Collective condensation and auto-aggregation of Escherichia coli in uniform acidic environments
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ABSTRACT:
SUBMITTER: Livne N
PROVIDER: S-EPMC11339372 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Acid resistance is an intrinsic characteristic of intestinal bacteria in order to survive passage through the stomach. Adenosine triphosphate (ATP), the ubiquitous chemical used to power metabolic reactions, activate signaling cascades, and form precursors of nucleic acids, was also found to be associated with the survival of Escherichia coli (E. coli) in acidic environments. The metabolic pathway responsible for elevating the level of ATP inside these bacteria during acid adaptation has been unclear. E. coli uses several mechanisms of ATP production, including oxidative phosphorylation, glycolysis and the oxidation of organic compounds. To uncover which is primarily used during adaptation to acidic conditions, we broadly analyzed the levels of gene transcription of multiple E. coli metabolic pathway components. Our findings confirmed that the primary producers of ATP in E. coli undergoing mild acidic stress are the glycolytic enzymes Glk, PykF and Pgk, which are also essential for survival under markedly acidic conditions. By contrast, the transcription of genes related to oxidative phosphorylation was downregulated, despite it being the major producer of ATP in neutral pH environments.
| S-EPMC7563387 | biostudies-literature
Project description:AimThe study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress.MethodsIn the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020).ResultsA large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001).ConclusionOur study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident.
| S-EPMC8123226 | biostudies-literature
Project description:Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes.
2013-03-01 | GSE44614 | GEO
Project description:MukB is a bacterial SMC (structural maintenance of chromosome) protein that regulates the global folding of the Escherichia coli chromosome by bringing distant DNA segments together. We report that moderate overproduction of MukB may lead, depending on strain and growth conditions, to transient growth arrest. In DH5α cells, overproduction of MukB or MukBEF using pBAD expression system triggered growth arrest 2.5 h after induction. The exit from growth arrest was accompanied by the loss of the overproducing plasmid and a decline in the abundance of MukBEF. The arrested cells showed a compound gene expression profile which can be characterized by the following features: (i) a broad and deep downregulation of ribosomal proteins (up to 80-fold); (ii) downregulation of groups of genes encoding enzymes involved in nucleotide metabolism, respiration, and central metabolism; (iii) upregulation of some of the genes responsive to general stress; and (iv) degradation of the patterns of spatial correlations in the transcriptional activity of the chromosome. The transcriptional state of the MukB induced arrest is most similar to stationary cells and cells recovered from stationary phase into a nutrient deprived medium, to amino acid starved cells and to the cells shifting from glucose to acetate. The mukB++ state is dissimilar from all examined transcriptional states generated by protein overexpression with the possible exception of RpoE and RpoH overexpression. Thus, the transcription profile of MukB-arrested cells can be described as a combination of responses typical for other growth-arrested cells and those for overproducers of DNA binding proteins with a particularly deep down-regulation of ribosomal genes.
| S-EPMC3871593 | biostudies-literature
Project description:In Escherichia coli, coordinated activation and deactivation of DnaA allows for proper timing of the initiation of chromosomal synthesis at the origin of replication (oriC) and assures initiation occurs once per cell cycle. In vitro, acidic phospholipids reactivate DnaA, and in vivo depletion of acidic phospholipids, results in growth arrest. Growth can be restored by the expression of a mutant form of DnaA, DnaA(L366K), or by oriC-independent DNA synthesis, suggesting acidic phospholipids are required for DnaA- and oriC-dependent replication. We observe here that when acidic phospholipids were depleted, replication was inhibited with a concomitant reduction of chromosomal content and cell mass prior to growth arrest. This global shutdown of biosynthetic activity was independent of the stringent response. Restoration of acidic phospholipid synthesis resulted in a resumption of DNA replication prior to restored growth, indicating a possible cell-cycle-specific growth arrest had occurred with the earlier loss of acidic phospholipids. Flow cytometry, thymidine uptake, and quantitative polymerase chain reaction data suggest that a deficiency in acidic phospholipids prolonged the time required to replicate the chromosome. We also observed that regardless of the cellular content of acidic phospholipids, expression of mutant DnaA(L366K) altered the DNA content-to-cell mass ratio.
| S-EPMC3535390 | biostudies-literature
Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature.
2014-03-31 | GSE37673 | GEO
Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature. 16 samples with 3 biological replicates each.
2014-03-31 | E-GEOD-37673 | biostudies-arrayexpress
Project description:Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes. An overnight culture of E coli (ancestor culture) was propagated in LB media with three different oxygen regimes during 150 days. One regime involved transfers under constant shaking (200rpm): Treatment A-Replica populations 1 and 2 , second regime consisted in a daily shift between shaking and static (no shaking) conditions: Treatment B-replica populations 3,4 and 5. The third regime involved transfers in constant static conditions: Treatment C-Populations 6 and 7. After 150 days and plating, 3 different colony types were selected by population (populations 6 and 7 only had 2 different morphologies). Morpholigies were marked as a, b, c in each population. cDNA was obtainned from each morphology after growing separately in LB medium, under they correspondant evolving condition until late logaritmic phase (0,6-0,7 in OD600). A total of 19 evolved forms were analyzed plus one ancestor. Each morphology was labeled in a dye-swap design and hybridized to the ancestor into genome-wide multi-strain E. coli (8x15K) microarrays.
2013-03-01 | E-GEOD-44614 | biostudies-arrayexpress
Project description:Enteroaggregative Escherichia coli (EAEC) is an emerging enteric pathogen in both developing and industrialized countries. EAEC is defined as a diarrheal pathogen based on its characteristic aggregative adherence to HEp-2 cells in culture and its biofilm formation on the intestinal mucosa. We have reported that the novel protein AatA, which is encoded on the EAEC virulence plasmid pAA2, localizes to the outer membrane and facilitates export of the dispersin Aap across the outer membrane. Because AatA is an E. coli efflux pump TolC homolog, we investigated the role of TolC in the virulence of EAEC. No difference in Aap secretion was observed between the wild type and its tolC mutant (042tolC). However, characteristic aggregation in high-glucose Dulbecco's minimal essential medium for the wild type was diminished for 042tolC. In a microtiter plate assay, there were significantly more planktonic cells for 042tolC than for the wild type, while there were significantly fewer spontaneously precipitated cells on the substratum for 042tolC than for the wild type. In a HEp-2 cell adherence test, 042tolC showed less aggregative adherence than did the wild type. The strong aggregation and aggregative adherence were restored in the complement strain with tolC. In a transwell assay, planktonic cells of 042tolC decreased when cocultured with the wild type or the complement, while precipitated cells of 042tolC increased when cocultured with them. These results suggest that TolC promotes the aggregation and adhesion of EAEC 042 by secreting an assumed humoral factor.
| S-EPMC2258836 | biostudies-literature
Project description:AimsIn cardiomyocytes, acute disturbances to intracellular pH (pHi) are promptly corrected by a system of finely tuned sarcolemmal acid-base transporters. However, these fluxes become thermodynamically re-balanced in acidic environments, which inadvertently causes their set-point pHi to fall outside the physiological range. It is unclear whether an adaptive mechanism exists to correct this thermodynamic challenge, and return pHi to normal.Methods and resultsFollowing left ventricle cryo-damage, a diffuse pattern of low extracellular pH (pHe) was detected by acid-sensing pHLIP. Despite this, pHi measured in the beating heart (13C NMR) was normal. Myocytes had adapted to their acidic environment by reducing Cl-/HCO3- exchange (CBE)-dependent acid-loading and increasing Na+/H+ exchange (NHE1)-dependent acid-extrusion, as measured by fluorescence (cSNARF1). The outcome of this adaptation on pHi is revealed as a cytoplasmic alkalinization when cells are superfused at physiological pHe. Conversely, mice given oral bicarbonate (to improve systemic buffering) had reduced myocardial NHE1 expression, consistent with a needs-dependent expression of pHi-regulatory transporters. The response to sustained acidity could be replicated in vitro using neonatal ventricular myocytes incubated at low pHe for 48 h. The adaptive increase in NHE1 and decrease in CBE activities was linked to Slc9a1 (NHE1) up-regulation and Slc4a2 (AE2) down-regulation. This response was triggered by intracellular H+ ions because it persisted in the absence of CO2/HCO3- and became ablated when acidic incubation media had lower chloride, a solution manoeuvre that reduces the extent of pHi-decrease. Pharmacological inhibition of FAK-family non-receptor kinases, previously characterized as pH-sensors, ablated this pHi autoregulation. In support of a pHi-sensing role, FAK protein Pyk2 (auto)phosphorylation was reduced within minutes of exposure to acidity, ahead of adaptive changes to pHi control.ConclusionsCardiomyocytes fine-tune the expression of pHi-regulators so that pHi is at least 7.0. This autoregulatory feedback mechanism defines physiological pHi and protects it during pHe vulnerabilities.
| S-EPMC9648823 | biostudies-literature