up, down and sideways: it does not really matter. Trends Biochem Sci 2012; 37:215-9. [PMID: 22444835 DOI: 10.1016/j.tibs.2012.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 10/28/2022]
Abstract
It is usually assumed that to ensure proper function, membrane proteins must be inserted in a unique topology. However, a number of dimeric small multidrug transporters can function in the membrane in various topologies. Thus, the dimers can be a random mixture of NiCi (N and C termini facing the cell cytoplasm) and NoCo (N and C termini facing the outside) orientation. In addition, the dimer functions whether the two protomers are parallel (N and C termini of both protomers on the same side of the membrane) or antiparallel (N and C termini of each protomer on opposite sides of the membrane). This unique phenomenon provides strong support for a simple mechanism of transport where the directionality is determined solely by the driving force.
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Affiliation(s)
- Shimon Schuldiner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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13
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Junge F, Haberstock S, Roos C, Stefer S, Proverbio D, Dötsch V, Bernhard F. Advances in cell-free protein synthesis for the functional and structural analysis of membrane proteins. N Biotechnol 2011; 28:262-71. [DOI: 10.1016/j.nbt.2010.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/28/2010] [Accepted: 07/04/2010] [Indexed: 11/25/2022]
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14
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Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010; 11:120. [PMID: 20167121 PMCID: PMC2834635 DOI: 10.1186/1471-2164-11-120] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE) revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. RESULTS The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs) and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. CONCLUSIONS High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.
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Affiliation(s)
- Matthew W Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
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15
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Ubarretxena-Belandia I, Stokes DL. Present and future of membrane protein structure determination by electron crystallography. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 81:33-60. [PMID: 21115172 DOI: 10.1016/b978-0-12-381357-2.00002-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins.
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Affiliation(s)
- Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Mt. Sinai School of Medicine, New York, New York, USA
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16
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Affiliation(s)
- Dale E Tronrud
- Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR 97403-1229, USA
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17
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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18
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EmrE, a model for studying evolution and mechanism of ion-coupled transporters. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:748-62. [DOI: 10.1016/j.bbapap.2008.12.018] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/23/2022]
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19
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Kajiyama Y, Otagiri M, Sekiguchi J, Kudo T, Kosono S. The MrpA, MrpB and MrpD subunits of the Mrp antiporter complex in Bacillus subtilis contain membrane-embedded and essential acidic residues. MICROBIOLOGY-SGM 2009; 155:2137-2147. [PMID: 19389778 DOI: 10.1099/mic.0.025205-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus subtilis Mrp is a unique Na+/H+ antiporter with a multicomponent structure consisting of the mrpABCDEFG gene products. We have previously reported that the conserved and putative membrane-embedded Glu-113, Glu-657, Asp-743 and Glu-747 of MrpA (ShaA) are essential for the transport function. In this study, we further investigated the functional involvement of the equivalent conserved acidic residues of other Mrp proteins in heterologous Escherichia coli and natural B. subtilis backgrounds. Asp-121 of MrpB and Glu-137 of MrpD were additionally identified to be essential for the transport function in both systems. Glu-137 of MrpD and Glu-113 of MrpA were found to be conserved in the homologous MrpD/MrpA proteins as well as in the homologous subunits of H+-translocating primary active transporters such as Nuo and Mbh, suggesting their critical role in ion binding. The remaining essential acidic residues clustered in the C-terminal domain of MrpA (Glu-657, Asp-743 and Glu-747) and MrpB (Asp-121); these subunits are fused in some Gram-negative species. It is possible that the MrpA, MrpB and MrpD subunits, which contain essential transmembrane acidic residues, form the ion translocation site(s) of the Mrp antiporter complex.
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Affiliation(s)
- Yusuke Kajiyama
- Department of Applied Biology, Shinshu University, Japan.,Environmental Molecular Biology Laboratory, RIKEN, Japan
| | - Masato Otagiri
- Environmental Molecular Biology Laboratory, RIKEN, Japan
| | | | - Toshiaki Kudo
- Graduate School of Integrated Science, Yokohama City University, Japan.,Environmental Molecular Biology Laboratory, RIKEN, Japan
| | - Saori Kosono
- Environmental Molecular Biology Laboratory, RIKEN, Japan
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20
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Poulsen BE, Rath A, Deber CM. The assembly motif of a bacterial small multidrug resistance protein. J Biol Chem 2009; 284:9870-5. [PMID: 19224913 DOI: 10.1074/jbc.m900182200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multidrug transporters such as the small multidrug resistance (SMR) family of bacterial integral membrane proteins are capable of conferring clinically significant resistance to a variety of common therapeutics. As antiporter proteins of approximately 100 amino acids, SMRs must self-assemble into homo-oligomeric structures for efflux of drug molecules. Oligomerization centered at transmembrane helix four (TM4) has been implicated in SMR assembly, but the full complement of residues required to mediate its self-interaction remains to be characterized. Here, we use Hsmr, the 110-residue SMR family member of the archaebacterium Halobacterium salinarum, to determine the TM4 residue motif required to mediate drug resistance and SMR self-association. Twelve single point mutants that scan the central portion of the TM4 helix (residues 85-104) were constructed and were tested for their ability to confer resistance to the cytotoxic compound ethidium bromide. Six residues were found to be individually essential for drug resistance activity (Gly(90), Leu(91), Leu(93), Ile(94), Gly(97), and Val(98)), defining a minimum activity motif of (90)GLXLIXXGV(98) within TM4. When the propensity of these mutants to dimerize on SDS-PAGE was examined, replacements of all but Ile resulted in approximately 2-fold reduction of dimerization versus the wild-type antiporter. Our work defines a minimum activity motif of (90)GLXLIXXGV(98) within TM4 and suggests that this sequence mediates TM4-based SMR dimerization along a single helix surface, stabilized by a small residue heptad repeat sequence. These TM4-TM4 interactions likely constitute the highest affinity locus for disruption of SMR function by directly targeting its self-assembly mechanism.
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Affiliation(s)
- Bradley E Poulsen
- Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8
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21
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Korkhov VM, Tate CG. An emerging consensus for the structure of EmrE. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:186-92. [PMID: 19171974 PMCID: PMC2631640 DOI: 10.1107/s0907444908036640] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 11/07/2008] [Indexed: 11/17/2022]
Abstract
The archetypical member of the small multidrug-resistance family is EmrE, a multidrug transporter that extrudes toxic polyaromatic cations from the cell coupled to the inward movement of protons down a concentration gradient. The architecture of EmrE was first defined from the analysis of two-dimensional crystals by cryoelectron microscopy (cryo-EM), which showed that EmrE was an unusual asymmetric dimer formed from a bundle of eight alpha-helices. The most favoured interpretation of the structure was that the monomers were oriented in opposite orientations in the membrane in an antiparallel orientation. A model was subsequently built based upon the cryo-EM data and evolutionary constraints and this model was consistent with mutagenic data indicating which amino-acid residues were important for substrate binding and transport. Two X-ray structures that differed significantly from the cryo-EM structure were subsequently retracted owing to a data-analysis error. However, the revised X-ray structure with substrate bound is extremely similar to the model built from the cryo-EM structure (r.m.s.d. of 1.4 A), suggesting that the proposed antiparallel orientation of the monomers is indeed correct; this represents a new structural paradigm in membrane-protein structures. The vast majority of mutagenic and biochemical data corroborate this structure, although cross-linking studies and recent EPR data apparently support a model of EmrE that contains parallel dimers.
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22
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Jeffrey PD. Analysis of errors in the structure determination of MsbA. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:193-9. [PMID: 19171975 PMCID: PMC2631635 DOI: 10.1107/s0907444909001292] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/12/2009] [Indexed: 11/13/2022]
Abstract
The determination of incorrect structures for the ABC transporter MsbA gave rise to questions of how this could have occurred. Methodological aspects of the MsbA structure determination are explored in light of this error.
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Affiliation(s)
- Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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23
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Bay DC, Rommens KL, Turner RJ. Small multidrug resistance proteins: A multidrug transporter family that continues to grow. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1814-38. [DOI: 10.1016/j.bbamem.2007.08.015] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 08/07/2007] [Accepted: 08/14/2007] [Indexed: 11/17/2022]
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24
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Sansuk K, Balog CIA, van der Does AM, Booth R, de Grip WJ, Deelder AM, Bakker RA, Leurs R, Hensbergen PJ. GPCR proteomics: mass spectrometric and functional analysis of histamine H1 receptor after baculovirus-driven and in vitro cell free expression. J Proteome Res 2008; 7:621-9. [PMID: 18177001 DOI: 10.1021/pr7005654] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human histamine H1 Receptor (hH1R) belongs to the family of G-protein coupled receptors (GPCRs), an attractive and proven class of drug targets in a wide range of therapeutic areas. However, due to the low amount of available purified protein and the hydrophobic nature of GPCRs, limited structural information is available on ligand-receptor interaction especially for the transmembrane (TM) domain regions where the majority of ligand-receptor interactions occur. During the last decades, proteomic techniques have increasingly become an important tool to reveal detailed information on the individual GPCR class, including post-translational modifications and characterizations of GPCRs binding pocket. Herein, we report the successful functional production and mass spectrometric characterization of the hH1R, after baculovirus-driven and in vitro cell-free expression. Using only MALDI-ToF, sequence coverage of more than 80%, including five hydrophobic TM domains was achieved. Moreover, we have identified an asparagine residue in the hH1R protein that is subject to N-linked glycosylation. This information would be valuable for drug discovery efforts by allowing us to further study H1R-ligand interactions using histaminergic ligands that covalently bind the hH1R, and eventually revealing binding sites of hH1R and other GPCRs.
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Affiliation(s)
- Kamonchanok Sansuk
- Leiden/Amsterdam Center for Drug Research (LACDR), Vrije Universiteit Amsterdam, Department of Medicinal Chemistry, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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25
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Choi S, Jeon J, Yang JS, Kim S. Common occurrence of internal repeat symmetry in membrane proteins. Proteins 2008; 71:68-80. [PMID: 17932930 DOI: 10.1002/prot.21656] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Symmetry plays significant roles in protein structure and function. Particularly, symmetric interfaces are known to act as switches for two-state conformational change. Membrane proteins often undergo two-state conformational change during the transport process of ion channels or the active/inactive transitions in receptors. Here, we provide the first comprehensive analyses of internal repeat symmetry in membrane proteins. We examined the known membrane protein structures and found that, remarkably, nearly half of them have internal repeat symmetry. Moreover, we found that the conserved cores of these internal repeats are positioned at the interface of symmetric units when they are mapped on structures. Because of the large sequence divergence that occurs between internal repeats, the inherent symmetry present in protein sequences often has only been detected after structure determination. We therefore developed a sensitive procedure to predict the internal repeat symmetry from sequence information and identified 4653 proteins that are likely to have internal repeat symmetry.
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Affiliation(s)
- Sungwon Choi
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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26
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High yield cell-free production of integral membrane proteins without refolding or detergents. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1237-50. [PMID: 18295592 DOI: 10.1016/j.bbamem.2008.01.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 01/02/2008] [Accepted: 01/28/2008] [Indexed: 11/21/2022]
Abstract
Integral membrane proteins act as critical cellular components and are important drug targets. However, difficulties in producing membrane proteins have hampered investigations of structure and function. In vivo production systems are often limited by cell toxicity, and previous in vitro approaches have required unnatural folding pathways using detergents or lipid solutions. To overcome these limitations, we present an improved cell-free expression system which produces high yields of integral membrane proteins without the use of detergents or refolding steps. Our cell-free reaction activates an Escherichia coli-derived cell extract for transcription and translation. Purified E. coli inner membrane vesicles supply membrane-bound components and the lipid environment required for insertion and folding. Using this system, we demonstrated successful synthesis of two complex integral membrane transporters, the tetracycline pump (TetA) and mannitol permease (MtlA), in yields of 570+/-50 microg/mL and 130+/-30 microg/mL of vesicle-associated protein, respectively. These yields are up to 400 times typical in vivo concentrations. Insertion and folding of these proteins are verified by sucrose flotation, protease digestion, and activity assays. Whereas TetA incorporates efficiently into vesicle membranes with over two-thirds of the synthesized protein being inserted, MtlA yields appear to be limited by insufficient concentrations of a membrane-associated chaperone.
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27
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Ravna AW, Sager G, Dahl SG, Sylte I. Membrane Transporters: Structure, Function and Targets for Drug Design. TOPICS IN MEDICINAL CHEMISTRY 2008. [DOI: 10.1007/7355_2008_023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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28
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Steiner-Mordoch S, Soskine M, Solomon D, Rotem D, Gold A, Yechieli M, Adam Y, Schuldiner S. Parallel topology of genetically fused EmrE homodimers. EMBO J 2007; 27:17-26. [PMID: 18059473 DOI: 10.1038/sj.emboj.7601951] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 11/14/2007] [Indexed: 11/09/2022] Open
Abstract
EmrE is a small H+-coupled multidrug transporter in Escherichia coli. Claims have been made for an antiparallel topology of this homodimeric protein. However, our own biochemical studies performed with detergent-solubilized purified protein support a parallel topology of the protomers. We developed an alternative approach to constrain the relative topology of the protomers within the dimer so that their activity can be assayed also in vivo before biochemical handling. Tandem EmrE was built with two identical monomers genetically fused tail to head (C-terminus of the first to N-terminus of the second monomer) with hydrophilic linkers of varying length. All the constructs conferred resistance to ethidium by actively removing it from the cytoplasm. The purified proteins bound substrate and transported methyl viologen into proteoliposomes by a proton-dependent mechanism. A tandem where one of the essential glutamates was replaced with glutamine transported only monovalent substrates and displayed a modified stoichiometry. The results support a parallel topology of the protomers in the functional dimer. The implications regarding insertion and evolution of membrane proteins are discussed.
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Affiliation(s)
- Sonia Steiner-Mordoch
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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29
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Agarwal V, Fink U, Schuldiner S, Reif B. MAS solid-state NMR studies on the multidrug transporter EmrE. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3036-43. [DOI: 10.1016/j.bbamem.2007.09.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 09/18/2007] [Accepted: 09/19/2007] [Indexed: 11/27/2022]
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30
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Ganas P, Mihasan M, Igloi GL, Brandsch R. A two-component small multidrug resistance pump functions as a metabolic valve during nicotine catabolism by Arthrobacter nicotinovorans. MICROBIOLOGY-SGM 2007; 153:1546-1555. [PMID: 17464069 DOI: 10.1099/mic.0.2006/004234-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genes nepAB of a small multidrug resistance (SMR) pump were identified as part of the pAO1-encoded nicotine regulon responsible for nicotine catabolism in Arthrobacter nicotinovorans. When [(14)C]nicotine was added to the growth medium the bacteria exported the (14)C-labelled end product of nicotine catabolism, methylamine. In the presence of the proton-motive force inhibitors 2,4-dinitrophenol (DNP), carbonyl cyanide m-chlorophenylhydrazone (CCCP) or the proton ionophore nigericin, export of methylamine was inhibited and radioactivity accumulated inside the bacteria. Efflux of [(14)C]nicotine-derived radioactivity from bacteria was also inhibited in a pmfR : cmx strain with downregulated nepAB expression. Because of low amine oxidase levels in the pmfR : cmx strain, gamma-N-methylaminobutyrate, the methylamine precursor, accumulated. Complementation of this strain with the nepAB genes, carried on a plasmid, restored the efflux of nicotine breakdown products. Both NepA and NepB were required for full export activity, indicating that they form a two-component efflux pump. NepAB may function as a metabolic valve by exporting methylamine, the end product of nicotine catabolism, and, in conditions under which it accumulates, the intermediate gamma-N-methylaminobutyrate.
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Affiliation(s)
- Petra Ganas
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Albrecht-Ludwigs University, Freiburg, Germany
| | - Marius Mihasan
- Department of Biochemistry, Alexandru-Ioan-Cuza University, Iasi, Romania
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Albrecht-Ludwigs University, Freiburg, Germany
| | - Gabor L Igloi
- Institute of Biology III, Albrecht-Ludwigs University, Freiburg, Germany
| | - Roderich Brandsch
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research, Albrecht-Ludwigs University, Freiburg, Germany
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31
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Abstract
EmrE, a multidrug transporter from Escherichia coli, functions as a homodimer of a small four-transmembrane protein. The membrane insertion topology of the two monomers is controversial. Although the EmrE protein was reported to have a unique orientation in the membrane, models based on electron microscopy and now defunct x-ray structures, as well as recent biochemical studies, posit an antiparallel dimer. We have now reanalyzed our x-ray data on EmrE. The corrected structures in complex with a transport substrate are highly similar to the electron microscopy structure. The first three transmembrane helices from each monomer surround the substrate binding chamber, whereas the fourth helices participate only in dimer formation. Selenomethionine markers clearly indicate an antiparallel orientation for the monomers, supporting a "dual topology" model.
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32
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Yan A, Guan Z, Raetz CRH. An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli. J Biol Chem 2007; 282:36077-89. [PMID: 17928292 DOI: 10.1074/jbc.m706172200] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modification of lipid A with the 4-amino-4-deoxy-L-arabinose (L-Ara4N) moiety is required for resistance to polymyxin and cationic antimicrobial peptides in Escherichia coli and Salmonella typhimurium. An operon of seven genes (designated pmrHFIJKLM in S. typhimurium), which is regulated by the PmrA transcription factor and is also present in E. coli, is necessary for the maintenance of polymyxin resistance. We previously elucidated the roles of pmrHFIJK in the biosynthesis and attachment of L-Ara4N to lipid A and renamed these genes arn-BCADT, respectively. We now propose functions for the last two genes of the operon, pmrL and pmrM. Chromosomal inactivation of each of these genes in an E. coli pmrA(c) parent switched its phenotype from polymyxin-resistant to polymyxin-sensitive. Lipid A was no longer modified with L-Ara4N, even though the levels of the lipid-linked donor of the L-Ara4N moiety, undecaprenyl phosphate-alpha-L-Ara4N, were not reduced in the mutants. However, the undecaprenyl phosphate-alpha-L-Ara4N present in the mutants was less concentrated on the periplasmic surface of the inner membrane, as judged by 4-5-fold reduced labeling with the inner membrane-impermeable amine reagent N-hydroxysulfosuccin-imidobiotin. In an arnT mutant of the same pmrA(c) parent, which lacks the enzyme that transfers the L-Ara4N unit to lipid A but retains the same high levels of undecaprenyl phosphate-alpha-L-Ara4N as the parent, N-hydroxysulfosuccinimidobiotin labeling was not reduced. These results implicate pmrL and pmrM, but not arnT, in transporting undecaprenyl phosphate-alpha-L-Ara4N across the inner membrane. PmrM and PmrL, now renamed ArnE and ArnF because of their involvement in L-Ara4N modification of lipid A, may be subunits of an undecaprenyl phosphate-alpha-L-Ara4N flippase.
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Affiliation(s)
- Aixin Yan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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33
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Abstract
Structure determination has already proven useful for lead optimization and direct drug design. The number of high-resolution structures available in public databases today exceeds 30,000 and will definitely aid in structure-based drug design. Structural genomics approaches covering whole genomes, topologically similar proteins or gene families are great assets for further progress in the development of new drugs. However, membrane proteins representing 70% of current drug targets are poorly characterized structurally. The problems have been related to difficulties in obtaining large amount of recombinant membrane proteins as well as their purification and structure determination. Structural genomics has proven successful in developing new methods in areas from expression to structure determination by studying a large number of target proteins in parallel.
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Affiliation(s)
- K Lundstrom
- Flamel Technologies, 33 Avenue du Dr. Georges Lévy, 69693 Vénissieux, France.
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34
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Schuldiner S. When biochemistry meets structural biology: the cautionary tale of EmrE. Trends Biochem Sci 2007; 32:252-8. [PMID: 17452106 DOI: 10.1016/j.tibs.2007.04.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2007] [Revised: 03/19/2007] [Accepted: 04/13/2007] [Indexed: 11/23/2022]
Abstract
When biochemistry meets structural biology a more complete understanding of the mechanism of biological macromolecules is usually achieved. Several high-resolution structures of ion-coupled transporters have enriched the understanding of mechanisms of substrate recognition, translocation and coupling of substrate fluxes. However, two X-ray structures of EmrE, the smallest ion-coupled multi-drug transporter, raised questions over the veracity of the structural model and represented a cautionary tale about the difficulty of determining the 3D structures of membrane proteins and the dangers of ignoring biochemical results. The 3D structures of EmrE have since been retracted because of faulty software, but the suggestion that the protomers in the dimer are in an antiparallel topological orientation sparked controversy that is still ongoing.
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Affiliation(s)
- Shimon Schuldiner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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35
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Affiliation(s)
- Brian W Matthews
- Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.
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36
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Respondek M, Madl T, Göbl C, Golser R, Zangger K. Mapping the orientation of helices in micelle-bound peptides by paramagnetic relaxation waves. J Am Chem Soc 2007; 129:5228-34. [PMID: 17397158 DOI: 10.1021/ja069004f] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many antimicrobial peptides form alpha-helices when bound to a membrane. In addition, around 80% of residues in membrane-bound proteins are found in alpha-helical regions. The orientation and location of such helical peptides and proteins in the membrane are key factors determining their function and activity. Here we present a new solution state NMR method for obtaining the orientation of helical peptides in a membrane-mimetic environment (micelle-bound) without any chemical perturbation of the peptide-micelle system. By monitoring proton longitudinal relaxation rates upon addition of the freely water-soluble and inert paramagnetic probe Gd(DTPA-BMA) to an alpha-helical peptide, a wavelike pattern with a periodicity of 3.6 residues per turn is observed. The tilt and azimuth (rotation) angle of the helix determine the shape of this paramagnetic relaxation wave and can be obtained by least-square fitting of measured relaxation enhancements. Results are presented for the 15-residue antimicrobial peptide CM15 which forms an amphipathic helix almost parallel to the surface of the micelle. Thus, a few fast experiments enable the identification of helical regions and determination of the helix orientation within the micelle without the need for covalent modification, isotopic labeling, or sophisticated equipment. This approach opens a path toward the topology determination of alpha-helical membrane-proteins without the need for a complete NOE-based structure determination.
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Affiliation(s)
- Michal Respondek
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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37
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Poget SF, Cahill SM, Girvin ME. Isotropic bicelles stabilize the functional form of a small multidrug-resistance pump for NMR structural studies. J Am Chem Soc 2007; 129:2432-3. [PMID: 17284035 PMCID: PMC2530891 DOI: 10.1021/ja0679836] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sébastien F Poget
- Biochemistry Department, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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38
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39
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Abstract
In the world of membrane proteins, topology defines an important halfway house between the amino-acid sequence and the fully folded three-dimensional structure. Although the concept of membrane-protein topology dates back at least 30 years, recent advances in the field of translocon-mediated membrane-protein assembly, proteome-wide studies of membrane-protein topology and an exponentially growing number of high-resolution membrane-protein structures have given us a deeper understanding of how topology is determined and of how it evolves.
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Affiliation(s)
- Gunnar von Heijne
- Center for Biomembrane Research and Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm.
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40
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Erni B. The mannose transporter complex: an open door for the macromolecular invasion of bacteria. J Bacteriol 2006; 188:7036-8. [PMID: 17015642 PMCID: PMC1636239 DOI: 10.1128/jb.01074-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Bernhard Erni
- Department of Chemistry and Biochemistry, University of Bern, Freiestr. 3, CH-3012 Bern, Switzerland.
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41
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Fleishman SJ, Harrington SE, Enosh A, Halperin D, Tate CG, Ben-Tal N. Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain. J Mol Biol 2006; 364:54-67. [PMID: 17005200 DOI: 10.1016/j.jmb.2006.08.072] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 08/25/2006] [Accepted: 08/25/2006] [Indexed: 11/24/2022]
Abstract
Small multidrug resistance (SMR) transporters contribute to bacterial resistance by coupling the efflux of a wide range of toxic aromatic cations, some of which are commonly used as antibiotics and antiseptics, to proton influx. EmrE is a prototypical small multidrug resistance transporter comprising four transmembrane segments (M1-M4) that forms dimers. It was suggested recently that EmrE molecules in the dimer have different topologies, i.e. monomers have opposite orientations with respect to the membrane plane. A 3-D structure of EmrE acquired by electron cryo-microscopy (cryo-EM) at 7.5 Angstroms resolution in the membrane plane showed that parts of the structure are related by quasi-symmetry. We used this symmetry relationship, combined with sequence conservation data, to assign the transmembrane segments in EmrE to the densities seen in the cryo-EM structure. A C alpha model of the transmembrane region was constructed by considering the evolutionary conservation pattern of each helix. The model is validated by much of the biochemical data on EmrE with most of the positions that were identified as affecting substrate translocation being located around the substrate-binding cavity. A suggested mechanism for proton-coupled substrate translocation in small multidrug resistance antiporters provides a mechanistic rationale to the experimentally observed inverted topology.
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Affiliation(s)
- Sarel J Fleishman
- Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
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42
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Soskine M, Mark S, Tayer N, Mizrachi R, Schuldiner S. On Parallel and Antiparallel Topology of a Homodimeric Multidrug Transporter. J Biol Chem 2006; 281:36205-12. [PMID: 17003034 DOI: 10.1074/jbc.m607186200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recently suggested antiparallel topology of EmrE has intriguing implications for many aspects of the biology of ion-coupled transporters. However, it is at odds with biochemical data that demonstrated the same topology for all protomers in the intact cell and with extensive cross-linking studies. To examine this apparent contradiction we chemically cross-linked dimers with a rigid bifunctional maleimide using Cys replacements at positions not permissible by an antiparallel topology. A purified cross-linked dimer binds substrate and transports it in proteoliposomes with kinetic constants similar to those of the non-cross-linked dimer. The cross-linked dimers do not interact with non-cross-linked dimers as judged from the fact that inactive mutants do not affect their activity (negative dominance). The results support the contention that EmrE with parallel topology is fully functional. We show that the detergents used in crystallization increase the fraction of monomers in solution. We suggest that the antiparallel orientation observed is a result of the arrangement of the monomers in the crystal. Functionality of EmrE with the suggested antiparallel orientation of the monomers remains to be characterized.
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Affiliation(s)
- Misha Soskine
- Alexander A. Silberman Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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43
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Klammt C, Schwarz D, Löhr F, Schneider B, Dötsch V, Bernhard F. Cell-free expression as an emerging technique for the large scale production of integral membrane protein. FEBS J 2006; 273:4141-53. [PMID: 16930130 DOI: 10.1111/j.1742-4658.2006.05432.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane proteins are highly underrepresented in structural data banks due to tremendous difficulties that occur upon approaching their structural analysis. Inefficient sample preparation from conventional cellular expression systems is in many cases the first major bottleneck. Preparative scale cell-free expression has now become an emerging alternative tool for the high level production of integral membrane proteins. Many toxic effects attributed to the overproduction of recombinant proteins are eliminated by cell-free expression as viable host cells are no longer required. A unique characteristic is the open nature of cell-free systems that offers a variety of options to manipulate the reaction conditions in order to protect or to stabilize the synthesized recombinant proteins. Detergents or lipids can easily be supplemented and membrane proteins can therefore be synthesized directly into a defined hydrophobic environment of choice that permits solubility and allows the functional folding of the proteins. Alternatively, cell-free produced precipitates of membrane proteins can efficiently be solubilized in mild detergents after expression. Highly valuable for structural approaches is the fast and efficient cell-free production of uniformly or specifically labeled proteins. A considerable number of membrane proteins from diverse families like prokaryotic small multidrug transporters or eukaryotic G-protein coupled receptors have been produced in cell-free systems in high amounts and in functionally active forms. We will give an overview about the current state of the art of this new approach with special emphasis on technical aspects as well as on the functional and structural characterization of cell-free produced membrane proteins.
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Affiliation(s)
- Christian Klammt
- Centre for Biomolecular Magnetic Resonance, University of Frankfurt/Main, Institute for Biophysical Chemistry, Frankfurt/Main, Germany
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44
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Wagner S, Bader ML, Drew D, de Gier JW. Rationalizing membrane protein overexpression. Trends Biotechnol 2006; 24:364-71. [PMID: 16820235 DOI: 10.1016/j.tibtech.2006.06.008] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 04/20/2006] [Accepted: 06/16/2006] [Indexed: 11/27/2022]
Abstract
Functional and structural studies of membrane proteins usually require overexpression of the proteins in question. Often, however, the 'trial and error' approaches that are mainly used to produce membrane proteins are not successful. Our rapidly increasing understanding of membrane protein insertion, folding and degradation means that membrane protein overexpression can be more rationalized, both at the level of the overexpression host and the overexpressed membrane protein. This change of mindset is likely to have a significant impact on membrane protein research.
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Affiliation(s)
- Samuel Wagner
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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45
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Fleishman SJ, Ben-Tal N. Progress in structure prediction of α-helical membrane proteins. Curr Opin Struct Biol 2006; 16:496-504. [PMID: 16822664 DOI: 10.1016/j.sbi.2006.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Revised: 06/05/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
Transmembrane (TM) proteins comprise 20-30% of the genome but, because of experimental difficulties, they represent less than 1% of the Protein Data Bank. The dearth of membrane protein structures makes computational prediction a potentially important means of obtaining novel structures. Recent advances in computational methods have been combined with experimental data to constrain the modeling of three-dimensional structures. Furthermore, threading and ab initio modeling approaches that were effective for soluble proteins have been applied to TM domains. Surprisingly, experimental structures, proteomic analyses and bioinformatics have revealed unexpected architectures that counter long-held views on TM protein structure and stability. Future computational and experimental studies aimed at understanding the thermodynamic and evolutionary bases of these architectural details will greatly enhance predictive capabilities.
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Affiliation(s)
- Sarel J Fleishman
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel-Aviv University Ramat Aviv 69978, Israel
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46
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Endo Y, Sawasaki T. Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 2006; 17:373-80. [PMID: 16828277 DOI: 10.1016/j.copbio.2006.06.009] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/01/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Following the success of genome sequencing projects, attention has now turned to studies of the structure and function of proteins. Although cell-based expression systems for protein production have been widely used, they have certain limitations in terms of the quality and quantity of the proteins produced and for high-throughput production. Many of these limitations can be circumvented by the use of cell-free translation systems. Among such systems, the wheat germ based system is of special interest for its eukaryotic nature; it has the significant advantage of producing eukaryotic multidomain proteins in a folded state. Several advances in the use of cell-free expression systems have been made in the past few years and successful applications of these systems to produce proteins for functional and structural biology studies have been reported.
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Affiliation(s)
- Yaeta Endo
- Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Japan.
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47
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Tate CG. Comparison of three structures of the multidrug transporter EmrE. Curr Opin Struct Biol 2006; 16:457-64. [PMID: 16828280 DOI: 10.1016/j.sbi.2006.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/15/2006] [Accepted: 06/22/2006] [Indexed: 11/30/2022]
Abstract
The small multidrug resistance proteins constitute a family of bacterial antiporters that confer multidrug resistance by H(+)-linked drug efflux across the bacterial cytoplasmic membrane. The structure of EmrE, the family archetype, has been determined by electron crystallography and shows that EmrE in the membrane is an asymmetric homodimer composed of a tightly packed bundle of eight alpha helices, six of which form the substrate-binding site, which has a single molecule of tetraphenylphosphonium at its centre. Two X-ray structures of EmrE have been determined; the first structure was of a non-native conformation of EmrE that formed a crystallographic tetramer, whereas EmrE in the second structure was an asymmetric dimer containing a single molecule of bound tetraphenylphosphonium. This recent EmrE structure bears a superficial resemblance to the electron crystallographic structure and the differences were ascribed to conformational changes. However, the biological relevance of these conformational differences is questionable.
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48
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Yin Y, He X, Szewczyk P, Nguyen T, Chang G. Structure of the multidrug transporter EmrD from Escherichia coli. Science 2006; 312:741-4. [PMID: 16675700 PMCID: PMC3152482 DOI: 10.1126/science.1125629] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
EmrD is a multidrug transporter from the Major Facilitator Superfamily that expels amphipathic compounds across the inner membrane of Escherichia coli. Here, we report the x-ray structure of EmrD determined to a resolution of 3.5 angstroms. The structure reveals an interior that is composed mostly of hydrophobic residues, which is consistent with its role transporting amphipathic molecules. Two long loops extend into the inner leaflet side of the cell membrane. This region can serve to recognize and bind substrate directly from the lipid bilayer. We propose that multisubstrate specificity, binding, and transport are facilitated by these loop regions and the internal cavity.
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Affiliation(s)
| | | | | | | | - Geoffrey Chang
- Corresponding author: Geoffrey Chang, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CB-105, La Jolla, CA 92037, Tel. (858) 784-9490, Fax (858) 784-9985,
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49
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Rotem D, Steiner-Mordoch S, Schuldiner S. Identification of tyrosine residues critical for the function of an ion-coupled multidrug transporter. J Biol Chem 2006; 281:18715-22. [PMID: 16672221 DOI: 10.1074/jbc.m602088200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aromatic residues may play several roles in integral membrane proteins, including direct interaction with substrates. In this work, we studied the contribution of tyrosine residues to the activity of EmrE, a small multidrug transporter from Escherichia coli that extrudes various drugs across the plasma membrane in exchange with protons. Each of five tyrosine residues was replaced by site-directed mutagenesis. Two of these residues, Tyr-40 and Tyr-60, can be partially replaced with hydroxyamino acids, but in the case of Tyr-40, replacement with either Ser or Thr generates a protein with modified substrate specificity. Replacement of Tyr-4 with either Trp or Phe generates a functional transporter. A Cys replacement at this position generates an uncoupled protein; it binds substrate and protons and transports the substrate downhill but is impaired in uphill substrate transport in the presence of a proton gradient. The role of these residues is discussed in the context of the published structures of EmrE.
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Affiliation(s)
- Dvir Rotem
- Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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50
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Kikukawa T, Nara T, Araiso T, Miyauchi S, Kamo N. Two-component bacterial multidrug transporter, EbrAB: Mutations making each component solely functional. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:673-9. [PMID: 16750162 DOI: 10.1016/j.bbamem.2006.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 04/03/2006] [Accepted: 04/04/2006] [Indexed: 11/24/2022]
Abstract
EbrAB in Bacillus subtilis belongs to a novel small multidrug resistance (SMR) family of multidrug efflux pumps. EmrE in Escherichia coli, a representative of SMR, functions as a homo-oligomer in the membrane. On the other hand, EbrAB requires a hetero-oligomeric configuration consisting of two polypeptides, EbrA and EbrB. Although both polypeptides have a high sequence similarity, expression of either single polypeptide does not confer the multidrug-resistance. We performed mutation studies on EbrA and B to determine why EbrAB requires the hetero-oligomerization. Mutants of EbrA and B lacking both the hydrophilic loops and the C-terminus regions conferred the multidrug-resistance solely by each protein. This suggests that the hydrophilic loops and the C-terminus regions constrain them to their respective conformations upon the formation of the functional hetero-oligomer.
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Affiliation(s)
- Takashi Kikukawa
- Laboratory of Biomolecular Systems, Creative Research Initiative Sosei (CRIS), Hokkaido University, Sapporo 001-0021, Japan.
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