scholarly journals Abstract OR-1: Condensed DNA Architecture in a Nucleoid of Escherichia coli

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S7-S7
Author(s):  
Yurii Krupyanskii ◽  
Nataliya Loiko ◽  
Olga Sokolova
Keyword(s):  
Stationary Phase ◽  
Liquid Crystalline ◽  
Environmental Changes ◽  
Dna Condensation ◽  
Bacterial Cells ◽  
E Coli ◽  
Flexible Response ◽  
Bacterial Nucleoid ◽  
As Stress ◽  
Condensed Dna

Background: Bacterial genomic DNA interacts with nucleoid-associated proteins (NAPs) and is located in a highly condensed and functional organized form in the nucleoid of the cell. The structure of the bacterial nucleoid is still awaiting its determination in high resolution. However, recent intensive research showed that condensed DNA in the bacterial nucleoid has a complex, hierarchically organized structure. Such architecture may only exist as a result of dynamic structural rearrangements, which characterize actively growing bacteria. Changes in environmental conditions are perceived by bacteria as stress. In the stationary phase caused by nutrient depletion, energy production processes become inefficient. Bacteria in the stationary phase use an energy-independent mechanism for maintaining an order to protect the DNA: the creation of stable structures, like those in inanimate nature. Cells develop into dormant forms that differ significantly in the structural organization from growing cells. Methods: Electron microscopy and synchrotron radiation diffraction studies were used to reveal distinct forms of DNA condensation in dormant E. coli cells. Results: The study made it possible to find the intracellular nanocrystalline, liquid crystalline, and folded nucleosome-like DNA structures, which were observed and described for the first time. Conclusion: The results of experiments made it possible to visualize the structures of the lower hierarchical tier of DNA compaction in the nucleoid of dormant cells. We hypothesized that the heterogeneity of bacterial cells allows for a flexible response to environmental changes and to surviving stress situations. Multiple types of DNA condensation in the same dormant E. coli cell increase the chances for rapid resumption of growth when conditions turn back to favorable.

scholarly journals Modifying TIMER, a slow-folding DsRed derivative, for optimal use in quickly-dividing bacteria

2021 ◽  
Author(s):  
Pavan Patel ◽  
Brendan J. O’Hara ◽  
Emily Aunins ◽  
Kimberly M. Davis
Keyword(s):  
Nitric Oxide ◽  
Cell Division ◽  
Stationary Phase ◽  
Yersinia Pseudotuberculosis ◽  
Fluorescent Protein ◽  
Bacterial Species ◽  
Bacterial Cells ◽  
E Coli ◽  
Slow Growing ◽  
Host Tissues

AbstractIt is now well appreciated that members of pathogenic bacterial populations exhibit heterogeneity in growth rates and metabolic activity, and it is known this can impact the ability to eliminate all members of the bacterial population during antibiotic treatment. It remains unclear which pathways promote slowed bacterial growth within host tissues, primarily because it has been difficult to identify and isolate slow growing bacteria from host tissues for downstream analyses. To overcome this limitation, we have developed a novel variant of TIMER, a slow-folding fluorescent protein, to identify subsets of slowly dividing bacteria within host tissues. The original TIMER folds too slowly for fluorescence accumulation in quickly replicating bacterial species (Escherichia coli, Yersinia pseudotuberculosis), however this TIMER42 variant accumulates signal in late stationary phase cultures of E. coli and Y. pseudotuberculosis. We show TIMER42 signal also accumulates during exposure to sources of nitric oxide (NO), suggesting TIMER42 signal detects growth-arrested bacterial cells. In a mouse model of Y. pseudotuberculosis deep tissue infection, TIMER42 signal is clearly detected, and primarily accumulates in bacteria expressing markers of stationary phase growth. There was not significant overlap between TIMER42 signal and NO-exposed subpopulations of bacteria within host tissues, suggesting NO stress was transient, allowing bacteria to recover from this stress and resume replication. This novel TIMER42 variant represents a new faster folding TIMER that will enable additional studies of slow-growing subpopulations of bacteria, specifically within bacterial species that quickly divide.Author SummaryWe have generated a variant of TIMER that can be used to mark slow-growing subsets of Yersinia pseudotuberculosis, which has a relatively short division time, similar to E. coli. We used a combination of site-directed and random mutagenesis to generate the TIMER42 variant, which has red fluorescent signal accumulation in post-exponential or stationary phase cells. We found that nitric oxide (NO) stress is sufficient to promote TIMER42 signal accumulation in culture, however within host tissues, TIMER42 signal correlates with a stationary phase reporter (dps). These results suggest NO may cause an immediate arrest in bacterial cell division, but during growth in host tissues exposure to NO is transient, allowing bacteria to recover from this stress and resume cell division. Thus instead of indicating a response to host stressors, TIMER42 signal accumulation within host tissues appears to identify slow-growing cells that are experiencing nutrient limitation.

scholarly journals Identification of a Dithiazoline Inhibitor of Escherichia colil,d-Carboxypeptidase A

2005 ◽  
Vol 49 (11) ◽  
pp. 4500-4507 ◽  
Author(s):  
Ellen Z. Baum ◽  
Steven M. Crespo-Carbone ◽  
Barbara Foleno ◽  
Sean Peng ◽  
Jamese J. Hilliard ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Phase Behavior ◽  
High Throughput Screening ◽  
Deletion Mutant ◽  
Inhibitory Concentration ◽  
Bacterial Cells ◽  
Carboxypeptidase A ◽  
E Coli ◽  
Bacterial Peptidoglycan

ABSTRACT The enzyme l,d-carboxypeptidase A is involved in the recycling of bacterial peptidoglycan and is essential in Escherichia coli during stationary phase. By high-throughput screening, we have identified a dithiazoline inhibitor of the enzyme with a 50% inhibitory concentration of 3 μM. The inhibitor appeared to cause lysis of E. coli during stationary phase, behavior that is similar to a previously described deletion mutant of l,d-carboxypeptidase A (M. F. Templin, A. Ursinus, and J.-V. Holtje, EMBO J. 18:4108-4117, 1999). As much as a one-log drop in CFU in stationary phase was observed upon treatment of E. coli with the inhibitor, and the amount of intracellular tetrapeptide substrate increased by approximately 33%, consistent with inhibition of the enzyme within bacterial cells. Stationary-phase targets such as l,d-carboxypeptidase A are largely underrepresented as targets of the antibiotic armamentarium but provide potential opportunities to interfere with bacterial growth and persistence.

scholarly journals Tombusvirus p19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts in E. coli

2019 ◽  
Author(s):  
Linfeng Huang ◽  
Padraig Deighan ◽  
Jingmin Jin ◽  
Yingxue Li ◽  
Elaine Lee ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Ectopic Expression ◽  
Antisense Transcription ◽  
Bacterial Cells ◽  
Rnase Iii ◽  
Antisense Transcripts ◽  
E Coli ◽  
Physiological Importance ◽  
Protein Levels ◽  
Bacterial Genes

AbstractAntisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form long double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. Ectopic expression of plant tombusvirus p19 in E. coli stabilizes ~21 bp dsRNA RNase III decay intermediates, which enabled us to characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA and total RNA. dsRNA formed at most bacterial genes in the bacterial chromosome and in a plasmid. The most abundant dsRNA clusters were mostly formed by divergent transcription of sense and antisense transcripts overlapping at their 5’-ends. The most abundant clusters included small RNAs, such as ryeA/ryeB, 4 toxin-antitoxin genes, and 3 tRNAs, and some longer coding genes, including rsd and cspD. The sense and antisense transcripts in abundant dsRNA clusters were more plentiful and had longer half-lives in RNase III mutant strains, suggesting that formation of dsRNAs promoted RNA decay at these loci. However, widespread changes in protein levels did not occur in RNase III mutant bacteria. Nonetheless, some proteins involved in antioxidant responses and glycolysis changed reproducibly. dsRNAs accumulated in bacterial cells lacking RNase III, increasing in stationary phase, and correlated with increased cell death in RNase III mutant bacteria in late stationary phase. The physiological importance of widespread antisense transcription in bacteria remains unclear but it may become important during environmental stress. Ectopic expression of p19 is a sensitive method for identifying antisense transcripts and RNase III cleavage sites in bacteria.

scholarly journals Morphological peculiarities of DNA-protein complexes in dormant Escherichia coli cells, subjected to prolonged starvation Condensation of DNA in dormant cells of Escherichia coli

2020 ◽  
Author(s):  
Natalia Loiko ◽  
Yana Danilova ◽  
Andrey Moiseenko ◽  
Vladislav Kovalenko ◽  
Ksenia Tereshkina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Liquid Crystalline ◽  
Environmental Changes ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Bacterial Cells ◽  
Ordered Structures ◽  
Extreme Stress ◽  
Different Types ◽  
Dps Protein

AbstractOne of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of Dps protein is tightly bound to nucleoid DNA. We demonstrated that the population of the dormant cell is structurally heterogeneous, which allows cells to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

scholarly journals Indole Pulse Signalling Regulates the Cytoplasmic pH ofE. coliin a Memory-Like Manner

2018 ◽  
Author(s):  
Ashraf Zarkan ◽  
Santiago Caño Muñiz ◽  
Jinbo Zhu ◽  
Kareem Al Nahas ◽  
Jehangir Cama ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Ph Regulation ◽  
Critical Role ◽  
Bacterial Cells ◽  
Cytoplasmic Ph ◽  
E Coli ◽  
Degree Of Protection ◽  
Bacterial Cell Membrane ◽  
Ph Range ◽  
Phase Entry

SUMMARYBacterial cells are critically dependent upon pH regulation. Most proteins function over a limited pH range and the pH gradient across the bacterial cell membrane is central to energy production and transduction1. Here we demonstrate that indole plays a critical role in the regulation of the cytoplasmic pH ofE. coli. Indole is an aromatic molecule with diverse signalling roles that in bacteria is produced from tryptophan by the enzyme tryptophanase (TnaA)2. Two modes of indole signalling have been described: persistent and pulse signalling. The latter is illustrated by the brief but intense elevation of intracellular indole during stationary phase entry3,4. We show thatE. colicells growing under conditions where no indole is produced maintain their cytoplasmic pH at 7.8 ± 0.2. In contrast, under conditions permitting indole production, pH is maintained at 7.2 ± 0.2. Experiments where indole was added experimentally to non-producing cultures showed that pH regulation results from pulse, rather than persistent, indole signalling. Furthermore, the application of an artificial pulse of either of two non-biological proton ionophores (DNP or CCCP) caused a similar effect, suggesting that the relevant property of indole in this context is its ability to conduct protons across the cytoplasmic membrane5. Additionally, we show that the effect of the indole pulse that occurs normally during stationary phase entry in rich medium remains as a “memory” to maintain the correct cytoplasmic pH until entry into the next stationary phase. The indole-mediated reduction in cytoplasmic pH may explain why indole providesE. coliwith a degree of protection against stresses, including some bactericidal antibiotics.

Toxic Effect of 2-ethyl (bicyclo[2.2.1] heptane) on Bacterial Cells

2019 ◽  
Vol 35 (6) ◽  
pp. 67-72 ◽  
Author(s):  
I.V. Manukhov ◽  
L.S. Yaguzhinsky ◽  
M.V. Bermeshev ◽  
M.A. Zisman ◽  
V.G. Pevgov ◽  
...  
Keyword(s):  
Toxic Effect ◽  
Atmospheric Oxygen ◽  
Inducible Promoter ◽  
Oxygen Species ◽  
Bacterial Cells ◽  
Unique Identifier ◽  
E Coli ◽  
Lux Biosensors ◽  
High Level ◽  
Ministry Of Higher Education

Toxic effect of 2-ethylnorbornane (2-ethyl(bicyclo[2.2.1]heptane) (EBH)) on bacteria has been studied using the E. coli pRecA-lux and E. coli pKatG- lux cells as lux-biosensors. It was shown that the addition of EBH to the incubation medium leads to death and growth retardation, high level oxidative stress and DNA damage in E. coli cells. It is assumed that the oxidation of EBH with atmospheric oxygen causes the formation of reactive oxygen species in the medium, which makes a major contribution to the toxicity of this substance. biosensor, luciferase, bioluminescence, inducible promoter, PrecA, PkatG The authors are grateful to Stanislav Filippovich Chalkin for the development of interdisciplinary ties in the scientific community. The work was financially supported by the Ministry of Higher Education and Science of Russia (Project Unique Identifier RFMEFI60417X0181, Agreement No. 14.604.21.0181 of 26.09.2017).

scholarly journals Precise regulation of the relative rates of surface area and volume synthesis in bacterial cells growing in dynamic environments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Handuo Shi ◽  
Yan Hu ◽  
Pascal D. Odermatt ◽  
Carlos G. Gonzalez ◽  
Lichao Zhang ◽  
...  
Keyword(s):  
Growth Rate ◽  
Time Delay ◽  
Surface Area ◽  
Environmental Changes ◽  
Volume Ratio ◽  
Dynamic Environments ◽  
Bacterial Cells ◽  
Bacterial Growth Rate ◽  
State Size ◽  
Insight Into

AbstractThe steady-state size of bacterial cells correlates with nutrient-determined growth rate. Here, we explore how rod-shaped bacterial cells regulate their morphology during rapid environmental changes. We quantify cellular dimensions throughout passage cycles of stationary-phase cells diluted into fresh medium and grown back to saturation. We find that cells exhibit characteristic dynamics in surface area to volume ratio (SA/V), which are conserved across genetic and chemical perturbations as well as across species and growth temperatures. A mathematical model with a single fitting parameter (the time delay between surface and volume synthesis) is quantitatively consistent with our SA/V experimental observations. The model supports that this time delay is due to differential expression of volume and surface-related genes, and that the first division after dilution occurs at a tightly controlled SA/V. Our minimal model thus provides insight into the connections between bacterial growth rate and cell shape in dynamic environments.

Mannose-Binding Activity of Escherichia coli: a Determinant of Attachment and Ingestion of the Bacteria by Macrophages

1980 ◽  
Vol 29 (2) ◽  
pp. 417-424
Author(s):  
Zvi Bar-Shavit ◽  
Rachel Goldman ◽  
Itzhak Ofek ◽  
Nathan Sharon ◽  
David Mirelman
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Pathogenic Bacteria ◽  
Binding Activity ◽  
Exponential Phase ◽  
Restrictive Temperature ◽  
Filamentous Bacteria ◽  
Phagocytic Cells ◽  
E Coli ◽  
Mannose Binding

Recently, it was suggested that a mannose-specific lectin on the bacterial cell surface is responsible for the recognition by phagocytic cells of certain nonopsonized Escherichia coli strains. In this study we assessed the interaction of two strains of E. coli at different phases of growth with a monolayer of mouse peritoneal macrophages and developed a direct method with [ 14 C]mannan to quantitate the bacterial mannose-binding activity. Normal-sized bacteria were obtained from logarithmic and stationary phases of growth. Nonseptated filamentous cells were formed by growing the organisms in the presence of cephalexin or at a restrictive temperature. Attachment to macrophages of all bacterial forms was inhibited by methyl α- d -mannoside and mannan but not by other sugars tested. The attachment of stationary phase and filamentous bacteria to macrophages, as well as their mannose-binding activity, was similar, whereas in the exponential-phase bacteria they were markedly reduced. The results show a linear relation between the two parameters ( R = 0.98, P < 0.001). The internalization of the filamentous cells attached to macrophages during 45 min of incubation was much less efficient (20%) compared to that of exponential-phase, stationary-phase, or antibody-coated filamentous bacteria (90%). The results indicate that the mannose-binding activity of E. coli determines the recognition of the organisms by phagocytes. They further suggest that administration of β-lactam antibiotics may impair elimination of certain pathogenic bacteria by inducing the formation of filaments which are inefficiently internalized by the host's phagocytic cells.

Phylogeny of Immunity, edited by R. T. Smith, M.D., P. A. Miescher, M.D., and R. A. Good, M.D. Gainesville, Florida: University of Florida Press, 1966, 276 pp. $15.00

PEDIATRICS ◽  
1968 ◽  
Vol 41 (4) ◽  
pp. 862-862
Author(s):  
Fred S. Rosen
Keyword(s):  
Environmental Changes ◽  
University Of Florida ◽  
E Coli ◽  
Immune Mechanisms ◽  
Biological Interest

It has been stated that the adaptability of higher organisms to environmental changes and stress is most vividly manifested by the organization of mind, the detoxifying versatility of liver, and the responsiveness of immune mechanisms. Thus, the evolutionary and developmental aspects of any of these systems are of broad biological interest, beyond the realm of the molecular biologists and their now incisive comprehension of E. coli. In two successive volumes the editors have assembled a distinguished collection of presentations in the balmy isolation of Sanibel Island, Florida.

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