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Optimal Strategy in E. coli Chemotaxis: An Information Theoretic Approach Lin Wang and Sima Setayeshgar Department of Physics, Indiana University, Bloomington, Indiana 47405 Focus Motivation Biochemical signaling is the most fundamental level of information processing in biological systems, where an external stimulus is measured and converted into a response. Photon counting in vision[1,2] Photon Molecule counting in chemotaxis[3] Δ[Ca2+], Δ[Na+], etc. Attractant Response of drosophila photoreceptor to photon absorption Model Validation E. coli varies its response to input signals with different statistics. Our goal is to understand how signal transduction pathways, such as the chemotaxis network, may adapt to the statistics of the fluctuating input so as to optimize the cell’s response. We construct a measure of the information transmission rate and investigate the role of varying response in maximizing this rate. Response of E. coli to change in external attractant concentration Chemotaxis Network Equations and Parameters Table I: Signal Transduction Network E. coli is the best-studied organism in molecular biology, providing an experimentally accessible basis for our understanding of fundamental cellular processes. Effect of τ on I/O relation Adaptation[9] Response r(s) to signals with μ=1 μM, σ2 = 1 μM2, τ = 0.1, 0.3, 0.8, 1 sec, respectively. For τ > 1 sec, the response does not vary significantly with . (This also holds true for signals with different mean values). 1 μm in length, 0.4 μm in radius 10 μm long, 45 nm in diameter n P1(n) P2(n) 0 0.02 0.00291 1 0.17 0.02 2 0.5 0.17 3 0.874 0.5 4 0.997 0.98 Variable network adaptation time in response to different step changes of concentration of external attractant, demonstrating increase in adaptation time with increasing stimulus step size Motor CCW and CW intervals[11] Table III: Initial Protein Levels Chemotaxis in E. coli - motion toward desirable chemicals and away from harmful ones - is an important behavioral response also shared by many other prokaryotic and eukaryotic cells. It is achieved through a series of modulated ‘runs’ and ‘tumbles’, leading to a biased random walk in the desired direction. Molecule Stimulus Signal Transduction Pathway [CheY-P] Motor Response Flagellar Bundling Motion From R. M. Berry, Encyclopedia of Life Sciences The chemotaxis signal transduction pathway in E. coli is a network of interacting proteins that converts an external stimulus (change in concentration of chemo-attractant / repellent) into an internal stimulus (change in concentration of intracellular response regulator, CheY-P) which in turn interacts with the flagella motor to bias the cell’s mean runtime. It is a model system for studying the properties of the two-component superfamily of receptor-regulated phosphorylation pathways in general. We use the well-characterized chemotaxis network in E. coli as a prototype for exploring general principles governing information processing in biological signaling networks. Adaptation Adaptation is an important and generic property of biological systems. Adaptive responses occur over a wide range of time scales, from fractions of a second in neural systems, to millions of years in the evolution of species. Adaptation Time Number 15684 18 Yp 0 0 R 250 0.29 E 6276 - B 1928 2.27 0 0 Simulating Reactions Reactions are simulated using Stochsim[5] package, a general platform for simulating reactions stochastically. Symbols: n: Number of molecules in reaction system n0: Number of pseudo-molecules NA: Avogadro constant p: Probability for a reaction to happen Δt: Simulation time step V: Simulation volume Uni-molecular reaction kn(n n0 ) t k p A B n0 Bi-molecular reaction kn( n n0 ) t p 2 N AV k A B C Motor response A simple threshold model[6] is used to model motor response. The motor switches state whenever CheY-P trace (blue trace) crosses the threshold (red line). [5] C. J. Morton-Firth et al. 1998 J. Theor. Biol.. 192 117-128 [6]T. Emonet et al. 2005 Bioinformatics 21 2714-2721 Adaptation to various step changes of aspartate. Blue: 1 μM; Red: 100 μM (simulation) In bacterial chemotaxis, adaptation occurs when the steady state response (running bias) returns precisely to the pre-stimulus level while the stimulus persists. It allows the system to compensate for the presence of continued stimulation and to be ready to respond to further stimuli. Mutual Information Furthermore, the dynamical properties of the network, such as the adaptation time, vary for different inputs. P(r ) P( s) r(s) s r I E[ P(r )] P(r ) E[ P(n | r )] r E[ P(r )] P log 2 PdP Here, s: input signal; P(s): probability distribution of signal r: response; P(r): probability distribution of response r(s): I-O relation, mapping s to r. n: noise P(n|r): probability distribution of noise distribution conditioned on response input, s : chemoattractant concentration output, r : CheY-P concentration [7] Spikes, Fred Rieke et al. 1997, p122-123 [8] N. Brenner et al. (2000) Neuron. 26 695-702 Effect of varying response The response, r (s1), to input signal s1 (with μ1=1 μM, σ12 = μ1, 1 = 1 sec) is used to map different input signals sk to output r’k (instead of using correct response r(sk) to each sk). The mutual information between r’k and sk is calculated as: ' P(rk ) P( sk ) r(s 1) r s I E[ P (r )] P(r ) E[ P(n | r )] ' k ' k ' k ' k r Distribution of CW (grey) and CCW (black) intervals in wild-type adapted cells The I/O mutual information rate is maximized when the response and the input signal are matched. Discussion: Our simulation results are in good agreement with experiments, providing an experimentally faithful computational framework for bacterial chemotaxis. [9] S. M. Block et al. 1982 Cell 31 215-226 [10] H. C. Berg et al. 1975 PNAS 72 3235-3239 [11] T. Emonet et al. 2005 Bioinformatics 21 2714-2721 Discussion: Intuitively, more information can be transmitted when input signal changes slowly. We show that as the time scale of changes in the input signal becomes comparable to the E. coli impulse response time (>0.8sec), the information transmission rate approaches a constant asymptotic value. Input-Output Relation Utilizing this realistic numerical implementation, we explore the chemotaxis network in E. coli from the standpoint of information-processing: Signal E. coli chemotaxis network Input signal Gaussian distributed time series for chemoattractant concentration with correlation time, : 2 As the statistics of the input stimulus varies, E. coli’s response adapts so as to maximize the mutual information between the input signal and the output. Conclusions Output Output Number of CheY-P molecules (s ) p( s) exp( ) 2 2 2 2 <s(0)s(t)> ~ exp(-t / ) 1 The average information that observation of Y provides about the signal X, is I, the mutual information of X and Y[7]. I is minimum (zero) when Y is independent of X, while it is maximum when Y is completely determined by X. The Input-Output (I/O) mutual information rate, I, is given by: Attractant: 30 μM aspartate. Repellent: 100 μM NiCl2 The I/O mutual information rate of E. coli chemotaxis network is plotted as a function of correlation time τ. The Gaussian distributed signals used here have means μ=1, 3, 5, and 10 μM, respectively. Concentration (μM) Y Bp Physical constants of motion: Cell speed: 20-30 μm/sec Mean run time: 1 sec Mean tumble time: 0.1 sec Effect of τ on I/O mutual information Table II: Activation Probabilities Courtesy of H. C. Berg lab) [4] Sourjik et al. (2002) PNAS. 99 123-127 Simulation Cell response (probability of CCW rotation of flagella, leading to running motion) when exposed to a step change of aspartate from 0 to 0.1 mM (left), 10 μM (right) beginning at 5 sec Adaptation time[10] Numerical Implementation E. coli Chemotaxis Perfect Adaptation[4] Experiment Δ[CheY-P] [1] R. C. Hardie et al. (2001) Nature 413, 186-193 [2] M. Postma et al. (1999) Biophysical Journal 77 1811-1823 [3] S. M. Block et al. 1982 Cell 31 215-226 Body size: Flagellum: Varying Statistics of Input The chemotaxis network in E. coli functions under varying environmental conditions. We have shown that as the statistics of the input stimulus change, the input-output relation varies. This adaptive behavior allows E. coli to extract “as much information as possible” from the input signal (by maximizing the mutual information between the input and output). Future Work Finding the input-output relation, r(s) Work in progress includes investigation of: Upper: Input = Gaussian distributed signal as a function of time {μ=3 μM, σ2 = μ, τ = 1 sec}. Lower : Output = system response to the input signal, as a function of time. Response function, r(s), as a function of input signal. Because of the stochastic nature, response to input signal varies. Each point represents the average value of response. Response, r(si), to input signals with {μi, σi2, τ = 1 sec} 1) Motor bias as the output of the chemotaxis network, by constructing a more physically realistic description of the motor response based on the statistical mechanics of switching between CW/CCW states. 2) Role of the variable network adaptation time, from the standpoint of optimizing information transmission.