Identification and Characterisation of Two Functional Antibiotic MATE Efflux Pumps in the Archaeon Halorubrum Amylolyticum

Overview

Journal NPJ Antimicrob Resist

Publisher Nature Portfolio

Date 2025 Jan 22

PMID 39843964

Authors

Asma A Fakhoury

Thomas P Thompson

Khondaker Miraz Rahman

Julianne Megaw

Matthew I McAteer

Timofey Skvortsov

Stephen A Kelly

Brendan F Gilmore

Affiliations

Soon will be listed here.

Abstract

Multidrug efflux pumps have been found to play a crucial role in drug resistance in bacteria and eukaryotes. In this study, we investigated the presence of functional multidrug and toxic compound extrusion (MATE) efflux pumps, inferred from whole genome sequencing, in the halophilic archaeon Halorubrum amylolyticum CSM52 using Hoechst 33342 dye accumulation and antimicrobial sensitivity tests in the presence and absence of efflux pump inhibitors (EPIs). The whole genome sequence of H. amylolyticum CSM52 contained two putative MATE-type efflux pump genes, which may contribute to the inherent resistance to conventional antimicrobial agents reported in archaea. Antimicrobial susceptibility of the wild-type H. amylolyticum CSM52 testing revealed a lack of sensitivity to a wide range of antimicrobials, including glycopeptides, aminoglycosides, macrolides, fluoroquinolones, tetracycline, and chloramphenicol. However, the presence of EPIs, such as thioridazine, fluoxetine, and chlorpromazine, significantly increased the susceptibility of H. amylolyticum CSM52 to a number of these antimicrobials, indicating the potential involvement of efflux pumps in the observed resistance. A molecular modelling study with EPIs and substrate antimicrobials provided important insights into the molecular interactions with the putative transporter. It suggests that the occupancy of the transporter channel by EPIs has the potential to impact the efflux of antimicrobials. Phylogenetic analysis of the amino acid sequences of both MATE pumps showed low similarity with bacterial representatives, suggesting the presence of novel and distinct MATE efflux pumps in archaea. Our findings provide the first experimental evidence of active antibiotic efflux mechanisms in archaea and their potential roles in antimicrobial resistance, broadening our understanding of mechanisms of archaeal antimicrobial resistance, an overlooked aspect of AMR research.

References

Tanaka Y, Hipolito C, Maturana A, Ito K, Kuroda T, Higuchi T . Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature. 2013; 496(7444):247-51. DOI: 10.1038/nature12014. View

Sioud M, Possot O, Elie C, Sibold L, Forterre P . Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme. J Bacteriol. 1988; 170(2):946-53. PMC: 210746. DOI: 10.1128/jb.170.2.946-953.1988. View

Ninio S, Schuldiner S . Characterization of an archaeal multidrug transporter with a unique amino acid composition. J Biol Chem. 2003; 278(14):12000-5. DOI: 10.1074/jbc.M213119200. View

Brent M . Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet. 2007; 9(1):62-73. DOI: 10.1038/nrg2220. View

Zhu M, Dai X . High Salt Cross-Protects from Antibiotic Treatment through Increasing Efflux Pump Expression. mSphere. 2018; 3(2). PMC: 5909119. DOI: 10.1128/mSphere.00095-18. View

Kaatz G, Moudgal V, Seo S, Kristiansen J . Phenothiazines and thioxanthenes inhibit multidrug efflux pump activity in Staphylococcus aureus. Antimicrob Agents Chemother. 2003; 47(2):719-26. PMC: 151737. DOI: 10.1128/AAC.47.2.719-726.2003. View

Neuberger A, van Veen H . Hoechst 33342 Is a Hidden "Janus" amongst Substrates for the Multidrug Efflux Pump LmrP. PLoS One. 2015; 10(11):e0141991. PMC: 4634932. DOI: 10.1371/journal.pone.0141991. View

Thompson T, Busetti A, Gilmore B . Quorum Sensing in Facilitates Cross-Domain Signaling between Archaea and Bacteria. Microorganisms. 2023; 11(5). PMC: 10223598. DOI: 10.3390/microorganisms11051271. View

Overbeek R, Bartels D, Vonstein V, Meyer F . Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev. 2007; 107(8):3431-47. DOI: 10.1021/cr068308h. View

10.

Dridi B, Fardeau M, Ollivier B, Raoult D, Drancourt M . The antimicrobial resistance pattern of cultured human methanogens reflects the unique phylogenetic position of archaea. J Antimicrob Chemother. 2011; 66(9):2038-44. DOI: 10.1093/jac/dkr251. View

11.

Drancourt M, Nkamga V, Lakhe N, Regis J, Dufour H, Fournier P . Evidence of Archaeal Methanogens in Brain Abscess. Clin Infect Dis. 2017; 65(1):1-5. DOI: 10.1093/cid/cix286. View

12.

Bartolucci S, Contursi P, Fiorentino G, Limauro D, Pedone E . Responding to toxic compounds: a genomic and functional overview of Archaea. Front Biosci (Landmark Ed). 2013; 18(1):165-89. DOI: 10.2741/4094. View

13.

Miyauchi S, Komatsubara M, Kamo N . In archaebacteria, there is a doxorubicin efflux pump similar to mammalian P-glycoprotein. Biochim Biophys Acta. 1992; 1110(2):144-50. DOI: 10.1016/0005-2736(92)90351-l. View

14.

Otsuka M, Yasuda M, Morita Y, Otsuka C, Tsuchiya T, Omote H . Identification of essential amino acid residues of the NorM Na+/multidrug antiporter in Vibrio parahaemolyticus. J Bacteriol. 2005; 187(5):1552-8. PMC: 1064000. DOI: 10.1128/JB.187.5.1552-1558.2005. View

15.

Kumawat M, Nabi B, Daswani M, Viquar I, Pal N, Sharma P . Role of bacterial efflux pump proteins in antibiotic resistance across microbial species. Microb Pathog. 2023; 181:106182. DOI: 10.1016/j.micpath.2023.106182. View

16.

Jagessar K, Mchaourab H, Claxton D . The N-terminal domain of an archaeal multidrug and toxin extrusion (MATE) transporter mediates proton coupling required for prokaryotic drug resistance. J Biol Chem. 2019; 294(34):12807-12814. PMC: 6709631. DOI: 10.1074/jbc.RA119.009195. View

17.

Dawson R, Locher K . Structure of a bacterial multidrug ABC transporter. Nature. 2006; 443(7108):180-5. DOI: 10.1038/nature05155. View

18.

Murota Y, Tabu K, Taga T . Requirement of ABC transporter inhibition and Hoechst 33342 dye deprivation for the assessment of side population-defined C6 glioma stem cell metabolism using fluorescent probes. BMC Cancer. 2016; 16(1):847. PMC: 5097359. DOI: 10.1186/s12885-016-2895-8. View

19.

Salah A, Elleboudy N, El-Housseiny G, Yassien M . Cloning and sequencing of lsaE efflux pump gene from MDR Enterococci and its role in erythromycin resistance. Infect Genet Evol. 2021; 94:105010. DOI: 10.1016/j.meegid.2021.105010. View

20.

Li X, Nikaido H . Efflux-mediated drug resistance in bacteria: an update. Drugs. 2009; 69(12):1555-623. PMC: 2847397. DOI: 10.2165/11317030-000000000-00000. View