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Article Dans Une Revue ISME Communications Année : 2024

HME, NFE and HAE-1 efflux pumps in gram-negative bacteria: a comprehensive phylogenetic and ecological approach

Résumé

Abstract The three primary resistance-nodulation-division (RND) efflux pump families (HME, NFE and HAE-1) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and qPCR analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches.
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Dates et versions

hal-04446672 , version 1 (03-04-2024)

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Paternité

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Josselin Bodilis, Olwen Simenel, Serge Michalet, Elisabeth Brothier, Thibault Meyer, et al.. HME, NFE and HAE-1 efflux pumps in gram-negative bacteria: a comprehensive phylogenetic and ecological approach. ISME Communications, 2024, 4 (1), pp.ycad018. ⟨10.1093/ismeco/ycad018⟩. ⟨hal-04446672⟩
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