scholarly journals DNA cytosine methylation at the lexA promoter of Escherichia coli is stationary phase specific

2021 ◽  
Author(s):  
Elizabeth B Lewis ◽  
Edwin Chen ◽  
Matthew J Culyba
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Cytosine Methylation ◽  
Sos Response ◽  
Phase Growth ◽  
Bacterial Dna ◽  
Cytosine Methyltransferase ◽  
Lexa Binding ◽  
The Impact ◽  
Dna Damage Response Pathway

Abstract The bacterial DNA damage response pathway (SOS response) is composed of a network of genes regulated by a single transcriptional repressor, LexA. The lexA promoter, itself, contains two LexA operators, enabling negative feedback. In Escherichia coli, the downstream operator contains a conserved DNA cytosine methyltransferase (Dcm) site that is predicted to be methylated to 5-methylcytosine (5mC) specifically during stationary phase growth, suggesting a regulatory role for DNA methylation in the SOS response. To test this, we quantified 5mC at the lexA locus, and then examined the effect of LexA on Dcm activity, as well as the impact of this 5mC mark on LexA binding, lexA transcription, and SOS response induction. We found that 5mC at the lexA promoter is specific to stationary phase growth, but that it does not affect lexA expression. Our data support a model where LexA binding at the promoter inhibits Dcm activity without an effect on the SOS regulon.

DNA cytosine methyltransferase enhances viability during prolonged stationary phase in Escherichia coli

2020 ◽  
Vol 367 (20) ◽  
Author(s):  
Kevin T Militello ◽  
Lara Finnerty-Haggerty ◽  
Ooha Kambhampati ◽  
Rebecca Huss ◽  
Rachel Knapp
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Wild Type ◽  
Bacterial Physiology ◽  
Phase Competition ◽  
Cytosine Methyltransferase ◽  
The Impact ◽  
Restriction Modification ◽  
Restriction Modification Systems

ABSTRACT In Escherichia coli, DNA cytosine methyltransferase (Dcm) methylates the second cytosine in the sequence 5′CCWGG3′ generating 5-methylcytosine. Dcm is not associated with a cognate restriction enzyme, suggesting Dcm impacts facets of bacterial physiology outside of restriction-modification systems. Other than gene expression changes, there are few phenotypes that have been identified in strains with natural or engineered Dcm loss, and thus Dcm function has remained an enigma. Herein, we demonstrate that Dcm does not impact bacterial growth under optimal and selected stress conditions. However, Dcm does impact viability in long-term stationary phase competition experiments. Dcm+ cells outcompete cells lacking dcm under different conditions. Dcm knockout cells have more RpoS-dependent HPII catalase activity than wild-type cells. Thus, the impact of Dcm on stationary phase may involve changes in RpoS activity. Overall, our data reveal a new role for Dcm during long-term stationary phase.

Contribution of SOS Genes to H2O2-induced Apoptosis-like Death in Escherichia Coli

2021 ◽  
Author(s):  
Heesu Kim ◽  
Dong Gun Lee
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Treatment Strategies ◽  
Sos Response ◽  
Bacterial Dna ◽  
E Coli ◽  
New Treatment ◽  
Induced Apoptosis ◽  
And Function ◽  
The Relationship

Abstract Hydrogen peroxide (H2O2) is a debriding agent that damages the microbial structure and function by generating various reactive oxygen species (ROS). H2O2-produced hydroxyl radical (OH∙) also exert oxidative stress on microorganisms. The spread of antibiotic resistance in bacteria is a serious issue worldwide, and greater efforts are needed to identify and characterize novel antibacterial mechanisms to develop new treatment strategies. Therefore, this study aimed to clarify the relationship between H2O2 and Escherichia coli and to elucidate a novel antibacterial mechanism(s) of H2O2. Following H2O2 exposure, increased levels of 8-hydroxyldeoxyguanosine and malondialdehyde indicated that H2O2 accelerates oxidation of bacterial DNA and lipids in E. coli. As oxidative damage worsened, the SOS response was triggered. Cell division arrest and resulting filamentation were identified in cells, indicating that LexA was involved in DNA replication. It was also verified that RecA, a representative SOS gene, helps self-cleavage of LexA and acts as a bacterial caspase-like protein. Our findings also showed that dinF is essential to preserve E. coli from H2O2-induced ROS, and furthermore, demonstrated that H2O2-induced SOS response and SOS genes participate differently in guarding E. coli from oxidative stress. As an extreme SOS response is considered apoptosis-like death (ALD) in bacteria, additional experiments were performed to examine the characteristics of ALD. DNA fragmentation and membrane depolarization appeared in H2O2-treated cells, suggesting that H2O2 causes ALD in E. coli. In conclusion, our investigations revealed that ALD is a novel antibacterial mode of action(s) of H2O2 with important contributions from SOS genes.

scholarly journals Nucleoids Dynamic in Escherichia coli: A Growth Phase Dependent Process

1970 ◽  
Vol 23 (2) ◽  
pp. 81-88 ◽  
Author(s):  
Ali Azam Talukder ◽  
M Anwar Hossain ◽  
Mamoru Yamada ◽  
Akira Ishihama
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Gene Silencing ◽  
Cell Survival ◽  
Growth Phase ◽  
Genomic Dna ◽  
Bacterial Dna ◽  
Escherichia Coli Cells ◽  
Dna Organization ◽  
Nucleoid Proteins

Bacterial DNA compacts in nucleoid bodies. The organization of nucleoid body depends on the association of genomic DNA with a numbers of histone-like proteins. The relax nucleoids organization in rapidly growing Escherichia coli cells associate with six major proteins, Fis, HU, Hfq, H-NS, StpA and IHF, but at stationary phase the nucleoids further tightly pack with Dps. The final steps of compact nucleoids formation occurs with association of MukBEF complex - a bacterial condensin. The change of nucleoid proteins composition in stationary phase accompanies compact DNA organization and genes silencing. Thus, compact nucleoid organization and gene silencing may be crucial for cell survival in stationary phase.Keywords: Escherichia coli, Nucleoid body, Nucleoid proteins, Nucleoid compaction, CondensinDOI: http://dx.doi.org/10.3329/bjm.v23i2.867 Bangladesh J Microbiol, Volume 23, Number 2, December 2006, pp 81-88

Growth and survival of uninjured and sublethally heat-injured Escherichia coli O157:H7 on beef extract medium as influenced by package atmosphere and storage temperature

1999 ◽  
Vol 45 (3) ◽  
pp. 263-268 ◽  
Author(s):  
Jeffrey J Semanchek ◽  
David A Golden ◽  
Robert C Williams
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Storage Temperature ◽  
Brain Heart Infusion ◽  
Escherichia Coli O157 ◽  
Phase Growth ◽  
Growth And Survival ◽  
E Coli ◽  
Beef Extract ◽  
And Storage

The effect of atmospheric composition and storage temperature on growth and survival of uninjured and sublethally heat-injured Escherichia coli O157:H7, inoculated onto brain heart infusion agar containing 0.3% beef extract (BEM), was determined. BEM plates were packaged in barrier bags in air, 100% CO2, 100% N2, 20% CO2 : 80% N2, and vacuum and were stored at 4, 10, and 37°C for up to 20 days. Package atmosphere and inoculum status (i.e., uninjured or heat-injured) influenced (P < 0.01) growth and survival of E. coli O157:H7 stored at all test temperatures. Growth of heat-injured E. coli O157:H7 was slower (P < 0.01) than uninjured E. coli O157:H7 stored at 37°C. At 37°C, uninjured E. coli O157:H7 reached stationary phase growth earlier than heat-injured populations. Uninjured E. coli O157:H7 grew during 10 days of storage at 10°C, while heat-injured populations declined during 20 days of storage at 10°C. Uninjured E. coli O157:H7 stored at 10°C reached stationary phase growth within approximately 10 days in all packaging atmospheres except CO2. Populations of uninjured and heat-injured E. coli O157:H7 declined throughout storage for 20 days at 4°C. Survival of uninjured populations stored at 4°C, as well as heat-injured populations stored at 4 and 10°C, was enhanced in CO2 atmosphere. Survival of heat-injured E. coli O157:H7 at 4 and 10°C was not different (P > 0.05). Uninjured and heat-injured E. coli O157:H7 are able to survive at low temperatures in the modified atmospheres used in this study.Key words: E. coli O157:H7, sublethal injury, modified atmosphere packaging.

Reaction of Surrogate Escherichia coli Serotype O157:H7 and Non-O157 Strains to Nutrient Starvation: Variation in Phenotype and Transcription of Stress Response Genes and Behavior on Lettuce Plants in the Field

2019 ◽  
Vol 82 (11) ◽  
pp. 1988-2000
Author(s):  
GREG BEZANSON ◽  
DAVID MADER ◽  
SHERRY FILLMORE ◽  
SUSAN BACH ◽  
PASCAL DELAQUIS
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Decay Rates ◽  
Leafy Vegetables ◽  
Broth Culture ◽  
Starvation Period ◽  
E Coli ◽  
Culture Cells ◽  
Stressed Cells ◽  
The Impact

ABSTRACT Preharvest contamination with bacteria borne by irrigation water may result in leafy vegetables serving as vehicles for transmission of Shiga toxin–producing Escherichia coli (STEC) to humans. The influence of starvation-associated stress on the behavior of non–toxin-producing strains of E. coli serotype O157:H7 and serotypes O26, O103, O111, and O145 was examined subsequent to their introduction to the phyllosphere of field-grown romaine lettuce as inocula simulating starved (96 h in sterile deionized water) and nutrient-depleted (24 h broth culture) cells. As with E. coli O157:H7, leaf populations of the non-O157 strains declined rapidly during the first 72 h postinoculation, displaying the biphasic decay curve typical of serotype O157:H7 isolates. Preinoculation treatment appeared not to influence decay rates greatly (P &gt; 0.5), but strain-specific differences (persistence period and attachment proficiency) indicated that serotype O103:H2 strain PARC445 was a better survivor. Also assessed was the impact of preinoculation treatment on phenotypes key to leaf colonization and survival and the expression of starvation stress–associated genes. The 96-h starvation period enhanced biofilm formation in one strain but reduced motility and autoinducer 2 formation in all five study strains relative to those characteristics in stationary-phase cells. Transcription of rpoS, dps, uspA, and gapA was reduced significantly (P &lt; 0.05) in starvation-stressed cells relative to that for exponential- and stationary-phase cultures. Strain-specific differences were observed; serotype O103:H2 PARC445 had greater downturns than did serotype O157:H7 and other non-O157 strains. Within this particular cohort, the behavior of the representative serotype O157:H7 strain, PARC443 (ATCC 700728), was not predictive of behavior of non-O157 members of this STEC group.

scholarly journals Metabolites potentiate nitrofurans in non-growing Escherichia coli

2020 ◽  
Author(s):  
Sandra J. Aedo ◽  
Juechun Tang ◽  
Mark P. Brynildsen
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Stationary Phase ◽  
Urinary Tract Infections ◽  
Contributing Factors ◽  
Bacterial Dna ◽  
E Coli ◽  
Artificial Urine ◽  
Tract Infections ◽  
Reducing Equivalents

Nitrofurantoin (NIT) is a broad-spectrum bactericidal antibiotic used in the treatment of urinary tract infections. It is a pro-drug that once activated by nitroreductases goes on to inhibit bacterial DNA, RNA, cell wall, and protein synthesis. Previous work has suggested that NIT retains considerable activity against non-growing bacteria. Here we have found that Escherichia coli (E. coli) grown to stationary phase in minimal or artificial urine media are not susceptible to NIT. Supplementation with glucose under conditions where cells remained non-growing (other essential nutrients were absent) sensitized cultures to NIT. We conceptualized NIT sensitivity as a multi-input AND gate, and lack of susceptibility as an insufficiency in one or more of those inputs. The inputs considered were an activating enzyme, cytoplasmic abundance of NIT, and reducing equivalents required for NIT activation. We systematically assessed the contribution of each of these inputs and found that NIT import and the level of activating enzyme were not contributing factors to the lack of susceptibility. Rather, evidence suggested that the low abundance of reducing equivalents is why stationary-phase E. coli are not killed by NIT, and catabolites can re-sensitize those cells. We found that this phenomenon also occurred when using nitrofurazone, which established generality to the nitrofuran antibiotic class. In addition, we observed that NIT activity against stationary-phase uropathogenic E. coli (UPEC) could also be potentiated through metabolite supplementation. These findings suggest that the combination of nitrofurans with specific metabolites could improve the outcome of uncomplicated urinary tract infections (UTIs).

Effect of RecA inactivation on quinolone susceptibility and the evolution of resistance in clinical isolates of Escherichia coli

2020 ◽  
Author(s):  
J Machuca ◽  
E Recacha ◽  
B Gallego-Mesa ◽  
S Diaz-Diaz ◽  
G Rojas-Granado ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Risk ◽  
Growth Curves ◽  
Sos Response ◽  
Quinolone Resistance ◽  
Clinical Isolates ◽  
Mutant Prevention Concentration ◽  
The Impact ◽  
Mutant Frequency ◽  
St131 Clone

Abstract Background SOS response suppression (by RecA inactivation) has been postulated as a therapeutic strategy for potentiating antimicrobials against Enterobacterales. Objectives To evaluate the impact of RecA inactivation on the reversion and evolution of quinolone resistance using a collection of Escherichia coli clinical isolates. Methods Twenty-three E. coli clinical isolates, including isolates belonging to the high-risk clone ST131, were included. SOS response was suppressed by recA inactivation. Susceptibility to fluoroquinolones was determined by broth microdilution, growth curves and killing curves. Evolution of quinolone resistance was evaluated by mutant frequency and mutant prevention concentration (MPC). Results RecA inactivation resulted in 2–16-fold reductions in fluoroquinolone MICs and modified EUCAST clinical category for several isolates, including ST131 clone isolates. Growth curves and time–kill curves showed a clear disadvantage (up to 10 log10 cfu/mL after 24 h) for survival in strains with an inactivated SOS system. For recA-deficient mutants, MPC values decreased 4–8-fold, with values below the maximum serum concentration of ciprofloxacin. RecA inactivation led to a decrease in mutant frequency (≥103-fold) compared with isolates with unmodified SOS responses at ciprofloxacin concentrations of 4×MIC and 1 mg/L. These effects were also observed in ST131 clone isolates. Conclusions While RecA inactivation does not reverse existing resistance, it is a promising strategy for increasing the effectiveness of fluoroquinolones against susceptible clinical isolates, including high-risk clone isolates.

scholarly journals Role of low-level quinolone resistance in generating tolerance in Escherichia coli under therapeutic concentrations of ciprofloxacin

2020 ◽  
Author(s):  
M Ortiz-Padilla ◽  
S Diaz-Diaz ◽  
J Machuca ◽  
A Tejada-Gonzalez ◽  
E Recacha ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sos Response ◽  
Resistance Mechanisms ◽  
Quinolone Resistance ◽  
Response Suppression ◽  
Bacterial Survival ◽  
Resistance Mutations ◽  
Low Level ◽  
Short Period ◽  
The Impact

Abstract Background Tolerance (including persistence) and resistance result in increased survival under antibiotic pressure. Objectives We evaluated the interplay between resistance and tolerance to ciprofloxacin under therapeutic and killing conditions to determine the contribution of low-level quinolone resistance (LLQR) mechanisms to tolerance. We also determined how the interaction between resistance (LLQR phenotypes) and tolerance was modified under SOS response suppression. Methods Twelve isogenic Escherichia coli strains harbouring quinolone resistance mechanisms combined with SOS response deficiency and six clinical E. coli isolates (LLQR or non-LLQR) were evaluated. Survival (tolerance or persistence) assays were used to measure surviving bacteria after a short period (up to 4 h) of bactericidal antibiotic treatment under therapeutic and killing concentrations of ciprofloxacin [1 mg/L, EUCAST/CLSI breakpoint for resistance; and 2.5 mg/L, peak serum concentration (Cmax) of this drug]. Results QRDR substitutions (S83L in GyrA alone or combined with S80R in ParC) significantly increased the fraction of tolerant bacteria (2–4 log10 cfu/mL) after exposure to ciprofloxacin at clinically relevant concentrations. The impact on tolerant bacteria due to SOS response suppression (including persistence mediated by the tisB gene) was reversed by LLQR mechanisms at therapeutic concentrations. Furthermore, no reduction in the fraction of tolerant bacteria due to SOS response suppression was observed when S83L in GyrA plus S80R in ParC were combined. Conclusions Tolerance and quinolone resistance mutations interact synergistically, giving LLQR mechanisms an additional role in allowing bacterial survival and evasion of therapeutic antimicrobial conditions by a combination of the two strategies. At clinically relevant concentrations, LLQR mechanisms reverse further impact of SOS response suppression in reducing bacterial tolerance.

scholarly journals Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Christina Kahramanoglou ◽  
Ana I. Prieto ◽  
Supriya Khedkar ◽  
Bettina Haase ◽  
Ankur Gupta ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Cytosine Methylation ◽  
Dna Cytosine Methylation
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