Reconstitution of energy-linked activities of the solubilized F1F0 ATP synthase from Bacillus subtilis

Deciphering meropenem persistence in Acinetobacter baumannii facilitates discovery of anti-persister activity of thymol

Decades of antibiotic misuse have accelerated the emergence of multi- and extensively drug-resistant bacteria. Bacterial pathogens employ several strategies such as antibiotic resistance, tolerance, and biofilm formation in response to extreme environments and antibiotic stress. Another crucial survival mechanism involves the stochastic generation of bacterial subpopulations known as persisters, which can endure high concentrations of antibiotics. Upon removal of antibiotic stress, these subpopulations revert back to their original phenotype which links them to the relapse and recalcitrance of chronic infections, a significant problem in clinical settings. Persistent infections are particularly notable in Acinetobacter baumannii, a top-priority ESKAPE pathogen, where carbapenems serve as last-resort antibiotics. Several reports indicate the rising therapeutic failure of carbapenems due to persistence, underscoring the importance of developing anti-persister therapeutics. In this study, we explored the mechanisms of transient persister formation in A. baumannii against meropenem. Our investigation revealed significant changes in membrane properties and energetics in meropenem persisters of A. baumannii, including a noteworthy increase in tolerance to other antibiotics. This understanding guided the evaluation of an in-house collection of GRAS status compounds for their potential anti-persister activity. The compound thymol demonstrated remarkable inhibitory activity against meropenem persisters of A. baumannii and other ESKAPE pathogens. Further investigation revealed its impact on persister cell physiology, including efflux pump inhibition and disruption of cellular respiration. Given our results, we propose a compelling strategy where thymol could be employed either as a monotherapy or in combination with meropenem in anti-persister therapeutics.

Mechanistic Studies of Antibiotic Adjuvants Reducing Kidney's Bacterial Loads upon Systemic Monotherapy

We describe the design and attributes of a linear pentapeptide-like derivative (C_14(ω5)OOc₁₀O) screened for its ability to elicit bactericidal competences of plasma constituents against Gram-negative bacteria (GNB). In simpler culture media, the lipopeptide revealed high aptitudes to sensitize resilient GNB to hydrophobic and/or efflux-substrate antibiotics, whereas in their absence, C_14(ω5)OOc₁₀O only briefly delayed bacterial proliferation. Instead, at low micromolar concentrations, the lipopeptide has rapidly lowered bacterial proton and ATP levels, although significantly less than upon treatment with its bactericidal analog. Mechanistic studies support a two-step scenario providing a plausible explanation for the lipopeptide’s biological outcomes against GNB: initially, C_14(ω5)OOc₁₀O permeabilizes the outer membrane similarly to polymyxin B, albeit in a manner not necessitating as much LPS-binding affinity. Subsequently, C_14(ω5)OOc₁₀O would interact with the inner membrane gently yet intensively enough to restrain membrane-protein functions such as drug efflux and/or ATP generation, while averting the harsher inner membrane perturbations that mediate the fatal outcome associated with bactericidal peers. Preliminary in vivo studies where skin wound infections were introduced in mice, revealed a significant efficacy in affecting bacterial viability upon topical treatment with creams containing C_14(ω5)OOc₁₀O, whereas synergistic combination therapies were able to secure the pathogen’s eradication. Further, capitalizing on the finding that C_14(ω5)OOc₁₀O plasma-potentiating concentrations were attainable in mice blood at sub-maximal tolerated doses, we used a urinary tract infection model to acquire evidence for the lipopeptide’s systemic capacity to reduce the kidney’s bacterial loads. Collectively, the data establish the role of C_14(ω5)OOc₁₀O as a compelling antibacterial potentiator and suggest its drug-like potential.

Targeting Superoxide dismutase confers enhanced Reactive Oxygen Species mediated eradication of Polymyxin B induced Acinetobacter baumannii persisters

Bacterial persisters represent non-inheritable drug tolerant population that are linked to recalcitrance of infections in healthcare settings. The rise of antibiotic resistance and depletion of new antibiotics in drug discovery pipeline has made the task of persister eradication more daunting. In the present study, we report that treatment of Acinetobacter baumannii with the last resort antibiotic polymyxin B displays continuous variation in tolerance among different clinical isolates. Mechanistically, Polymyxin B persisters exhibit disruption of proton motive force led delocalisation of cell division protein to attain a growth arrested phenotype. Tolerance studies on mutant strains revealed that superoxide dismutase (sodB) activity is a major contributor in tolerance of A. baumannii to polymyxin B. Using a dual fluorescence based persister detection system, screening of various antibiotics was performed to eradicate polymyxin B induced persisters of A. baumannii Rifampicin exhibited eradication of polymyxin B tolerant population by log reduction of 6 in magnitude against different clinical isolates of A. baumannii We establish that enhanced generation of ROS by rifampicin leads to clearance of these polymyxin B persisters. It was further demonstrated, as a proof of concept, that rifampicin potentiates the killing of polymyxin B persisters in murine wound infection model. We found that the effects were linked to significant down regulation of sodB by rifampicin, which contributes to higher generation of ROS in polymyxin B tolerant cells. In view of these results, we propose that the combination of polymyxin B and rifampicin is an effective antipersister strategy in clearing polymyxin B induced A. baumannii persisters.

C-terminal regulatory domain of the ε subunit of Fo F1 ATP synthase enhances the ATP-dependent H+ pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis

The ε subunit of F_oF₁‐ATPase/synthase (F_oF₁) plays a crucial role in regulating F_oF₁ activity. To understand the physiological significance of the ε subunit‐mediated regulation of F_oF₁ in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C‐terminal regulatory domain of the ε subunit (ε^∆C). Analyses using inverted membrane vesicles revealed that the ε^∆C mutation decreased ATPase activity and the ATP‐dependent H⁺‐pumping activity of F_oF₁. To enhance the effects of ε^∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε^∆C mutant strain). Interestingly, growth of the ∆rrn8 ε^∆C mutant stalled at late‐exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε^∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C‐terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP‐dependent H⁺‐pumping activity of F_oF₁.

Mutation Q259L in subunit beta in Bacillus subtilis ATP synthase attenuates ADP-inhibition and decreases fitness in mixed cultures

The ATPase activity of H⁺-F_OF₁-ATP synthase (F_OF₁) is down-regulated by several mechanisms. The most universal of them found in bacterial, chloroplast and mitochondrial enzymes is non-competitive inhibition by MgADP (ADP-inhibition). When MgADP binds in a catalytic site in the absence of phosphate, the nucleotide might be trapped instead of being released and replaced by new MgATP. In this case the enzyme becomes inactivated, and MgADP release is required for re-activation. The degree of ADP-inhibition varies between different organisms: it is strong in mitochondrial and chloroplast F_OF₁ and in enzymes of some bacteria (including Bacillus PS3 sp., and Bacillus subtilis), but in F_OF₁ of Escherichia coli it is much weaker. It was shown that mutation betaGln259Leu in Bacillus PS3 F_OF₁ noticeably relieves its strong ADP-inhibition. In this work, we introduced the same mutation in F_OF₁ from B. subtilis. ADP-inhibition in the mutant F_OF₁ was also attenuated in comparison to the wild-type enzyme. The ATPase activity in membrane preparations was 3 fold higher in the mutant. Mutant enzyme was capable of ATP-driven proton pumping, and its ATPase activity was stimulated by dissipation of the protonmotive force, implying that the coupling efficiency between ATP hydrolysis and proton transport was not impaired by the mutation. We observed no effect of mutation on the growth rate of B. subtilis in pure cultures. However, in competition growth experiments when the wild type and the mutant strains were cultivated together in mixed cultures, the wild type strain always crowded out the mutant. To our knowledge, this is the first demonstration of the negative effect of F_OF₁ ADP-inhibition attenuation in vivo.

A broad-spectrum bactericidal lipopeptide with anti-biofilm properties

Previous studies of the oligoacyllysyl (OAK) series acyl-lysyl-lysyl-aminoacyl-lysine-amide, suggested their utility towards generating robust linear lipopeptide-like alternatives to antibiotics, although to date, none exhibited potent broad-spectrum bactericidal activity. To follow up on this premise, we produced a new analog (C₁₄KKc₁₂K) and investigated its properties in various media. Mechanistic studies suggest that C₁₄KKc₁₂K uses a non-specific membrane-disruptive mode of action for rapidly reducing viability of Gram-negative bacteria (GNB) similarly to polymyxin B (PMB), a cyclic lipopeptide used as last resort antibiotic. Indeed, C₁₄KKc₁₂K displayed similar affinity for lipopolysaccharides and induced cell permeabilization associated with rapid massive membrane depolarization. Unlike PMB however, C₁₄KKc₁₂K was also bactericidal to Gram-positive bacteria (GPB) at or near the minimal inhibitory concentration (MIC), as assessed against a multispecies panel of >50 strains, displaying MIC₅₀ at 3 and 6 µM, respectively for GPB and GNB. C₁₄KKc₁₂K retained activity in human saliva, reducing the viability of cultivable oral microflora by >99% within two minutes of exposure, albeit at higher concentrations, which, nonetheless, were similar to the commercial gold standard, chlorhexidine. This equipotent bactericidal activity was also observed in pre-formed biofilms of Streptococcus mutans, a major periodontal pathogen. Such compounds therefore, may be useful for eradication of challenging poly-microbial infections.

Controlling bacterial infections by inhibiting proton-dependent processes

Bacterial resistance to antibiotics is recognized as one of the greatest threats in modern healthcare, taking a staggering toll worldwide. New approaches for controlling bacterial infections must be designed, eventually combining multiple strategies for complimentary therapies. This review explores an old/new paradigm for multi-targeted antibacterial therapy, focused at disturbing bacterial cytoplasmic membrane functions at sub minimal inhibitory concentrations, namely through superficial physical alterations of the bilayer, thereby perturbing transmembrane signals transduction. Such a paradigm may have the advantage of fighting the infection while avoiding many of the known resistance mechanisms. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.

ε subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition

MgADP inhibition, which is considered as a part of the regulatory system of ATP synthase, is a well-known process common to all F₁-ATPases, a soluble component of ATP synthase. The entrapment of inhibitory MgADP at catalytic sites terminates catalysis. Regulation by the ε subunit is a common mechanism among F₁-ATPases from bacteria and plants. The relationship between these two forms of regulatory mechanisms is obscure because it is difficult to distinguish which is active at a particular moment. Here, using F₁-ATPase from Bacillus subtilis (BF₁), which is strongly affected by MgADP inhibition, we can distinguish MgADP inhibition from regulation by the ε subunit. The ε subunit did not inhibit but activated BF₁. We conclude that the ε subunit relieves BF₁ from MgADP inhibition.

ATP synthase in slow- and fast-growing mycobacteria is active in ATP synthesis and blocked in ATP hydrolysis direction

ATP synthase is a validated drug target for the treatment of tuberculosis, and ATP synthase inhibitors are promising candidate drugs for the treatment of infections caused by other slow-growing mycobacteria, such as Mycobacterium leprae and Mycobacterium ulcerans. ATP synthase is an essential enzyme in the energy metabolism of Mycobacterium tuberculosis; however, no biochemical data are available to characterize the role of ATP synthase in slow-growing mycobacterial strains. Here, we show that inverted membrane vesicles from the slow-growing model strain Mycobacterium bovis BCG are active in ATP synthesis, but ATP synthase displays no detectable ATP hydrolysis activity and does not set up a proton-motive force (PMF) using ATP as a substrate. Treatment with methanol as well as PMF activation unmasked the ATP hydrolysis activity, indicating that the intrinsic subunit ɛ and inhibitory ADP are responsible for the suppression of hydrolytic activity. These results suggest that the enzyme is needed for the synthesis of ATP, not for the maintenance of the PMF. For the development of new antimycobacterial drugs acting on ATP synthase, screening for ATP synthesis inhibitors, but not for ATP hydrolysis blockers, can be regarded as a promising strategy.

Membrane potential is important for bacterial cell division

Many cell division-related proteins are located at specific positions in the bacterial cell, and this organized distribution of proteins requires energy. Here, we report that the proton motive force, or more specifically the (trans)membrane potential, is directly involved in protein localization. It emerged that the membrane potential modulates the distribution of several conserved cell division proteins such as MinD, FtsA, and the bacterial cytoskeletal protein MreB. We show for MinD that this is based on the membrane potential stimulated binding of its C-terminal amphipathic helix. This function of the membrane potential has implications for how these morphogenetic proteins work and provide an explanation for the effects observed with certain antimicrobial compounds.

Inhibition of ATP hydrolysis by thermoalkaliphilic F1Fo-ATP synthase is controlled by the C terminus of the epsilon subunit

The F(1)F(o)-ATP synthases of alkaliphilic bacteria exhibit latent ATPase activity, and for the thermoalkaliphile Bacillus sp. strain TA2.A1, this activity is intrinsic to the F(1) moiety. To study the mechanism of ATPase inhibition, we developed a heterologous expression system in Escherichia coli to produce TA2F(1) complexes from this thermoalkaliphile. Like the native F(1)F(o)-ATP synthase, the recombinant TA2F(1) was blocked in ATP hydrolysis activity, and this activity was stimulated by the detergent lauryldimethylamine oxide. To determine if the C-terminal domain of the epsilon subunit acts as an inhibitor of ATPase activity and if an electrostatic interaction plays a role, a TA2F(1) mutant with either a truncated epsilon subunit [i.e., TA2F(1)(epsilon(DeltaC))] or substitution of basic residues in the second alpha-helix of epsilon with nonpolar alanines [i.e., TA2F(1)(epsilon(6A))] was constructed. Both mutants showed ATP hydrolysis activity at low and high concentrations of ATP. Treatment of the purified F(1)F(o)-ATP synthase and TA2F(1)(epsilon(WT)) complex with proteases revealed that the epsilon subunit was resistant to proteolytic digestion. In contrast, the epsilon subunit of TA2F(1)(epsilon(6A)) was completely degraded by trypsin, indicating that the C-terminal arm was in a conformation where it was no longer protected from proteolytic digestion. In addition, ATPase activity was not further activated by protease treatment when compared to the untreated control, supporting the observation that epsilon was responsible for inhibition of ATPase activity. To study the effect of the alanine substitutions in the epsilon subunit in the entire holoenzyme, we reconstituted recombinant TA2F(1) complexes with F(1)-stripped native membranes of strain TA2.A1. The reconstituted TA2F(o)F(1)(epsilon(WT)) was blocked in ATP hydrolysis and exhibited low levels of ATP-driven proton pumping consistent with the F(1)F(o)-ATP synthase in native membranes. Reconstituted TA2F(o)F(1)(epsilon(6A)) exhibited ATPase activity that correlated with increased ATP-driven proton pumping, confirming that the epsilon subunit also inhibits ATPase activity of TA2F(o)F(1).

Alkaline pH homeostasis in bacteria: new insights

The capacity of bacteria to survive and grow at alkaline pH values is of widespread importance in the epidemiology of pathogenic bacteria, in remediation and industrial settings, as well as in marine, plant-associated and extremely alkaline ecological niches. Alkali-tolerance and alkaliphily, in turn, strongly depend upon mechanisms for alkaline pH homeostasis, as shown in pH shift experiments and growth experiments in chemostats at different external pH values. Transcriptome and proteome analyses have recently complemented physiological and genetic studies, revealing numerous adaptations that contribute to alkaline pH homeostasis. These include elevated levels of transporters and enzymes that promote proton capture and retention (e.g., the ATP synthase and monovalent cation/proton antiporters), metabolic changes that lead to increased acid production, and changes in the cell surface layers that contribute to cytoplasmic proton retention. Targeted studies over the past decade have followed up the long-recognized importance of monovalent cations in active pH homeostasis. These studies show the centrality of monovalent cation/proton antiporters in this process while microbial genomics provides information about the constellation of such antiporters in individual strains. A comprehensive phylogenetic analysis of both eukaryotic and prokaryotic genome databases has identified orthologs from bacteria to humans that allow better understanding of the specific functions and physiological roles of the antiporters. Detailed information about the properties of multiple antiporters in individual strains is starting to explain how specific monovalent cation/proton antiporters play dominant roles in alkaline pH homeostasis in cells that have several additional antiporters catalyzing ostensibly similar reactions. New insights into the pH-dependent Na(+)/H(+) antiporter NhaA that plays an important role in Escherichia coli have recently emerged from the determination of the structure of NhaA. This review highlights the approaches, major findings and unresolved problems in alkaline pH homeostasis, focusing on the small number of well-characterized alkali-tolerant and extremely alkaliphilic bacteria.