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High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration Dependent

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Abstract

Overexpression of tripartite efflux pump systems in gram-negative bacteria is a principal component of antibiotic resistance. High-yield purification of the outer membrane component of these systems will enable biochemical and structural interrogation of their mechanisms of action and allow testing of compounds that target them. However, preparation of these proteins is typically hampered by low yields, requiring laborious large-scale efforts. If refolding conditions can be found, refolding these proteins from inclusion bodies can lead to increased yields as compared to membrane isolations. A classical method for refolding outer membrane proteins involves unfolding inclusion bodies in urea followed by refolding in lipid or detergent micelles. However, that method has not yet been successful in refolding tripartite efflux pump TolC. Here, we find that refolding TolC from inclusion bodies requires an additional oligomerization enhancing step of sample concentration. We show that by our method of refolding, homotrimeric TolC remains folded in SDS-PAGE, retains binding to an endogenous ligand, and recapitulates the known crystal structure by single particle cryoEM analysis. We find that TolC refolding is concentration dependent. We then extended our method to refolding CmeC, a homologous protein from Campylobacter jejuni, and find that concentration-dependent oligomerization is a general feature of these systems. Because outer membrane efflux pump components are ubiquitous across gram-negative species, we anticipate that incorporating a concentration step in refolding protocols will promote correct refolding allowing for reliable, high-yield preparation of this family of proteins.

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Acknowledgements

We gratefully acknowledge Rik Dhar, Alex Little, and Jaden Anderson for discussions and feedback, Rajeev Misra for the pTrc vector containing the TolC gene, and Vasileios Petrou for guidance on nanodiscs.

Funding

The Gordon and Betty Moore Inventor Fellowship to JSGS and NIGMS award DP2GM128201 to Joanna Slusky, and P20GM103638 and Kansas INBRE, P20 GM103418 and 2K12GM063651 to Jimmy Budiardjo. We are also grateful for inspiration and mentorship from Stephen White. Our understanding of membrane protein folding is richer for your contributions and conferences are more fun when you are there. Thank you for leading the way in asking the important questions. Happy birthday and many happy returns.

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Author notes

  1. S. Jimmy Budiardjo and Ayotunde Paul Ikujuni have contributed equally to this work.

Authors and Affiliations

  1. Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS, 66045-7534, USA

    S. Jimmy Budiardjo & Joanna S. G. Slusky

  2. Department of Molecular Biosciences, The University of Kansas, 2030 Becker Dr., Lawrence, KS, 66045-7534, USA

    Ayotunde Paul Ikujuni, Andrés Cordova & Joanna S. G. Slusky

  3. Rutgers CryoEM & Nanoimaging Facility, and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA

    Emre Firlar & Jason T. Kaelber

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  1. S. Jimmy Budiardjo
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  2. Ayotunde Paul Ikujuni
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Correspondence to Joanna S. G. Slusky.

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Budiardjo, S.J., Ikujuni, A.P., Firlar, E. et al. High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration Dependent. J Membrane Biol 254, 41–50 (2021). https://doi.org/10.1007/s00232-020-00161-y

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