133 research outputs found
Self-organized partitioning of dynamically localized proteins in bacterial cell division
The Min proteins are equally partitioned between daughter cells at division.The mechanism allowing this accurate distribution is intrinsic to the Min system.Individual oscillations appear in each daughter cell before cytokinesis is completed.Diffusion through the gradually constricting septum is key to this process
Predicting chemical environments of bacteria from receptor signaling
Sensory systems have evolved to respond to input stimuli of certain
statistical properties, and to reliably transmit this information through
biochemical pathways. Hence, for an experimentally well-characterized sensory
system, one ought to be able to extract valuable information about the
statistics of the stimuli. Based on dose-response curves from in vivo
fluorescence resonance energy transfer (FRET) experiments of the bacterial
chemotaxis sensory system, we predict the chemical gradients chemotactic
Escherichia coli cells typically encounter in their natural environment. To
predict average gradients cells experience, we revaluate the phenomenological
Weber's law and its generalizations to the Weber-Fechner law and fold-change
detection. To obtain full distributions of gradients we use information theory
and simulations, considering limitations of information transmission from both
cell-external and internal noise. We identify broad distributions of
exponential gradients, which lead to log-normal stimuli and maximal drift
velocity. Our results thus provide a first step towards deciphering the
chemical nature of complex, experimentally inaccessible cellular
microenvironments, such as the human intestine.Comment: DG and GM contributed equally to this wor
Effects of receptor modification and temperature on dynamics of sensory complexes in Escherichia coli chemotaxis
<p>Abstract</p> <p>Background</p> <p>Extracellular stimuli in chemotaxis of <it>Escherichia coli </it>and other bacteria are processed by large clusters of sensory complexes. The stable core of these clusters is formed by transmembrane receptors, a kinase CheA, and an adaptor CheW, whereas adaptation enzymes CheR and CheB dynamically associate with the clusters via interactions with receptors and/or CheA. Several biochemical studies have indicated the dependence of the sensory complex stability on the adaptive modification state of receptors and/or on temperature, which may potentially allow environment-dependent tuning of its signalling properties. However, the extent of such regulation <it>in vivo </it>and its significance for chemotaxis remained unclear.</p> <p>Results</p> <p>Here we used fluorescence recovery after photobleaching (FRAP) to confirm <it>in vivo </it>that the exchange of CheA and CheW shows a modest dependency on the level of receptor modification/activity. An even more dramatic effect was observed for the exchange kinetics of CheR and CheB, indicating that their association with clusters may depend on the ability to bind substrate sites on receptors and on the regulatory phosphorylation of CheB. In contrast, environmental temperature did not have a discernible effect on stability of the cluster core. Strain-specific loss of <it>E. coli </it>chemotaxis at high temperature could instead be explained by a heat-induced reduction in the chemotaxis protein levels. Nevertheless, high basal levels of chemotaxis and flagellar proteins in common wild type strains MG1655 and W3110 enabled these strains to maintain their chemotactic ability up to 42°C.</p> <p>Conclusions</p> <p>Our results confirmed that clusters formed by less modified receptors are more dynamic, which can explain the previously observed adjustment of the chemotaxis response sensitivity according to the level of background stimulation. We further propose that the dependency of CheR exchange on the availability of unmethylated sites on receptors is important to improve the overall chemotaxis efficiency by suppressing molecular noise under conditions of high ligand concentrations. Moreover, the observed stability of the cluster core at high temperature is in line with the overall thermal robustness of the chemotaxis pathway and allows maintenance of chemotaxis up to 42°C in the common wild type strains of <it>E. coli</it>.</p
Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments
In bacterial chemotaxis, several types of receptors form mixed clusters. Receptor adaptation is shown to depend on the receptor's own conformational state rather than on the cluster's global activity, enabling cells to differentiate stimuli in complex environments
Exponential signaling gain at the receptor level enhances signal-to-noise ratio in bacterial chemotaxis
Peer reviewedPublisher PD
Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway
Protein–protein interactions play key roles in virtually all cellular processes, often forming complex regulatory networks. A powerful tool to study interactions in vivo is fluorescence resonance energy transfer (FRET), which is based on the distance-dependent energy transfer from an excited donor to an acceptor fluorophore. Here, we used FRET to systematically map all protein interactions in the chemotaxis signaling pathway in Escherichia coli, one of the most studied models of signal transduction, and to determine stimulation-induced changes in the pathway. Our FRET analysis identified 19 positive FRET pairs out of the 28 possible protein combinations, with 9 pairs being responsive to chemotactic stimulation. Six stimulation-dependent and five stimulation-independent interactions were direct, whereas other interactions were apparently mediated by scaffolding proteins. Characterization of stimulation-induced responses revealed an additional regulation through activity dependence of interactions involving the adaptation enzyme CheB, and showed complex rearrangement of chemosensory receptors. Our study illustrates how FRET can be efficiently employed to study dynamic protein networks in vivo
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Mechanism of bidirectional thermotaxis in Escherichia coli.
In bacteria various tactic responses are mediated by the same cellular pathway, but sensing of physical stimuli remains poorly understood. Here, we combine an in-vivo analysis of the pathway activity with a microfluidic taxis assay and mathematical modeling to investigate the thermotactic response of Escherichia coli. We show that in the absence of chemical attractants E. coli exhibits a steady thermophilic response, the magnitude of which decreases at higher temperatures. Adaptation of wild-type cells to high levels of chemoattractants sensed by only one of the major chemoreceptors leads to inversion of the thermotactic response at intermediate temperatures and bidirectional cell accumulation in a thermal gradient. A mathematical model can explain this behavior based on the saturation-dependent kinetics of adaptive receptor methylation. Lastly, we find that the preferred accumulation temperature corresponds to optimal growth in the presence of the chemoattractant serine, pointing to a physiological relevance of the observed thermotactic behavior
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Background: Computational identification of new drug targets is a major goal of pharmaceutical bioinformatics. Results: This paper presents a machine learning strategy to study and validate essential enzymes of a metabolic network. Each single enzyme was characterized by its local network topology, gene homologies and co-expression, and flux balance analyses. A machine learning system was trained to distinguish between essential and non-essential reactions. It was validated by a comprehensive experimental dataset, which consists of the phenotypic outcomes from single knockout mutants of Escherichia coli (KEIO collection). We yielded very reliable results with high accuracy (93%) and precision (90%). We show that topologic, genomic and transcriptomic features describing the network are sufficient for defining the essentiality of a reaction. These features do not substantially depend on specific media conditions and enabled us to apply our approach also for less specific media conditions, like the lysogeny broth rich medium. Conclusion: Our analysis is feasible to validate experimental knockout data of high throughput screens, can be used to improve flux balance analyses and supports experimental knockout screens to define drug targets
Chemotactic response and adaptation dynamics in Escherichia coli
Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia
coli is integral for detecting chemicals over a wide range of background
concentrations, ultimately allowing cells to swim towards sources of attractant
and away from repellents. Its biochemical mechanism based on methylation and
demethylation of chemoreceptors has long been known. Despite the importance of
adaptation for cell memory and behavior, the dynamics of adaptation are
difficult to reconcile with current models of precise adaptation. Here, we
follow time courses of signaling in response to concentration step changes of
attractant using in vivo fluorescence resonance energy transfer measurements.
Specifically, we use a condensed representation of adaptation time courses for
efficient evaluation of different adaptation models. To quantitatively explain
the data, we finally develop a dynamic model for signaling and adaptation based
on the attractant flow in the experiment, signaling by cooperative receptor
complexes, and multiple layers of feedback regulation for adaptation. We
experimentally confirm the predicted effects of changing the enzyme-expression
level and bypassing the negative feedback for demethylation. Our data analysis
suggests significant imprecision in adaptation for large additions.
Furthermore, our model predicts highly regulated, ultrafast adaptation in
response to removal of attractant, which may be useful for fast reorientation
of the cell and noise reduction in adaptation.Comment: accepted for publication in PLoS Computational Biology; manuscript
(19 pages, 5 figures) and supplementary information; added additional
clarification on alternative adaptation models in supplementary informatio
Variable sizes of Escherichia coli chemoreceptor signaling teams
Like many sensory receptors, bacterial chemotaxis receptors form clusters. In bacteria, large-scale clusters are subdivided into signaling teams that act as ‘antennas' allowing detection of ligands with remarkable sensitivity. The range of sensitivity is greatly extended by adaptation of receptors to changes in concentrations through covalent modification. However, surprisingly little is known about the sizes of receptor signaling teams. Here, we combine measurements of the signaling response, obtained from in vivo fluorescence resonance energy transfer, with the statistical method of principal component analysis, to quantify the size of signaling teams within the framework of the previously successful Monod–Wyman–Changeux model. We find that size of signaling teams increases 2- to 3-fold with receptor modification, indicating an additional, previously unrecognized level of adaptation of the chemotaxis network. This variation of signaling-team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations
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