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Feedback control architecture and the bacterial chemotaxis network.
PMCID: PMC3088647This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance
Feedback control architecture & the bacterial chemotaxis network
Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to ‘reset’ (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a ‘cascade control’ feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance
Relationship between cellular response and behavioral variability in bacterial chemotaxis
Bacterial chemotaxis in Escherichia coli is a canonical system for the study
of signal transduction. A remarkable feature of this system is the coexistence
of precise adaptation in population with large fluctuating cellular behavior in
single cells (Korobkova et al. 2004, Nature, 428, 574). Using a stochastic
model, we found that the large behavioral variability experimentally observed
in non-stimulated cells is a direct consequence of the architecture of this
adaptive system. Reversible covalent modification cycles, in which methylation
and demethylation reactions antagonistically regulate the activity of
receptor-kinase complexes, operate outside the region of first-order kinetics.
As a result, the receptor-kinase that governs cellular behavior exhibits a
sigmoidal activation curve. This curve simultaneously amplifies the inherent
stochastic fluctuations in the system and lengthens the relaxation time in
response to stimulus. Because stochastic fluctuations cause large behavioral
variability and the relaxation time governs the average duration of runs in
response to small stimuli, cells with the greatest fluctuating behavior also
display the largest chemotactic response. Finally, Large-scale simulations of
digital bacteria suggest that the chemotaxis network is tuned to simultaneously
optimize the random spread of cells in absence of nutrients and the cellular
response to gradients of attractant.Comment: 15 pages, 4 figures, Supporting information available here
http://cluzel.uchicago.edu/data/emonet/arxiv_070531_supp.pd
Limits of feedback control in bacterial chemotaxis
Inputs to signaling pathways can have complex statistics that depend on the
environment and on the behavioral response to previous stimuli. Such behavioral
feedback is particularly important in navigation. Successful navigation relies
on proper coupling between sensors, which gather information during motion, and
actuators, which control behavior. Because reorientation conditions future
inputs, behavioral feedback can place sensors and actuators in an operational
regime different from the resting state. How then can organisms maintain proper
information transfer through the pathway while navigating diverse environments?
In bacterial chemotaxis, robust performance is often attributed to the zero
integral feedback control of the sensor, which guarantees that activity returns
to resting state when the input remains constant. While this property provides
sensitivity over a wide range of signal intensities, it remains unclear how
other parameters affect chemotactic performance, especially when considering
that the swimming behavior of the cell determines the input signal. Using
analytical models and simulations that incorporate recent experimental
evidences about behavioral feedback and flagellar motor adaptation we identify
an operational regime of the pathway that maximizes drift velocity for various
environments and sensor adaptation rates. This optimal regime is outside the
dynamic range of the motor response, but maximizes the contrast between run
duration up and down gradients. In steep gradients, the feedback from
chemotactic drift can push the system through a bifurcation. This creates a
non-chemotactic state that traps cells unless the motor is allowed to adapt.
Although motor adaptation helps, we find that as the strength of the feedback
increases individual phenotypes cannot maintain the optimal operational regime
in all environments, suggesting that diversity could be beneficial.Comment: Corrected one typo. First two authors contributed equally. Notably,
there were various typos in the values of the parameters in the model of
motor adaptation. The results remain unchange
PID Control of Biochemical Reaction Networks
Principles of feedback control have been shown to naturally arise in
biological systems and successfully applied to build synthetic circuits. In
this work we consider Biochemical Reaction Networks (CRNs) as a paradigm for
modelling biochemical systems and provide the first implementation of a
derivative component in CRNs. That is, given an input signal represented by the
concentration level of some species, we build a CRN that produces as output the
concentration of two species whose difference is the derivative of the input
signal. By relying on this component, we present a CRN implementation of a
feedback control loop with Proportional-Integral-Derivative (PID) controller
and apply the resulting control architecture to regulate the protein expression
in a microRNA regulated gene expression model.Comment: 8 Pages, 4 figures, Submitted to CDC 201
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