Use of a Bacterial Luciferase Monitoring System To Estimate Real-Time Dynamics of Intracellular Metabolism in Escherichia coli

De novo evolution of antibiotic resistance to Oct-TriA1

The rise of antimicrobial resistance as a global health concern has led to a strong interest in compounds able to inhibit the growth of bacteria without detectable levels of resistance evolution. A number of these compounds have been reported in recent years, including the tridecaptins, a small family of lipopeptides typified by the synthetic analogue octyl-tridecaptin A1. Hypothesizing that prior reports of negligible resistance evolution have been due in part to limitations in the laboratory evolution systems used, we have attempted to select for resistant mutants using a soft agar gradient evolution (SAGE) system developed by our lab. Following optimization of the media conditions by incorporation of the anti-synaeresis agent xanthan gum into the agar matrix, we successfully evolved high-level resistance to both octyl-tridecaptin A1 as well as the challenging lipopeptide antibiotic polymyxin B. Decreased tridecaptin susceptibility was linked to mutations in outer membrane proteins ompC, lptD and mlaA, with the effect of these genes confirmed through a mix of allelic replacement and knockout studies. Overall, this work demonstrates the robust evolutionary potential of bacteria, even in the face of challenging antimicrobial agents.

Constitutive glucose dehydrogenase elevates intracellular NADPH levels and luciferase luminescence in Bacillus subtilis

BACKGROUND

Genetic modifications in Bacillus subtilis have allowed the conversion of myo-inositol into scyllo-inositol, which is proposed as a therapeutic agent for Alzheimer's disease. This conversion comprises two reactions catalyzed by two distinct inositol dehydrogenases, IolG and IolW. The IolW-mediated reaction requires the intracellular regeneration of NADPH, and there appears to be a limit to the endogenous supply of NADPH, which may be one of the rate-determining factors for the conversion of inositol. The primary mechanism of NADPH regeneration in this bacterium remains unclear.

RESULTS

The gdh gene of B. subtilis encodes a sporulation-specific glucose dehydrogenase that can use NADP⁺ as a cofactor. When gdh was modified to be constitutively expressed, the intracellular NADPH level was elevated, increasing the conversion of inositol. In addition, the bacterial luciferase derived from Photorhabdus luminescens became more luminescent in cells in liquid culture and colonies on culture plates.

CONCLUSION

The results indicated that the luminescence of luciferase was representative of intracellular NADPH levels. Luciferase can therefore be employed to screen for mutations in genes involved in NADPH regeneration in B. subtilis, and artificial manipulation to enhance NADPH regeneration can promote the production of substances such as scyllo-inositol.

Exploiting Catabolite Repression and Stringent Response to Control Delay and Multimodality of Bioluminescence Signal by Metal Whole-Cell Biosensors: Interplay between Metal Bioavailability and Nutritional Medium Conditions

The time-dependent response of metal-detecting whole-cell luminescent bacterial sensors is impacted by metal speciation/bioavailability in solution. The comprehensive understanding of such connections requires the consideration of the bacterial energy metabolism at stake and the effects of supplied food on cells’ capability to convert bioaccumulated metals into light. Accordingly, we investigated the time response (48 h assay) of PzntA-luxCDABE Escherichia coli Cd biosensors in media differing with respect to sources of amino acids (tryptone or Lysogeny Broth) and carbon (glucose, xylose and mixtures thereof). We show that the resulting coupling between the stringent cell response and glucose/xylose-mediated catabolite repressions lead to well-defined multimodalities and shapes of the bioluminescence signal over time. Based on a recent theory for the time–response of metal-sensing luminescent bacteria, successful theoretical reconstructions of the bioluminescence signals are reported under all Cd concentrations (0–20 nM) and nutritive conditions examined. This analysis leads to the evaluation of time-dependent cell photoactivity and qualitative information on metal speciation/bioavailability in solution. Biosensor performance and the position, shape, number, and magnitude of detected peaks are discussed in relation to the metabolic pathways operative during the successive light emission modes identified here over time. Altogether, the results clarify the contributions of metal/nutrient bio-availabilities and food quality to cell response typology.

Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli

Acetate overflow refers to the metabolism by which a large part of carbon incorporated as glucose into Escherichia coli cells is catabolized and excreted as acetate into the medium. We previously found that mutants for the acetate overflow pathway enzymes phosphoacetyltransferase (Pta) and acetate kinase (AckA) showed significant diauxic growth after glucose depletion in E. coli. Here, we analyzed the underlying mechanism in the pta mutant. Proteomic and other analyses revealed an increase in pyruvate dehydrogenase complex subunits and a decrease in glyoxylate shunt enzymes, which resulted from pyruvate accumulation. Since restoration of these enzyme levels by overexpressing PdhR (pyruvate-sensing transcription factor) or deleting iclR (gene encoding a pyruvate- and glyoxylate-sensing transcription factor) alleviated the growth lag of the pta mutant after glucose depletion, these changes were considered as the reason for the phenotype. Given the evidence for decreased coenzyme A (HS-CoA) levels in the pta mutant, the growth inhibition after glucose depletion was partly explained by limited availability of HS-CoA in the cell. The findings provide insights into the role of acetate overflow in metabolic regulation, which may be useful for biotechnological applications.

Improved Aliivibrio fischeri based-toxicity assay: Graphene-oxide as a sensitivity booster with a mobile-phone application

Recently, many bioluminescence-based applications have arisen in several fields, such as biosensing, bioimaging, molecular biology, and human health diagnosis. Among all bioluminescent organisms, Aliivibrio fischeri (A. fischeri) is a bioluminescent bacterium used to carry out water toxicity assays since the late 1970s. Since then, several commercial A. fischeri-based products have been launched to the market, as these bacteria are considered as a gold standard for water toxicity assessment worldwide. However, the aforementioned commercial products rely on expensive equipment, requiring several reagents and working steps, as well as high-trained personnel to perform the assays and analyze the output data. For these reasons, in this work, we have developed for the first time a mobile-phone-based sensing platform for water toxicity assessment in just 5 min using two widespread pesticides as model analytes. To accomplish this, we have established new methodologies to enhance the bioluminescent signal of A. fischeri based on the bacterial culture in a solid media and/or using graphene oxide. Finally, we have addressed the biocompatibility of graphene oxide to A. fischeri, boosting the sensitivity of the toxicity assays and the bacterial growth of the lyophilized bacterial cultures for more user-friendly storage.

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.

Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH₂) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH₂ under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited.

The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important implications for how microorganisms persist in energy-limited environments, such as reduced sediments under changing redox conditions. From an applied perspective, this work has important implications for microbially catalyzed processes on electrodes, particularly with regard to understanding models of cellular conversion of electrons from cathodes to microbially synthesized products.