Accumulation of glutamate by osmotically stressed Escherichia coli is dependent on pH

Development of the autonomous lab system to support biotechnology research

In this study, we developed the autonomous lab (ANL), which is a system based on robotics and artificial intelligence (AI) to conduct biotechnology experiments and formulate scientific hypotheses. This system was designed with modular devices and Bayesian optimization algorithms, allowing it to effectively run a closed loop from culturing to preprocessing, measurement, analysis, and hypothesis formulation. As a case study, we used the ANL to optimize medium conditions for a recombinant Escherichia coli strain, which overproduces glutamic acid. The results demonstrated that our autonomous system successfully replicated the experimental techniques, such as sample preparation and data measurement, and improved both the cell growth rate and the maximum cell growth. The ANL offers a versatile and scalable solution for various applications in the field of bioproduction, with the potential to improve efficiency and reliability of experimental processes in the future.

New two-stage pH combined with dissolved oxygen control strategy for cyclic β-1,2 glucans synthesis

On the basis of a novel two-stage pH combined with dissolved oxygen (DO) control strategy in fed-batch fermentation, this research addresses the influence of pH on cyclic β-1,2-glucans (CβGs) biosynthesis and melanin accumulation during the production of CβGs by Rhizobium radiobacter ATCC 13,333. Under these optimal fermentation conditions, the maximum cell concentration and CβGs concentration in a 7-L stirred-tank fermenter were 7.94 g L^-1 and 3.12 g L^-1, which were the maximum production reported for R. radiobacter. The melanin concentration of the fermentation broth was maintained at a low level, which was beneficial to the subsequent separation and purification of the CβGs. In addition, a neutral extracellular oligosaccharide (COGs-1) purified by the two-stage pH combined with DO control strategy fermentation medium was structurally characterized. Structural analyses indicated that COGs-1 was a family of unbranched cyclic oligosaccharides composed of only β-1,2-linked D-glucopyranose residues with degree of polymerization between 17 and 23, namely CβGs. This research provides a reliable source of CβGs and structural basis for further studies of biological activity and function. KEY POINTS: • A two-stage pH combined with DO control strategy was proposed for CβGs production and melanin biosynthesis by Rhizobium radiobacter. • The final extracellular CβGs production reached 3.12 g L^-1, which was the highest achieved by Rhizobium radiobacter. • The existence of CβGs could be detected by TLC quickly and accurately.

Environmental Conditions Affecting GABA Production in Lactococcus lactis NCDO 2118

GABA (γ-aminobutyric acid) production has been widely described as an adaptive response to abiotic stress, allowing bacteria to survive in harsh environments. This work aimed to clarify and understand the relationship between GABA production and bacterial growth conditions, with particular reference to osmolarity. For this purpose, Lactococcus lactis NCDO 2118, a GABA-producing strain, was grown in glucose-supplemented chemically defined medium containing 34 mM L-glutamic acid, and different concentrations of salts (chloride, sulfate or phosphate ions) or polyols (sorbitol, glycerol). Unexpectedly, our data demonstrated that GABA production was not directly related to osmolarity. Chloride ions were the most significant factor influencing GABA yield in response to acidic stress while sulfate ions did not enhance GABA production. We demonstrated that the addition of chloride ions increased the glutamic acid decarboxylase (GAD) synthesis and the expression of the gadBC genes. Finally, under fed-batch conditions in a complex medium supplemented with 0.3 M NaCl and after a pH shift to 4.6, L. lactis NCDO 2118 was able to produce up to 413 mM GABA from 441 mM L-glutamic acid after only 56 h of culture, revealing the potential of L. lactis strains for intensive production of this bioactive molecule.

Augmentation of bacterial homeostasis by regulating in situ buffer capacity: Significance of total dissolved salts over acidogenic metabolism

During anaerobic fermentation, consequent accumulation of acidic fermented products leads to the failure of pH homeostasis. The present study aimed to comprehend the changes in buffering capacity with addition of sodium salts of hydroxide, bicarbonate and phosphate. The results showed notable augmentation in buffer capacity and cumulative hydrogen production (CHP) compared to control. The influential factor is the amount of undissociated volatile fatty acids released that affected the cell metabolism and consequently biohydrogen generation. It is inferred that among the tested salts, sodium bicarbonate has substantial buffering capacity (β, 0.035± mol) ensuing maximum CHP (468± mL). Besides, bioelectrochemical analysis revealed variations in redox currents that aligned with biohydrogen production. The study provides valuable information on the role of inorganic dissolved salts that would be required to regulate H₂ generation and acidogenesis in the aspects of acid-gas phase system.

Evaluation of Honey and Rice Syrup as Replacements for Sorbitol in the Production of Restructured Duck Jerky

The aim of this study was to evaluate the potential of natural humectants such as honey and rice syrup to replace sorbitol in the production of restructured duck jerky. Each humectant was mixed at 3%, 6%, and 10% (wt/wt) concentrations with the marinating solution. The values of water activity and the moisture-to-protein ratio of all of the samples were maintained below 0.75. Jerky samples treated with honey retained more moisture than those exposed to other treatments. Among all samples, those treated with 10% sorbitol produced the highest processing yield and the lowest shear force values. The highest L* value and the lowest b* value were observed for the sorbitol-treated sample, followed by the rice syrup- and honey-treated samples. Duck jerky samples treated with 10% honey showed the highest scores for the sensory parameters evaluated. The overall acceptability scores of samples treated with rice syrup were comparable with those of samples treated with sorbitol. Microscopic observation of restructured duck jerky samples treated with honey showed stable forms and smaller pores when compared with other treatments.

Osmotic Stress

Escherichia coli and Salmonella encounter osmotic pressure variations in natural environments that include host tissues, food, soil, and water. Osmotic stress causes water to flow into or out of cells, changing their structure, physics, and chemistry in ways that perturb cell functions. E. coli and Salmonella limit osmotically induced water fluxes by accumulating and releasing electrolytes and small organic solutes, some denoted compatible solutes because they accumulate to high levels without disturbing cell functions. Osmotic upshifts inhibit membrane-based energy transduction and macromolecule synthesis while activating existing osmoregulatory systems and specifically inducing osmoregulatory genes. The osmoregulatory response depends on the availability of osmoprotectants (exogenous organic compounds that can be taken up to become compatible solutes). Without osmoprotectants, K+ accumulates with counterion glutamate, and compatible solute trehalose is synthesized. Available osmoprotectants are taken up via transporters ProP, ProU, BetT, and BetU. The resulting compatible solute accumulation attenuates the K+ glutamate response and more effectively restores cell hydration and growth. Osmotic downshifts abruptly increase turgor pressure and strain the cytoplasmic membrane. Mechanosensitive channels like MscS and MscL open to allow nonspecific solute efflux and forestall cell lysis. Research frontiers include (i) the osmoadaptive remodeling of cell structure, (ii) the mechanisms by which osmotic stress alters gene expression, (iii) the mechanisms by which transporters and channels detect and respond to osmotic pressure changes, (iv) the coordination of osmoregulatory programs and selection of available osmoprotectants, and (v) the roles played by osmoregulatory mechanisms as E. coli and Salmonella survive or thrive in their natural environments.

Exposure of Salmonella enterica Serovar Typhimurium to Three Humectants Used in the Food Industry Induces Different Osmoadaptation Systems

Common salt (NaCl) is frequently used by the food industry to add flavor and to act as a humectant in order to reduce the water content of a food product. The improved health awareness of consumers is leading to a demand for food products with reduced salt content; thus, manufacturers require alternative water activity-reducing agents which elicit the same general effects as NaCl. Two examples include KCl and glycerol. These agents lower the water activity of a food matrix and also contribute to limit the growth of the microbiota, including foodborne pathogens. Little is currently known about how foodborne pathogens respond to these water activity-lowering agents. Here we examined the response of Salmonella enterica serovar Typhimurium 4/74 to NaCl, KCl, and glycerol at three time points, using a constant water activity level, compared with the response of a control inoculum. All conditions induced the upregulation of gluconate metabolic genes after 6 h of exposure. Bacteria exposed to NaCl and KCl demonstrated the upregulation of the osmoprotective transporter mechanisms encoded by the proP, proU, and osmU (STM1491 to STM1494) genes. Glycerol exposure elicited the downregulation of these osmoadaptive mechanisms but stimulated an increase in lipopolysaccharide and membrane protein-associated genes after 1 h. The most extensive changes in gene expression occurred following exposure to KCl. Because many of these genes were of unknown function, further characterization may identify KCl-specific adaptive processes that are not stimulated by NaCl. This study shows that the response of S. Typhimurium to different humectants does not simply reflect reduced water activity and likely involves systems that are linked to specific humectants.

The Escherichia coli Acid Stress Response and Its Significance for Pathogenesis

Escherichia coli has a remarkable ability to survive low pH and possesses a number of different genetic systems that enable it to do this. These may be expressed constitutively, typically in stationary phase, or induced by growth under a variety of conditions. The activities of these systems have been implicated in the ability of E. coli to pass the acidic barrier of the stomach and to become established in the gastrointestinal tract, something causing serious infections. However, much of the work characterizing these systems has been done on standard laboratory strains of E. coli and under conditions which do not closely resemble those found in the human gut. Here we review what is known about acid resistance in E. coli as a model laboratory organism and in the context of its lifestyle as an inhabitant-sometimes an unwelcome one-of the human gut.

Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery

The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.

Coping with low pH: molecular strategies in neutralophilic bacteria

As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.

A computational kinetic model of diffusion for molecular systems

Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10-100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS.

Physicochemical Characteristics of Beef Jerky Cured with Salted-fermented Anchovy and Shrimp

The aim of this study is to evaluate the availability of salted and fermented fish (SFF) including salted and fermented anchovy (SFA) and shrimp (SFS) as a marinade of beef jerky. In curing solutions, half (SFA 1 and SFS 1) or whole (SFA 2 and SFS 2) salt-water was replaced with SFF juices. Higher water activity (a_w) was found in the beef jerky cured with SFFs than the control (C) (p< 0.05). The SFFs had the effect of causing a decrease in hardness and an increase in cohesiveness (p<0.05). Among the treatment samples, springiness was the highest in SFA2 and SFS2 (p<0.05) and the lowest values of Warner-Bratzler shear force were found in SFA1 and SFA2 (p<0.05). The SFFs also had the effect of increasing the flavor of the sensory properties; however, color measurements from both the instrumental surface color (L*, a*, b*, chroma, and hue angle) and color of sensory evaluation were decreased by addition of SFFs (p<0.05). Therefore, we conclude the SFFs can improve the texture and sensory properties of the beef jerky. In particular, the SFS is a good ingredient for the curing solution. However, studies are still needed on improving the a_w, pH, and surface color of the beef jerky to apply the SFFs for making beef jerky.

Functional reconstitution and osmoregulatory properties of the ProU ABC transporter from Escherichia coli

The ATP-binding cassette (ABC) transporter ProU from Escherichia coli translocates a wide range of compatible solutes and contributes to the regulation of cell volume, which is particularly important when the osmolality of the environment fluctuates. We have purified the components of ProU, i.e., the substrate-binding protein ProX, the nucleotide-binding protein ProV and the transmembrane protein ProW, and reconstituted the full transporter complex in liposomes. We engineered a lipid anchor to ProX for surface tethering of this protein to ProVW-containing proteoliposomes. We show that glycine betaine binds to ProX with high-affinity and is transported via ProXVW in an ATP-dependent manner. The activity ProU is salt and anionic lipid-dependent and mimics the ionic strength-gating of transport of the homologous OpuA system.

Functional dissection of N-acetylglutamate synthase (ArgA) of Pseudomonas aeruginosa and restoration of its ancestral N-acetylglutamate kinase activity

In many microorganisms, the first step of arginine biosynthesis is catalyzed by the classical N-acetylglutamate synthase (NAGS), an enzyme composed of N-terminal amino acid kinase (AAK) and C-terminal histone acetyltransferase (GNAT) domains that bind the feedback inhibitor arginine and the substrates, respectively. In NAGS, three AAK domain dimers are interlinked by their N-terminal helices, conforming a hexameric ring, whereas each GNAT domain sits on the AAK domain of an adjacent dimer. The arginine inhibition of Pseudomonas aeruginosa NAGS was strongly hampered, abolished, or even reverted to modest activation by changes in the length/sequence of the short linker connecting both domains, supporting a crucial role of this linker in arginine regulation. Linker cleavage or recombinant domain production allowed the isolation of each NAGS domain. The AAK domain was hexameric and inactive, whereas the GNAT domain was monomeric/dimeric and catalytically active although with ∼50-fold-increased and ∼3-fold-decreased K(m)(glutamate) and k(cat) values, respectively, with arginine not influencing its activity. The deletion of N-terminal residues 1 to 12 dissociated NAGS into active dimers, catalyzing the reaction with substrate kinetics and arginine insensitivity identical to those for the GNAT domain. Therefore, the interaction between the AAK and GNAT domains from different dimers modulates GNAT domain activity, whereas the hexameric architecture appears to be essential for arginine inhibition. We proved the closeness of the AAK domains of NAGS and N-acetylglutamate kinase (NAGK), the enzyme that catalyzes the next arginine biosynthesis step, shedding light on the origin of classical NAGS, by showing that a double mutation (M26K L240K) in the isolated NAGS AAK domain elicited NAGK activity.

Manipulating the permeation of charged compounds through the MscL nanovalve

MscL is a bacterial mechanosensor that serves as a biological emergency release valve, releasing cytoplasmic solutes to the environment on osmotic downshock. Previous studies have recognized that this channel has properties that make it ideal for use as a triggered nanovalve for vesicular-based targeted drug-release devices. One can even change the modality of the sensor. Briefly, the introduction of charges into the MscL pore lumen gates the channel in the absence of membrane tension; thus, by inserting compounds that acquire a charge on exposure to an alternative stimulus, such as light or pH, into the pore of the channel, controllable nanoswitches that detect these alternative modalities have been engineered. However, a charge in the pore lumen could not only encourage actuation of the nanopore but also have a significant influence on the permeation of large charged compounds, which would thus have important implications for the efficiency of drug-release devices. In this study, we used in vivo and electrophysiological approaches to demonstrate that the introduction of a charge into pore lumen of MscL does indeed influence the permeation of charged molecules. These effects were more drastic for larger compounds and, surprisingly, were related to the orientation of the MscL channel in the membrane.

Transit through the flea vector induces a pretransmission innate immunity resistance phenotype in Yersinia pestis

Yersinia pestis, the agent of plague, is transmitted to mammals by infected fleas. Y. pestis exhibits a distinct life stage in the flea, where it grows in the form of a cohesive biofilm that promotes transmission. After transmission, the temperature shift to 37 degrees C induces many known virulence factors of Y. pestis that confer resistance to innate immunity. These factors are not produced in the low-temperature environment of the flea, however, suggesting that Y. pestis is vulnerable to the initial encounter with innate immune cells at the flea bite site. In this study, we used whole-genome microarrays to compare the Y. pestis in vivo transcriptome in infective fleas to in vitro transcriptomes in temperature-matched biofilm and planktonic cultures, and to the previously characterized in vivo gene expression profile in the rat bubo. In addition to genes involved in metabolic adaptation to the flea gut and biofilm formation, several genes with known or predicted roles in resistance to innate immunity and pathogenicity in the mammal were upregulated in the flea. Y. pestis from infected fleas were more resistant to phagocytosis by macrophages than in vitro-grown bacteria, in part attributable to a cluster of insecticidal-like toxin genes that were highly expressed only in the flea. Our results suggest that transit through the flea vector induces a phenotype that enhances survival and dissemination of Y. pestis after transmission to the mammalian host.

Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non-ionic osmotica

Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using Escherichia coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above approximately 1.0 Os kg(-1) causes a dose-dependent K(+) leak from the cell, resulting in a substantial decrease in cytosolic K(+) content and a concurrent accumulation of Na(+) in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K(+) uptake. Ion flux data are consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K(+) uptake to efflux. Microarray experiments reveal that about 40% of upregulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic and non-ionic osmotica. The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K(+) transporters for bacterial adaptation to hyperosmotic stress.

Effects of acid adaptation and modified marinades on survival of postdrying Salmonella contamination on beef jerky during storage

This study was undertaken to evaluate the survival of acid-adapted and nonadapted Salmonella cultures inoculated after drying on beef jerky that had been treated with marinades before drying at 60 degrees C for 10 h. Beef slices were (i) not treated prior to refrigeration at 4 degrees C for 24 h (control [C]); (ii) marinated with traditional marinade (TM), (iii) marinated with TM modified with 1.2% sodium lactate, 9% acetic acid, and 68% soy sauce containing 5% ethanol (MM) at twice the amount used in the TM treatment; (iv) dipped into 5% acetic acid and then marinated with TM (AATM); and (v) dipped into 1% Tween 20, then dipped into 5% acetic acid, and then marinated with TM (TWTM); after each treatment, meat slices were refrigerated at 4 degrees C for 24 h prior to drying. Dried slices were inoculated with acid-adapted or nonadapted Salmonella (ca. 5.7 log CFU/cm2) prior to aerobic storage at 25 degrees C for 60 days. Tryptic soy agar with 0.1% pyruvate, as well as xylose-lysine-tergitol 4 (XLT4) agar, was used to determine survivor counts. Bacterial decreases achieved with the different treatments were found to be in the following order: TWTM (5.4 to 6.3 log units) > or = AATM > or = MM > C > or = TM (2.9 to 5.1 log units). Acid-adapted Salmonella decreased faster than nonadapted Salmonella for all treatments. Bacterial populations decreased to below the detection limit (-0.4 log CFU/cm2) in as few as 14 days or remained detectable by direct plating after 60 days of storage, depending on acid adaptation, treatment, and agar media. The results of this study indicate that the modified marinades used in jerky processing and the low water activity of the dried product provide antimicrobial effects against possible postprocessing contamination with Salmonella, while the preparation of cultures under acid-adaptation conditions did not increase Salmonella survival during storage and may have reduced it.

Bacterial strategies to inhabit acidic environments

Bacteria can inhabit a wide range of environmental conditions, including extremes in pH ranging from 1 to 11. The primary strategy employed by bacteria in acidic environments is to maintain a constant cytoplasmic pH value. However, many data demonstrate that bacteria can grow under conditions in which pH values are out of the range in which cytoplasmic pH is kept constant. Based on these observations, a novel notion was proposed that bacteria have strategies to survive even if the cytoplasm is acidified by low external pH. Under these conditions, bacteria are obliged to use acid-resistant systems, implying that multiple systems having the same physiological role are operating at different cytoplasmic pH values. If this is true, it is quite likely that bacteria have genes that are induced by environmental stimuli under different pH conditions. In fact, acid-inducible genes often respond to another factor(s) besides pH. Furthermore, distinct genes might be required for growth or survival at acid pH under different environmental conditions because functions of many systems are dependent on external conditions. Systems operating at acid pH have been described to date, but numerous genes remain to be identified that function to protect bacteria from an acid challenge. Identification and analysis of these genes is critical, not only to elucidate bacterial physiology, but also to increase the understanding of bacterial pathogenesis.

The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system

Inducible bacterial amino acid decarboxylases are expressed at the end of active cell division to counteract acidification of the extracellular environment during fermentative growth. It has been proposed that acid resistance in some enteric bacteria strictly relies on a glutamic acid-dependent system. The Escherichia coli chromosome contains distinct genes encoding two biochemically identical isoforms of glutamic acid decarboxylase, GadA and GadB. The gadC gene, located downstream of gadB, has been proposed to encode a putative antiporter implicated in the export of gamma-aminobutyrate, the glutamic acid decarboxylation product. In the present work, we provide in vivo evidence that gadC is co-transcribed with gadB and that the functional glutamic acid-dependent system requires the activities of both GadA/B and GadC. We also found that expression of gad genes is positively regulated by acidic shock, salt stress and stationary growth phase. Mutations in hns, the gene for the histone-like protein H-NS, cause derepressed expression of the gad genes, whereas the rpoS mutation abrogates gad transcription even in the hns background. According to our results, the master regulators H-NS and RpoS are hierarchically involved in the transcriptional control of gad expression: H-NS prevents gad expression during the exponential growth whereas the alternative sigma factor RpoS relieves H-NS repression during the stationary phase, directly or indirectly accounting for transcription of gad genes.

Control of acid resistance in Escherichia coli

Acid resistance (AR) in Escherichia coli is defined as the ability to withstand an acid challenge of pH 2.5 or less and is a trait generally restricted to stationary-phase cells. Earlier reports described three AR systems in E. coli. In the present study, the genetics and control of these three systems have been more clearly defined. Expression of the first AR system (designated the oxidative or glucose-repressed AR system) was previously shown to require the alternative sigma factor RpoS. Consistent with glucose repression, this system also proved to be dependent in many situations on the cyclic AMP receptor protein. The second AR system required the addition of arginine during pH 2.5 acid challenge, the structural gene for arginine decarboxylase (adiA), and the regulator cysB, confirming earlier reports. The third AR system required glutamate for protection at pH 2.5, one of two genes encoding glutamate decarboxylase (gadA or gadB), and the gene encoding the putative glutamate:gamma-aminobutyric acid antiporter (gadC). Only one of the two glutamate decarboxylases was needed for protection at pH 2.5. However, survival at pH 2 required both glutamate decarboxylase isozymes. Stationary phase and acid pH regulation of the gad genes proved separable. Stationary-phase induction of gadA and gadB required the alternative sigma factor sigmaS encoded by rpoS. However, acid induction of these enzymes, which was demonstrated to occur in exponential- and stationary-phase cells, proved to be sigmaS independent. Neither gad gene required the presence of volatile fatty acids for induction. The data also indicate that AR via the amino acid decarboxylase systems requires more than an inducible decarboxylase and antiporter. Another surprising finding was that the sigmaS-dependent oxidative system, originally thought to be acid induced, actually proved to be induced following entry into stationary phase regardless of the pH. However, an inhibitor produced at pH 8 somehow interferes with the activity of this system, giving the illusion of acid induction. The results also revealed that the AR system affording the most effective protection at pH 2 in complex medium (either Luria-Bertani broth or brain heart infusion broth plus 0.4% glucose) is the glutamate-dependent GAD system. Thus, E. coli possesses three overlapping acid survival systems whose various levels of control and differing requirements for activity ensure that at least one system will be available to protect the stationary-phase cell under naturally occurring acidic environments.