Biology subjects

Abramovitch, R. B.

Publications and source records attributed to Abramovitch, R. B..

10 recordsLinked to original sources

bioRxiv2026

Combined lactate- and phosphate-dependent cytoplasmic acidification drives Mycobacterium tuberculosis growth arrest at acidic pH

Mycobacterium tuberculosis (Mtb) cultured in minimal medium at acidic pH arrests its growth when provided specific single carbon sources, including glycerol, propionate, and lactate, a phenomenon we refer to as acid growth arrest. To define mechanisms of acid growth arrest on lactate, transposon mutants that suppress growth arrest were selected. Four mutants had insertions in phoT and one had an insertion in pstC2, both components of a phosphate ABC transporter. Mtb grows in minimal media supplemented with lactate at acidic pH when phosphate is depleted, showing that Mtb growth arrest on lactate is dependent on phosphate. The combination of lactate and phosphate at acidic pH causes cytoplasmic acidification below pH 6.7 in wild type Mtb, but a phoT::Tn mutant maintains a cytoplasmic pH of >7.2. Membrane potential in wild type Mtb is slightly decreased by lactate in a dose-dependent manner but is higher in the phoT::Tn mutant. Thus, acidic pH, phosphate, and lactate act together to dissipate proton motive force (PMF), a stress that is associated with acid growth arrest. Transcriptional profiling further supports that lactate causes PMF stress including induction of electron transport chain genes. The phoT::Tn mutant grown in lactate at acidic pH upregulates the senX3/regX3 regulon and using a regX3 mutant, we demonstrate that growth on lactate at low phosphate requires regX3. We propose a model where 1) the combined impact of acidic pH, lactate, and phosphate drives cytoplasmic pH acidification and decreased PMF, thus promoting acid growth arrest, and 2) low phosphate or a mutated phosphate transporter causes upregulation of senX3-regX3, which may induce ESX-5 and PPE/PE-based import mechanisms, thereby altering the mycomembrane or nutrient uptake in a manner that promotes growth on lactate at acidic pH. ImportanceMycobacterium tuberculosis (Mtb) grows well on lactate as a sole carbon source at neutral pH, but not at acidic pH. This study sought to understand why there is a pH-dependent growth restriction on lactate. A genetic selection for mutants that can grow on lactate at acidic pH identified mutants defective in phosphate transport. We found that limiting phosphate through depleting extracellular availability or inactivating a phosphate transporter promotes growth on lactate at acidic pH, and that this growth is dependent on the phosphate responsive two-component regulatory system SenX3-RegX3. Furthermore, we show that lactate, phosphate, and acidic pH combine to cause cytoplasmic pH acidification, a metabolic stress that is associated with acid growth arrest on lactate.

microbiology↗

bioRxiv2025

Mycobacterium tuberculosis growth arrest on propionate at acidic pH is suppressed by mutations in phoPR and pyrazinamide treatment

Mycobacterium tuberculosis (Mtb) arrests its growth at acidic pH, when grown on specific single carbon sources, including propionate. However, Mtb grows well on propionate at pH 7.0, supporting that propionate can support growth as a sole carbon source. To understand the basis of the propionate-driven growth arrest at acidic pH, we performed a forward genetic selection for mutants that enable growth on propionate at pH 5.7. All the selected mutants had insertions in the two-component regulatory genes phoR or phoP. We hypothesized that growth arrest at acidic pH is caused by PhoPR diverting carbon from central carbon metabolism towards lipid anabolism and that when PhoPR is inactivated, growth is promoted through metabolizing propionate by the methyl citrate cycle (MCC) into pyruvate, a permissive carbon source for growth at acidic pH. Using chemical inhibition and mutants of the MCC pathway, we demonstrate that the enhanced growth is dependent on the MCC. Furthermore, stimulating lipid synthesis via the methylmalonyl-CoA pathway by adding vitamin B12 restricts growth in the{Delta} phoPR mutant and, conversely, restricting lipid anabolism by inhibiting the triacylglycerol (TAG) synthase tgs1 enhances growth of the{Delta} phoPR mutant. Notably, CoA pools increased in the{Delta} phoPR mutant grown on propionate, directly supporting our model. Given the role of CoA metabolism in pyrazinamide sensitivity, we examined Mtb sensitivity to pyrazinamide on propionate at acidic pH and, surprisingly, observed that pyrazinamide treatment of WT Mtb suppresses growth arrest on propionate at acidic pH. In contrast, the phoPR mutant has enhanced sensitivity to pyrazinamide. Together, these findings support that propionate-driven growth arrest at acidic pH is caused by metabolic remodeling that is regulated by PhoPR and is associated with pyrazinamide sensitivity. ImportanceWhen grown on certain single carbon sources, such as propionate, Mtb arrests its growth at acidic pH and establishes a state of non-replicating persistence (NRP). To understand the genetic basis of this growth restriction, a genetic selection was performed to identify mutants unable to arrest growth at acidic pH with propionate as a sole carbon source. The selection exclusively identified mutants in the PhoPR two-component regulatory system, which functions to modulate cell envelope lipids and redox homeostasis through the upregulation of lipid synthesis at acidic pH. Using genetic and chemical inhibition studies, we demonstrate that PhoPR arrests growth at acidic pH by diverting carbon away from the methyl citrate cycle towards lipid anabolism. Surprisingly, treatment of Mtb with pyrazinamide at acidic pH on propionate, also enabled growth. Therefore, this study defines new mechanisms by which Mtb integrates environmental signaling to regulate growth, metabolism, and drug susceptibility. These findings are relevant to pathogenesis, as PhoPR is essential for growth in macrophages and animals, environments with varying pH and carbon source availability, depending on immune pressures. These data suggest that drug susceptibility may be impacted by enhanced growth and metabolic capacity of Mtb in acidic and propionate-rich environments, such as the within the macrophage or the granuloma.

microbiology↗

bioRxiv2022

Carbon dioxide regulates Mycobacterium tuberculosis PhoPR signaling and virulence

The Mycobacterium tuberculosis (Mtb) two-component regulatory system, PhoPR, is implicated in pH-sensing within the macrophage because it is strongly induced by acidic pH both in vitro and the macrophage phagosome. The carbonic anhydrase (CA) inhibitor ethoxzolamide (ETZ) inhibits PhoPR signaling supporting the hypothesis that CO2 may also play a role in regulating PhoPR. Here, we show that increasing CO2 concentration induces PhoPR signaling, and its induction is independent of medium pH. We also show that at acidic pH 5.7, a normally strong inducer of PhoPR signaling, that increasing CO2 from 0.5% to 5% further induces the pathway. Based on these findings, we propose that PhoPR functions as a CO2 sensor. Mtb has three CA (CanA, CanB, and CanC) and using CRISPR interference knockdowns and gene deletion mutants, we assessed which CAs regulate PhoPR signaling and virulence. We first examined if CA played a role in Mtb pathogenesis and observed that CanB was required for virulence in macrophages, where the knockdown strain had ~1 log reduction in virulence. To further define the interplay of CO2 and Mtb signaling, we conducted transcriptional profiling experiments at varying pH and CO2 concentrations. As hypothesized, we observed the induction of PhoPR at acidic pH is dependent on CO2 concentration, with a subset of core PhoPR regulon genes dependent on both 5% CO2 and acidic pH for their induction, including expression of the ESX-1 secretion system. Transcriptional profiling also revealed core CO2 responsive genes that were differentially expressed independently of the PhoPR regulon or the acidic pH-inducible regulon. Notably, genes regulated by a second two component regulatory system, TrcRS, are associated with adaptation to changes in CO2.

microbiology↗

bioRxiv2021

ppe51 variants promote non-replicating Mycobacterium tuberculosis to grow at acidic pH by selectively promoting glycerol uptake

In defined media supplemented with single carbon sources, Mycobacterium tuberculosis (Mtb) exhibits carbon source specific growth restriction. When supplied glycerol as the sole carbon source at pH 5.7, Mtb establishes a metabolically active state of nonreplicating persistence known as acid growth arrest. We hypothesized that acidic growth arrest on glycerol is not a metabolic restriction, but rather an adaptive response. To test this hypothesis, we conducted forward genetic screens that identified several Mtb mutants that could grow under these restrictive conditions. All of the mutants were mapped to the ppe51 gene and resulted in three amino acid substitution - S211R, E215K, and A228D. Expression of the PPE51 variants in Mtb promoted growth at acidic pH showing that the mutant alleles are sufficient to cause the dominant gain-of-function, enhanced acid growth (eag) phenotype. Testing growth on other single carbon sources showed the PPE51 variants specifically enhanced growth on glycerol, suggesting ppe51 plays a role in glycerol uptake. Using radiolabeled glycerol, enhanced glycerol uptake was observed in Mtb expressing the PPE51 (S211R) variant, with glycerol overaccumulation in triacylglycerol. Notably, the eag phenotype is deleterious for growth in macrophages, where the mutants have selectively faster replication and reduced in virulence in activated macrophages as compared to resting macrophages. Recombinant PPE51 protein exhibited differential thermostability in the WT or S211R variants in the presence of glycerol, supporting the eag substitutions alter PPE51-glycerol interactions. Together, these findings support that PPE51 variants selectively promote glycerol uptake and that slowed growth at acidic pH is an important adaptive mechanism required for macrophage pathogenesis.

microbiology↗

bioRxiv2021

AC2P20 selectively kills M. tuberculosis at acidic pH by depleting free thiols

Mycobacterium tuberculosis (Mtb) senses and adapts to host immune cues as part of its pathogenesis. One environmental cue sensed by Mtb is the acidic pH of its host niche in the macrophage phagosome. Disrupting the ability of Mtb to sense and adapt to acidic pH has the potential to reduce survival of Mtb in macrophages. Previously, a high throughput screen of a [~]220,000 compound small molecule library was conducted to discover chemical probes that inhibit Mtb growth at acidic pH. The screen discovered chemical probes that kill Mtb at pH 5.7 but are inactive at pH 7.0. In this study, AC2P20 was prioritized for continued study to test the hypothesis that it was targeting Mtb pathways associated with pH-driven adaptation. RNAseq transcriptional profiling studies showed AC2P20 modulates expression of genes associated with redox homeostasis. Gene enrichment analysis revealed that the AC2P20 transcriptional profile had significant overlap with a previously characterized pH-selective inhibitor, AC2P36. Like AC2P36, we show that AC2P20 kills Mtb by selectively depleting free thiols at acidic pH. Mass spectrometry studies show the formation of a disulfide bond between AC2P20 and reduced glutathione, supporting a mechanism where AC2P20 is able to deplete intracellular thiols and dysregulate redox homeostasis. The observation of two independent molecules targeting free thiols to kill Mtb at acidic pH further supports that Mtb has restricted redox homeostasis and sensitivity to thiol-oxidative stress at acidic pH.

microbiology↗

bioRxiv2019

Identification of new MmpL3 inhibitors by untargeted and targeted mutant screens defines MmpL3 domains with differential resistance

The Mycobacterium tuberculosis (Mtb) mycolic acid flippase MmpL3 has been the proposed target for multiple inhibitors with diverse chemical scaffolds. This diversity in chemical scaffolds has made it difficult to predict compounds that inhibit MmpL3 without whole genome sequencing of isolated resistant mutants. Here we describe the identification of four new inhibitors that select for resistance mutations in mmpL3. Using these resistant mutants, we conducted a targeted whole-cell phenotypic screen of 163 novel Mtb growth inhibitors for differential growth inhibition of wild type Mtb as compared to a pool of twenty-four unique mmpL3 mutants. The screen successfully identified six additional putative MmpL3 inhibitors. The compounds were bactericidal both in vitro and against intracellular Mtb. Mtb cells treated with these compounds were shown to accumulate trehalose monomycolate and have reduced levels of trehalose dimycolate, supporting MmpL3 as the target. The inhibitors were mycobacteria specific with several also showing activity against the non-tuberculosis mycobacterial species M. abscessus. Cluster analysis of cross resistance profiles generated by dose response experiments for each combination of 13 MmpL3 inhibitors against each of the 24 mmpL3 mutants defined two clades of inhibitors and two clades of mmpL3 mutants. Pairwise combination studies of the inhibitors revealed interactions that were specific to the clades identified in the cross-resistance profiling. Additionally, modeling of resistance substitutions to the MmpL3 crystal structure revealed clade specific localization of the residues to specific domains of MmpL3, with the clades showing differential resistance. Several compounds exhibited high solubility and stability in microsomes and low cytotoxicity in macrophages, supporting their further development. The combined study of multiple mutants and novel compounds provides new insights into structure-function interactions of MmpL3 and small molecule inhibitors.

microbiology↗

bioRxiv2019

Remodeling of Mycobacterium tuberculosis lipids regulates prpCD during acid growth arrest

Mycobacterium tuberculosis (Mtb) establishes a state of non-replicating persistence when it is cultured at acidic pH with glycerol as a sole carbon source. Growth can be restored by spontaneous mutations in the ppe51 gene or supplementation with pyruvate, supporting that acid growth arrests is a genetically controlled, adaptive process and not simply a physiological limitation associated with acidic pH. Transcriptional profiling identified the methylcitrate synthase and methylcitrate dehydratase genes (prpC and prpD, respectively) as being selectively induced during acid growth arrest. prpCD along with isocitrate lyase (icl) enable Mtb to detoxify propionyl-CoA through the methylcitrate cycle. The goal of this study was to examine mechanisms underlying the regulation of prpCD during acid growth arrest. Induction of prpCD during acid growth arrest was reduced when the medium was supplemented with vitamin B12 (which enables an alternative propionate detoxification pathway) and enhanced in an icl mutant (which is required for the propionate detoxification), suggesting that Mtb is responding to elevated levels of propionyl-CoA during acidic growth arrest. We hypothesized that an endogenous source of propionyl-CoA generated during metabolism of methyl-branched lipids may be regulating prpCD. Using Mtb radiolabeled with 14C-propionate or 14C-acetate, it was observed that lipids are remodeled during acid growth arrest, with triacylglycerol being catabolized and sulfolipid and trehalose dimycolate being synthesized. Blocking TAG lipolysis using the lipase inhibitor tetrahydrolipstatin, resulted in enhanced prpC induction during acid growth arrest, suggesting that lipid remodeling may function, in part, to detoxify propionate. Notably, prpC was not induced during acid growth arrest when using lactate instead of glycerol. We propose that metabolism of glycerol at acidic pH may result in the accumulation of propionyl-CoA and that lipid remodeling may function as a detoxification mechanism.\n\nImportanceDuring infection, Mycobacterium tuberculosis (Mtb) colonizes acidic environments, such as the macrophage phagosome and granuloma. Understanding regulatory and metabolic adaptations that occur in response to acidic pH can provide insights int0 mechanisms used by the bacterium to adapt to the host. We have previously shown that Mtb exhibits pH-dependent metabolic adaptations and requires anaplerotic enzymes, such as Icl1/2 and PckA, to grow optimally at acidic pH. Additionally, we have observed that Mtb can only grow on specific carbon sources at acidic pH. Together these findings show that Mtb integrates environmental pH and carbon source to regulate its metabolism. In this study, it is shown that Mtb remodels its lipids and modulates the expression of propionyl-CoA detoxifying genes prpCD when grown on glycerol at acidic pH. This finding suggests that lipid remodeling at acidic pH may contribute to detoxification of propionyl-CoA, by incorporating the metabolite into methyl-branched cell envelope lipids.

microbiology↗

bioRxiv2018

Inhibition of Mycobacterium tuberculosis DosRST two-component regulatory system signaling by targeting response regulator DNA binding and sensor kinase heme

Mycobacterium tuberculosis (Mtb) possesses a two-component regulatory system, DosRST, that enables Mtb to sense host immune cues and establish a state of non-replicating persistence (NRP). NRP bacteria are tolerant to several anti-mycobacterial drugs and are thought to play a role in the long course of tuberculosis (TB) therapy. Therefore, small molecules that inhibit Mtb from establishing or maintaining NRP could reduce the reservoir of drug tolerant bacteria and function as an adjunct therapy to reduce treatment time. Previously, we reported the discovery of six novel chemical inhibitors of DosRST, named HC101A-106A, from a whole cell, reporter-based phenotypic high throughput screen. Here, we report functional and mechanism of action studies of HC104A and HC106A. RNAseq transcriptional profiling shows that the compounds downregulate genes of the DosRST regulon. Both compounds reduce hypoxia-induced triacylglycerol synthesis by ~50%. HC106A inhibits Mtb survival during hypoxia-induced NRP, however, HC104A did not inhibit survival during NRP. An electrophoretic mobility assay shows that HC104A inhibits DosR DNA binding in a dose-dependent manner, indicating that HC104A may function by directly targeting DosR. In contrast, UV-visible spectroscopy studies suggest HC106A directly targets the histidine kinase heme, via a mechanism that is distinct from the oxidation and alkylation of heme previously observed with artemisinin (HC101A). Synergistic interactions were observed when DosRST inhibitors were examined in pair-wise combinations with the strongest potentiation observed between artemisinin paired with HC102A, HC103A, or HC106A. Our data collectively show that the DosRST pathway can be inhibited by multiple distinct mechanisms.

microbiology↗

bioRxiv2017

Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest

Mycobacterium tuberculosis (Mtb) senses and adapts to acidic environments during the course of infection. Acidic pH-dependent adaptations include the induction of metabolic genes associated with anaplerosis and growth arrest on specific carbon sources. In this study, reverse and forward genetic studies were undertaken to define new mechanisms underlying pH-dependent adaptations. Here we report that deletion of isocitrate lyase (icl1/2) or phosphoenolpyruvate carboxykinase (pckA) results in reduced growth at acidic pH and altered metabolite profiles, supporting that remodeling of anaplerotic metabolism is required for pH-dependent adaptation. Mtb cultured at pH 5.7 in minimal medium containing glycerol as a single carbon source exhibits an acid growth arrest phenotype, where the bacterium is non-replicating but viable and metabolically active. The bacterium uptakes and metabolizes glycerol and maintains ATP pools during acid growth arrest and becomes tolerant to detergent stress and the antibiotics isoniazid and rifampin. A forward genetic screen identified mutants that do not arrest their growth at acidic pH, including four enhanced acid growth (eag) mutants with three distinct mutations in the PPE gene MT3221. Overexpression of the MT3221(S211R) variant protein in wild type Mtb results in enhanced acid growth and reduced drug tolerance. Together, these findings provide new evidence for a genetic and physiological basis for acid growth arrest and support that growth arrest is an adaptive process and not simply a physiological limitation associated with acidic pH.\n\nAuthor SummaryThe bacterium Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis in humans. During infection Mtb colonizes a variety of environments that have acidic environments and Mtb must adapt to these environments to cause disease. One of these adaptations is that Mtb slows and arrests its growth at acidic pH, and the goal of this study was to examine the genetics and physiology of these pH-dependent adaptations. We found that Mtb modifies its metabolism at acidic pH and that these adaptations are required for optimal growth. We also found that acidic pH and specific nutrient sources can promote the bacterium to enter a state of dormancy, called acid growth arrest, where the bacterium becomes tolerant to antibiotics. Mutants were identified that do not arrest their growth at acidic, revealing that acid growth arrest is a genetically controlled process. Overall, understanding how Mtb adapts to acidic pH has revealed pathway that are required for virulence and drug tolerance and thus may identify new targets for drug development that may function to shorten the course of TB therapy.

microbiology↗

bioRxiv2016

Acidic pH-dependent depletion of Mycobacterium tuberculosis thiol pools potentiates antibiotics and oxidizing agents

Mycobacterium tuberculosis (Mtb) must sense and adapt to immune pressures such as acidic pH and reactive oxygen species (ROS) during pathogenesis. The goal of this study was to isolate compounds that inhibit acidic pH resistance, thus defining virulence pathways that are vulnerable to chemotherapy. Here we report that the acidic pH-dependent compound AC2P36 depletes intracellular thiol pools, sensitizes Mtb to killing by acidic pH, and potentiates the bactericidal activity of isoniazid, clofazimine, and oxidizing agents. We show that the pHdependent activity of AC2P36 is associated with metabolic stress at acidic pH and a pHdependent accumulation of intracellular ROS. Mechanism of action studies show that AC2P36 directly depletes Mtb thiol pools. These data support a model where chemical depletion of Mtb thiol pools at acidic pH enhances sensitivity to oxidative damage, resulting in bacterial killing and potentiation of antibiotics.

microbiology↗