scholarly journals Molecular Design of a Signaling System Influences Noise in Protein Abundance under Acid Stress in Different Gammaproteobacteria

2020 ◽  
Vol 202 (16) ◽  
Author(s):  
Sophie Brameyer ◽  
Elisabeth Hoyer ◽  
Sebastian Bibinger ◽  
Korinna Burdack ◽  
Jürgen Lassak ◽  
...  
Keyword(s):  
Copy Number ◽  
Molecular Design ◽  
Ph Sensor ◽  
Acid Stress ◽  
Acid Resistance ◽  
Signaling System ◽  
Content Type ◽  
Signaling Systems ◽  
E Coli ◽  
Cad System

ABSTRACT Bacteria have evolved different signaling systems to sense and adapt to acid stress. One of these systems, the CadABC system, responds to a combination of low pH and lysine availability. In Escherichia coli, the two signals are sensed by the pH sensor and transcription activator CadC and the cosensor LysP, a lysine-specific transporter. Activated CadC promotes the transcription of the cadBA operon, which codes for the lysine decarboxylase CadA and the lysine/cadaverine antiporter CadB. The copy number of CadC is controlled translationally. Using a bioinformatics approach, we identified the presence of CadC with ribosomal stalling motifs together with LysP in species of the Enterobacteriaceae family. In contrast, we identified CadC without stalling motifs in species of the Vibrionaceae family, and the LysP cosensor is missing. Therefore, we compared the outputs of the Cad system in single cells of the distantly related organisms E. coli and Vibrio campbellii using fluorescently tagged CadB as the reporter. We observed a heterogeneous output in E. coli, and all the V. campbellii cells produced CadB. The copy number of the pH sensor CadC in E. coli was extremely low (≤4 molecules per cell), but it was 10-fold higher in V. campbellii. An increase in the CadC copy number in E. coli correlated with a decrease in heterogeneous behavior. This study demonstrated how small changes in the design of a signaling system allow a homogeneous output and, thus, adaptation of Vibrio species that rely on the CadABC system as the only acid resistance system. IMPORTANCE Acid resistance is an important property for bacteria, such as Escherichia coli, to survive acidic environments like the human gastrointestinal tract. E. coli possesses both passive and inducible acid resistance systems to counteract acidic environments. Thus, E. coli evolved sophisticated signaling systems to sense and appropriately respond to environmental acidic stress by regulating the activity of its three inducible acid resistance systems. One of these systems is the Cad system, which is induced only under moderate acidic stress in a lysine-rich environment by the pH-responsive transcriptional regulator CadC. The significance of our research lies in identifying the molecular design of the Cad systems in different proteobacteria and their target expression noise at the single-cell level during acid stress conditions.

scholarly journals BaeSR, Involved in Envelope Stress Response, Protects against Lysogenic Conversion by Shiga Toxin 2-Encoding Phages

2015 ◽  
Vol 83 (4) ◽  
pp. 1451-1457 ◽  
Author(s):  
Lejla Imamovic ◽  
Alexandre Martínez-Castillo ◽  
Carmen Benavides ◽  
Maite Muniesa
Keyword(s):  
Stress Responses ◽  
Shiga Toxin ◽  
Phage Infection ◽  
Bacterial Cells ◽  
Content Type ◽  
Signaling Systems ◽  
E Coli ◽  
Envelope Stress ◽  
Lysogenic Conversion

Infection and lysogenic conversion with Shiga toxin-encoding bacteriophages (Stx phages) drive the emergence of new Shiga toxin-producingEscherichia colistrains. Phage attachment to the bacterial surface is the first stage of phage infection. Envelope perturbation causes activation of envelope stress responses in bacterial cells. Although many external factors are known to activate envelope stress responses, the role of these responses in the phage-bacterium interaction remains unexplored. Here, we investigate the link between three envelope signaling systems inE. coli(RcsBC, CpxAR, and BaeSR) and Stx2 phage infection by determining the success of bacterial lysogenic conversion. For this purpose,E. coliDH5α wild-type (WT) and mutant strains lacking RcsBC, CpxAR, or BaeSR signaling systems were incubated with a recombinant Stx2 phage (933W). Notably, the number of lysogens obtained with the BaeSR mutant was 5 log10units higher than with the WT, and the same differences were observed when using 7 different Stx2 phages. To assess whether the membrane receptor used by Stx phages, BamA, was involved in the differences observed,bamAgene expression was monitored by reverse transcription-quantitative PCR (RT-qPCR) in all host strains. A 4-fold-higherbamAexpression level was observed in the BaeSR mutant than in the WT strain, suggesting that differential expression of the receptor used by Stx phages accounted for the increase in the number of lysogenization events. Establishing the link between the role of stress responses and phage infection has important implications for understanding the factors affecting lysogenic conversion, which drives the emergence of new pathogenic clones.

scholarly journals Evolutionary Silence of the Acid Chaperone Protein HdeB in Enterohemorrhagic Escherichia coli O157:H7

2011 ◽  
Vol 78 (4) ◽  
pp. 1004-1014 ◽  
Author(s):  
Michelle Q. Carter ◽  
Jacqueline W. Louie ◽  
Clifton K. Fagerquist ◽  
Omar Sultan ◽  
William G. Miller ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acid Resistance ◽  
Significant Loss ◽  
Enterohemorrhagic Escherichia Coli ◽  
Survival Strategies ◽  
Start Codon ◽  
Divergent Evolution ◽  
Content Type ◽  
E Coli ◽  
K 12

ABSTRACTThe periplasmic chaperones HdeA and HdeB are known to be important for cell survival at low pH (pH < 3) inEscherichia coliandShigellaspp. Here we investigated the roles of HdeA and HdeB in the survival of various enterohemorrhagicE. coli(EHEC) following exposure to pH 2.0. Similar to K-12 strains, the acid protections conferred by HdeA and HdeB in EHEC O145 were significant: loss of HdeA and HdeB led to over 100- to 1,000-fold reductions in acid survival, depending on the growth condition of prechallenge cells. However, this protection was much less inE. coliO157:H7 strains. Deletion ofhdeBdid not affect the acid survival of cells, and deletion ofhdeAled to less than a 5-fold decrease in survival. Sequence analysis of thehdeABoperon revealed a point mutation at the putative start codon of thehdeBgene in all 26E. coliO157:H7 strains analyzed, which shifted the ATG start codon to ATA. This mutation correlated with the lack of HdeB inE. coliO157:H7; however, the plasmid-borne O157-hdeBwas able to restore partially the acid resistance in anE. coliO145ΔhdeABmutant, suggesting the potential function of O157-HdeB as an acid chaperone. We conclude thatE. coliO157:H7 strains have evolved acid survival strategies independent of the HdeA/B chaperones and are more acid resistant than nonpathogenic K-12 for cells grown under nonfavorable culturing conditions such as in Luria-Bertani no-salt broth at 28°C. These results suggest a divergent evolution of acid resistance mechanisms withinE. coli.

scholarly journals Improved Acetic Acid Resistance in Saccharomyces cerevisiae by Overexpression of theWHI2Gene Identified through Inverse Metabolic Engineering

2016 ◽  
Vol 82 (7) ◽  
pp. 2156-2166 ◽  
Author(s):  
Yingying Chen ◽  
Lisa Stabryla ◽  
Na Wei
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Acetic Acid ◽  
Metabolic Engineering ◽  
Acid Stress ◽  
Acid Resistance ◽  
Biofuel Production ◽  
Gene Target ◽  
Content Type ◽  
Inverse Metabolic Engineering ◽  
Acetic Acid Resistance

ABSTRACTDevelopment of acetic acid-resistantSaccharomyces cerevisiaeis important for economically viable production of biofuels from lignocellulosic biomass, but the goal remains a critical challenge due to limited information on effective genetic perturbation targets for improving acetic acid resistance in the yeast. This study employed a genomic-library-based inverse metabolic engineering approach to successfully identify a novel gene target,WHI2(encoding a cytoplasmatic globular scaffold protein), which elicited improved acetic acid resistance inS. cerevisiae. Overexpression ofWHI2significantly improved glucose and/or xylose fermentation under acetic acid stress in engineered yeast. TheWHI2-overexpressing strain had 5-times-higher specific ethanol productivity than the control in glucose fermentation with acetic acid. Analysis of the expression ofWHI2gene products (including protein and transcript) determined that acetic acid induced endogenous expression of Whi2 inS. cerevisiae. Meanwhile, thewhi2Δ mutant strain had substantially higher susceptibility to acetic acid than the wild type, suggesting the important role of Whi2 in the acetic acid response inS. cerevisiae. Additionally, overexpression ofWHI2and of a cognate phosphatase gene,PSR1, had a synergistic effect in improving acetic acid resistance, suggesting that Whi2 might function in combination with Psr1 to elicit the acetic acid resistance mechanism. These results improve our understanding of the yeast response to acetic acid stress and provide a new strategy to breed acetic acid-resistant yeast strains for renewable biofuel production.

scholarly journals D-Methionine and D-Phenylalanine Improve Lactococcus lactis F44 Acid Resistance and Nisin Yield by Governing Cell Wall Remodeling

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Hao Wu ◽  
Ershu Xue ◽  
Ning Zhi ◽  
Qianqian Song ◽  
Kairen Tian ◽  
...  
Keyword(s):  
Amino Acids ◽  
Cell Wall ◽  
Lactococcus Lactis ◽  
Acid Stress ◽  
Acid Tolerance ◽  
Acid Resistance ◽  
Cell Wall Synthesis ◽  
Nisin Production ◽  
Content Type ◽  
Nisin Yield

ABSTRACT Lactococcus lactis encounters various environmental challenges, especially acid stress, during its growth. The cell wall can maintain the integrity and shape of the cell under environmental stress, and d-amino acids play an important role in cell wall synthesis. Here, by analyzing the effects of 19 different d-amino acids on the physiology of L. lactis F44, we found that exogenously supplied d-methionine and d-phenylalanine increased the nisin yield by 93.22% and 101.29%, respectively, as well as significantly increasing the acid resistance of L. lactis F44. The composition of the cell wall in L. lactis F44 with exogenously supplied d-Met or d-Phe was further investigated via a vancomycin fluorescence experiment and a liquid chromatography-mass spectrometry assay, which demonstrated that d-Met could be incorporated into the fifth position of peptidoglycan (PG) muropeptides and d-Phe could be added to the fourth and fifth positions. Moreover, overexpression of the PG synthesis gene murF further enhanced the levels of d-Met and d-Phe involved in PG and increased the survival rate under acid stress and the nisin yield of the strain. This study reveals that the exogenous supply of d-Met or d-Phe can change the composition of the cell wall and influence acid tolerance as well as nisin yield in L. lactis. IMPORTANCE As d-amino acids play an important role in cell wall synthesis, we analyzed the effects of 19 different d-amino acids on L. lactis F44, demonstrating that d-Met and d-Phe can participate in peptidoglycan (PG) synthesis and improve the acid resistance and nisin yield of this strain. murF overexpression further increased the levels of d-Met and d-Phe incorporated into PG and contributed to the acid resistance of the strain. These findings suggest that d-Met and d-Phe can be incorporated into PG to improve the acid resistance and nisin yield of L. lactis, and this study provides new ideas for the enhancement of nisin production.

scholarly journals Distinct Transcriptional Profiles and Phenotypes Exhibited by Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-Associated Outbreak

2011 ◽  
Vol 78 (2) ◽  
pp. 455-463 ◽  
Author(s):  
Craig T. Parker ◽  
Jennifer L. Kyle ◽  
Steven Huynh ◽  
Michelle Q. Carter ◽  
Maria T. Brandl ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acid Stress ◽  
The United States ◽  
Clinical Isolates ◽  
Content Type ◽  
Transcriptional Profiles ◽  
E Coli ◽  
Large Outbreak ◽  
Altered Gene ◽  
Feral Pig

ABSTRACTIn 2006, a large outbreak ofEscherichia coliO157:H7 was linked to the consumption of ready-to-eat bagged baby spinach in the United States. The likely sources of preharvest spinach contamination were soil and water that became contaminated via cattle or feral pigs in the proximity of the spinach fields. In this study, we compared the transcriptional profiles of 12E. coliO157:H7 isolates that possess the same two-enzyme pulsed-field gel electrophoresis (PFGE) profile and are related temporally or geographically to the above outbreak. TheseE. coliO157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig. The three clinical isolates and two spinach bag isolates grown in cultures to stationary phase showed decreased expression of many σS-regulated genes, includinggadA,osmE,osmY, andkatE, compared with the soil, water, cow, feral pig, and the other three spinach bag isolates. The decreased expression of these σS-regulated genes was correlated with the decreased resistance of the isolates to acid stress, osmotic stress, and oxidative stress but increases in scavenging ability. We also observed that intraisolate variability was much more pronounced among the clinical and spinach isolates than among the environmental isolates. Together, the transcriptional and phenotypic differences of the spinach outbreak isolates ofE. coliO157:H7 support the hypothesis that some variants within the spinach bag retained characteristics of the preharvest isolates, whereas other variants with altered gene expression and phenotypes infected the human host.

scholarly journals Collaborative Regulation of Escherichia coli Glutamate-Dependent Acid Resistance by Two AraC-Like Regulators, GadX and GadW (YhiW)

2002 ◽  
Vol 184 (24) ◽  
pp. 7001-7012 ◽  
Author(s):  
Zhuo Ma ◽  
Hope Richard ◽  
Don L. Tucker ◽  
Tyrrell Conway ◽  
John W. Foster
Keyword(s):  
Escherichia Coli ◽  
Acid Stress ◽  
Acid Resistance ◽  
Negative Regulator ◽  
Receptor Protein ◽  
Growth Media ◽  
Infectious Dose ◽  
E Coli ◽  
Control Circuits

ABSTRACT An important feature of Escherichia coli pathogenesis is an ability to withstand extremely acidic environments of pH 2 or lower. This acid resistance property contributes to the low infectious dose of pathogenic E. coli species. One very efficient E. coli acid resistance system encompasses two isoforms of glutamate decarboxylase (gadA and gadB) and a putative glutamate:γ-amino butyric acid (GABA) antiporter (gadC). The system is subject to complex controls that vary with growth media, growth phase, and growth pH. Previous work has revealed that the system is controlled by two sigma factors, two negative regulators (cyclic AMP receptor protein [CRP] and H-NS), and an AraC-like regulator called GadX. Earlier evidence suggested that the GadX protein acts both as a positive and negative regulator of the gadA and gadBC genes depending on environmental conditions. New data clarify this finding, revealing a collaborative regulation between GadX and another AraC-like regulator called GadW (previously YhiW). GadX and GadW are DNA binding proteins that form homodimers in vivo and are 42% homologous to each other. GadX activates expression of gadA and gadBC at any pH, while GadW inhibits GadX-dependent activation. Regulation of gadA and gadBC by either regulator requires an upstream, 20-bp GAD box sequence. Northern blot analysis further indicates that GadW represses expression of gadX. The results suggest a control circuit whereby GadW interacts with both the gadA and gadX promoters. GadW clearly represses gadX and, in situations where GadX is missing, activates gadA and gadBC. GadX, however, activates only gadA and gadBC expression. CRP also represses gadX expression. It does this primarily by repressing production of sigma S, the sigma factor responsible for gadX expression. In fact, the acid induction of gadA and gadBC observed when rich-medium cultures enter stationary phase corresponds to the acid induction of sigma S production. These complex control circuits impose tight rein over expression of the gadA and gadBC system yet provide flexibility for inducing acid resistance under many conditions that presage acid stress.

scholarly journals Escherichia coli O157 : H7 glutamate- and arginine-dependent acid-resistance systems protect against oxidative stress during extreme acid challenge

Microbiology ◽  
2009 ◽  
Vol 155 (3) ◽  
pp. 805-812 ◽  
Author(s):  
Bradley L. Bearson ◽  
In Soo Lee ◽  
Thomas A. Casey
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Hydrogen Peroxide ◽  
Acid Stress ◽  
Acid Resistance ◽  
Dependent Manner ◽  
Bacterial Survival ◽  
E Coli ◽  
Stress Protection ◽  
Acid Challenge

Micro-organisms may simultaneously encounter multiple stresses in their environment. To investigate the protection that several known Escherichia coli O157 : H7 acid-resistance systems might provide against both oxidative and acid stress, the addition of diamide, a membrane-permeable thiol-specific oxidizing agent, or hydrogen peroxide were used concurrent with acid challenge at pH 2.5 to determine bacterial survival. The addition of either diamide or hydrogen peroxide decreased bacterial survival in a dose-dependent manner for E. coli O157 : H7 during challenge at pH 2.5 following overnight growth in LB MES pH 5.5 (acid-resistance system 1, AR1). In contrast, the presence of either glutamate or arginine during challenge provided significant protection against diamide- and hydrogen peroxide-induced oxidative stress during pH 2.5 acid challenge. Oxidative stress protection during acid challenge required gadC and adiA for the glutamate- (AR2) and arginine- (AR3) dependent acid-resistance systems, respectively. In addition, maximal protection against oxidative stress in the presence of glutamate required a low external pH (pH 2.5), since pH 5.5 did not protect. This study demonstrates that the glutamate- and arginine-dependent acid-resistance systems of E. coli O157 : H7 can simultaneously protect against oxidative stress during extreme acid challenge.

scholarly journals Products of the Escherichia coli Acid Fitness Island Attenuate Metabolite Stress at Extremely Low pH and Mediate a Cell Density-Dependent Acid Resistance

2007 ◽  
Vol 189 (7) ◽  
pp. 2759-2768 ◽  
Author(s):  
Aaron K. Mates ◽  
Atef K. Sayed ◽  
John W. Foster
Keyword(s):  
Escherichia Coli ◽  
Organic Acids ◽  
Regulatory Protein ◽  
Resistance Mechanism ◽  
Acid Stress ◽  
Acid Resistance ◽  
Cell Contact ◽  
Density Dependent ◽  
E Coli ◽  
Cell Densities

ABSTRACT Escherichia coli has an ability, rare among the Enterobacteriaceae, to survive extreme acid stress under various host (e.g., human stomach) and nonhost (e.g., apple cider) conditions. Previous microarray studies have exposed a cluster of 12 genes at 79 centisomes collectively called an acid fitness island (AFI). Four AFI genes, gadA, gadX, gadW, and gadE, were already known to be involved in an acid resistance system that consumes an intracellular proton through the decarboxylation of glutamic acid. However, roles for the other eight AFI gene products were either unknown or subject to conflicting findings. Two new aspects of acid resistance are described that require participation of five of the remaining eight AFI genes. YhiF (a putative regulatory protein), lipoprotein Slp, and the periplasmic chaperone HdeA protected E. coli from organic acid metabolites produced during fermentation once the external pH was reduced to pH 2.5. HdeA appears to handle protein damage caused when protonated organic acids diffuse into the cell and dissociate, thereby decreasing internal pH. In contrast, YhiF- and Slp-dependent systems appear to counter the effects of the organic acids themselves, specifically succinate, lactate, and formate, but not acetate. A second phenomenon was defined by two other AFI genes, yhiD and hdeD, encoding putative membrane proteins. These proteins participate in an acid resistance mechanism exhibited only at high cell densities (>108 CFU per ml). Density-dependent acid resistance does not require any demonstrable secreted factor and may involve cell contact-dependent activation. These findings further define the complex physiology of E. coli acid resistance.

scholarly journals Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli

2015 ◽  
Vol 81 (23) ◽  
pp. 8118-8125 ◽  
Author(s):  
Marta Veses-Garcia ◽  
Xuan Liu ◽  
Daniel J. Rigden ◽  
John G. Kenny ◽  
Alan J. McCarthy ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acid Resistance ◽  
Lytic Cycle ◽  
Acid Decarboxylase ◽  
O157 Strain ◽  
Data Set ◽  
Content Type ◽  
E Coli ◽  
Before And After ◽  
The Impact

ABSTRACTShiga-toxigenic bacteriophages are converting lambdoid phages that impart the ability to produce Shiga toxin to their hosts. Little is known about the function of most of the genes carried by these phages or the impact that lysogeny has on theEscherichia colihost. Here we use next-generation sequencing to compare the transcriptomes ofE. colistrains infected with an Stx phage, before and after triggering of the bacterial SOS response that initiates the lytic cycle of the phage. We were able to discriminate between bacteriophage genes expressed in the lysogenic and lytic cycles, and we describe transcriptional changes that occur in the bacterial host as a consequence of Stx phage carriage. Having identified upregulation of the glutamic acid decarboxylase (GAD) operon, confirmed by reverse transcription-quantitative PCR (RT-qPCR), we used phenotypic assays to establish the ability of the Stx prophage to confer a greater acid resistance phenotype on theE. colihost. Known phage regulators were overexpressed inE. coli, and the acid resistance of the recombinant strains was tested. The phage-encoded transcriptional regulator CII was identified as the controller of the acid response in the lysogen. Infection of anE. coliO157 strain, from which integrated Stx prophages were previously removed, showed increased acid resistance following infection with a nontoxigenic phage, ϕ24B. In addition to demonstrating this link between Stx phage carriage andE. coliacid resistance, with its implications for survival postingestion, the data set provides a number of other potential insights into the impact of lambdoid phage carriage on the biology ofE. coli.

scholarly journals Acetoin Synthesis Acquisition Favors Escherichia coli Growth at Low pH

2014 ◽  
Vol 80 (19) ◽  
pp. 6054-6061 ◽  
Author(s):  
Bram Vivijs ◽  
Pieter Moons ◽  
Abram Aertsen ◽  
Chris W. Michiels
Keyword(s):  
Escherichia Coli ◽  
Culture Media ◽  
Acid Stress ◽  
Low Ph ◽  
Phase Cell ◽  
Acid Fermentation ◽  
Serratia Plymuthica ◽  
Content Type ◽  
E Coli ◽  
Acetoin Production

ABSTRACTSome members of the familyEnterobacteriaceaeferment sugars via the mixed-acid fermentation pathway. This yields large amounts of acids, causing strong and sometimes even lethal acidification of the environment. Other family members employ the 2,3-butanediol fermentation pathway, which generates comparatively less acidic and more neutral end products, such as acetoin and 2,3-butanediol. In this work, we equippedEscherichia coliMG1655 with thebudABoperon, encoding the acetoin pathway, fromSerratia plymuthicaRVH1 and investigated how this affected the ability ofE. colito cope with acid stress during growth. Acetoin fermentation prevented lethal medium acidification byE. coliin lysogeny broth (LB) supplemented with glucose. It also supported growth and higher stationary-phase cell densities in acidified LB broth with glucose (pH 4.10 to 4.50) and in tomato juice (pH 4.40 to 5.00) and reduced the minimal pH at which growth could be initiated. On the other hand, the acetoin-producing strain was outcompeted by the nonproducer in a mixed-culture experiment at low pH, suggesting a fitness cost associated with acetoin production. Finally, we showed that acetoin production profoundly changes the appearance ofE. colion several diagnostic culture media. NaturalE. colistrains that have laterally acquiredbudABgenes may therefore have escaped detection thus far. This study demonstrates the potential importance of acetoin fermentation in the ecology ofE. coliin the food chain and contributes to a better understanding of the microbiological stability and safety of acidic foods.

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