scholarly journals Control and regulation of acetate overflow in Escherichia coli

2020 ◽  
Author(s):  
Pierre Millard ◽  
Brice Enjalbert ◽  
Sandrine Uttenweiler-Joseph ◽  
Jean-Charles Portais ◽  
Fabien Létisse
Keyword(s):  
Escherichia Coli ◽  
Glucose Metabolism ◽  
Kinetic Model ◽  
Local Control ◽  
Overflow Metabolism ◽  
Central Metabolism ◽  
Global Regulator ◽  
E Coli ◽  
By Products ◽  
Acetate Overflow

AbstractOverflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli – global control of the central metabolism and local control of the acetate pathway – but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviors and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.

scholarly journals Control and regulation of acetate overflow in Escherichia coli

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Pierre Millard ◽  
Brice Enjalbert ◽  
Sandrine Uttenweiler-Joseph ◽  
Jean-Charles Portais ◽  
Fabien Létisse
Keyword(s):  
Escherichia Coli ◽  
Glucose Metabolism ◽  
Kinetic Model ◽  
Local Control ◽  
Overflow Metabolism ◽  
Central Metabolism ◽  
Global Regulator ◽  
E Coli ◽  
By Products ◽  
Acetate Overflow

Overflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli – global control of the central metabolism and local control of the acetate pathway – but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviours and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control, and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.

scholarly journals Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0139507 ◽  
Author(s):  
Ahmad A. Mannan ◽  
Yoshihiro Toya ◽  
Kazuyuki Shimizu ◽  
Johnjoe McFadden ◽  
Andrzej M. Kierzek ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Open System ◽  
Central Metabolism ◽  
E Coli ◽  
Metabolic Fluxes ◽  
Genome Scale

scholarly journals Escherichia coliLrp regulates one-third of the genome via direct, cooperative, and indirect routes

2018 ◽  
Author(s):  
Grace M. Kroner ◽  
Michael B. Wolfe ◽  
Peter L. Freddolino
Keyword(s):  
Escherichia Coli ◽  
Crucial Role ◽  
Regulatory Activity ◽  
Global Regulator ◽  
Full Spectrum ◽  
Global Trends ◽  
Cooperative Action ◽  
E Coli ◽  
Physiological Conditions ◽  
Regulatory Behavior

AbstractThe global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions. Lrp has previously been shown to activate or repress approximately 10% of genes inEscherichia coli. However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study. We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding. The overall regulatory behavior of Lrp, which as we now show regulates 35% ofE. coligenes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.

scholarly journals Overlapping stimulons arising in response to divergent stresses in Escherichia coli

2021 ◽  
Author(s):  
Huijing Wang ◽  
GW McElfresh ◽  
Nishantha Wijesuriya ◽  
Adam Podgorny ◽  
Andrew D Hecht ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Differential Expression Analysis ◽  
Stringent Response ◽  
Coli Strain ◽  
Growth Media ◽  
Overflow Metabolism ◽  
Rna Seq ◽  
E Coli

Cellular responses to stress can cause a similar change in some facets of fitness even if the stresses are different. Lactose as a sole carbon source for Escherichia coli is an established example: too little causes starvation while excessive lactose import causes toxicity as a side-effect. In an E. coli strain that is robust to osmotic and ionic differences in growth media, B REL606, the rate of antibiotic-tolerant persister formation is elevated in both starvation-inducing and toxicity-inducing concentrations of lactose in comparison to less stressful intermediate concentrations. Such similarities between starvation and toxification raise the question of how much the global stress response stimulon differs between them. We hypothesized that a common stress response is conserved between the two conditions, but that a previously shown threshold driving growth rate heterogeneity in a lactose-toxifying medium would reveal that the growing fraction of cells in that medium to be missing key stress responses that curb growth. To test this, we performed RNA-seq in three representative conditions for differential expression analysis. In comparison to nominally unstressed cultures, both stress conditions showed global shifts in gene expression, with informative similarities and differences. Functional analysis of pathways, gene ontology terms, and clusters of orthogonal groups revealed signatures of overflow metabolism, membrane component shifts, and altered cytosolic and periplasmic contents in toxified cultures. Starving cultures showed an increased tendency toward stringent response-like regulatory signatures. Along with other emerging evidence, our results show multiple possible pathways to stress responses, persistence, and possibly other phenotypes. These results suggest a set of overlapping responses that drives emergence of stress-tolerant phenotypes in diverse conditions.

scholarly journals Overflow Metabolism in Escherichia coli during Steady-State Growth: Transcriptional Regulation and Effect of the Redox Ratio

2006 ◽  
Vol 72 (5) ◽  
pp. 3653-3661 ◽  
Author(s):  
G. N. Vemuri ◽  
E. Altman ◽  
D. P. Sangurdekar ◽  
A. B. Khodursky ◽  
M. A. Eiteman
Keyword(s):  
Escherichia Coli ◽  
Consumption Rate ◽  
Nadh Oxidase ◽  
Glucose Consumption ◽  
Tca Cycle ◽  
Overflow Metabolism ◽  
Glucose Consumption Rate ◽  
Redox Ratio ◽  
E Coli ◽  
Acetate Formation

ABSTRACT Overflow metabolism in the form of aerobic acetate excretion by Escherichia coli is an important physiological characteristic of this common industrial microorganism. Although acetate formation occurs under conditions of high glucose consumption, the genetic mechanisms that trigger this phenomenon are not clearly understood. We report on the role of the NADH/NAD ratio (redox ratio) in overflow metabolism. We modulated the redox ratio in E. coli through the expression of Streptococcus pneumoniae (water-forming) NADH oxidase. Using steady-state chemostat cultures, we demonstrated a strong correlation between acetate formation and this redox ratio. We furthermore completed genome-wide transcription analyses of a control E. coli strain and an E. coli strain overexpressing NADH oxidase. The transcription results showed that in the control strain, several genes involved in the tricarboxylic acid (TCA) cycle and respiration were repressed as the glucose consumption rate increased. Moreover, the relative repression of these genes was alleviated by expression of NADH oxidase and the resulting reduced redox ratio. Analysis of a promoter binding site upstream of the genes which correlated with redox ratio revealed a degenerate sequence with strong homology with the binding site for ArcA. Deletion of arcA resulted in acetate reduction and increased the biomass yield due to the increased capacities of the TCA cycle and respiration. Acetate formation was completely eliminated by reducing the redox ratio through expression of NADH oxidase in the arcA mutant, even at a very high glucose consumption rate. The results provide a basis for studying new regulatory mechanisms prevalent at reduced NADH/NAD ratios, as well as for designing more efficient bioprocesses.

scholarly journals A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jun Zhang ◽  
Wen Luo ◽  
Zhiyuan Wang ◽  
Xiaoyan Chen ◽  
Pengmei Lv ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Synthesis ◽  
Bacillus Subtilis ◽  
Culture System ◽  
Fermentation Process ◽  
Tryptophan Metabolism ◽  
E Coli ◽  
Novel Strategy ◽  
By Products ◽  
Metabolomics Analysis

AbstractTo develop an economically feasible fermentation process, this study designed a novel bioprocess based on the co-culture of engineered Bacillus subtilis and Escherichia coli for the co-production of extracellular D-psicose and intracellular lipase. After optimizing the co-culture bioprocess, 11.70 g/L of D-psicose along with 16.03 U/mg of lipase was obtained; the glucose and fructose were completely utilized. Hence, the conversion rate of D-psicose reached 69.54%. Compared with mono-culture, lipase activity increased by 58.24%, and D-psicose production increased by 7.08%. In addition, the co-culture bioprocess was explored through metabolomics analysis, which included 168 carboxylic acids and derivatives, 70 organooxygen compounds, 34 diazines, 32 pyridines and derivatives, 30 benzene and substituted derivatives, and other compounds. It also could be found that the relative abundance of differential metabolites in the co-culture system was significantly higher than that in the mono-culture system. Pathway analysis revealed that, tryptophan metabolism and β-alanine metabolism had the highest correlation and played an important role in the co-culture system; among them, tryptophan metabolism regulates protein synthesis and β-alanine metabolism, which is related to the formation of metabolic by-products. These results confirm that the co-cultivation of B. subtilis and E. coli can provide a novel idea for D-psicose and lipase biorefinery, and are beneficial for the discovery of valuable secondary metabolites such as turanose and morusin.

scholarly journals Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli

2017 ◽  
Vol 199 (13) ◽  
Author(s):  
Dagmara I. Kisiela ◽  
Matthew Radey ◽  
Sandip Paul ◽  
Stephen Porter ◽  
Kseniya Polukhina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Adaptive Dynamics ◽  
Transcriptional Regulators ◽  
Index Patient ◽  
Transcriptional Analysis ◽  
Global Regulator ◽  
Blood Isolate ◽  
Content Type ◽  
E Coli ◽  
Sepsis Model

ABSTRACT We analyzed the within-household evolution of two household-associated Escherichia coli strains from pandemic clonal group ST131-H30, using isolates recovered from five individuals within two families, each of which had a distinct strain. Family 1's strain was represented by a urine isolate from the index patient (older sister) with recurrent cystitis and a blood isolate from her younger sister with fatal urosepsis. Family 2's strain was represented by a urine isolate from the index patient (father) with pyelonephritis and renal abscesses, blood and kidney drainage isolates from the daughter with emphysematous pyelonephritis, and urine and fecal isolates from the mother with cystitis. Collectively, the several variants of each family's strain had accumulated a total of 8 (family 1) and 39 (family 2) point mutations; no two isolates were identical. Of the 47 total mutations, 36 resulted in amino acid changes or truncation of coded proteins. Fourteen such mutations (39%) targeted genes encoding transcriptional regulators, and 9 (25%) involved DNA-binding transcription factors (TFs), which significantly exceeded the relative contribution of TF genes to the isolates' genomes (∼6%). At least one-half of the transcriptional regulator mutations were inactivating, based on phenotypic and/or transcriptional analysis. In particular, inactivating mutations in the global regulator LrhA (repressor of type 1 fimbriae and flagella) occurred in the blood isolates from both households and increased the virulence of E. coli strains in a murine sepsis model. The results indicate that E. coli undergoes adaptive evolution between and/or within hosts, generating subpopulations with distinctive phenotypes and virulence potential. IMPORTANCE The clonal evolution of bacterial strains associated with interhost transmission is poorly understood. We characterized the genome sequences of clonal descendants of two Escherichia coli strains, recovered at different time points from multiple individuals within two households who had different types of urinary tract infection. We found evidence that the E. coli strains underwent extensive mutational diversification between and within these individuals, driven disproportionately by inactivation of transcriptional regulators. In urosepsis isolates, the mutations observed in the global regulator LrhA increased bacterial virulence in a murine sepsis model. Our findings help in understanding the adaptive dynamics and strategies of E. coli during short-term natural evolution.

scholarly journals Multiple functions of l0036 in the regulation of the pathogenicity island of enterohaemorrhagic Escherichia coli O157:H7

2005 ◽  
Vol 393 (2) ◽  
pp. 591-599 ◽  
Author(s):  
Nien-Pei Tsai ◽  
Yi-Chih Wu ◽  
Jenn-Wei Chen ◽  
Chih-Feng Wu ◽  
Chi-Meng Tzeng ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Current Knowledge ◽  
Regulatory Gene ◽  
Pathogenicity Island ◽  
Negative Regulator ◽  
Multiple Point ◽  
Global Regulator ◽  
Multiple Functions ◽  
E Coli ◽  
Enterohaemorrhagic Escherichia Coli

Diarrhoeagenic enterohaemorrhagic Escherichia coli and enteropathogenic E. coli attach to human intestinal epithelium and efface brush-border microvilli, forming an A/E (attaching and effacing) lesion. These human pathogens are phenotypically similar to the mouse pathogen Citrobacter rodentium. Genetically, they all have a homologous set of virulent genes involved in the A/E lesion, and these genes are organized on a LEE (locus of enterocyte effacement), a pathogenicity island. This island comprises 41 specific open reading frames, of which most are organized at five operons, LEE1, LEE2, LEE3, LEE4 and tir (LEE5). The expression of the LEE genes is regulated in a complicated manner, and current knowledge is that there are at least two positive regulators, Ler (LEE-encoded regulator) and GrlA (global regulator of LEE activator), and one negative regulator, called GrlR (global regulator of LEE repressor). In enterohaemorrhagic E. coli, GrlA is encoded by l0043, whereas GrlR is encoded by l0044. Here we report a fourth regulatory gene located in LEE3, namely l0036. Its expression is tightly controlled. When overexpressed, this factor, named Mpc (multiple point controller), interacts with Ler and suppresses the expression of the LEE proteins. When the translation is not initiated or terminated before maturation, the type III secretion of effectors is completely abolished. Therefore, together with the fact that several cis elements reside in the region that l0036 spans, l0036 appeared to have multiple functions in the regulation of LEE expression.

scholarly journals pSM19035-encoded ζ toxin induces stasis followed by death in a subpopulation of cells

Microbiology ◽  
2006 ◽  
Vol 152 (8) ◽  
pp. 2365-2379 ◽  
Author(s):  
Virginia S. Lioy ◽  
M. Teresa Martín ◽  
Ana G. Camacho ◽  
Rudi Lurz ◽  
Haike Antelmann ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Proliferation ◽  
Minimal Medium ◽  
Time Window ◽  
Constitutive Expression ◽  
Protein Translation ◽  
Cellular Level ◽  
Global Regulator ◽  
E Coli ◽  
Toxin Accumulation

The toxin–antitoxin operon of pSM19035 encodes three proteins: the ω global regulator, the ε labile antitoxin and the stable ζ toxin. Accumulation of ζ toxin free of ε antitoxin induced loss of cell proliferation in both Bacillus subtilis and Escherichia coli cells. Induction of a ζ variant (ζY83C) triggered stasis, in which B. subtilis cells were viable but unable to proliferate, without selectively affecting protein translation. In E. coli cells, accumulation of free ζ toxin induced stasis, but this was fully reversed by expression of the ε antitoxin within a defined time window. The time window for reversion of ζ toxicity by expression of ε antitoxin was dependent on the initial cellular level of ζ. After 240 min of constitutive expression, or inducible expression of high levels of ζ toxin for 30 min, expression of ε failed to reverse the toxic effect exerted by ζ in cells growing in minimal medium. Under the latter conditions, ζ inhibited replication, transcription and translation and finally induced death in a fraction (∼50 %) of the cell population. These results support the view that ζ interacts with its specific target and reversibly inhibits cell proliferation, but accumulation of ζ might lead to cell death due to pleiotropic effects.

scholarly journals Characterization of DNA-binding specificity and analysis of binding sites of the Pseudomonas aeruginosa global regulator, Vfr, a homologue of the Escherichia coli cAMP receptor protein

Microbiology ◽  
2006 ◽  
Vol 152 (12) ◽  
pp. 3485-3496 ◽  
Author(s):  
Kristen J. Kanack ◽  
Laura J. Runyen-Janecky ◽  
Evan P. Ferrell ◽  
Sang-Jin Suh ◽  
Susan E. H. West
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Receptor Protein ◽  
Camp Receptor Protein ◽  
Global Regulator ◽  
E Coli ◽  
Consensus Binding Sequence ◽  
Target Sequences ◽  
Camp Receptor ◽  
Binding Sequence

Vfr, a global regulator of Pseudomonas aeruginosa virulence factors, is a homologue of the Escherichia coli cAMP receptor protein, CRP. Vfr is 91 % similar to CRP and maintains many residues important for CRP to bind cAMP, bind DNA, and interact with RNA polymerase at target promoters. While vfr can complement an E. coli crp mutant in β-galactosidase production, tryptophanase production and catabolite repression, crp can only complement a subset of Vfr-dependent phenotypes in P. aeruginosa. Using specific CRP binding site mutations, it is shown that Vfr requires the same nucleotides as CRP for optimal transcriptional activity from the E. coli lac promoter. In contrast, CRP did not bind Vfr target sequences in the promoters of the toxA and regA genes. Footprinting analysis revealed Vfr protected sequences upstream of toxA, regA, and the quorum sensing regulator lasR, that are similar to but significantly divergent from the CRP consensus binding sequence, and Vfr causes similar DNA bending to CRP in bound target sequences. Using a preliminary Vfr consensus binding sequence deduced from the Vfr-protected sites, Vfr target sequences were identified upstream of the virulence-associated genes plcN, plcHR, pbpG, prpL and algD, and in the vfr/orfX, argH/fimS, pilM/ponA intergenic regions. From these sequences the Vfr consensus binding sequence, 5′-ANWWTGNGAWNY : AGWTCACAT-3′, was formulated. This study suggests that Vfr shares many of the same functions as CRP, but has specialized functions, at least in terms of DNA target sequence binding, required for regulation of a subset of genes in its regulon.

Sign in / Sign up

Export Citation Format

Share Document