HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance

Duval, Manuel; D, Dar; Carvalho, Frédéric A.; Rocha, Eduardo P. C.; Sorek, Rotem; Cossart, Pascale

doi:10.1073/pnas.1810555115

Cited by 48 publications

(74 citation statements)

References 37 publications

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“…7), demonstrating that the ribosome-associated HrpA and SCO2532 proteins indeed contribute to resistance to translation-targeting antibiotics. Interestingly, the strain lacking HflX ribosomeassociated GTPase showed a significant effect on sensitivity to erythromycin (fourfold), supporting a previous report that a hflX homolog mediates erythromycin resistance (47,48). Complementation of the hrpA, SCO2532, or hflX gene restored resistance to erythromycin or tetracycline (except SCO2532 to tetracycline sensitivity), further supporting that these proteins directly mediate antibiotic resistance.…”

Section: Category (No Of Genes) Asupporting

confidence: 81%

The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition

Lee

Yoo

Kim

et al. 2020

mBio

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Bacteria that encounter antibiotics can efficiently change their physiology to develop resistance. This intrinsic antibiotic resistance is mediated by multiple pathways, including a regulatory system(s) that activates specific genes. In some Streptomyces and Mycobacterium spp., the WblC/WhiB7 transcription factor is required for intrinsic resistance to translation-targeting antibiotics. Wide conservation of WblC/WhiB7 within Actinobacteria indicates a critical role of WblC/WhiB7 in developing resistance to such antibiotics. Here, we identified 312 WblC target genes in Streptomyces coelicolor, a model antibiotic-producing bacterium, using a combined analysis of RNA sequencing and chromatin immunoprecipitation sequencing. Interestingly, WblC controls many genes involved in translation, in addition to previously identified antibiotic resistance genes. Moreover, WblC promotes translation rate during antibiotic stress by altering the ribosome-associated protein composition. Our genome-wide analyses highlight a previously unappreciated antibiotic resistance mechanism that modifies ribosome composition and maintains the translation rate in the presence of sub-MIC levels of antibiotics. IMPORTANCE The emergence of antibiotic-resistant bacteria is one of the top threats in human health. Therefore, we need to understand how bacteria acquire resistance to antibiotics and continue growth even in the presence of antibiotics. Streptomyces coelicolor, an antibiotic-producing soil bacterium, intrinsically develops resistance to translation-targeting antibiotics. Intrinsic resistance is controlled by the WblC/WhiB7 transcription factor that is highly conserved within Actinobacteria, including Mycobacterium tuberculosis. Here, identification of the WblC/WhiB7 regulon revealed that WblC/WhiB7 controls ribosome maintenance genes and promotes translation in the presence of antibiotics by altering the composition of ribosome-associated proteins. Also, the WblC-mediated ribosomal alteration is indeed required for resistance to translation-targeting antibiotics. This suggests that inactivation of the WblC/WhiB7 regulon could be a potential target to treat antibiotic-resistant mycobacteria.

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Section: Category (No Of Genes) Asupporting

confidence: 81%

The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition

Lee

Yoo

Kim

et al. 2020

mBio

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“…Both classes of proteins show homology to the translation factors, EF-G and EF-Tu, and actively trigger the release of the antibiotic bound to the ribosome (14,(36)(37)(38)(39). Dissociation of ribosomes stalled in the presence of antibiotics and rescue of mRNA has, however, not been described as a mechanism of antibiotic resistance until very recently, when Duval et al (29) demonstrated that deletion of Listeria monocytogenes hflX-r (lmo0762) confers sensitivity to erythromycin and lincomycin and results in accumulation of 70S ribosomes in the mutant strain on antibiotic exposure. Interestingly, L. monocytogenes encodes 2 HflX paralogs, only 1 of which is involved in antibiotic resistance.…”

Section: Discussionmentioning

confidence: 99%

“…Although binding of macrolides has been shown to interfere with the GTPase activity of E. coli HflX, the E. coli HflX has not been shown to be directly involved in antibiotic resistance (28). Recently, the hflX-r gene from Listeria monocytogenes was shown to confer macrolide resistance (29). We demonstrate here that Mab-HflX (MAB_3042c) and Ms-HflX (MSMEG_2736) are required for macrolide-lincosamide resistance in M. abscessus and M. smegmatis, conferring equivalent resistance as the erm genes, by an erm-independent pathway.…”

Section: Significancementioning

confidence: 99%

Mycobacterial HflX is a ribosome splitting factor that mediates antibiotic resistance

Rudra

Hurst-Hess

Cotten

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Antibiotic resistance in bacteria is typically conferred by proteins that function as efflux pumps or enzymes that modify either the drug or the antibiotic target. Here we report an unusual mechanism of resistance to macrolide-lincosamide antibiotics mediated by mycobacterial HflX, a conserved ribosome-associated GTPase. We show that deletion of thehflXgene in the pathogenicMycobacterium abscessus, as well as the nonpathogenicMycobacterium smegmatis, results in hypersensitivity to the macrolide-lincosamide class of antibiotics. Importantly, the level of resistance provided byMab_hflXis equivalent to that conferred byerm41, implying thathflXconstitutes a significant resistance determinant inM. abscessus. We demonstrate that mycobacterial HflX associates with the 50S ribosomal subunits in vivo and can dissociate purified 70S ribosomes in vitro, independent of GTP hydrolysis. The absence of HflX in aΔMs_hflXstrain also results in a significant accumulation of 70S ribosomes upon erythromycin exposure. Finally, a deletion of either the N-terminal or the C-terminal domain of HflX abrogates ribosome splitting and concomitantly abolishes the ability of mutant proteins to mediate antibiotic tolerance. Together, our results suggest a mechanism of macrolide-lincosamide resistance in which the mycobacterial HflX dissociates antibiotic-stalled ribosomes and rescues the bound mRNA. Given the widespread presence ofhflXgenes, we anticipate this as a generalized mechanism of macrolide resistance used by several bacteria.

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“…We note that a few of the predicted core gene alleles are of genes previously associated to resistance against the corresponding antibiotic, if not necessarily in the target organism or mechanistically established. For instance, an HflX-like protein is known to confer resistance in erythromycin in Listeria monocytogenes through ribosome recycling [52], and it is possible that the hflX gene discovered here may similarly confer resistance in S. aureus. In Helicobacter pylori, oppD was found to be significantly induced by gentamicin exposure [53].…”

Section: Characterization Of Candidate Novel Amr Genesmentioning

confidence: 97%

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

et al. 2020

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The evolution of antimicrobial resistance (AMR) poses a persistent threat to global public health. Sequencing efforts have already yielded genome sequences for thousands of resistant microbial isolates and require robust computational tools to systematically elucidate the genetic basis for AMR. Here, we present a generalizable machine learning workflow for identifying genetic features driving AMR based on constructing reference strain-agnostic pan-genomes and training random subspace ensembles (RSEs). This workflow was applied to the resistance profiles of 14 antimicrobials across three urgent threat pathogens encompassing 288 Staphylococcus aureus, 456 Pseudomonas aeruginosa, and 1588 Escherichia coli genomes. We find that feature selection by RSE detects known AMR associations more reliably than common statistical tests and previous ensemble approaches, identifying a total of 45 known AMR-conferring genes and alleles across the three organisms, as well as 25 candidate associations backed by domain-level annotations. Furthermore, we find that results from the RSE approach are consistent with existing understanding of fluoroquinolone (FQ) resistance due to mutations in the main drug targets, gyrA and parC, in all three organisms, and suggest the mutational landscape of those genes with respect to FQ resistance is simple. As larger datasets become available, we expect this approach to more reliably predict AMR determinants for a wider range of microbial pathogens.

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HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance

Cited by 48 publications

References 37 publications

The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition

The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition

Mycobacterial HflX is a ribosome splitting factor that mediates antibiotic resistance

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

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