DOI QR코드

DOI QR Code

Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Suggests an Alternative Assembly Mode

  • Kim, Jin-Sik (Department of Manufacturing Pharmacy, Pusan National University) ;
  • Jeong, Hyeongseop (Division of Electron Microscopic Research, Korea Basic Science Institute) ;
  • Song, Saemee (Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University) ;
  • Kim, Hye-Yeon (Division of Magnetic Resonance, Korea Basic Science Institute) ;
  • Lee, Kangseok (Department of Life Science, Chung-Ang University) ;
  • Hyun, Jaekyung (Division of Electron Microscopic Research, Korea Basic Science Institute) ;
  • Ha, Nam-Chul (Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University)
  • Received : 2014.10.17
  • Accepted : 2014.11.18
  • Published : 2015.02.28

Abstract

Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the ${\alpha}$-barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.

Keywords

References

  1. Du, D., Wang, Z., James, N.R., Voss, J.E., Klimont, E., Ohene- Agyei, T., Venter, H., Chiu, W., and Luisi, B.F. (2014). Structure of the AcrAB-TolC multidrug efflux pump. Nature 509, 512-515. https://doi.org/10.1038/nature13205
  2. Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132. https://doi.org/10.1107/S0907444904019158
  3. Fralick, J.A. (1996). Evidence that TolC is required for functioning of the Mar/AcrAB efflux pump of Escherichia coli. J. Bacteriol. 178, 5803-5805. https://doi.org/10.1128/jb.178.19.5803-5805.1996
  4. Goddard, T.D., Huang, C.C., and Ferrin, T.E. (2007). Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157, 281-287. https://doi.org/10.1016/j.jsb.2006.06.010
  5. Hinchliffe, P., Symmons, M.F., Hughes, C., and Koronakis, V. (2013). Structure and operation of bacterial tripartite pumps. Annu. Rev. Microbiol. 67, 221-242. https://doi.org/10.1146/annurev-micro-092412-155718
  6. Janganan, T.K., Bavro, V.N., Zhang, L., Matak-Vinkovic, D., Barrera, N.P., Venien-Bryan, C., Robinson, C.V., Borges-Walmsley, M.I., and Walmsley, A.R. (2011). Evidence for the assembly of a bacterial tripartite multidrug pump with a stoichiometry of 3:6:3. J. Biol. Chem. 286, 26900-26912. https://doi.org/10.1074/jbc.M111.246595
  7. Kim, H.M., Xu, Y., Lee, M., Piao, S., Sim, S.H., Ha, N.C., and Lee, K. (2010). Functional interrelationships between the AcrA hairpin tip region and the TolC aperture tip region for the formation of bacterial tripartite efflux pump AcrAB-TolC. J. Bacteriol. 192, 4498-4503. https://doi.org/10.1128/JB.00334-10
  8. Koronakis, V., Sharff, A., Koronakis, E., Luisi, B., and Hughes, C. (2000). Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405, 914-919. https://doi.org/10.1038/35016007
  9. Lee, M., Jun, S.Y., Yoon, B.Y., Song, S., Lee, K., and Ha, N.C. (2012). Membrane fusion proteins of type I secretion system and tripartite efflux pumps share a binding motif for TolC in gram-negative bacteria. PLoS One 7, e40460. https://doi.org/10.1371/journal.pone.0040460
  10. Lewis, K. (2000). Translocases: a bacterial tunnel for drugs and proteins. Curr. Biol. 10, R678-681. https://doi.org/10.1016/S0960-9822(00)00682-5
  11. Lobedanz, S., Bokma, E., Symmons, M.F., Koronakis, E., Hughes, C., and Koronakis, V. (2007). A periplasmic coiled-coil interface underlying TolC recruitment and the assembly of bacterial drug efflux pumps. Proc. Natl. Acad. Sci. USA 104, 4612-4617. https://doi.org/10.1073/pnas.0610160104
  12. Ma, D., Cook, D.N., Alberti, M., Pon, N.G., Nikaido, H., and Hearst, J.E. (1993). Molecular cloning and characterization of acrA and acrE genes of Escherichia coli. J. Bacteriol. 175, 6299-6313. https://doi.org/10.1128/jb.175.19.6299-6313.1993
  13. Martins, A., and Amaral, L. (2012). Screening for efflux pump systems of bacteria by the new acridine orange agar method. In Vivo 26, 203-206.
  14. Mikolosko, J., Bobyk, K., Zgurskaya, H.I., and Ghosh, P. (2006). Conformational flexibility in the multidrug efflux system protein AcrA. Structure 14, 577-587. https://doi.org/10.1016/j.str.2005.11.015
  15. Mima, T., Joshi, S., Gomez-Escalada, M., and Schweizer, H.P. (2007). Identification and characterization of TriABC-OpmH, a triclosan efflux pump of Pseudomonas aeruginosa requiring two membrane fusion proteins. J. Bacteriol. 189, 7600-7609. https://doi.org/10.1128/JB.00850-07
  16. Morshed, S.R., Lei, Y., Yoneyama, H., and Nakae, T. (1995). Expression of genes associated with antibiotic extrusion in Pseudomonas aeruginosa. Biochem. Biophys. Res. Commun. 210, 356-362. https://doi.org/10.1006/bbrc.1995.1669
  17. Murakami, S., Nakashima, R., Yamashita, E., and Yamaguchi, A. (2002). Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419, 587-593. https://doi.org/10.1038/nature01050
  18. Narita, S., Eda, S., Yoshihara, E., and Nakae, T. (2003). Linkage of the efflux-pump expression level with substrate extrusion rate in the MexAB-OprM efflux pump of Pseudomonas aeruginosa. Biochem. Biophys. Res. Commun. 308, 922-926. https://doi.org/10.1016/S0006-291X(03)01512-2
  19. Nikaido, H., and Zgurskaya, H.I. (1999). Antibiotic efflux mechanisms. Curr. Opin. Infect Dis. 12, 529-536. https://doi.org/10.1097/00001432-199912000-00001
  20. Rouquette-Loughlin, C.E., Balthazar, J.T., and Shafer, W.M. (2005). Characterization of the MacA-MacB efflux system in Neisseria gonorrhoeae. J. Antimicrob. Chemother 56, 856-860. https://doi.org/10.1093/jac/dki333
  21. Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., and Pos, K.M. (2006). Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science 313, 1295-1298. https://doi.org/10.1126/science.1131542
  22. Stegmeier, J.F., Polleichtner, G., Brandes, N., Hotz, C., and Andersen, C. (2006). Importance of the adaptor (membrane fusion) protein hairpin domain for the functionality of multidrug efflux pumps. Biochemistry 45, 10303-10312. https://doi.org/10.1021/bi060320g
  23. Su, C.C., Long, F., Zimmermann, M.T., Rajashankar, K.R., Jernigan, R.L., and Yu, E.W. (2011). Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. Nature 470, 558-562. https://doi.org/10.1038/nature09743
  24. Symmons, M.F., Bokma, E., Koronakis, E., Hughes, C., and Koronakis, V. (2009). The assembled structure of a complete tripartite bacterial multidrug efflux pump. Proc. Natl. Acad. Sci. USA 106, 7173-7178. https://doi.org/10.1073/pnas.0900693106
  25. Tamura, N., Murakami, S., Oyama, Y., Ishiguro, M., and Yamaguchi, A. (2005). Direct interaction of multidrug efflux transporter AcrB and outer membrane channel TolC detected via site-directed disulfide cross-linking. Biochemistry 44, 11115-11121. https://doi.org/10.1021/bi050452u
  26. Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., and Ludtke, S.J. (2007). EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46. https://doi.org/10.1016/j.jsb.2006.05.009
  27. Touze, T., Eswaran, J., Bokma, E., Koronakis, E., Hughes, C., and Koronakis, V. (2004). Interactions underlying assembly of the Escherichia coli AcrAB-TolC multidrug efflux system. Mol. Microbiol. 53, 697-706. https://doi.org/10.1111/j.1365-2958.2004.04158.x
  28. Trepout, S., Taveau, J.C., Benabdelhak, H., Granier, T., Ducruix, A., Frangakis, A.S., and Lambert, O. (2010). Structure of reconstituted bacterial membrane efflux pump by cryo electron tomography. Biochim. Biophys. Acta 1798, 1953-1960. https://doi.org/10.1016/j.bbamem.2010.06.019
  29. Xu, Y., Sim, S.H., Nam, K.H., Jin, X.L., Kim, H.M., Hwang, K.Y., Lee, K., and Ha, N.C. (2009). Crystal structure of the periplasmic region of MacB, a noncanonic ABC transporter. Biochemistry 48, 5218-5225. https://doi.org/10.1021/bi900415t
  30. Xu, Y., Sim, S.H., Song, S., Piao, S., Kim, H.M., Jin, X.L., Lee, K., and Ha, N.C. (2010). The tip region of the MacA alpha-hairpin is important for the binding to TolC to the Escherichia coli MacABTolC pump. Biochem. Biophys. Res. Commun. 394, 962-965. https://doi.org/10.1016/j.bbrc.2010.03.097
  31. Xu, Y., Lee, M., Moeller, A., Song, S., Yoon, B.Y., Kim, H.M., Jun, S.Y., Lee, K., and Ha, N.C. (2011a). Funnel-like hexameric assembly of the periplasmic adapter protein in the tripartite multidrug efflux pump in gram-negative bacteria. J. Biol. Chem. 286, 17910-17920. https://doi.org/10.1074/jbc.M111.238535
  32. Xu, Y., Song, S., Moeller, A., Kim, N., Piao, S., Sim, S.H., Kang, M., Yu, W., Cho, H.S., Chang, I., et al. (2011b). Functional implications of an intermeshing cogwheel-like interaction between TolC and MacA in the action of macrolide-specific efflux pump MacAB-TolC. J. Biol. Chem. 286, 13541-13549. https://doi.org/10.1074/jbc.M110.202598
  33. Xu, Y., Moeller, A., Jun, S.Y., Lee, M., Yoon, B.Y., Kim, J.S., Lee, K., and Ha, N.C. (2012). Assembly and channel opening of the outer membrane protein in tripartite drug efflux pumps of Gramnegative bacteria. J. Biol. Chem. 287, 11740-11750. https://doi.org/10.1074/jbc.M111.329375
  34. Yum, S., Xu, Y., Piao, S., Sim, S.H., Kim, H.M., Jo, W.S., Kim, K.J., Kweon, H.S., Jeong, M.H., Jeon, H., et al. (2009). Crystal structure of the periplasmic component of a tripartite macrolidespecific efflux pump. J. Mol. Biol. 387, 1286-1297. https://doi.org/10.1016/j.jmb.2009.02.048

Cited by

  1. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism vol.5, pp.1, 2015, https://doi.org/10.1038/srep16441
  2. Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria vol.24, pp.3, 2016, https://doi.org/10.1016/j.str.2015.12.012
  3. Catch me if you can: a biotinylated proteoliposome affinity assay for the investigation of assembly of the MexA-MexB-OprM efflux pump from Pseudomonas aeruginosa vol.6, 2015, https://doi.org/10.3389/fmicb.2015.00541
  4. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota vol.9, pp.390, 2017, https://doi.org/10.1126/scitranslmed.aal4069
  5. An overview of bacterial efflux pumps and computational approaches to study efflux pump inhibitors vol.8, pp.2, 2016, https://doi.org/10.4155/fmc.15.173
  6. Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC vol.24, pp.2, 2016, https://doi.org/10.1016/j.str.2015.12.007
  7. Multidrug efflux pumps as main players in intrinsic and acquired resistance to antimicrobials vol.28, 2016, https://doi.org/10.1016/j.drup.2016.06.007
  8. An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump vol.6, 2017, https://doi.org/10.7554/eLife.24905
  9. Hexameric assembly of membrane fusion protein YknX of the sporulation delaying efflux pump from Bacillus amyloliquefaciens 2017, https://doi.org/10.1016/j.bbrc.2017.09.059
  10. The ins and outs of RND efflux pumps in Escherichia coli vol.6, 2015, https://doi.org/10.3389/fmicb.2015.00587
  11. Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins vol.11, pp.4, 2016, https://doi.org/10.1371/journal.pone.0152733
  12. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies vol.6, 2015, https://doi.org/10.3389/fmicb.2015.00513
  13. Structure, mechanism and cooperation of bacterial multidrug transporters vol.33, 2015, https://doi.org/10.1016/j.sbi.2015.07.015
  14. Mechanisms of envelope permeability and antibiotic influx and efflux in Gram-negative bacteria vol.2, pp.3, 2017, https://doi.org/10.1038/nmicrobiol.2017.1
  15. Structure of the MacAB–TolC ABC-type tripartite multidrug efflux pump vol.2, 2017, https://doi.org/10.1038/nmicrobiol.2017.70
  16. Tripartite assembly of RND multidrug efflux pumps vol.7, 2016, https://doi.org/10.1038/ncomms10731
  17. Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations vol.120, pp.9, 2016, https://doi.org/10.1021/acs.jpcb.5b11942
  18. Assembly and operation of bacterial tripartite multidrug efflux pumps vol.23, pp.5, 2015, https://doi.org/10.1016/j.tim.2015.01.010
  19. Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model vol.53, pp.6, 2015, https://doi.org/10.1007/s12275-015-5248-4
  20. Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition vol.9, pp.1, 2018, https://doi.org/10.1038/s41467-017-02493-1
  21. Structure of a MacAB-like efflux pump from Streptococcus pneumoniae vol.9, pp.1, 2018, https://doi.org/10.1038/s41467-017-02741-4
  22. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System vol.6, pp.2296-634X, 2018, https://doi.org/10.3389/fcell.2018.00128
  23. Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis vol.9, pp.1664-302X, 2019, https://doi.org/10.3389/fmicb.2018.03322
  24. Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system vol.57, pp.3, 2019, https://doi.org/10.1007/s12275-019-8520-1
  25. Structural basis of RND-type multidrug exporters vol.6, pp.None, 2015, https://doi.org/10.3389/fmicb.2015.00327
  26. Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa vol.6, pp.None, 2015, https://doi.org/10.3389/fmicb.2015.00660
  27. AcrB-AcrA Fusion Proteins That Act as Multidrug Efflux Transporters vol.198, pp.2, 2016, https://doi.org/10.1128/jb.00587-15
  28. Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family vol.7, pp.1, 2015, https://doi.org/10.1128/ecosalplus.esp-0019-2015
  29. Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump vol.429, pp.24, 2017, https://doi.org/10.1016/j.jmb.2017.09.018
  30. Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis vol.59, pp.5, 2015, https://doi.org/10.1021/acs.jcim.8b00957
  31. Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly vol.5, pp.11, 2015, https://doi.org/10.1021/acsinfecdis.9b00273
  32. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC vol.10, pp.1, 2015, https://doi.org/10.1038/s41467-019-10512-6
  33. Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa vol.42, pp.12, 2019, https://doi.org/10.14348/molcells.2019.0168
  34. AcrB: a mean, keen, drug efflux machine vol.1459, pp.1, 2015, https://doi.org/10.1111/nyas.14239
  35. A Comparative Review on Current and Future Drug Targets Against Bacteria & Malaria vol.21, pp.None, 2020, https://doi.org/10.2174/1389450121666200129103618
  36. Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump vol.7, pp.None, 2015, https://doi.org/10.3389/fmolb.2020.00166
  37. Site-Directed Mutagenesis Reveals Crucial Residues in Escherichia coli Resistance-Nodulation-Division Efflux Pump OqxB vol.26, pp.6, 2020, https://doi.org/10.1089/mdr.2019.0165
  38. Probing the Dynamics of AcrB Through Disulfide Bond Formation vol.5, pp.34, 2015, https://doi.org/10.1021/acsomega.0c02921
  39. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria vol.6, pp.9, 2020, https://doi.org/10.1021/acsinfecdis.0c00384
  40. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria vol.121, pp.9, 2015, https://doi.org/10.1021/acs.chemrev.1c00055
  41. Ever-Adapting RND Efflux Pumps in Gram-Negative Multidrug-Resistant Pathogens: A Race against Time vol.10, pp.7, 2021, https://doi.org/10.3390/antibiotics10070774
  42. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA vol.20, pp.None, 2022, https://doi.org/10.1016/j.csbj.2021.11.042