A role for the periplasmic adaptor protein AcrA in vetting substrate access to the RND efflux transporter AcrB.
Adaptor Proteins, Signal Transducing
/ metabolism
Anti-Bacterial Agents
/ metabolism
Bacterial Outer Membrane Proteins
/ metabolism
Biological Transport
Escherichia coli Proteins
/ genetics
Membrane Transport Proteins
/ genetics
Multidrug Resistance-Associated Proteins
/ genetics
Periplasm
/ metabolism
Salmonella typhimurium
/ genetics
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
19 03 2022
19 03 2022
Historique:
received:
19
10
2021
accepted:
14
03
2022
entrez:
20
3
2022
pubmed:
21
3
2022
medline:
20
4
2022
Statut:
epublish
Résumé
Tripartite resistance-nodulation-division (RND) efflux pumps, such as AcrAB-TolC of Salmonella Typhimurium, contribute to antibiotic resistance and comprise an inner membrane RND-transporter, an outer membrane factor, and a periplasmic adaptor protein (PAP). The role of the PAP in the assembly and active transport process remains poorly understood. Here, we identify the functionally critical residues involved in PAP-RND-transporter binding between AcrA and AcrB and show that the corresponding RND-binding residues in the closely related PAP AcrE, are also important for its interaction with AcrB. We also report a residue in the membrane-proximal domain of AcrA, that when mutated, differentially affects the transport of substrates utilising different AcrB efflux channels, namely channels 1 and 2. This supports a potential role for the PAP in sensing the substrate-occupied state of the proximal binding pocket of the transporter and substrate vetting. Understanding the PAP's role in the assembly and function of tripartite RND pumps can guide novel ways to inhibit their function to combat antibiotic resistance.
Identifiants
pubmed: 35306531
doi: 10.1038/s41598-022-08903-9
pii: 10.1038/s41598-022-08903-9
pmc: PMC8934357
doi:
Substances chimiques
Adaptor Proteins, Signal Transducing
0
Anti-Bacterial Agents
0
Bacterial Outer Membrane Proteins
0
Escherichia coli Proteins
0
Membrane Transport Proteins
0
Multidrug Resistance-Associated Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4752Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M01116X/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N002776/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M02623X/1
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s).
Références
Ventola, C. L. The antibiotic resistance crisis: Part 1: causes and threats. Pharm. Ther. 40, 277–283 (2015).
Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O. & Piddock, L. J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 13, 42–51 (2015).
pubmed: 25435309
doi: 10.1038/nrmicro3380
Du, D. et al. Multidrug efflux pumps: Structure, function and regulation. Nat. Rev. Microbiol. 16, 523–539 (2018).
pubmed: 30002505
doi: 10.1038/s41579-018-0048-6
Colclough, A. L. et al. RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance. Future Microbiol. 15, 143–157 (2020).
pubmed: 32073314
doi: 10.2217/fmb-2019-0235
Li, X. Z., Plesiat, P. & Nikaido, H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin. Microbiol. Rev. 28, 337–418 (2015).
pubmed: 25788514
pmcid: 4402952
doi: 10.1128/CMR.00117-14
Zwama, M. & Nishino, K. Ever-adapting RND efflux pumps in gram-negative multidrug-resistant pathogens: A race against time. Antibiotics 10, 774 (2021).
pubmed: 34201908
pmcid: 8300642
doi: 10.3390/antibiotics10070774
Neuberger, A., Du, D. & Luisi, B. F. Structure and mechanism of bacterial tripartite efflux pumps. Res. Microbiol. 169, 401–413 (2018).
pubmed: 29787834
doi: 10.1016/j.resmic.2018.05.003
Alav, I. et al. Structure, assembly, and function of tripartite efflux and type 1 secretion systems in gram-negative bacteria. Chem. Rev. 121, 5479–5596 (2021).
pubmed: 33909410
pmcid: 8277102
doi: 10.1021/acs.chemrev.1c00055
Nishino, K. & Yamaguchi, A. Analysis of a complete library of putative drug transporter genes in Escherichia coli. J. Bacteriol. 183, 5803–5812 (2001).
pubmed: 11566977
pmcid: 99656
doi: 10.1128/JB.183.20.5803-5812.2001
Nishino, K., Latifi, T. & Groisman, E. A. Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium. Mol. Microbiol. 59, 126–141 (2006).
pubmed: 16359323
doi: 10.1111/j.1365-2958.2005.04940.x
Zhang, Y. et al. The multidrug efflux pump MdtEF protects against nitrosative damage during the anaerobic respiration in Escherichia coli. J. Biol. Chem. 286, 26576–26584 (2011).
pubmed: 21642439
pmcid: 3143622
doi: 10.1074/jbc.M111.243261
Horiyama, T. & Nishino, K. AcrB, AcrD, and MdtABC multidrug efflux systems are involved in enterobactin export in Escherichia coli. PLoS ONE 9, e108642 (2014).
pubmed: 25259870
pmcid: 4178200
doi: 10.1371/journal.pone.0108642
Buckner, M. M. et al. Beyond antimicrobial resistance: evidence for a distinct role of the AcrD efflux pump in Salmonella biology. MBio 7, e01916-16 (2016).
pubmed: 27879336
pmcid: 5120143
doi: 10.1128/mBio.01916-16
Wang-Kan, X. et al. Lack of AcrB efflux function confers loss of virulence on Salmonella enterica serovar Typhimurium. MBio 8, e00968-17 (2017).
pubmed: 28720734
pmcid: 5516257
doi: 10.1128/mBio.00968-17
Wang-Kan, X. et al. Metabolomics reveal potential natural substrates of AcrB in Escherichia coli and Salmonella enterica Serovar Typhimurium. MBio 12, e00109-21 (2021).
pubmed: 33785633
pmcid: 8092203
doi: 10.1128/mBio.00109-21
Schaffner, S. H. et al. Extreme acid modulates fitness trade-offs of multidrug efflux pumps MdtEF-TolC and AcrAB-TolC in Escherichia coli K-12. Appl. Environ. Microbiol. 87, e0072421 (2021).
pubmed: 34085861
doi: 10.1128/AEM.00724-21
Nishino, K., Hayashi-Nishino, M. & Yamaguchi, A. H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multidrug efflux genes acrEF. Antimicrob. Agents Chemother. 53, 3541–3543 (2009).
pubmed: 19506059
pmcid: 2715579
doi: 10.1128/AAC.00371-09
Symmons, M. F., Marshall, R. L. & Bavro, V. N. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies. Front. Microbiol. 6, 513 (2015).
pubmed: 26074901
pmcid: 4446572
doi: 10.3389/fmicb.2015.00513
Du, D. et al. Structure of the AcrAB-TolC multidrug efflux pump. Nature 509, 512–515 (2014).
pubmed: 24747401
pmcid: 4361902
doi: 10.1038/nature13205
Wang, Z. et al. An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. Elife 6, e24905 (2017).
pubmed: 28355133
pmcid: 5404916
doi: 10.7554/eLife.24905
Ge, Q., Yamada, Y. & Zgurskaya, H. The C-terminal domain of AcrA is essential for the assembly and function of the multidrug efflux pump AcrAB-TolC. J. Bacteriol. 191, 4365–4371 (2009).
pubmed: 19411330
pmcid: 2698478
doi: 10.1128/JB.00204-09
McNeil, H. E. et al. Identification of binding residues between periplasmic adapter protein (PAP) and RND efflux pumps explains PAP-pump promiscuity and roles in antimicrobial resistance. PLoS Pathog. 15, e1008101 (2019).
pubmed: 31877175
pmcid: 6975555
doi: 10.1371/journal.ppat.1008101
De Angelis, F. et al. Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems. Proc. Natl. Acad. Sci. USA 107, 11038–11043 (2010).
pubmed: 20534468
pmcid: 2890744
doi: 10.1073/pnas.1003908107
Chacon, K. N., Mealman, T. D., McEvoy, M. M. & Blackburn, N. J. Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins. Proc. Natl. Acad. Sci. USA 111, 15373–15378 (2014).
pubmed: 25313055
pmcid: 4217431
doi: 10.1073/pnas.1411475111
Lu, S. & Zgurskaya, H. I. MacA, a periplasmic membrane fusion protein of the macrolide transporter MacAB-TolC, binds lipopolysaccharide core specifically and with high affinity. J. Bacteriol. 195, 4865–4872 (2013).
pubmed: 23974027
pmcid: 3807484
doi: 10.1128/JB.00756-13
Elkins, C. A. & Nikaido, H. Chimeric analysis of AcrA function reveals the importance of its C-terminal domain in its interaction with the AcrB multidrug efflux pump. J. Bacteriol. 185, 5349–5356 (2003).
pubmed: 12949086
pmcid: 193755
doi: 10.1128/JB.185.18.5349-5356.2003
Alav, I., Bavro, V. N. & Blair, J. M. A. Interchangeability of periplasmic adaptor proteins AcrA and AcrE in forming functional efflux pumps with AcrD in Salmonella enterica serovar Typhimurium. J. Antimicrob. Chemother. 76, 2558–2564 (2021).
pubmed: 34278432
pmcid: 8446912
doi: 10.1093/jac/dkab237
Zwama, M. et al. Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition. Nat. Commun. 9, 124 (2018).
pubmed: 29317622
pmcid: 5760665
doi: 10.1038/s41467-017-02493-1
Nakashima, R., Sakurai, K., Yamasaki, S., Nishino, K. & Yamaguchi, A. Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket. Nature 480, 565–569 (2011).
pubmed: 22121023
doi: 10.1038/nature10641
Tam, H. K. et al. Binding and transport of carboxylated drugs by the multidrug transporter AcrB. J. Mol. Biol. 432, 861–877 (2020).
pubmed: 31881208
doi: 10.1016/j.jmb.2019.12.025
Glavier, M. et al. Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex. Nat. Commun. 11, 4948 (2020).
pubmed: 33009415
pmcid: 7532149
doi: 10.1038/s41467-020-18770-5
Tsutsumi, K. et al. Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism. Nat. Commun. 10, 1520 (2019).
pubmed: 30944318
pmcid: 6447562
doi: 10.1038/s41467-019-09463-9
Mikolosko, J., Bobyk, K., Zgurskaya, H. I. & Ghosh, P. Conformational flexibility in the multidrug efflux system protein AcrA. Structure 14, 577–587 (2006).
pubmed: 16531241
pmcid: 1997295
doi: 10.1016/j.str.2005.11.015
Tam, H. K. et al. Allosteric drug transport mechanism of multidrug transporter AcrB. Nat. Commun. 12, 3889 (2021).
pubmed: 34188038
pmcid: 8242077
doi: 10.1038/s41467-021-24151-3
Schuster, S., Vavra, M. & Kern, W. V. Evidence of a substrate-discriminating entrance channel in the lower porter domain of the multidrug resistance efflux pump AcrB. Antimicrob. Agents Chemother. 60, 4315–4323 (2016).
pubmed: 27161641
pmcid: 4914648
doi: 10.1128/AAC.00314-16
Murakami, S., Nakashima, R., Yamashita, E. & Yamaguchi, A. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419, 587–593 (2002).
pubmed: 12374972
doi: 10.1038/nature01050
Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T. & Yamaguchi, A. Crystal structures of a multidrug transporter reveal a functionally rotating mechanism. Nature 443, 173–179 (2006).
pubmed: 16915237
doi: 10.1038/nature05076
Zwama, M. & Yamaguchi, A. Molecular mechanisms of AcrB-mediated multidrug export. Res. Microbiol. 169, 372–383 (2018).
pubmed: 29807096
doi: 10.1016/j.resmic.2018.05.005
Daury, L. et al. Tripartite assembly of RND multidrug efflux pumps. Nat. Commun. 7, 10731 (2016).
pubmed: 26867482
pmcid: 4754349
doi: 10.1038/ncomms10731
Sennhauser, G., Amstutz, P., Briand, C., Storchenegger, O. & Grutter, M. G. Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PLoS Biol. 5, e7 (2007).
pubmed: 17194213
doi: 10.1371/journal.pbio.0050007
Chen, M. et al. In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution. Structure 30, 107–113 (2022).
pubmed: 34506732
doi: 10.1016/j.str.2021.08.008
Wray, C. & Sojka, W. J. Experimental Salmonella typhimurium infection in calves. Res. Vet. Sci. 25, 139–143 (1978).
pubmed: 364573
doi: 10.1016/S0034-5288(18)32968-0
Smith, H. E. & Blair, J. M. Redundancy in the periplasmic adaptor proteins AcrA and AcrE provides resilience and an ability to export substrates of multidrug efflux. J. Antimicrob. Chemother. 69, 982–987 (2014).
pubmed: 24302652
doi: 10.1093/jac/dkt481
CLSI. Performance standards for antimicrobial susceptibility testing, 30th edition, 30th edn. Clinical and Laboratory Standards Institute (2020).
Brezovsky, J., Kozlikova, B. & Damborsky, J. Computational analysis of protein tunnels and channels. Methods Mol. Biol. 1685, 25–42 (2018).
pubmed: 29086302
doi: 10.1007/978-1-4939-7366-8_3
Schrödinger. The PyMOL Molecular Graphics System. 2.5.2 edn. Schrödinger LLC (2022).
Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320-324 (2014).
pubmed: 24753421
pmcid: 4086106
doi: 10.1093/nar/gku316