Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β′ Subunit

Stefan, Maxwell; Ugur, Fatima S.; Garcia, George A.

doi:10.1128/aac.00164-18

Cited by 27 publications

(43 citation statements)

References 49 publications

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“…6 suggest that termination could play a role in rif resistance, consistent with the observed changes in termination caused by mutations at the D516, H526, and I572 residues of rpoB (70). These findings may relate to rif resistance in M. tuberculosis (50), as recent work in that organism has implicated termination efficiency as the mechanism underlying the cost of resistance (51).…”

Section: Discussionsupporting

confidence: 68%

“…We expect transcriptional profiles to be predictive of collateral sensitivity, as has been shown for chemogenomic profiles (49), to the extent that both reflect the molecular mechanisms underlying adaptation and the cost of resistance. These efforts may offer another avenue to manage resistance in bacterial infections that are treated with rif, such as Mycoplasma tuberculosis (50,51). Our approach to find extreme antagonistic gene-drug pairs is scalable and can facilitate the systematic design of antagonistically interacting drug combinations by providing targets-the gene mutations-against which a second drug may be developed.…”

Section: Introductionmentioning

confidence: 99%

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Extreme Antagonism Arising from Gene-Environment Interactions

Wytock

Zhang

Jinich

et al. 2020

Biophysical Journal

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Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this interpretation ignores extreme antagonistic interactions wherein an otherwise deleterious perturbation compensates for the function lost due to a prior perturbation. Here, we report on gene-environment interactions involving genetic mutations that are deleterious in a permissive environment but beneficial in a specific environment that restricts growth. These extreme antagonistic interactions constitute gene-environment analogs of synthetic rescues previously observed for gene-gene interactions. Our approach uses two independent adaptive evolution steps to address the lack of experimental methods to systematically identify such extreme interactions. We apply the approach to Escherichia coli by successively adapting it to defined glucose media without and with the antibiotic rifampicin. The approach identified multiple mutations that are beneficial in the presence of rifampicin and deleterious in its absence. The analysis of transcription shows that the antagonistic adaptive mutations repress a stringent response-like transcriptional program, while non-antagonistic mutations have an opposite transcriptional profile. Our approach represents a step toward the systematic characterization of extreme antagonistic gene-drug interactions, which can be used to identify targets to select against antibiotic resistance. Statement of Significance Mutations that are deleterious in the absence of an antibiotic can become beneficial in its presence, which is an example of an extreme antagonistic gene-environment interaction. Such antagonism is of biophysical significance because it reflects non-local interactions mediated by intracellular networks rather than direct physical or chemical interactions. We develop and apply a forwardevolution experimental approach to systematically identify these interactions using DNA and RNA sequencing. These analyses reveal differences in the expression of the translational machinery between antagonistic and non-antagonistic mutations. Our findings demonstrate how distinct single-base pair mutations within the same gene can have divergent phenotypic consequences, which give rise to antagonistic interactions that can be explored in addressing antibiotic resistance.

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Section: Discussionsupporting

confidence: 68%

Section: Introductionmentioning

confidence: 99%

Extreme Antagonism Arising from Gene-Environment Interactions

Wytock

Zhang

Jinich

et al. 2020

Biophysical Journal

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“…L452P confers only low-level rifampin resistance, whereas mutations at position 435 (including D435Y and D435G) are associated with distinctly higher rifampin MICs (50), and in LAM4/KZN acquisition of D435G likely augmented rifampin resistance versus the L452P single mutant (51). Recent studies have implicated changes in protein stability (52) and transcriptional efficiency (53) as important determinants of how putative compensatory mutations impact fitness in rifampin-resistant Mtb . Although in our analysis D435G and I1106T only partially offset the destabilizing effects of L452P, multiple studies suggest that the compensatory effects of D435G may not be related exclusively to its effects on protein stability.…”

Section: Discussionmentioning

confidence: 99%

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Brown

Challagundla

Baugh

et al. 2019

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

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Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating whole-genome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.

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“…As shown in Figure 1 , I491V, also reported by Comas et al (2011) , is located at the interface between the α and β’ subunits; A734V is near the interface between the β and β’ subunits; G594E maps to a region between the two α helices, and the substitution of glycine with glutamate changes the charge of the side chain from neutral to negative. Interestingly, Stefan et al recently reported similar findings that F452L and V483G, two mutants of RpoC near I491V, displayed a compensatory effect on RpoB S450L mutated RNA polymerase in vitro by recovering the defects of open-promoter complex stability and elongation rate, enhancing termination efficiency and RNA primer hydrolysis ( Stefan et al, 2018 ). Their work demonstrates the possibility of and underlying mechanism of mutations in RpoC compensating for functional defects of RNA polymerase resulting from mutations in RpoB.…”

Section: Resultsmentioning

confidence: 88%

Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis

Zhou

et al. 2018

Front. Microbiol.

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Multidrug-resistant tuberculosis (TB), defined as TB resistant to the two first-line drugs, isoniazid and rifampin, is a serious challenge to global TB eradication efforts. Although mutations in rpoA or rpoC have been proposed to compensate for this fitness cost due to rpoB mutation in rifampicin-resistant Mycobacterium tuberculosis mutants, whether the compensatory effect exists and the underlying mechanisms of compensation remain unclear. Here, we used RNA sequencing to investigate the global transcriptional profiles of 6 rifampin-resistant clinical isolates with either single mutation in rpoB or dual mutations in rpoB/rpoC, as well as 3 rifampin-susceptible clinical isolates, trying to prove the potential compensatory effect of rpoC by transcriptomic alteration. In rifampin-free conditions, rpoC mutation was associated with M. tuberculosis upregulation of ribosomal protein-coding genes, dysregulation of growth-related essential genes and balancing the expression of arginine and glutamate synthesis-associated genes. Upon rifampin exposure of M. tuberculosis isolates, rpoC mutations were associated with the upregulation of the oxidative phosphorylation machinery, which was inhibited in the rpoB single mutants, as well as stabilization of the expression of rifampin-regulated essential genes and balancing the expression of genes involved in metabolism of sulfur-containing amino acids. Taken together, our data suggest that rpoC mutation may compensate for the fitness defect of rifampicin-resistant M. tuberculosis by altering gene expression in response to rifampin exposure.

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Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β′ Subunit

Cited by 27 publications

References 49 publications

Extreme Antagonism Arising from Gene-Environment Interactions

Extreme Antagonism Arising from Gene-Environment Interactions

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis

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