Skip to main content

Biochemical Reconstitution and Characterization of Multicomponent Drug Efflux Transporters

  • Protocol
  • First Online:
Bacterial Multidrug Exporters

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1700))

Abstract

Efflux pumps are the major determinants in bacterial multidrug resistance. In Gram-negative bacteria, efflux transporters are organized as macromolecular tripartite machineries that span the two-membrane cell envelope of the bacterium. Biochemical data on purified proteins are essential to draw a mechanistic picture of this highly dynamical, multicomponent, efflux system. We describe protocols for the reconstitution and the in vitro study of transporters belonging to RND and ABC superfamilies: the AcrAB–TolC and MacAB–TolC efflux systems from Escherichia coli and the MexAB–OprM efflux pump from Pseudomonas aeruginosa.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Nikaido H, Vaara M (1985) Molecular basis of bacterial outer membrane permeability. Microbiol Rev 49:1–32

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Lomovskaya O, Lewis K (1992) Emr, an Escherichia coli locus for multidrug resistance. Proc Natl Acad Sci U S A 89:8938–8942

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ma D, Cook DN, Alberti M, Pon NG, Nikaido H, Hearst JE (1993) Molecular cloning and characterization of acrA and acrE genes of Escherichia coli. J Bacteriol 175:6299–6313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lomovskaya O, Zgurskaya HI, Totrov M, Watkins WJ (2007) Waltzing transporters and ‘the dance macabre’ between humans and bacteria. Nat Rev Drug Discov 6:56–65

    Article  CAS  PubMed  Google Scholar 

  5. Nikaido H (2001) Preventing drug access to targets: cell surface permeability barriers and active efflux in bacteria. Semin Cell Dev Biol 12:215–223

    Article  CAS  PubMed  Google Scholar 

  6. Zgurskaya HI, Krishnamoorthy G, Tikhonova EB, Lau SY, Stratton KL (2003) Mechanism of antibiotic efflux in Gram-negative bacteria. Front Biosci 8:s862–s873

    Article  CAS  PubMed  Google Scholar 

  7. Dinh T, Paulsen IT, Saier MH Jr (1994) A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of gram-negative bacteria. J Bacteriol 176:3825–3831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Aires JR, Nikaido H (2005) Aminoglycosides are captured from both periplasm and cytoplasm by the AcrD multidrug efflux transporter of Escherichia coli. J Bacteriol 187:1923–1929

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Krishnamoorthy G, Tikhonova EB, Zgurskaya HI (2008) Fitting periplasmic membrane fusion proteins to inner membrane transporters: mutations that enable Escherichia coli AcrA to function with Pseudomonas aeruginosa MexB. J Bacteriol 190:691–698

    Article  CAS  PubMed  Google Scholar 

  10. Zgurskaya HI, Nikaido H (1999) Bypassing the periplasm: reconstitution of the AcrAB multidrug efflux pump of Escherichia coli. Proc Natl Acad Sci U S A 96:7190–7195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Andersen C, Hughes C, Koronakis V (2001) Protein export and drug efflux through bacterial channel-tunnels. Curr Opin Cell Biol 13:412–416

    Article  CAS  PubMed  Google Scholar 

  12. Thanabalu T, Koronakis E, Hughes C, Koronakis V (1998) Substrate-induced assembly of a contiguous channel for protein export from E. coli: reversible bridging of an inner-membrane translocase to an outer membrane exit pore. EMBO J 17:6487–6496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Paulsen IT, Chen J, Nelson KE, Saier MH Jr (2001) Comparative genomics of microbial drug efflux systems. J Mol Microbiol Biotechnol 3:145–150

    CAS  PubMed  Google Scholar 

  14. Saier MH Jr, Beatty JT, Goffeau A, Harley KT, Heijne WH, Huang SC, Jack DL, Jahn PS, Lew K, Liu J, Pao SS, Paulsen IT, Tseng TT, Virk PS (1999) The major facilitator superfamily. J Mol Microbiol Biotechnol 1:257–279

    CAS  PubMed  Google Scholar 

  15. Tseng TT, Gratwick KS, Kollman J, Park D, Nies DH, Goffeau A, Saier MH Jr (1999) The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J Mol Microbiol Biotechnol 1:107–125

    CAS  PubMed  Google Scholar 

  16. Saier MH Jr, Paulsen IT, Sliwinski MK, Pao SS, Skurray RA, Nikaido H (1998) Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria. FASEB J 12:265–274

    CAS  PubMed  Google Scholar 

  17. Verchere A, Dezi M, Adrien V, Broutin I, Picard M (2015) In vitro transport activity of the fully assembled MexAB-OprM efflux pump from Pseudomonas aeruginosa. Nat Commun 6:6890

    Article  CAS  PubMed  Google Scholar 

  18. Modali SD, Zgurskaya HI (2011) The periplasmic membrane proximal domain of MacA acts as a switch in stimulation of ATP hydrolysis by MacB transporter. Mol Microbiol 81:937–951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tikhonova EB, Dastidar V, Rybenkov VV, Zgurskaya HI (2009) Kinetic control of TolC recruitment by multidrug efflux complexes. Proc Natl Acad Sci U S A 106:16416–16421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tikhonova EB, Devroy VK, Lau SY, Zgurskaya HI (2007) Reconstitution of the Escherichia coli macrolide transporter: the periplasmic membrane fusion protein MacA stimulates the ATPase activity of MacB. Mol Microbiol 63:895–910

    Article  CAS  PubMed  Google Scholar 

  21. Goldberg M, Pribyl T, Juhnke S, Nies DH (1999) Energetics and topology of CzcA, a cation/proton antiporter of the resistance-nodulation-cell division protein family. J Biol Chem 274:26065–26070

    Article  CAS  PubMed  Google Scholar 

  22. Lu S, Zgurskaya HI (2012) Role of ATP binding and hydrolysis in assembly of MacAB-TolC macrolide transporter. Mol Microbiol 86:1132–1143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Su CC, Long F, Zimmermann MT, Rajashankar KR, Jernigan RL, Yu EW (2011) Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. Nature 470:558–562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, Yu EW (2009) Crystal structure of the membrane fusion protein CusB from Escherichia coli. J Mol Biol 393:342–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lin HT, Bavro VN, Barrera NP, Frankish HM, Velamakanni S, van Veen HW, Robinson CV, Borges-Walmsley MI, Walmsley AR (2009) MacB ABC transporter is a dimer whose ATPase activity and macrolide-binding capacity are regulated by the membrane fusion protein MacA. J Biol Chem 284:1145–1154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Welch A, Awah CU, Jing S, van Veen Hendrik W, Venter H (2010) Promiscuous partnering and independent activity of MexB, the multidrug transporter protein from Pseudomonas aeruginosa. Biochem J 430:355–364

    Article  CAS  PubMed  Google Scholar 

  27. Verchère A, Broutin I, Picard M (2012) Photo-induced proton gradients for the in vitro investigation of bacterial efflux pumps. Sci Rep 2:306

    Article  PubMed  PubMed Central  Google Scholar 

  28. Kapoor V, Wendell D (2013) Engineering bacterial efflux pumps for solar-powered bioremediation of surface waters. Nano Lett 13:2189–2193

    Article  CAS  PubMed  Google Scholar 

  29. Picard M, Verchère A, Broutin I (2012) Monitoring the active transport of efflux pumps after their reconstitution into proteoliposomes: caveats and keys. Anal Biochem 420:194–196

    Article  CAS  PubMed  Google Scholar 

  30. Zgurskaya HI, Nikaido H (1999) AcrA is a highly asymmetric protein capable of spanning the periplasm. J Mol Biol 285:409–420

    Article  CAS  PubMed  Google Scholar 

  31. Mokhonov V, Mokhonova E, Yoshihara E, Masui R, Sakai M, Akama H, Nakae T (2005) Multidrug transporter MexB of Pseudomonas aeruginosa: overexpression, purification, and initial structural characterization. Protein Expr Purif 40:91–100

    Article  CAS  PubMed  Google Scholar 

  32. Trépout S, Taveau JC, Benabdelhak H, Granier T, Ducruix A, Frangakis AS, Lambert O (2010) Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography. Biochim Biophys Acta Biomembr 1798:1953–1960

    Article  Google Scholar 

  33. Gilson L, Mahanty HK, Kolter R (1990) Genetic analysis of an MDR-like export system: the secretion of colicin V. EMBO J 9:3875–3894

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Phan G, Benabdelhak H, Lascombe MB, Benas P, Rety S, Picard M, Ducruix A, Etchebest C, Broutin I (2010) Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel. Structure 18:507–517

    Article  CAS  PubMed  Google Scholar 

  35. Ponchon L, Catala M, Seijo B, El Khouri M, Dardel F, Nonin-Lecomte S, Tisné C (2013) Co-expression of RNA–protein complexes in Escherichia coli and applications to RNA biology. Nucleic Acids Res 41:e150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Ames BN (1966) Assay of inorganic phosphate, total phosphate and phospholipids. Methods Enzymol VIII:115–118

    Article  Google Scholar 

  37. Randerath E, Randerath K (1967) Ion-exchange thin-layer chromatography: XVI. Techniques for preparation and analysis of oligonucleotides. J Chromatogr 31:485–499

    Article  CAS  PubMed  Google Scholar 

  38. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Lopez O, de la Maza A, Coderch L, Lopez-Iglesias C, Wehrli E, Parra JL (1998) Direct formation of mixed micelles in the solubilization of phospholipid liposomes by Triton X-100. FEBS Lett 426:314–318

    Article  CAS  PubMed  Google Scholar 

  40. Ntsogo Enguene VY, Verchère A, Phan G, Broutin I, Picard M (2015) 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. Front Microbiol 6:541

    PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Martin Picard or Helen I. Zgurskaya .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Picard, M., Tikhonova, E.B., Broutin, I., Lu, S., Verchère, A., Zgurskaya, H.I. (2018). Biochemical Reconstitution and Characterization of Multicomponent Drug Efflux Transporters. In: Yamaguchi, A., Nishino, K. (eds) Bacterial Multidrug Exporters. Methods in Molecular Biology, vol 1700. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7454-2_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7454-2_8

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7452-8

  • Online ISBN: 978-1-4939-7454-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics