In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth The specific pH values of cellular compartments affect virtually all biochemical processes, including enzyme activity, protein folding and redox state. Accurate, sensitive and compartmentspecific measurements of intracellular pH (pH i ) dynamics in living cells are therefore crucial to the understanding of stress response and adaptation. We used the pH-sensitive GFP derivative 'ratiometric pHluorin' expressed in the cytosol and in the mitochondrial matrix of growing Saccharomyces cerevisiae to assess the variation in cytosolic pH (pH cyt ) and mitochondrial pH (pH mit ) in response to nutrient availability, respiratory chain activity, shifts in environmental pH and stress induced by addition of sorbic acid. The in vivo measurement allowed accurate determination of organelle-specific pH, determining a constant pH cyt of 7.2 and a constant pH mit of 7.5 in cells exponentially growing on glucose. We show that pH cyt and pH mit are differentially regulated by carbon source and respiratory chain inhibitors. Upon glucose starvation or sorbic acid stress, pH i decrease coincided with growth stasis. Additionally, pH i and growth coincided similarly in recovery after addition of glucose to glucose-starved cultures or after recovery from a sorbic acid pulse. We suggest a relation between pH i and cellular energy generation, and therefore a relation between pH i and growth. INTRODUCTIONMicrobes are able to adapt to a wide range of stressful environments such as deviant temperature, high or low osmotic pressure, oxidative stress and exposure to weak organic acids. The mechanisms by which they adapt to these environments are often poorly understood. To study these adaptive responses we rely on techniques that focus on various levels of cellular regulation, such as transcription profiles, protein levels and metabolic flux analysis. However, global physiological parameters such as intracellular pH (pH i ) affect nearly all processes in a living cell. pH i directly influences the redox state of the cell by influencing the NAD + /NADH equilibrium (Veine et al., 1998) and determines pH gradients necessary for transport over membranes (Goffeau & Slayman, 1981;Wohlrab & Flowers, 1982). Additionally, the effect of pH is very prominent in enzyme kinetics, as pH influences ionization states of acidic or basic amino acid side-chains and thereby influences the structure, solubility and activity of most, if not all, enzymes.The different organelles in the cell all maintain their own specific pH, which is used to define and maintain the processes associated with each organelle. Yeast vacuoles, for instance, are reported to have an acidic pH (Preston et al., 1989;Brett et al., 2005; Martínez-Muñoz & Kane, 2008). The proton gradient across the vacuolar membrane has been shown to be essential for the transport of various compounds (Nishimura et al., 1998;Ohsumi & Anraku, ...

Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites, and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, the results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30% of the B. subtilis genome.A number of bacterial species such as bacilli and clostridia have the ability to form dormant spores. The spore has a specialized and complex structure, enabling the organism to survive for a long time under harsh environmental conditions and in the absence of nutrients. When triggered by specific nutrients, the spore is capable of breaking dormancy (germination) and initiating vegetative growth (34, 52). The Bacillus subtilis spore is composed of a dehydrated central compartment (the spore core) engulfed by two protective outer layers: a thick spore-specific peptidoglycan layer known as the spore cortex and a multilayered protein structure known as the coat (12).The process of endospore formation in Bacillus subtilis has been studied in great detail. Studies have revealed a highly ordered and strictly regulated program ensuring the correct coordination of various aspects of the sporulation process, such as asymmetric cell division, prespore engulfment, spore maturation, and mother cell lysis (22). The sporulation program involves the timed activation of several mother cell and forespore compartment-and sporulation stage-dependent RNA polymerase sigma factors that transcribe specific sets of sporulation genes. Eventually, the sporulation program results in the lysis of the mother cell and the release of a dormant spore (22).The process of spore germination and outgrowth has been studies in less detail. Spore germination is initiated when the spore senses the appropriate trigger molecules, often simple sugars and/or amino acids. The germinant molecules are sensed by germination receptors. This, by an unknown mechanism, leads to an irreversible commitment of a spore to germination. The germinating spore initially releases Zn 2ϩ and H ϩ (65). Simultaneously (and probably as a consequence), the pH of the spore core rises from 6.5 to 7.7. In a second stage, the germinating spore releases the spore core's large supply of dipicolinic acid (pyridine-2,6-dicarboxylic acid), and the spore core is rehydrated. Subsequently, cortex lytic enzymes are activated and the protective spore peptidoglycan cortex is degraded. This enables the germinating spore to hydrate the spore core further and to swell. These germination events coincide with a loss of...

Oxygen availability is the major determinant of the metabolic modes adopted by Escherichia coli. Although much is known about E. coli gene expression and metabolism under fully aerobic and anaerobic conditions, the intermediate oxygen tensions that are encountered in natural niches are understudied. Here, for the first time, the transcript profiles of E. coli K-12 across the physiologically significant range of oxygen availabilities are described. These suggested a progressive switch to aerobic respiratory metabolism and a remodeling of the cell envelope as oxygen availability increased. The transcriptional responses were consistent with changes in the abundance of cytochrome bd and bo and the outer membrane protein OmpW. The observed transcript and protein profiles result from changes in the activities of regulators that respond to oxygen itself or to metabolic and environmental signals that are sensitive to oxygen availability (aerobiosis). A probabilistic model (TFInfer) was used to predict the activity of the indirect oxygen-sensing two-component system ArcBA across the aerobiosis range. The model implied that the activity of the regulator ArcA correlated with aerobiosis but not with the redox state of the ubiquinone pool, challenging the idea that ArcA activity is inhibited by oxidized ubiquinone. The amount of phosphorylated ArcA correlated with the predicted ArcA activities and with aerobiosis, suggesting that fermentation product-mediated inhibition of ArcB phosphatase activity is the dominant mechanism for regulating ArcA activity under the conditions used here.The bacterium and model organism Escherichia coli K-12 has three basic metabolic modes: aerobic respiration, anaerobic respiration, and fermentation (1, 2). There is a hierarchy in which aerobic respiration is preferred to anaerobic respiration, which in turn is preferred to fermentation (1). This hierarchy reflects the relative amounts of energy that can be conserved by these metabolic modes, and oxygen availability is the major signal that governs which metabolic mode is adopted.Many environments, both natural (host intestinal tract) and man-made (bioreactors), are characterized by the presence of oxygen gradients and/or regions of variable oxygen availability (3, 4). Thus, how patterns of gene expression adapt across the range of physiologically relevant oxygen availabilities is important for the efficiency of biotechnological processes that use E. coli as a cell factory and for competitiveness in natural environments (4). However, obtaining reproducible data from E. coli cultures at low oxygen tensions is technically demanding, and the overwhelming majority of the relevant literature reports the results of experiments with fully aerobic or anaerobic cultures. Furthermore, as indicated by Alexeeva et al. (5), in the relatively few attempts to study E. coli grown at intermediate oxygen tensions, it was apparent that neither dissolved oxygen tension nor the gas input to a chemostat accurately describes the responses of the culture to changes in ...

Spore-forming bacteria are a special problem for the food industry as some of them are able to survive preservation processes. Bacillus spp. spores can remain in a dormant, stress resistant state for a long period of time. Vegetative cells are formed by germination of spores followed by a more extended outgrowth phase. Spore germination and outgrowth progression are often very heterogeneous and therefore, predictions of microbial stability of food products are exceedingly difficult. Mechanistic details of the cause of this heterogeneity are necessary. In order to examine spore heterogeneity we made a novel closed air-containing chamber for live imaging. This chamber was used to analyze Bacillus subtilis spore germination, outgrowth, as well as subsequent vegetative growth. Typically, we examined around 90 starting spores/cells for ≥4 hours per experiment. Image analysis with the purposely built program “SporeTracker” allows for automated data processing from germination to outgrowth and vegetative doubling. In order to check the efficiency of the chamber, growth and division of B. subtilis vegetative cells were monitored. The observed generation times of vegetative cells were comparable to those obtained in well-aerated shake flask cultures. The influence of a heat stress of 85°C for 10 min on germination, outgrowth, and subsequent vegetative growth was investigated in detail. Compared to control samples fewer spores germinated (41.1% less) and fewer grew out (48.4% less) after the treatment. The heat treatment had a significant influence on the average time to the start of germination (increased) and the distribution and average of the duration of germination itself (increased). However, the distribution and the mean outgrowth time and the generation time of vegetative cells, emerging from untreated and thermally injured spores, were similar.

The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL-and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (fab) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward the fab inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of B. subtilis to sorbic acid stress.

Species from the genus Bacillus have the ability to form endospores, dormant cellular forms that are able to survive heat and acid preservation techniques commonly used in the food industry. Resistance characteristics of spores towards various environmental stresses are in part attributed to their coat proteins. Previously, 70 proteins have been assigned to the spore coat of Bacillus subtilis using SDS-PAGE, 2-DE gel approaches, protein localization studies and genome-wide transcriptome studies. Here, we present a "gel-free" protocol that is capable of comprehensive B. subtilis spore coat protein extraction and addresses the insoluble coat fraction. Using LC-MS/MS we identified 55 proteins from the insoluble B. subtilis spore coat protein fraction, of which 21 are putative novel spore coat proteins not assigned to the spore coat until now. Identification of spore coat proteins from a B. subtilis food-spoilage isolate corroborated a generic and "applied" use of our protocol. To develop specific and sensitive spore detection and/or purification systems from food stuff or patient material, suitable protein targets can be derived from our proteomic approach. Finally, the protocol can be extended to study cross-linking among the spore coat proteins as well as for their quantification.

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Phage shock proteins (Psp) and their homologues are found in species from the three domains of life: Bacteria, Archaea and Eukarya (e.g. higher plants). In enterobacteria, the Psp response helps to maintain the proton motive force (PMF) of the cell when the inner membrane integrity is impaired. The presumed ability of ArcB to sense redox changes in the cellular quinone pool and the strong decrease of psp induction in ΔubiG or ΔarcAB backgrounds suggest a link between the Psp response and the quinone pool. The authors now provide evidence indicating that the physiological signal for inducing psp by secretin-induced stress is neither the quinone redox state nor a drop in PMF. Neither the loss of the H+-gradient nor the dissipation of the electrical potential alone is sufficient to induce the Psp response. A set of electron transport mutants differing in their redox states due to the lack of a NADH dehydrogenase and a quinol oxidase, but retaining a normal PMF displayed low levels of psp induction inversely related to oxidised ubiquinone levels under microaerobic growth and independent of PMF. In contrast, cells displaying higher secretin induced psp expression showed increased levels of ubiquinone. Taken together, this study suggests that not a single but likely multiple signals are needed to be integrated to induce the Psp response.Electronic supplementary materialThe online version of this article (doi:10.1007/s00284-011-9869-5) contains supplementary material, which is available to authorized users.