Specific growth rate and not cell density controls the general stress response in Escherichia coli

Understanding and computational design of genetic circuits of metabolic networks

The expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli's strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli's circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.

Gut microbiota-derived butyrate selectively interferes with growth of carbapenem-resistant Escherichia coli based on their resistance mechanism

We investigated consequences of resistance acquisition in Escherichia coli clinical isolates during anaerobic (continuous culture) growth and examined their sensitivity to butyrate, a hallmark metabolite of healthy gut microbiota. Strains were stratified based on carrying either a carbapenemase (CARB) or displaying porin malfunctioning (POR). POR displayed markedly altered growth efficiencies, lower membrane stability and increased sensitivity to butyrate compared with CARB. Major differences in global gene expression between the two groups during anaerobic growth were revealed involving increased expression of alternative substrate influx routes, the stringent response and iron acquisition together with lower expression of various stress response systems in POR. Longitudinal analyses during butyrate wash-in showed common responses for all strains as well as specific features of POR that displayed strong initial "overshoot" reactions affecting various stress responses that balanced out over time. Results were partly reproduced in a mutant strain verifying porin deficiencies as the major underlying mechanism for results observed in clinical isolates. Furthermore, direct competition experiments confirmed butyrate as key for amplifying fitness disadvantages based on porin malfunctioning. Results provide new (molecular) insights into ecological consequences of resistance acquisition and can assist in developing measures to prevent colonization and infection based on the underlying resistance mechanism.

Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species

Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats massively synthesize proteins that are not utilized in the conditions they currently experience. Based on resource allocation models, recent studies have begun to reconcile the costs and benefits of these conditionally unutilized proteins (CUPs) in the context of varying environmental conditions. Such massive synthesis of CUPs is crucial to consider in different areas of modern microbiology, from the systematic investigation of cell physiology, via the prediction of evolution in laboratory and natural environments, to the rational design of strains in biotechnology applications.

Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models

Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade-offs between cellular objectives such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long-term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework.

The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705

Bifidobacteria are saccharolytic bacteria that are able to metabolize a relatively large range of carbohydrates through their unique central carbon metabolism known as the “bifid-shunt”. Carbohydrates have been shown to modulate the growth rate of bifidobacteria, but unlike for other genera (e.g., E. coli or L. lactis), the impact it may have on the overall physiology of the bacteria has not been studied in detail to date. Using glucose and galactose as model substrates in Bifidobacterium longum NCC 2705, we established that the strain displayed fast and slow growth rates on those carbohydrates, respectively. We show that these differential growth conditions are accompanied by global transcriptional changes and adjustments of central carbon fluxes. In addition, when grown on galactose, NCC 2705 cells were significantly smaller, exhibited an expanded capacity to import and metabolized different sugars and displayed an increased acid-stress resistance, a phenotypic signature associated with generalized fitness. We predict that part of the observed adaptation is regulated by the previously described bifidobacterial global transcriptional regulator AraQ, which we propose to reflect a catabolite-repression-like response in B. longum. With this manuscript, we demonstrate that not only growth rate but also various physiological characteristics of B. longum NCC 2705 are responsive to the carbon source used for growth, which is relevant in the context of its lifestyle in the human infant gut where galactose-containing oligosaccharides are prominent.

Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space

Near space (20 to 100 km in altitude) is an extreme environment with high radiation and extreme cold, making it difficult for organisms to survive. However, many studies had shown that there were still microbes living in this extremely harsh environment. It was particularly important to study which factors affected the survival of microorganisms living in near space after exposure to irradiation, as this was related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. Survival after radiation was probably influenced by the growth condition before radiation, which is called the memory effect. In this research, we used different growth conditions to affect the growth of Deinococcus radiodurans and lyophilized bacteria in exponential phase to maintain the physiological state at this stage. Then high-altitude scientific balloon exposure experiments were carried out by using the Chinese Academy of Sciences Balloon-Borne Astrobiology Platform (CAS-BAP) at Dachaidan, Qinghai, China (37°44'N, 95°21'E). The aim was to investigate which factors influence survival after near-space exposure. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. If the differences in growth rate were caused by differences in nutrition, the survival rate and growth rate were positively correlated. Moreover, the addition of paraquat and Mn2+ during the growth phase can also increase survival. This finding may help to deepen the understanding of the mechanics of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space. IMPORTANCE Earth's near space is an extreme environment with high radiation and extreme cold. Which factors affect the survival of microbes in near space is related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. We performed several exposure experiments with Deinococcus radiodurans in near space to investigate which factors influence the survival rate after near-space exposure; that is, there was a relationship between survival after radiation and the growth condition before radiation. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. This finding may help to deepen the understanding of the mechanism of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space.

Dynamic Interplay between O2 Availability, Growth Rates, and the Transcriptome of Yarrowia lipolytica

Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps Yarrowia lipolytica-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h−1, the largest simulated volume (90 m3) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h−1. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that Y. lipolytica can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for Y. lipolytica-based strain engineering, thereby accelerating bioprocess development.

Assessing the growth kinetics and stoichiometry of Escherichia coli at the single-cell level

Microfluidic cultivation and single-cell analysis are inherent parts of modern microbial biotechnology and microbiology. However, implementing biochemical engineering principles based on the kinetics and stoichiometry of growth in microscopic spaces remained unattained. We here present a novel integrated framework that utilizes distinct microfluidic cultivation technologies and single-cell analytics to make the fundamental math of process-oriented biochemical engineering applicable at the single-cell level. A combination of non-invasive optical cell mass determination with sub-pg sensitivity, microfluidic perfusion cultivations for establishing physiological steady-states, and picoliter batch reactors, enabled the quantification of all physiological parameters relevant to approximate a material balance in microfluidic reaction environments. We determined state variables (biomass concentration based on single-cell dry weight and mass density), biomass synthesis rates, and substrate affinities of cells grown in microfluidic environments. Based on this data, we mathematically derived the specific kinetics of substrate uptake and growth stoichiometry in glucose-grown Escherichia coli with single-cell resolution. This framework may initiate microscale material balancing beyond the averaged values obtained from populations as a basis for integrating heterogeneous kinetic and stoichiometric single-cell data into generalized bioprocess models and descriptions.

Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures while upregulating anaerobic respiratory chains

Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 μM) is characterized by lower biomass yield, higher acetate accumulation and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, previous studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. Here, the effect of iron availability on the energy metabolism of E. coli has been investigated. It was established that aerobic cultures growing under limiting iron conditions showed lower ATP yield per glucose, lower growth rate and lower TCA cycle activity and respiration, at the same time as increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independent of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiratory chain. In conditions of iron excess, some iron-requiring terminal reductases of the respiratory chain, that were thought to function only under anaerobiosis, were used by the E. coli, when in aerobic conditions, to maintain high respiratory activity. This allowed it to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase and catalase) and the iron-sulfur cluster repair systems.

Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects

Microbial populations often contain persister cells, which reduce the extinction risk upon sudden stresses. Persister cell formation is deeply intertwined with physiology. Due to this complexity, it cannot be satisfactorily understood by focusing only on mechanistic, physiological or evolutionary aspects. In this review, we take an integrative biology perspective to identify common principles of persister cell formation, which might be applicable across evolutionary-distinct microbes. Persister cells probably evolved to cope with a fundamental trade-off between cellular stress and growth tasks, as any biosynthetic resource investment in growth-supporting proteins is at the expense of stress tasks and vice versa. Natural selection probably favours persister cell subpopulation formation over a single-phenotype strategy, where each cell is prepared for growth and stress to a suboptimal extent, since persister cells can withstand harsher environments and their coexistence with growing cells leads to a higher fitness. The formation of coexisting phenotypes requires bistable molecular circuitry. Bistability probably emerges from growth-modulated, positive feedback loops in the cell's growth versus stress control network, involving interactions between sigma factors, guanosine pentaphosphate and toxin-antitoxin (TA) systems. We conclude that persister cell formation is most likely a response to a sudden reduction in growth rate, which can be achieved by antibiotic addition, nutrient starvation, sudden stresses, nutrient transitions or activation of a TA system.

Central Metabolism and Growth Rate Impacts on Hydrogen and Carbon Isotope Fractionation During Amino Acid Synthesis in E. coli

Compound specific stable isotope analysis (CSIA) of amino acids from bacterial biomass is a newly emerging powerful tool for exploring central carbon metabolism pathways and fluxes. By comparing isotopic values and fractionations relative to water and growth substrate, the impact of variable flow path for metabolites through different central metabolic pathways, perturbations of these paths, and their resultant consequences on intracellular pools and resultant biomass may be elucidated. Here, we explore the effects that central carbon metabolism and growth rate can have on stable hydrogen (δ2H) and carbon (δ13C) compound specific isotopic values of amino acids, and whether diagnostic isotopic fingerprints are revealed by these paired analyses. We measured δ2H and δ13C in amino acids in the wild type Escherichia coli (MG1655) across a range of growth rates in chemostat cultures to address the unknown isotopic consequences as metabolic fluxes are shuffled between catabolic and anabolic metabolisms. Additionally, two E. coli knockout mutants, one with deficiency in glycolysis -pgi (LC1888) and another inhibiting the oxidative pentose phosphate pathway (OPPP) -zwf (LC1889), were grown on glucose and used as a comparison against the wild type E. coli (MG1655) to address the isotopic changes of amino acids produced in these perturbed metabolic pathways. Amino acid δ2H values, which collectively vary in composition by more than 400‰, are altered along with δ13C values demonstrating fundamental shifts in central metabolic pathways and/or fluxes. Within our linear discriminant analysis with a simple model organism to examine potential amino acid fingerprinting, our knockout strains and variable growth rate samples plot across a wider array of organism classification than merely within the boundaries of other bacterial data.

The Resistance Mechanism Governs Physiological Adaptation of Escherichia coli to Growth With Sublethal Concentrations of Carbapenem

Factors governing resistance in carbapenem-resistant Enterobacteriaceae are manifold. Despite ample research efforts, underlying molecular mechanisms are still only partly understood. Furthermore, little is known on (eco)physiological consequences from resistance acquisition originating from distinct mechanisms in respective bacteria.

In this study, we examined physiological adaptation of Escherichia coli clinical isolates exhibiting two distinct resistance mechanisms–either carrying a carbapenemase (n = 4, CARB) or alterations in porin-encoding genes (n = 6, POR)–during growth with sublethal concentrations of ertapenem in chemostat culture. Basic growth parameters based on optical density and flow-cytometric analyses as well as global gene expression patterns using RNA-Seq were recorded. We demonstrate that strategies to deal with the antibiotic were distinct between strains of the two groups, where (increased) expression of carbapenemases was the major response in CARB, whereas wide-spread alterations in gene-expression that promoted a survival-like phenotype was observed in POR. The response in POR was accompanied with “costs of resistance” resulting in reduced growth efficiencies compared with CARB that are intrinsic to that group and were also observed during growth without antibiotic challenge, however, at lower levels. All strains showed similar minimal inhibitory concentrations and did not form phylogenetic groups, indicating that results cannot be attributed to distinct resistance levels or phylogenetic relationships, but are indeed based on the resistance mechanism.

Study of the contribution of active defense mechanisms to ciprofloxacin tolerance in Escherichia coli growing at different rates

Using rpoS, tolC, ompF, and recA knockouts, we investigated their effect on the physiological response and lethality of ciprofloxacin in E. coli growing at different rates on glucose, succinate or acetate. We have shown that, regardless of the strain, the degree of changes in respiration, membrane potential, NAD⁺/NADH ratio, ATP and glutathione (GSH) strongly depends on the initial growth rate and the degree of its inhibition. The deletion of the regulator of the general stress response RpoS, although it influenced the expression of antioxidant genes, did not significantly affect the tolerance to ciprofloxacin at all growth rates. The mutant lacking TolC, which is a component of many E. coli efflux pumps, showed the same sensitivity to ciprofloxacin as the parent. The absence of porin OmpF slowed down the entry of ciprofloxacin into cells, prolonged growth and shifted the optimal bactericidal concentration towards higher values. Deficiency of RecA, a regulator of the SOS response, dramatically altered the late phase of the SOS response (SOS-dependent cell death), preventing respiratory inhibition and a drop in membrane potential. The recA mutation inverted GSH fluxes across the membrane and abolished ciprofloxacin-induced H₂S production. All studied mutants showed an inverse linear relationship between logCFU ml^-1 and the specific growth rate. Mutations shifted the plot of this dependence relative to the parental strain according to their significance for ciprofloxacin tolerance. The crucial role of the SOS system is confirmed by dramatic shift down of this plot in the recA mutant.

Recombinant Protein Production with Escherichia coli in Glucose and Glycerol Limited Chemostats

Recently, there has been a resurgence of interest in continuous bioprocessing as a cost-optimised production strategy, driven by a rising global requirement for recombinant proteins used as biological drugs. This strategy could provide several benefits over traditional batch processing, including smaller bioreactors, smaller facilities, and overall reduced plant footprints and investment costs. Continuous processes may also offer improved product quality and minimise heterogeneity, both in the culture and in the product. In this paper, a model protein, green fluorescent protein (GFP) mut3*, was used to test the recombinant protein expression in an Escherichia coli strain with industrial relevance grown in chemostat. An important factor in enabling stable productivity in continuous cultures is the carbon source. We have studied the viability and heterogeneity of the chemostat cultures using a chemically defined medium based on glucose or glycerol as the single carbon source. As a by-product of biodiesel production, glycerol is expected to become a sustainable alternative substrate to glucose. We have found that although glycerol gives a higher cell density, it also generates higher heterogeneity in the culture and a less stable recombinant protein production. We suggest that manipulating the balance between different subpopulations to increase the proportion of productive cells may be a possible solution for making glycerol a successful alternative to glucose.

Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions

Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism’s ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and Escherichia coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We, therefore, generated RNAseq and TraDIS data on a uropathogenic E. coli strain grown at either pH 7 or pH 5.5 in the presence or absence of three SCFAs (acetic, propionic and butyric), either aerobically or anaerobically. Our analysis identifies both known and novel pathways as being likely to be important under these conditions. There is no simple correlation between gene expression and fitness, but we found a significant overlap in KEGG pathways that are predicted to be enriched following analysis of the data from the two methods, and the majority of these showed a fitness signature that would be predicted from the gene expression data, assuming expression to be adaptive. Genes which are not in the E. coli core genome were found to be particularly likely to show a positive correlation between level of expression and contribution to fitness.

Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms

Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.

Discovery, development and exploitation of steady-state biofilms

Early in vitro biofilm models go back even beyond the invention of the word 'biofilm'. In the dental field, biofilms were simply known as dental plaque and many of the first in vitro models were termed 'artificial mouth microcosm plaques'. The purpose of this review is to highlight important elements of research from over the years regarding in vitro biofilm models, including data from our own laboratories. This helps us to interpret the models and point the way to the future development of biofilm testing. Many hypotheses regarding biofilm phenomena, particularly ecology, metabolism and physiology of volatile sulphur compounds (VSCs) and volatile organic compound (VOC) production could potentially be supported or disproved. In this way, the methods we use for screening biologically active agents including inhibitors, biocides and antimicrobial compounds in general can be improved. Hopefully, any lessons learnt in the past may be of value for the future. In this review, we focus around the need for growth rate controlled long-term biofilms; being continuously monitored using recent technical advances in bioluminescence, selective real-time electrodes, pH electrodes and continuous on-line analysis of the gas phase (both qualitatively and quantitatively). These features allow for accurate determination of growth rate and/or metabolic rate as well as pave the way towards automated assays and fine control of metabolism; impossible to achieve according to conventional biofilm theory. We also attempt to address the questions; can biofilm systems be improved to maintain long term 'real' or 'true' steady states over weeks or months, or are we limited to quasi-steady state systems for a limited period of time.

A Bayesian non-parametric mixed-effects model of microbial growth curves

Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters. However, estimation of these parameters from data is confounded by random effects such as experimental variability, batch effects or differences in experimental material. A systematic statistical method to identify and correct for such confounding effects in population growth data is not currently available. Further, our previous work has demonstrated that parametric models are insufficient to explain and predict microbial response under non-standard growth conditions. Here we develop a hierarchical Bayesian non-parametric model of population growth that identifies the latent growth behavior and response to perturbation, while simultaneously correcting for random effects in the data. This model enables more accurate estimates of the biological effect of interest, while better accounting for the uncertainty due to technical variation. Additionally, modeling hierarchical variation provides estimates of the relative impact of various confounding effects on measured population growth.

Study of the relationship between extracellular superoxide and glutathione production in batch cultures of Escherichia coli

Aerobically growing Escherichia coli generates superoxide flux into the periplasm via the oxidation of dihydromenaquinone and simultaneously carries out continuous transmembrane cycling of glutathione (GSH). Here we have shown that, under the conditions of a gradual decrease in dissolved oxygen (dO₂), characteristic of batch culture, the global regulatory system ArcB/ArcA can play an important role in the coordinated control of extracellular superoxide and GSH fluxes and their interaction with intracellular antioxidant systems. The lowest superoxide production was observed in the menA and arcB mutants, while the atpA, atpC and atpE mutants generated superoxide 1.3-1.5 times faster than the parent. The share of exported glutathione in the ubiC, atpA, atpC, and atpE mutants was 2-3 times higher compared to the parent. A high direct correlation (r = 0.87, p = 0.01) between extracellular superoxide and GSH was revealed. The menA and arcB mutants, as well as the cydD mutant lacking the GSH export system CydDC, were not capable of GSH excretion with a decrease in dO₂, which indicates a positive control of GSH export by ArcB. In contrast, ArcB downregulates sodA, therefore, an inverse correlation (r = -0.86, p = 0.013) between superoxide production and sodA expression was observed.

Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions

Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we used a high-throughput automated microscopy assay to quantify the impact of deleting >1500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondrial membrane potential - but not amount - varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.

Transcriptome analysis of a Pseudomonas aeruginosasn-glycerol-3-phosphate dehydrogenase mutant reveals a disruption in bioenergetics

Pseudomonas aeruginosa causes acute and chronic human infections and is the major cause of morbidity and mortality in cystic fibrosis (CF) patients. We previously determined that the sn-glycerol-3-phosphate dehydrogenase encoded by glpD plays a larger role in P. aeruginosa physiology beyond its role in glycerol metabolism. To better understand the effect of a glpD mutation on P. aeruginosa physiology we compared the transcriptomes of P. aeruginosa strain PAO1 and the PAO1ΔglpD mutant using RNA-seq analysis. We determined that a null mutation of glpD significantly altered amino acid metabolism in P. aeruginosa and affected the production of intermediates that are channelled into the tricarboxylic acid cycle. Moreover, the loss of glpD induced a general stress response mediated by RpoS in P. aeruginosa. Several other phenotypes observed for the P. aeruginosa glpD mutant include increased persister cell formation, reduced extracellular ATP accumulation and increased heat output. Taken together, these findings implicate sn-glycerol-3-phosphate dehydrogenase as a key player in energy metabolism in P. aeruginosa.

Severely Heat Injured Survivors of E. coli O157:H7 ATCC 43888 Display Variable and Heterogeneous Stress Resistance Behavior

Although minimal food processing strategies aim to eliminate foodborne pathogens and spoilage microorganisms through a combination of mild preservation techniques, little is actually known on the resistance behavior of the small fraction of microorganisms surviving an inimical treatment. In this study, the conduct of severely heat stressed survivors of E. coli O157:H7 ATCC 43888, as an indicator for the low infectious dose foodborne enterohemorrhagic strains, was examined throughout their resuscitation and outgrowth. Despite the fact that these survivors were initially sublethally injured, they were only marginally more sensitive to a subsequent heat treatment and actually much more resistant to a subsequent high hydrostatic pressure (HHP) shock in comparison with unstressed control cells. Throughout further resuscitation, however, their initial HHP resistance rapidly faded out, while their heat resistance increased and surpassed the initial heat resistance of unstressed control cells. Results also indicated that the population eventually emerging from the severely heat stressed survivors heterogeneously consisted of both growing and non-growing cells. Together, these observations provide deeper insights into the particular behavior and heterogeneity of stressed foodborne pathogens in the context of food preservation.

Engineering E. coli for large-scale production - Strategies considering ATP expenses and transcriptional responses

Microbial producers such as Escherichia coli are evolutionarily trained to adapt to changing substrate availabilities. Being exposed to large-scale production conditions, their complex, multilayered regulatory programs are frequently activated because they face changing substrate supply due to limited mixing. Here, we show that E. coli can adopt both short- and long-term strategies to withstand these stress conditions. Experiments in which glucose availability was changed over a short time scale were performed in a two-compartment bioreactor system. Quick metabolic responses were observed during the first 30s of glucose shortage, and after 70s, fundamental transcriptional programs were initiated. Since cells are fluctuating under simulated large-scale conditions, this scenario represents a continuous on/off switching of about 600 genes. Furthermore, the resulting ATP maintenance demands were increased by about 40-50%, allowing us to conclude that hyper-producing strains could become ATP-limited under large-scale production conditions. Based on the observed transcriptional patterns, we identified a number of candidate gene deletions that may reduce unwanted ATP losses. In summary, we present a theoretical framework that provides biological targets that could be used to engineer novel E. coli strains such that large-scale performance equals laboratory-scale expectations.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.

Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase

The physiological adaptation to stationary growth by Pseudomonas putida F1, a model organism for the degradation of aromatic compounds, was investigated by proteome-wide label-free quantification.The data unveiled that entrance to the stationary phase did not involve an abrupt switch within the P. putida F1 proteome, but rather an ongoing adaptation that started already during the mid-exponential growth phase. The proteomic adaptations involved a clear increase in amino acid degradation capabilities and a loss of transcriptional as well as translational capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. The results show that it is important to consider significant sample variations when exponentially growing cultures are studied alone or compared across proteomic or transcriptomic literature. All MS data have been deposited in the ProteomeXchange with identifier PXD001219 (http://proteomecentral.proteomexchange.org/dataset/PXD001219).

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage

Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method—FitFlow—that enables the sorting of subpopulations by growth rate. The slow-growing subpopulation shows a transcriptional stress response, but, more surprisingly, these cells have reduced RNA polymerase fidelity and exhibit a DNA damage response. As DNA damage is often caused by oxidative stress, we test the addition of an antioxidant, and find that it reduces the size of the slow-growing population. More generally, we find a significantly altered transcriptome in the slow-growing subpopulation that only partially resembles that of cells growing slowly due to environmental and culture conditions. Slow-growing cells upregulate transposons and express more chromosomal, viral and plasmid-borne transcripts, and thus explore a larger genotypic—and so phenotypic — space.

Isogenic cells growing in the same environment show a large degree of variability. Here, by sorting yeast cells based on growth rate, the authors show that the slow-growing subpopulation exhibits stress responses, a high level of transcriptional diversity, and decreased RNA polymerase fidelity.

Physiological, biomass elemental composition and proteomic analyses of Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited chemostat growth

Escherichia coli physiological, biomass elemental composition and proteome acclimations to ammonium-limited chemostat growth were measured at four levels of nutrient scarcity controlled via chemostat dilution rate. These data were compared with published iron- and glucose-limited growth data collected from the same strain and at the same dilution rates to quantify general and nutrient-specific responses. Severe nutrient scarcity resulted in an overflow metabolism with differing organic byproduct profiles based on limiting nutrient and dilution rate. Ammonium-limited cultures secreted up to 35% of the metabolized glucose carbon as organic byproducts with acetate representing the largest fraction; in comparison, iron-limited cultures secreted up to 70 % of the metabolized glucose carbon as lactate, and glucose-limited cultures secreted up to 4% of the metabolized glucose carbon as formate. Biomass elemental composition differed with nutrient limitation; biomass from ammonium-limited cultures had a lower nitrogen content than biomass from either iron- or glucose-limited cultures. Proteomic analysis of central metabolism enzymes revealed that ammonium- and iron-limited cultures had a lower abundance of key tricarboxylic acid (TCA) cycle enzymes and higher abundance of key glycolysis enzymes compared with glucose-limited cultures. The overall results are largely consistent with cellular economics concepts, including metabolic tradeoff theory where the limiting nutrient is invested into essential pathways such as glycolysis instead of higher ATP-yielding, but non-essential, pathways such as the TCA cycle. The data provide a detailed insight into ecologically competitive metabolic strategies selected by evolution, templates for controlling metabolism for bioprocesses and a comprehensive dataset for validating in silico representations of metabolism.

Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth

For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya), were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σ^D with σ^S. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow, carbon-limited growth, whereas RpoS is primarily involved in the regulation of stress response systems necessary for the survival of this bacterium under hunger conditions.

Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2-4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.

Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase “core enzyme” (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σ^S-associated RNA polymerase form (Eσ^S) during transition from exponential to stationary phase. We identified 63 binding sites for Eσ^S overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the σ^S-encoding rpoS gene. Eσ^S binding did not always correlate with an increase in transcription level, suggesting that, at some σ^S-dependent promoters, Eσ^S might remain poised in a pre-initiation state upon binding. A large fraction of Eσ^S-binding sites corresponded to promoters recognized by RNA polymerase associated with σ⁷⁰ or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, Eσ^S appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of Eσ^S in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.

Microbial growth and physiology: a call for better craftsmanship

Virtually every microbiological experiment starts with the cultivation of microbes. Consequently, as originally pointed out by Monod (1949), handling microbial cultures is a fundamental methodology of microbiology and mastering different cultivation techniques should be part of every microbiologist’s craftsmanship. This is particularly important for research in microbial physiology, as the composition and behavior of microbes is strongly dependent on their growth environment. It has been pointed out repeatedly by eminent microbiologists that we should give more attention to the media and culturing conditions. However, this is obviously not adhered to with sufficient rigor as mistakes in basic cultivation principles are frequently found in the published research literature. The most frequent mistakes are the use of inappropriate growth media and little or no control of the specific growth rate, and some examples will be discussed here in detail. Therefore, this is a call for better microbiological craftsmanship when cultivating microbial cultures for physiological experiments. This call is not only addressed to researchers but it is probably even more important for the teaching of our discipline.

Survival kinetics of starving bacteria is biphasic and density-dependent

In the lifecycle of microorganisms, prolonged starvation is prevalent and sustaining life during starvation periods is a vital task. In the literature, it is commonly assumed that survival kinetics of starving microbes follows exponential decay. This assumption, however, has not been rigorously tested. Currently, it is not clear under what circumstances this assumption is true. Also, it is not known when such survival kinetics deviates from exponential decay and if it deviates, what underlying mechanisms for the deviation are. Here, to address these issues, we quantitatively characterized dynamics of survival and death of starving E. coli cells. The results show that the assumption--starving cells die exponentially--is true only at high cell density. At low density, starving cells persevere for extended periods of time, before dying rapidly exponentially. Detailed analyses show intriguing quantitative characteristics of the density-dependent and biphasic survival kinetics, including that the period of the perseverance is inversely proportional to cell density. These characteristics further lead us to identification of key underlying processes relevant for the perseverance of starving cells. Then, using mathematical modeling, we show how these processes contribute to the density-dependent and biphasic survival kinetics observed. Importantly, our model reveals a thrifty strategy employed by bacteria, by which upon sensing impending depletion of a substrate, the limiting substrate is conserved and utilized later during starvation to delay cell death. These findings advance quantitative understanding of survival of microbes in oligotrophic environments and facilitate quantitative analysis and prediction of microbial dynamics in nature. Furthermore, they prompt revision of previous models used to analyze and predict population dynamics of microbes.

Growth-dependent photoinactivation kinetics of Enterococcus faecalis

AIMS

To investigate how the growth stage of Enterococcus faecalis affects its photoinactivation in clear water.

METHODS AND RESULTS

Enterococcus faecalis were grown in batch cultures to four different growth stages or grown in chemostats set at four different dilution rates, then harvested and exposed to full spectrum or UVB-blocked simulated sunlight. Experiments were conducted in triplicate in clear water with no added sensitizers. Decay curves were shoulder-log linear and were generally not statistically different in experiments conducted under full spectrum light. Shoulders were longer and first order inactivation rates smaller when experiments were seeded with cells grown to stationary as compared to exponential phase, and for slower growing cells when experiments were done under UVB-blocked light. Chemostat-sourced bacteria generally showed less variability among replicates than batch-sourced cells.

CONCLUSIONS

The physiological state of cells and the method via which they are being generated may affect the photoinactivation experimental results.

SIGNIFICANCE AND IMPACT OF THE STUDY

Photoinactivation experiments conducted with exponential phase cells may overestimate the photoinactivation kinetics in the environment, particular if UVB-independent mechanisms predominate. Chemostat-sourced cells are likely to provide more consistent experimental results than batch-sourced cells.

The functional basis of adaptive evolution in chemostats

Two of the central problems in biology are determining the molecular basis of adaptive evolution and understanding how cells regulate their growth. The chemostat is a device for culturing cells that provides great utility in tackling both of these problems: it enables precise control of the selective pressure under which organisms evolve and it facilitates experimental control of cell growth rate. The aim of this review is to synthesize results from studies of the functional basis of adaptive evolution in long-term chemostat selections using Escherichia coli and Saccharomyces cerevisiae. We describe the principle of the chemostat, provide a summary of studies of experimental evolution in chemostats, and use these studies to assess our current understanding of selection in the chemostat. Functional studies of adaptive evolution in chemostats provide a unique means of interrogating the genetic networks that control cell growth, which complements functional genomic approaches and quantitative trait loci (QTL) mapping in natural populations. An integrated approach to the study of adaptive evolution that accounts for both molecular function and evolutionary processes is critical to advancing our understanding of evolution. By renewing efforts to integrate these two research programs, experimental evolution in chemostats is ideally suited to extending the functional synthesis to the study of genetic networks.

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

Bistable expression of virulence genes in salmonella leads to the formation of an antibiotic-tolerant subpopulation

The bistable expression of virulence genes in Salmonella allows a clonal population to hedge its bets: one subpopulation suffers a growth cost, but is tolerant to antibiotics.

Phenotypic heterogeneity can confer clonal groups of organisms with new functionality. A paradigmatic example is the bistable expression of virulence genes in Salmonella typhimurium, which leads to phenotypically virulent and phenotypically avirulent subpopulations. The two subpopulations have been shown to divide labor during S. typhimurium infections. Here, we show that heterogeneous virulence gene expression in this organism also promotes survival against exposure to antibiotics through a bet-hedging mechanism. Using microfluidic devices in combination with fluorescence time-lapse microscopy and quantitative image analysis, we analyzed the expression of virulence genes at the single cell level and related it to survival when exposed to antibiotics. We found that, across different types of antibiotics and under concentrations that are clinically relevant, the subpopulation of bacterial cells that express virulence genes shows increased survival after exposure to antibiotics. Intriguingly, there is an interplay between the two consequences of phenotypic heterogeneity. The bet-hedging effect that arises through heterogeneity in virulence gene expression can protect clonal populations against avirulent mutants that exploit and subvert the division of labor within these populations. We conclude that bet-hedging and the division of labor can arise through variation in a single trait and interact with each other. This reveals a new degree of functional complexity of phenotypic heterogeneity. In addition, our results suggest a general principle of how pathogens can evade antibiotics: Expression of virulence factors often entails metabolic costs and the resulting growth retardation could generally increase tolerance against antibiotics and thus compromise treatment.

Scientists have recently realized that nature and nurture are not the only determinants of an individual's traits; some organisms also use random molecular processes to generate phenotypic variation among genetically identical individuals. This raises the question of whether such phenotypic variation could be beneficial and what such possible benefits might be. Working with pathogenic Salmonella bacteria, we discovered that phenotypic variation in one single trait—the expression of virulence genes—provides this pathogen with two critical benefits. First, it leads to the division of labor between different phenotypic variants that allows for effective host colonization, and second, it provides tolerance to antibiotics through a “bet-hedging” mechanism. Our results provide a new perspective on how phenotypic differences between individuals can provide benefits to clonal groups of organisms. At the same time, this study contributes to explaining why some pathogens can evade treatment, and could help to find new and better ways for controlling infectious disease.

Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli

Laboratory-based evolution and whole-genome sequencing can link genotype and phenotype. We used evolution of acid resistance in exponential phase Escherichia coli to study resistance to a lethal stress. Iterative selection at pH 2.5 generated five populations that were resistant to low pH in early exponential phase. Genome sequencing revealed multiple mutations, but the only gene mutated in all strains was evgS, part of a two-component system that has already been implicated in acid resistance. All these mutations were in the cytoplasmic PAS domain of EvgS, and were shown to be solely responsible for the resistant phenotype, causing strong upregulation at neutral pH of genes normally induced by low pH. Resistance to pH 2.5 in these strains did not require the transporter GadC, or the sigma factor RpoS. We found that EvgS-dependent constitutive acid resistance to pH 2.5 was retained in the absence of the regulators GadE or YdeO, but was lost if the oxidoreductase YdeP was also absent. A deletion in the periplasmic domain of EvgS abolished the response to low pH, but not the activity of the constitutive mutants. On the basis of these results we propose a model for how EvgS may become activated by low pH.

Specific growth rate determines the sensitivity of Escherichia coli to lactic acid stress: implications for predictive microbiology

This study tested the hypothesis that sensitivity of Escherichia coli to lactic acid at concentrations relevant for fermented sausages (pH 4.6, 150 mM lactic acid, aw = 0.92, temperature = 20 or 27°C) increases with increasing growth rate. For E. coli strain 683 cultured in TSB in chemostat or batch, subsequent inactivation rates when exposed to lactic acid stress increased with increasing growth rate at harvest. A linear relationship between growth rate at harvest and inactivation rate was found to describe both batch and chemostat cultures. The maximum difference in T90, the estimated times for a one-log reduction, was 10 hours between bacteria harvested during the first 3 hours of batch culture, that is, at different growth rates. A 10-hour difference in T90 would correspond to measuring inactivation at 33°C or 45°C instead of 37°C based on relationships between temperature and inactivation. At similar harvest growth rates, inactivation rates were lower for bacteria cultured at 37°C than at 15-20°C. As demonstrated for E. coli 683, culture conditions leading to variable growth rates may contribute to variable lactic acid inactivation rates. Findings emphasize the use and reporting of standardised culture conditions and can have implications for the interpretation of data when developing inactivation models.

Physiological and proteomic analysis of Escherichia coli iron-limited chemostat growth

Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area of study. Escherichia coli K-12 metabolism was studied at four levels of iron limitation in chemostats using physiological and proteomic analyses. The data documented an E. coli acclimation gradient where progressively more severe iron scarcity resulted in a larger percentage of substrate carbon being directed into an overflow metabolism accompanied by a decrease in biomass yield on glucose. Acetate was the primary secreted organic by-product for moderate levels of iron limitation, but as stress increased, the metabolism shifted to secrete primarily lactate (∼70% of catabolized glucose carbon). Proteomic analysis reinforced the physiological data and quantified relative increases in glycolysis enzyme abundance and decreases in tricarboxylic acid (TCA) cycle enzyme abundance with increasing iron limitation stress. The combined data indicated that E. coli responds to limiting iron by investing the scarce resource in essential enzymes, at the cost of catabolic efficiency (i.e., downregulating high-ATP-yielding pathways containing enzymes with large iron requirements, like the TCA cycle). Acclimation to iron-limited growth was contrasted experimentally with acclimation to glucose-limited growth to identify both general and nutrient-specific acclimation strategies. While the iron-limited cultures maximized biomass yields on iron and increased expression of iron acquisition strategies, the glucose-limited cultures maximized biomass yields on glucose and increased expression of carbon acquisition strategies. This study quantified ecologically competitive acclimations to nutrient limitations, yielding knowledge essential for understanding medically relevant bacterial responses to host and to developing intervention strategies.

Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell-cell interactions

Variation of mutation rate at a particular site in a particular genotype, in other words mutation rate plasticity (MRP), can be caused by stress or ageing. However, mutation rate control by other factors is less well characterized. Here we show that in wild-type Escherichia coli (K-12 and B strains), the mutation rate to rifampicin resistance is plastic and inversely related to population density: lowering density can increase mutation rates at least threefold. This MRP is genetically switchable, dependent on the quorum-sensing gene luxS--specifically its role in the activated methyl cycle--and is socially mediated via cell-cell interactions. Although we identify an inverse association of mutation rate with fitness under some circumstances, we find no functional link with stress-induced mutagenesis. Our experimental manipulation of mutation rates via the social environment raises the possibility that such manipulation occurs in nature and could be exploited medically.

sigmaS, a major player in the response to environmental stresses in Escherichia coli: role, regulation and mechanisms of promoter recognition

Bacterial cells often face hostile environmental conditions, to which they adapt by activation of stress responses. In Escherichia coli, environmental stresses resulting in significant reduction in growth rate stimulate the expression of the rpoS gene, encoding the alternative σ factor σ(S). The σ(S) protein associates with RNA polymerase, and through transcription of genes belonging to the rpoS regulon allows the activation of a 'general stress response', which protects the bacterial cell from harmful environmental conditions. Each step of this process is finely tuned in order to cater to the needs of the bacterial cell: in particular, selective promoter recognition by σ(S) is achieved through small deviations from a common consensus DNA sequence for both σ(S) and the housekeeping σ(70). Recognition of specific DNA elements by σ(S) is integrated with the effects of environmental signals and the interaction with regulatory proteins, in what represents a fascinating example of multifactorial regulation of gene expression. In this report, we discuss the function of the rpoS gene in the general stress response, and review the current knowledge on regulation of rpoS expression and on promoter recognition by σ(S).

Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates

Microorganisms extensively reorganize gene expression to adjust growth rate to changes in growth conditions. At the genomic scale, we measured the contribution of both transcription and transcript stability to regulating messenger RNA (mRNA) concentration in Escherichia coli. Transcriptional control was the dominant regulatory process. Between growth rates of 0.10 and 0.63 h(-1), there was a generic increase in the bulk mRNA transcription. However, many transcripts became less stable and the median mRNA half-life decreased from 4.2 to 2.8 min. This is the first evidence that mRNA turnover is slower at extremely low-growth rates. The destabilization of many, but not all, transcripts at high-growth rate correlated with transcriptional upregulation of genes encoding the mRNA degradation machinery. We identified five classes of growth-rate regulation ranging from mainly transcriptional to mainly degradational. In general, differential stability within polycistronic messages encoded by operons does not appear to be affected by growth rate. We show here that the substantial reorganization of gene expression involving downregulation of tricarboxylic acid cycle genes and acetyl-CoA synthetase at high-growth rates is controlled mainly by transcript stability. Overall, our results demonstrate that the control of transcript stability has an important role in fine-tuning mRNA concentration during changes in growth rate.

Growth rate affects the responses of the green alga Tetraselmis suecica to external perturbations

Acclimation to environmental changes involves a modification of the expressed proteome and metabolome. The reproductive advantage associated with the higher fitness that acclimation provides to the new conditions more than compensates for the costs of acclimation. To exploit such an advantage, however, the duration of the perturbation must be sufficiently long relative to the growth rate. Otherwise, a selective pressure may exist in favour of responses that minimize changes in carbon allocation and resource use and do not require reversal of the acclimation after the perturbation ceases (compositional homeostasis). We hypothesize that the choice between acclimation and homeostasis depends on the duration of the perturbation relative to the length of the cell cycle. To test this hypothesis, we cultured the green alga Tetraselmis suecica at two growth rates and subjected the cultures to three environmental perturbations. Carbon allocation was studied with Fourier transform infrared (FTIR) spectroscopy; elemental stoichiometry was investigated by total reflection X-ray fluorescence (TXRF) spectroscopy. Our data confirmed that growth rate is a crucial factor for C allocation in response to external changes, with a higher degree of compositional homeostasis in cells with lower growth rate.

Different levels of catabolite repression optimize growth in stable and variable environments

This study uses experimentally evolved brewer's yeasts to explore the costs and benefits of different nutrient-switching strategies when energy sources vary or remain constant.

Organisms respond to environmental changes by adapting the expression of key genes. However, such transcriptional reprogramming requires time and energy, and may also leave the organism ill-adapted when the original environment returns. Here, we study the dynamics of transcriptional reprogramming and fitness in the model eukaryote Saccharomyces cerevisiae in response to changing carbon environments. Population and single-cell analyses reveal that some wild yeast strains rapidly and uniformly adapt gene expression and growth to changing carbon sources, whereas other strains respond more slowly, resulting in long periods of slow growth (the so-called “lag phase”) and large differences between individual cells within the population. We exploit this natural heterogeneity to evolve a set of mutants that demonstrate how the frequency and duration of changes in carbon source can favor different carbon catabolite repression strategies. At one end of this spectrum are “specialist” strategies that display high rates of growth in stable environments, with more stringent catabolite repression and slower transcriptional reprogramming. The other mutants display less stringent catabolite repression, resulting in leaky expression of genes that are not required for growth in glucose. This “generalist” strategy reduces fitness in glucose, but allows faster transcriptional reprogramming and shorter lag phases when the cells need to shift to alternative carbon sources. Whole-genome sequencing of these mutants reveals that mutations in key regulatory genes such as HXK2 and STD1 adjust the regulation and transcriptional noise of metabolic genes, with some mutations leading to alternative gene regulatory strategies that allow “stochastic sensing” of the environment. Together, our study unmasks how variable and stable environments favor distinct strategies of transcriptional reprogramming and growth.

When microbes grow in a mixture of different nutrients, they repress the metabolism of nonpreferred nutrients such as complex carbohydrates until preferred nutrients, like glucose, are depleted. While this “catabolite repression” allows cells to use the most efficient nutrients first, it also comes at a cost because the switch to nonpreferred nutrients requires the de-repression of specific genes, and during this transition cells must temporarily stop dividing. Naively, one might expect that cells would activate the genes needed to resume growth in the new environment as quickly as possible. However, we find that the length of the growth lag that occurs when yeast cells are switched from the preferred carbon source glucose to alternative nutrients like maltose, galactose, or ethanol differs between wild yeast strains. By repeatedly alternating a slow-switching strain between glucose and maltose, we obtained mutants that show shortened lag phases. Although these variants can switch rapidly between carbon sources, they show reduced growth rates in environments where glucose is available continuously. Further analysis revealed that mutations in genes like HXK2 cause variations in the degree of catabolite repression, with some mutants showing leaky or stochastic maltose gene expression. Together, these results reveal how different gene regulation strategies can affect fitness in variable or stable environments.