Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity

AbstractNucleotide-based signaling molecules (NSMs) are widespread in bacteria and eukaryotes, where they control important physiological and behavioral processes. In bacteria, NSM-based regulatory networks are highly complex, entailing large numbers of enzymes involved in the synthesis and degradation of active signaling molecules. How the converging input from multiple enzymes is transformed into robust and unambiguous cellular responses has remained unclear. Here we show that Escherichia coli converts dynamic changes of c-di-GMP into discrete binary signaling states, thereby generating heterogeneous populations with either high or low c-di-GMP. This is mediated by an ultrasensitive switch protein, PdeL, which senses the prevailing cellular concentration of the signaling molecule and couples this information to c-di-GMP degradation and transcription feedback boosting its own expression. We demonstrate that PdeL acts as a digital filter that facilitates precise developmental transitions, confers cellular memory, and generates functional heterogeneity in bacterial populations to evade phage predation. Based on our findings, we propose that bacteria apply ultrasensitive regulatory switches to convert dynamic changes of NSMs into binary signaling modes to allow robust decision-making and bet-hedging for improved overall population fitness.

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Predicting experimental designs leading to rewiring of transcription program and evolution of anticipatory regulation in E. coli

10.1101/2020.08.20.259606 ◽

2020 ◽

Author(s):

Anjali Mahilkar ◽

Akshat Mall ◽

Supreet Saini

Keyword(s):

Regulatory Networks ◽

Quantitative Model ◽

Environmental Cues ◽

Anticipatory Response ◽

Experimental Conditions ◽

Bacterial Populations ◽

E Coli ◽

Temporal Cues ◽

Darwinian Fitness ◽

Pentose Sugar

AbstractEnvironmental cues in an ecological niche are temporal. In response to these temporal cues, bacteria have been known to exhibit learning or conditioning, whereby they trigger response to a yet to appear cue, anticipating its actual arrival in the near future. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature in the regulatory networks in microorganisms. However, the conditions under which an anticipatory response optimizes cellular fitness are not known. Nor has evolution of anticipatory regulation in laboratory conditions been experimentally demonstrated. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and present the key variables in cellular physiology associated with response to the cues whose modulation is likely to lead to evolution of anticipatory regulatory response. We predict experimental conditions, which are likely to lead to demonstration of rewiring of regulation, and evolution of anticipatory response in bacterial populations. Using inputs from the modeling results, we evolve E. coli in alternating environments of the pentose sugar rhamnose and paraquat, which induces oxidative stress. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. Thus, we argue that in niches where environmental stimuli have a cyclical nature, conditioning evolves in a population as an adaptive response.

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STUDIES ON BACTERIEMIA

Journal of Experimental Medicine ◽

10.1084/jem.105.2.113 ◽

1957 ◽

Vol 105 (2) ◽

pp. 113-124 ◽

Cited By ~ 14

Author(s):

David E. Rogers ◽

Marian Ann Melly

Keyword(s):

Polymorphonuclear Leukocytes ◽

Blood Stream ◽

Bacterial Populations ◽

E Coli ◽

Vascular Bed ◽

Large Numbers ◽

Minute Period ◽

Initial Clearance ◽

In Transit

Large numbers of E. coli were rapidly removed from the blood stream of rabbits at rates which initially paralleled the removal of similar numbers of staphylococci. Splanchnic tissues removed approximately two-thirds of the circulating bacilli in transit through the liver and spleen. In contrast to the cessation of splanchnic trapping noted 20 to 40 minutes following the injection of staphylococci, splanchnic trapping of E. coli continued unchanged for 3 to 5 hours unless the splanchnic tissues were dearly reseeding the blood stream. This resulted in the continued disappearance of E. coli over a 60 to 90 minute period, and differed from the constant bacteriemia maintained beyond 20 minutes after the injection of staphylococci. Some of the differences in the initial clearance of these two microorganisms appeared to relate to differences in host leukocyte-bacterium relationships. In vitro studies indicated that E. coli were rapidly killed following ingestion by rabbit polymorphonuclear leukocytes. Staphylococci survive such ingestion. The injection of E. coli was followed by a prolonged granulocytopenia with evidence of sequestration of granulocytes within the pulmonary vascular bed. The injection of staphylococci was followed by a transient leukopenia, with rapid return of granulocytes to the circulation (15). It appears probable that E. coli ingested by sequestered leukocytes are destroyed within the cell, and that leukocytes do not reenter the circulation containing living E. coli. Such intraleukocytic residence in the blood stream has been shown to be of possible importance in the maintenance of staphylococcal bacteriemia (14). An increasing E. coli bacteriemia occurred rapidly after the initial clearance period, indicating that many sequestered bacilli remained viable. Increasing bacteriemia also occurs 3 to 5 hours after the injection of staphylococci. The bacterial or host cell mechanisms which allow this secondary resurgence of bacterial populations are currently under investigation.

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The comparison of the diversity of activated sludge plants

Water Science & Technology ◽

10.2166/wst.1998.0585 ◽

1998 ◽

Vol 37 (4-5) ◽

pp. 71-78 ◽

Cited By ~ 16

Author(s):

Thomas P. Curtis ◽

Noel G. Craine

Keyword(s):

Cluster Analysis ◽

Activated Sludge ◽

Treatment Process ◽

Denaturing Gradient Gel Electrophoresis ◽

Optimal Sampling ◽

Bacterial Populations ◽

Large Numbers ◽

Probable Presence ◽

Gradient Gel Electrophoresis ◽

Sampling Regime

The explicit engineering of bacterial populations requires that we know which organisms perform which tasks. The comparison of the bacterial diversity of activated sludge plants may give important information about the functions of different bacteria. This difficult task may be made easier by the use of technologies based on 16S rRNA based techniques. In this study we have used denaturing gradient gel electrophoresis (DGGE) to determine the optimal sampling regime for comparative studies and used cluster analysis to show how plants may be quantitatively compared. We sought evidence of spatial, diurnal and intrasample variation in a number of sites. No evidence for variation was found in the plants studied and we concluded that a single sample of an activated sludge plant was sufficient for a plant to plant comparison. The cluster analysis was able to distinguish between plants, though further work is required to find the most appropriate basis for such comparisons. We found organisms from raw sewage in the mixed liquor samples, these organisms may have no functional significance in the treatment process and thus complicate plant to plant comparisons as will the probable presence of heteroduplex rDNA products. Nevertheless we believe that these drawbacks do not outweigh the advantages of being able to take and compare relatively large numbers of samples.

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The AIDA Autotransporter System Is Associated with F18 and Stx2e in Escherichia coli Isolates from Pigs Diagnosed with Edema Disease and Postweaning Diarrhea

Clinical and Diagnostic Laboratory Immunology ◽

10.1128/cdli.8.1.143-149.2001 ◽

2001 ◽

Vol 8 (1) ◽

pp. 143-149 ◽

Cited By ~ 64

Author(s):

Ulla Niewerth ◽

Andreas Frey ◽

Thomas Voss ◽

Chantal Le Bouguénec ◽

Georg Baljer ◽

...

Keyword(s):

Escherichia Coli ◽

Western Blot ◽

Virulence Factors ◽

Rapid Screening ◽

Edema Disease ◽

E Coli ◽

Large Numbers ◽

High Prevalence ◽

Pcr Method ◽

Postweaning Diarrhea

ABSTRACT Pathogenic Escherichia coli strains are known to cause edema disease (ED) and postweaning diarrhea (PWD) in piglets. Although the exact mechanisms of pathogenicity that lead to ED-PWD remain to be elucidated, E. coli-borne Shiga-like toxin and adhesion-mediating virulence factors such as F18 adhesin or F4 fimbriae are believed to play a central role in ED-PWD. In light of these observations we investigated whether another E. coliadhesin, the plasmid-encoded AIDA (adhesin involved in diffuse adherence) might also be present in ED-PWD-causing E. coli isolates. For rapid screening for the AIDA system in large numbers of isolates, a multiplex PCR method along with a duplex Western blot procedure was developed. When screening 104 strains obtained from pigs with or without ED-PWD, we observed a high prevalence of the AIDA operon in porcine E. coli isolates, with over 25% of all strains being AIDA positive, and we could demonstrate a significant association of the intact AIDA gene (orfB) with ED-PWD, while defects in orfB were associated with the absence of disease. Although our data hint toward a contribution of AIDA to ED-PWD, further studies will be necessary since the presence of the AIDA genes was also associated with the presence of the Shiga-like toxin and F18 adhesin genes, two reported virulence factors for ED-PWD.

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Fermented liquid feed can reduce E. coli bloom at farrowing and prevent constipation problems during lactation

Proceedings of the British Society of Animal Science ◽

10.1017/s175275620001228x ◽

2003 ◽

Vol 2003 ◽

pp. 69-69

Author(s):

V. Demečková ◽

C.A. Tsourgiannis ◽

P.H. Brooks ◽

A. Campbell

Keyword(s):

Microbial Load ◽

Swine Production ◽

Gastrointestinal Infections ◽

E Coli ◽

Neonatal Pigs ◽

Liquid Feed ◽

Pathogen Load ◽

Laxative Effect ◽

Large Numbers

Gastrointestinal infections associated with E. coli represent a serious problem for neonatal pigs. These bacteria are present in the sow’s intestine in large numbers but increase dramatically just prior to farrowing due to stress occasioned by movement and parturition (Maclean and Thomas, 1974). Consequently, just 24 hours after farrowing, E.coli are found in high numbers (over 108/g) in the faeces of piglets. However, at this stage of its life the piglet is not equipped to deal with such a large microbial load and unless immunological assistance is provided, they have very little chance of survival. In pigs, all immunological assistance at birth is concentrated in the mother’s colostrum. Thus elimination, or at least minimizing, all the factors which negatively affect the sow’s ability to produce sufficient amount of milk becomes essential challenge of each efficient swine production. The main aim of this study was to investigate the potential of fermented liquid feed (FLF) to control the pathogen load within the piglet’s environment by reducing the rapid E. coli multiplication in sows associated with farrowing. The possible laxative effect of FLF, in order to prevent constipation and the problems it causes during farrowing, was also examined.

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Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

Applied and Environmental Microbiology ◽

10.1128/aem.02203-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 110-118 ◽

Cited By ~ 29

Author(s):

Adelumola Oladeinde ◽

Thomas Bohrmann ◽

Kelvin Wong ◽

S. T. Purucker ◽

Ken Bradshaw ◽

...

Keyword(s):

Decay Rate ◽

Fecal Indicator Bacteria ◽

Decay Rates ◽

Indicator Bacteria ◽

Source Tracking ◽

Fecal Indicator ◽

Bacterial Populations ◽

Content Type ◽

E Coli ◽

Decay Dynamic

ABSTRACTUnderstanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (Escherichia coliand enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of theE. colipopulation (P< 0.0001), with a rate of −0.176 day−1for the shaded treatment and −0.297 day−1for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (P> 0.05). In addition,E. colipopulations showed a significant growth rate (0.881 day−1) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate ofE. colipopulations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers thanE. coliconcentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic ofE. colipopulations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.

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Protozoa abundance, growth, and bacterivory in the water column, on sedimenting particles, and in the sediment of Halifax Harbor

Canadian Journal of Microbiology ◽

10.1139/m90-149 ◽

1990 ◽

Vol 36 (12) ◽

pp. 859-863 ◽

Cited By ~ 6

Author(s):

James A. Novitsky

Keyword(s):

Bacterial Community ◽

Water Column ◽

Sediment Surface ◽

Metabolic Inhibitor ◽

Optimum Conditions ◽

Bacterial Populations ◽

Protozoan Grazing ◽

Large Numbers ◽

Doubling Times

The role of protozoan grazing in controlling bacterial populations was examined in four microbial habitats in Halifax Harbor, Canada: the water column, setting particles, the sediment–water interface, and the sediment. Large numbers of protozoans were found in all habitats although most (>56%) were small (<5 μm) flagellates. Protozoans larger than 10 μm were rarely observed; protozoans >20 μm were never observed. Protozoans were also observed to a depth of 9 cm below the sediment surface although efforts to culture viable protozoa failed except for the top 1 cm. The use of the metabolic inhibitor cycloheximide with and without colchicine to selectively inhibit eucaryotic metabolism was shown to severely affect procaryotic metabolism in sediment (and presumably particle and water) samples. Using fluorescently labelled bacteria as food, and under optimum conditions, up to 42% of the Protozoa population exhibited active grazing within 7 h. Using protozoan and bacterial community sizes and doubling times, it was calculated that each protozoan in Halifax Harbor would have to consume 13–118 bacteria per hour for the enumerated nanoplanktonic (<20 μm) Protozoa to be the sole control of the size of the bacterial community. Key words: marine, Protozoa, bacterivory, particles, bacteria.

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Microbiological Examination of some ImportedCanned and Frozen Foods

Baghdad Science Journal ◽

10.21123/bsj.5.2.237-242 ◽

2008 ◽

Vol 5 (2) ◽

pp. 237-242

Author(s):

Baghdad Science Journal

Keyword(s):

Microbial Contamination ◽

Human Consumption ◽

Frozen Foods ◽

E Coli ◽

Food Items ◽

Cell Counts ◽

Bacterial Indicator ◽

Large Numbers ◽

Microbiological Examination ◽

Canned Foods

A number of juices, jams, canned foods and frozen fishes available in local markets were inspected with respect to microbial contamination. We have determined the total viable bacterial cell counts in these samples and the number of g(-) lactose fermentors as a bacterial indicator of food spoilage. The results indicated that most of the food items inspected, were contaminated with large numbers of different species of g(-) ,g(+), yeast and fungi and some were contained more than the maximum permissible number of pathogenic g(-) enteric E-coli, which render these food items unsafe for human consumption.

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Universal attenuators and their interactions with feedback loops in gene regulatory networks

10.1101/074716 ◽

2016 ◽

Author(s):

Dianbo Liu ◽

Luca Albergante ◽

Timothy J Newman

Keyword(s):

Gene Expression ◽

Gene Regulatory Networks ◽

Gene Networks ◽

Regulatory Networks ◽

Human Cancer ◽

Cancer Cell Line ◽

Feedback Loops ◽

Human Cancer Cell ◽

E Coli ◽

Gene Regulatory

AbstractUsing a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LRCs act as attenuators. This observation implies a progressively weaker functionality of LRCs as their length increases. When analysing the preponderance of LRCs in the GRNs of E. coli K12 and several other organisms, we find that very long LRCs are essentially absent. In both E. coli and M. tuberculosis we find that four-gene LRCs are intimately linked to identical feedback loops that are involved in potentially chaotic stress response, indicating that the dynamics of these potentially destabilising motifs are strongly restrained under homeostatic conditions. The same relationship is observed in a human cancer cell line (K562), and we postulate that four-gene LRCs act as “universal attenuators”. These findings suggest a role for long LRCs in dampening variation in gene expression, thereby protecting cell identity, and in controlling dramatic shifts in cell-wide gene expression through inhibiting chaos-generating motifs.In briefWe present a general principle that linear regulatory chains exponentially attenuate the range of expression in gene regulatory networks. The discovery of a universal interplay between linear regulatory chains and genetic feedback loops in microorganisms and a human cancer cell line is analysed and discussed.HighlightsWithin gene networks, linear regulatory chains act as exponentially strong attenuators of upstream variationBecause of their exponential behaviour, linear regulatory chains beyond a few genes provide no additional functionality and are rarely observed in gene networks across a range of different organismsNovel interactions between four-gene linear regulatory chains and feedback loops were discovered in E. coli, M. tuberculosis and human cancer cells, suggesting a universal mechanism of control.

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Microbiological Status of Fresh Beef Cuts

Journal of Food Protection ◽

10.4315/0362-028x-69.6.1456 ◽

2006 ◽

Vol 69 (6) ◽

pp. 1456-1459 ◽

Cited By ~ 13

Author(s):

J. D. STOPFORTH ◽

M. LOPES ◽

J. E. SHULTZ ◽

R. R. MIKSCH ◽

M. SAMADPOUR

Keyword(s):

Total Coliform ◽

Incidence Rates ◽

Microbial Populations ◽

Plate Count ◽

Bacterial Populations ◽

E Coli ◽

Coliform Count ◽

Processing Plants ◽

Aerobic Plate Count ◽

Whole Muscle

Fresh beef samples (n = 1,022) obtained from two processing plants in the Midwest (July to December 2003) were analyzed for levels of microbial populations (total aerobic plate count, total coliform count, and Escherichia coli count) and for the presence or absence of E. coli O157:H7 and Salmonella. A fresh beef cut sample was a 360-g composite of 6-g portions excised from the surface of 60 individual representative cuts in a production lot. Samples of fresh beef cuts yielded levels of 4.0 to 6.2, 1.1 to 1.8, and 0.8 to 1.0 log CFU/g for total aerobic plate count, total coliform count, and E. coli count, respectively. There did not appear to be substantial differences or obvious trends in bacterial populations on different cuts. These data may be useful in establishing a baseline or a benchmark of microbiological levels of contamination of beef cuts. Mean incidence rates of E. coli O157:H7 and Salmonella on raw beef cuts were 0.3 and 2.2%, respectively. Of the 1,022 samples analyzed, cuts testing positive for E. coli O157:H7 included top sirloin butt (0.9%) and butt, ball tip (2.1%) and for Salmonella included short loins (3.4%), strip loins (9.6%), rib eye roll (0.8%), shoulder clod (3.4%), and clod, top blade (1.8%). These data provide evidence of noticeable incidence of pathogens on whole muscle beef and raise the importance of such contamination on product that may be mechanically tenderized. Levels of total aerobic plate count, total coliform count, and E. coli count did not (P ≥ 0.05) appear to be associated with the presence of E. coli O157:H7 and Salmonella on fresh beef cuts. E. O157:H7 was exclusively isolated from cuts derived from the sirloin area of the carcass. Salmonella was exclusively isolated from cuts derived from the chuck, rib, and loin areas of the carcass. Results of this study suggest that contamination of beef cuts may be influenced by the region of the carcass from which they are derived.

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