1
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Blanchini F, Colaneri P, Giordano G, Zorzan I. Vertex results for the robust analysis of uncertain biochemical systems. J Math Biol 2022; 85:35. [PMID: 36123409 PMCID: PMC9485104 DOI: 10.1007/s00285-022-01799-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/06/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022]
Abstract
We consider the problem of assessing the sensitivity of uncertain biochemical systems in the presence of input perturbations (either constant or periodic) around a stable steady state.
In particular, we propose approaches for the robust sensitivity analysis of systems with uncertain parameters assumed to take values in a hyper-rectangle. We highlight vertex results, which allow us to check whether a property is satisfied for all parameter choices in the hyper-rectangle by simply checking whether it is satisfied for all parameter choices at the vertices of the hyper-rectangle. We show that, for a vast class of systems, including (bio)chemical reaction networks with mass-action kinetics, the system Jacobian has a totally multiaffine structure (namely, all minors of the Jacobian matrix are multiaffine functions of the uncertain parameters), which can be exploited to obtain several vertex results. We consider different problems: robust non-singularity; robust stability of the steady-state; robust steady-state sensitivity analysis, in the case of constant perturbations; robust frequency-response sensitivity analysis, in the presence of periodic perturbations; and robust adaptation analysis. The developed theory is then applied to gain insight into some examples of uncertain biochemical systems, including the incoherent feed-forward loop, the coherent feed-forward loop, the Brusselator oscillator and the Goldbeter oscillator.
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Affiliation(s)
- Franco Blanchini
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche, University of Udine, Udine, Italy
| | - Patrizio Colaneri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy.,IEIIT-CNR, Turin, Italy
| | - Giulia Giordano
- Department of Industrial Engineering, University of Trento, Trento, Italy.
| | - Irene Zorzan
- Department of Information Engineering, University of Padova, Padua, Italy.,Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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2
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Mochizuki A. A structural approach to understanding enzymatic regulation of chemical reaction networks. Biochem J 2022; 479:1265-1283. [PMID: 35713414 PMCID: PMC9246345 DOI: 10.1042/bcj20210545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/02/2022]
Abstract
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex systems, i.e. chemical reaction network. One of the largest missions in modern biology is to understand behaviors of such systems logically based on information of network structures. However, there are series of obstacles to study dynamical behaviors of complex network systems in biology. For example, network structure does not provide sufficient information to determine details of the dynamical behaviors. In this review, I will introduce a novel mathematical theory, structural sensitivity analysis, by which the responses of reaction systems upon the changes in enzyme activities/amounts are determined from network structure alone. The patterns of responses exhibit characteristic features, localization and hierarchy, depending on the topology of the network. The theory also shows that ranges of enzymatic regulations are governed by a mathematical law characterized by local topology of substructures. These findings imply that the network topology is one of the origins of biological robustness.
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Affiliation(s)
- Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
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3
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Giordano G. Ceramide-transfer protein-mediated ceramide transfer is a structurally tunable flow-inducing mechanism with structural feed-forward loops. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180494. [PMID: 30110462 PMCID: PMC6030332 DOI: 10.1098/rsos.180494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
This paper considers two models of ceramide-transfer protein (CERT)-mediated ceramide transfer at the trans-Golgi network proposed in the literature, short distance shuttle and neck swinging, and seeks structural (parameter-free) features of the two models, which rely exclusively on the peculiar interaction network and not on specific parameter values. In particular, it is shown that both models can be seen as flow-inducing systems, where the flows between pairs of species are tuned by the concentrations of other species, and suitable external inputs can structurally regulate ceramide transfer. In the short distance shuttle model, the amount of transferred ceramide is structurally tuned by active protein kinase D (PKD), both directly and indirectly, in a coherent feed-forward loop motif. In the neck-swinging model, the amount of transferred ceramide is structurally tuned by active PI4KIIIβ, while active PKD has an ambivalent effect, due to the presence of an incoherent feed-forward loop motif that directly inhibits ceramide transfer and indirectly promotes it; the structural role of active PKD is to favour CERT mobility in the cytosol. It is also shown that the influences among key variables often have structurally determined steady-state signs, which can help falsify the models against experimental traces.
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Affiliation(s)
- Giulia Giordano
- Delft Center for Systems and Control, Delft University of Technology (TU Delft), 2628 CD Delft, The Netherlands
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4
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Naik P, Wang JP, Sederoff R, Chiang V, Williams C, Ducoste JJ. Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis. PLoS One 2018; 13:e0193896. [PMID: 29509777 PMCID: PMC5839572 DOI: 10.1371/journal.pone.0193896] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/19/2018] [Indexed: 11/18/2022] Open
Abstract
Lignin is a polymer present in the secondary cell walls of all vascular plants. It is a known barrier to pulping and the extraction of high-energy sugars from cellulosic biomass. The challenge faced with predicting outcomes of transgenic plants with reduced lignin is due in part to the presence of unique protein-protein interactions that influence the regulation and metabolic flux in the pathway. Yet, it is unclear why certain plants have evolved to create these protein complexes. In this study, we use mathematical models to investigate the role that the protein complex, formed specifically between Ptr4CL3 and Ptr4CL5 enzymes, have on the monolignol biosynthesis pathway. The role of this Ptr4CL3-Ptr4CL5 enzyme complex on the steady state flux distribution was quantified by performing Monte Carlo simulations. The effect of this complex on the robustness and the homeostatic properties of the pathway were identified by performing sensitivity and stability analyses, respectively. Results from these robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex. Specifically, the presence of Ptr4CL3-Ptr4CL5 complex increased the stability of the pathway by 22%. The robustness in the pathway is maintained due to the presence of multiple enzyme isoforms as well as the presence of alternative pathways resulting from the presence of the Ptr4CL3-Ptr4CL5 complex.
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Affiliation(s)
- Punith Naik
- Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Vincent Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Cranos Williams
- Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Joel J. Ducoste
- Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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5
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Edgington MP, Tindall MJ. Mathematical Analysis of the Escherichia coli Chemotaxis Signalling Pathway. Bull Math Biol 2018; 80:758-787. [PMID: 29404879 PMCID: PMC5862969 DOI: 10.1007/s11538-018-0400-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022]
Abstract
We undertake a detailed mathematical analysis of a recent nonlinear ordinary differential equation (ODE) model describing the chemotactic signalling cascade within an Escherichia coli cell. The model includes a detailed description of the cell signalling cascade and an average approximation of the receptor activity. A steady-state stability analysis reveals the system exhibits one positive real steady state which is shown to be asymptotically stable. Given the occurrence of a negative feedback between phosphorylated CheB (CheB-P) and the receptor state, we ask under what conditions the system may exhibit oscillatory-type behaviour. A detailed analysis of parameter space reveals that whilst variation in kinetic rate parameters within known biological limits is unlikely to lead to such behaviour, changes in the total concentration of the signalling proteins do. We postulate that experimentally observed overshoot behaviour can actually be described by damped oscillatory dynamics and consider the relationship between overshoot amplitude, total cell protein concentration and the magnitude of the external ligand stimulus. Model reductions in the full ODE model allow us to understand the link between phosphorylation events and the negative feedback between CheB-P and receptor methylation, as well as elucidate why some mathematical models exhibit overshoot and others do not. Our paper closes by discussing intercell variability of total protein concentration as a means of ensuring the overall survival of a population as cells are subjected to different environments.
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Affiliation(s)
- Matthew P Edgington
- Department of Mathematics and Statistics, University of Reading, Whiteknights, PO Box 220, Reading, RG6 6AX, UK.,The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Marcus J Tindall
- Department of Mathematics and Statistics, University of Reading, Whiteknights, PO Box 220, Reading, RG6 6AX, UK. .,Institute for Cardiovascular and Metabolic Research, University of Reading, Whiteknights, PO Box 218, Reading, RG6 6AA, UK.
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6
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Paulick A, Jakovljevic V, Zhang S, Erickstad M, Groisman A, Meir Y, Ryu WS, Wingreen NS, Sourjik V. Mechanism of bidirectional thermotaxis in Escherichia coli. eLife 2017; 6:26607. [PMID: 28826491 PMCID: PMC5578741 DOI: 10.7554/elife.26607] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/01/2017] [Indexed: 12/17/2022] Open
Abstract
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. Many bacteria can move towards or away from chemicals, heat and other stimuli in their environment. The ability of bacteria to move in response to nutrients and other chemicals, known as chemotaxis, is the best understood of these phenomena. Bacteria generally swim in a fairly random way and frequently change direction. During chemotaxis, however, the bacteria sense changes in the concentrations of a chemical in their surroundings and this biases the direction in which they swim so that they spend more time swimming towards or away from the source of the chemical. The bacteria have various receptor proteins that can detect different chemicals. For example, the Tar and Tsr receptors can recognize chemicals called aspartate and serine, respectively, which are – amongst other things – nutrients that are used to build proteins. Tar and Tsr are also involved in the response to temperature, referred to as thermotaxis. At low temperatures, a bacterium Escherichia coli will move towards sources of heat. Yet when the bacteria detect both serine and aspartate they may reverse the response and move towards colder areas instead. However, it was not clear why the bacteria do this, and what roles Tar and Tsr play in this response. Paulick et al. have now combined approaches that directly visualise signalling inside living bacteria and that track the movements of individual bacterial cellswith mathematical modelling to investigate thermotaxis in E. coli. The experiments show that the bacteria’s behaviour could be explained by interplay between the responses mediated by Tar and Tsr. In the absence of both serine and aspartate, both receptors stimulate heat-seeking responses, causing the bacteria to move towards hotter areas. When only aspartate is present, Tsr continues to stimulate the heat-seeking response, but the aspartate causes Tar to switch to promoting a cold-seeking response instead. This leads to the bacteria accumulating in areas of intermediate temperature. In the presence of serine only, the bacteria behave in a similar way because the receptors swap roles so that Tsr stimulates the cold-seeking response, while Tar promotes the heat-seeking one. The intermediate temperature at which the bacteria accumulate in response to serine is also around the optimal temperature for E.coli growth in presence of this chemical, suggesting that thermotaxis might play an important role in allowing bacteria to survive and grow in many different environments, including in the human body. Thus, understanding how chemotaxis and thermotaxis are regulated may lead to new ways to control how bacteria behave in patients and natural environments.
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Affiliation(s)
- Anja Paulick
- Max Planck Institute for Terrestrial Microbiology and LOEWE Research Center for Synthetic Microbiology, Marburg, Germany
| | | | - SiMing Zhang
- Department of Physics and Donnelly Centre, University of Toronto, Toronto, Canada
| | - Michael Erickstad
- Departments of Physics, University of California, San Diego, United States
| | - Alex Groisman
- Departments of Physics, University of California, San Diego, United States
| | - Yigal Meir
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - William S Ryu
- Department of Physics and Donnelly Centre, University of Toronto, Toronto, Canada
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Research Center for Synthetic Microbiology, Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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7
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Savir Y, Martynov A, Springer M. Achieving global perfect homeostasis through transporter regulation. PLoS Comput Biol 2017; 13:e1005458. [PMID: 28414718 PMCID: PMC5411106 DOI: 10.1371/journal.pcbi.1005458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/01/2017] [Accepted: 03/16/2017] [Indexed: 01/04/2023] Open
Abstract
Nutrient homeostasis-the maintenance of relatively constant internal nutrient concentrations in fluctuating external environments-is essential to the survival of most organisms. Transcriptional regulation of plasma membrane transporters by internal nutrient concentrations is typically assumed to be the main mechanism by which homeostasis is achieved. While this mechanism is homeostatic we show that it does not achieve global perfect homeostasis-a condition where internal nutrient concentrations are completely independent of external nutrient concentrations for all external nutrient concentrations. We show that the criterion for global perfect homeostasis is that transporter levels must be inversely proportional to net nutrient flux into the cell and that downregulation of active transporters (activity-dependent regulation) is a simple and biologically plausible mechanism that meets this criterion. Activity-dependent transporter regulation creates a trade-off between robustness and efficiency, i.e., the system's ability to withstand perturbation in external nutrients and the transporter production rate needed to maintain homeostasis. Additionally, we show that a system that utilizes both activity-dependent transporter downregulation and regulation of transporter synthesis by internal nutrient levels can create a system that mitigates the shortcomings of each of the individual mechanisms. This analysis highlights the utility of activity-dependent regulation in achieving homeostasis and calls for a re-examination of the mechanisms of regulation of other homeostatic systems.
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Affiliation(s)
- Yonatan Savir
- Department of Physiology, Biophysics and Systems Biology, Faculty of Medicine, Technion, Haifa, Israel
| | - Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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8
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Okada T, Mochizuki A. Law of Localization in Chemical Reaction Networks. PHYSICAL REVIEW LETTERS 2016; 117:048101. [PMID: 27494502 DOI: 10.1103/physrevlett.117.048101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 06/06/2023]
Abstract
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g., metabolic pathways. Here we developed a theory to predict the sensitivity, i.e., the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. Nonzero response patterns turn out to exhibit two characteristic features, localization and hierarchy. We present a general theorem connecting sensitivity with network topology that explains these characteristic patterns. Our results imply that network topology is an origin of biological robustness. Finally, we suggest a strategy to determine real networks from experimental measurements.
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Affiliation(s)
- Takashi Okada
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
- CREST, JST 4-1-8 Honcho, Kawaguchi 332-0012, Japan
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9
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Computing the structural influence matrix for biological systems. J Math Biol 2015; 72:1927-58. [PMID: 26395779 DOI: 10.1007/s00285-015-0933-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 08/26/2015] [Indexed: 12/20/2022]
Abstract
We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.
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10
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11
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Feng S, Ollivier JF, Swain PS, Soyer OS. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Res 2015; 43:e123. [PMID: 26101250 PMCID: PMC4627059 DOI: 10.1093/nar/gkv595] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx.
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Affiliation(s)
- Song Feng
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Peter S Swain
- SynthSys, The University of Edinburgh, Edinburgh, United Kingdom
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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12
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Bosdriesz E, Molenaar D, Teusink B, Bruggeman FJ. How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization. FEBS J 2015; 282:2029-44. [PMID: 25754869 PMCID: PMC4672707 DOI: 10.1111/febs.13258] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/02/2015] [Accepted: 03/02/2015] [Indexed: 01/20/2023]
Abstract
Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. This is exemplified for Escherichia coli by the increase of its ribosomal protein-fraction with growth rate, which precisely matches the increased protein synthesis demand. These findings and others have led to the hypothesis that E. coli aims to maximize its growth rate in environments that support growth. However, what kind of regulatory strategy is required for a robust, optimal adjustment of the ribosome concentration to the prevailing condition is still an open question. In the present study, we analyze the ppGpp-controlled mechanism of ribosome expression used by E. coli and show that this mechanism maintains the ribosomes saturated with its substrates. In this manner, overexpression of the highly abundant ribosomal proteins is prevented, and limited resources can be redirected to the synthesis of other growth-promoting enzymes. It turns out that the kinetic conditions for robust, optimal protein-partitioning, which are required for growth rate maximization across conditions, can be achieved with basic biochemical interactions. We show that inactive ribosomes are the most suitable ‘signal’ for tracking the intracellular nutritional state and for adjusting gene expression accordingly, as small deviations from optimal ribosome concentration cause a huge fractional change in ribosome inactivity. We expect to find this control logic implemented across fast-growing microbial species because growth rate maximization is a common selective pressure, ribosomes are typically highly abundant and thus costly, and the required control can be implemented by a small, simple network.
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Affiliation(s)
- Evert Bosdriesz
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
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13
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Abstract
The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A short-term memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis.
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14
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Straube R. Reciprocal regulation as a source of ultrasensitivity in two-component systems with a bifunctional sensor kinase. PLoS Comput Biol 2014; 10:e1003614. [PMID: 24809699 PMCID: PMC4014401 DOI: 10.1371/journal.pcbi.1003614] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/24/2014] [Indexed: 01/31/2023] Open
Abstract
Two-component signal transduction systems, where the phosphorylation state of a regulator protein is modulated by a sensor kinase, are common in bacteria and other microbes. In many of these systems, the sensor kinase is bifunctional catalyzing both, the phosphorylation and the dephosphorylation of the regulator protein in response to input signals. Previous studies have shown that systems with a bifunctional enzyme can adjust the phosphorylation level of the regulator protein independently of the total protein concentrations – a property known as concentration robustness. Here, I argue that two-component systems with a bifunctional enzyme may also exhibit ultrasensitivity if the input signal reciprocally affects multiple activities of the sensor kinase. To this end, I consider the case where an allosteric effector inhibits autophosphorylation and, concomitantly, activates the enzyme's phosphatase activity, as observed experimentally in the PhoQ/PhoP and NRII/NRI systems. A theoretical analysis reveals two operating regimes under steady state conditions depending on the effector affinity: If the affinity is low the system produces a graded response with respect to input signals and exhibits stimulus-dependent concentration robustness – consistent with previous experiments. In contrast, a high-affinity effector may generate ultrasensitivity by a similar mechanism as phosphorylation-dephosphorylation cycles with distinct converter enzymes. The occurrence of ultrasensitivity requires saturation of the sensor kinase's phosphatase activity, but is restricted to low effector concentrations, which suggests that this mode of operation might be employed for the detection and amplification of low abundant input signals. Interestingly, the same mechanism also applies to covalent modification cycles with a bifunctional converter enzyme, which suggests that reciprocal regulation, as a mechanism to generate ultrasensitivity, is not restricted to two-component systems, but may apply more generally to bifunctional enzyme systems. Bacteria often use two-component systems to sense and respond to environmental changes, which involves autophosphorylation of a sensor kinase and phosphotransfer to a cognate response regulator. However, despite conservation of this ‘classical’ scheme there exist substantial variations in the mechanism of phosphotransfer among systems. Also, many sensor kinases exhibit phosphatase activity raising the question whether such a bifunctional architecture enables special regulatory properties in the response behavior to input signals. According to previous studies, classical two-component systems are unlikely to produce sigmoidal response curves (ultrasensitivity) if the sensor protein is bifunctional. Here, I argue that this is not necessarily true if the input stimulus (allosteric effector) reciprocally affects multiple activities of the sensor kinase, as it seems to be common for bifunctional enzymes. To this end, I propose and analyze an extension of the experimentally well-supported Batchelor-Goulian model which shows that ultrasensitivity requires a high-affinity effector and saturation of the phosphatase activity. The underlying mechanism involves sequestration of the effector by the sensor kinase which restricts the occurrence of ultrasensitivity to sufficiently low effector concentrations. Hence, this operating regime might be useful to sense effector limitations or to amplify weak input signals.
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Affiliation(s)
- Ronny Straube
- Analysis and Redesign of Biological Networks Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail:
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15
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Česka M, Šafránek D, Dražan S, Brim L. Robustness analysis of stochastic biochemical systems. PLoS One 2014; 9:e94553. [PMID: 24751941 PMCID: PMC3994026 DOI: 10.1371/journal.pone.0094553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/18/2014] [Indexed: 11/18/2022] Open
Abstract
We propose a new framework for rigorous robustness analysis of stochastic biochemical systems that is based on probabilistic model checking techniques. We adapt the general definition of robustness introduced by Kitano to the class of stochastic systems modelled as continuous time Markov Chains in order to extensively analyse and compare robustness of biological models with uncertain parameters. The framework utilises novel computational methods that enable to effectively evaluate the robustness of models with respect to quantitative temporal properties and parameters such as reaction rate constants and initial conditions. We have applied the framework to gene regulation as an example of a central biological mechanism where intrinsic and extrinsic stochasticity plays crucial role due to low numbers of DNA and RNA molecules. Using our methods we have obtained a comprehensive and precise analysis of stochastic dynamics under parameter uncertainty. Furthermore, we apply our framework to compare several variants of two-component signalling networks from the perspective of robustness with respect to intrinsic noise caused by low populations of signalling components. We have successfully extended previous studies performed on deterministic models (ODE) and showed that stochasticity may significantly affect obtained predictions. Our case studies demonstrate that the framework can provide deeper insight into the role of key parameters in maintaining the system functionality and thus it significantly contributes to formal methods in computational systems biology.
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Affiliation(s)
- Milan Česka
- Systems Biology Laboratory at Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - David Šafránek
- Systems Biology Laboratory at Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Sven Dražan
- Systems Biology Laboratory at Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Luboš Brim
- Systems Biology Laboratory at Faculty of Informatics, Masaryk University, Brno, Czech Republic
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16
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Neumann S, Løvdok L, Bentele K, Meisig J, Ullner E, Paldy FS, Sourjik V, Kollmann M. Exponential signaling gain at the receptor level enhances signal-to-noise ratio in bacterial chemotaxis. PLoS One 2014; 9:e87815. [PMID: 24736435 PMCID: PMC3988002 DOI: 10.1371/journal.pone.0087815] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/01/2014] [Indexed: 11/18/2022] Open
Abstract
Cellular signaling systems show astonishing precision in their response to external stimuli despite strong fluctuations in the molecular components that determine pathway activity. To control the effects of noise on signaling most efficiently, living cells employ compensatory mechanisms that reach from simple negative feedback loops to robustly designed signaling architectures. Here, we report on a novel control mechanism that allows living cells to keep precision in their signaling characteristics – stationary pathway output, response amplitude, and relaxation time – in the presence of strong intracellular perturbations. The concept relies on the surprising fact that for systems showing perfect adaptation an exponential signal amplification at the receptor level suffices to eliminate slowly varying multiplicative noise. To show this mechanism at work in living systems, we quantified the response dynamics of the E. coli chemotaxis network after genetically perturbing the information flux between upstream and downstream signaling components. We give strong evidence that this signaling system results in dynamic invariance of the activated response regulator against multiplicative intracellular noise. We further demonstrate that for environmental conditions, for which precision in chemosensing is crucial, the invariant response behavior results in highest chemotactic efficiency. Our results resolve several puzzling features of the chemotaxis pathway that are widely conserved across prokaryotes but so far could not be attributed any functional role.
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Affiliation(s)
- Silke Neumann
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Linda Løvdok
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kajetan Bentele
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Johannes Meisig
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Ekkehard Ullner
- Department of Physics and Institute for Complex Systems and Mathematical Biology (ICSMB), Aberdeen, United Kingdom
| | - Ferencz S. Paldy
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Markus Kollmann
- Department Biologie, Heinrich-Heine-Universität, Düsseldorf, Düsseldorf, Germany
- * E-mail:
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17
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Link H, Christodoulou D, Sauer U. Advancing metabolic models with kinetic information. Curr Opin Biotechnol 2014; 29:8-14. [PMID: 24534671 DOI: 10.1016/j.copbio.2014.01.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/18/2014] [Accepted: 01/23/2014] [Indexed: 12/21/2022]
Abstract
Kinetic models are crucial to quantitatively understand and predict how functional behavior emerges from dynamic concentration changes of cellular components. The current challenge is on resolving uncertainties about parameter values of reaction kinetics. Additionally, there are also major structural uncertainties due to unknown molecular interactions and only putatively assigned regulatory functions. What if one or few key regulators of biochemical reactions are missing in a metabolic model? By reviewing current advances in building kinetic models of metabolism, we found that such models experience a paradigm shift away from fitting parameters towards identifying key regulatory interactions.
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Affiliation(s)
- Hannes Link
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland.
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18
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Anderson DF, Enciso GA, Johnston MD. Stochastic analysis of biochemical reaction networks with absolute concentration robustness. J R Soc Interface 2014; 11:20130943. [PMID: 24522780 DOI: 10.1098/rsif.2013.0943] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' (ACR) on a wide class of biologically relevant, deterministically modelled mass-action systems. We show here that fundamentally different conclusions about the long-term behaviour of such systems are reached if the systems are instead modelled with stochastic dynamics and a discrete state space. Specifically, we characterize a large class of models that exhibit convergence to a positive robust equilibrium in the deterministic setting, whereas trajectories of the corresponding stochastic models are necessarily absorbed by a set of states that reside on the boundary of the state space, i.e. the system undergoes an extinction event. If the time to extinction is large relative to the relevant timescales of the system, the process will appear to settle down to a stationary distribution long before the inevitable extinction will occur. This quasi-stationary distribution is considered for two systems taken from the literature, and results consistent with ACR are recovered by showing that the quasi-stationary distribution of the robust species approaches a Poisson distribution.
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Affiliation(s)
- David F Anderson
- Department of Mathematics, University of Wisconsin, , Madison, WI, USA
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19
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Jeschke M, Baumgärtner S, Legewie S. Determinants of cell-to-cell variability in protein kinase signaling. PLoS Comput Biol 2013; 9:e1003357. [PMID: 24339758 PMCID: PMC3854479 DOI: 10.1371/journal.pcbi.1003357] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/06/2013] [Indexed: 12/28/2022] Open
Abstract
Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds (‘pathway sensitivity’) and the maximal activation level upon strong stimulation. Minimal kinase cascades with gradual dose-response behavior show strong variability, because the pathway sensitivity and the maximal activation level cannot be simultaneously invariant. Negative feedback regulation resolves this trade-off and coordinately reduces fluctuations in the pathway sensitivity and maximal activation. Feedbacks acting at different levels in the cascade control different aspects of the dose-response curve, thereby synergistically reducing the variability. We also investigated more complex, ultrasensitive signaling cascades capable of switch-like decision making, and found that these can be inherently robust to protein concentration fluctuations. We describe how the cell-to-cell variability of ultrasensitive signaling systems can be actively regulated, e.g., by altering the expression of phosphatase(s) or by feedback/feedforward loops. Our calculations reveal that slow transcriptional negative feedback loops allow for variability suppression while maintaining switch-like decision making. Taken together, we describe design principles of signaling cascades that promote robustness. Our results may explain why certain signaling cascades like the yeast pheromone pathway show switch-like decision making with little cell-to-cell variability. Cells sense their surroundings and respond to soluble factors in the extracellular space. Extracellular factors frequently induce heterogeneous responses, thereby restricting the biological outcome to a fraction of the cell population. However, the question arises how such cell-to-cell variability can be controlled, because some cellular systems show a very homogenous response at a defined level of an extracellular stimulus. We derived an analytical framework to systematically characterize the cell-to-cell variability of intracellular signaling pathways which transduce external signals. We analyzed how heterogeneity arises from fluctuations in the total concentrations of signaling proteins because this is the main source of variability in eukaryotic systems. We find that signaling pathways can be highly variable or inherently invariant, depending on the kinetic parameters and the structural features of the cascade. Our results indicate that the cell-to-cell variability can be reduced by negative feedback in the cascade or by signaling crosstalk between parallel pathways. We precisely define the role of negative feedback loops in variability suppression, and show that different aspects of the dose-response curve can be controlled, depending on the feedback kinetics and site of action in the cascade. This work constitutes a first step towards a systematic understanding of cell-to-cell variability in signal transduction.
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Affiliation(s)
| | | | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany
- * E-mail:
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20
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Streif S, Kim KKK, Rumschinski P, Kishida M, Shen DE, Findeisen R, Braatz RD. Robustness Analysis, Prediction and Estimation for Uncertain Biochemical Networks. ACTA ACUST UNITED AC 2013. [DOI: 10.3182/20131218-3-in-2045.00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Blüthgen N, Legewie S. Robustness of signal transduction pathways. Cell Mol Life Sci 2013; 70:2259-69. [PMID: 23007845 PMCID: PMC11113274 DOI: 10.1007/s00018-012-1162-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/05/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
Signal transduction pathways transduce information about the outside of the cell to the nucleus, regulating gene expression and cell fate. To reliably inform the cell about its surroundings, information transfer has to be robust against typical perturbation that a cell experiences. Robustness of several mammalian signaling pathways has been studied recently by quantitative experimentation and using mathematical modeling. Here, we review these studies, and describe the emerging concepts of robustness and the underlying mechanisms.
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Affiliation(s)
- Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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22
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Abstract
We propose a model of parameter learning for signal transduction, where the objective function is defined by signal transmission efficiency. We apply this to learn kinetic rates as a form of evolutionary learning, and look for parameters which satisfy the objective. This is a novel approach compared to the usual technique of adjusting parameters only on the basis of experimental data. The resulting model is self-organizing, i.e. perturbations in protein concentrations or changes in extracellular signaling will automatically lead to adaptation. We systematically perturb protein concentrations and observe the response of the system. We find compensatory or co-regulation of protein expression levels. In a novel experiment, we alter the distribution of extracellular signaling, and observe adaptation based on optimizing signal transmission. We also discuss the relationship between signaling with and without transients. Signaling by transients may involve maximization of signal transmission efficiency for the peak response, but a minimization in steady-state responses. With an appropriate objective function, this can also be achieved by concentration adjustment. Self-organizing systems may be predictive of unwanted drug interference effects, since they aim to mimic complex cellular adaptation in a unified way.
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Affiliation(s)
- Gabriele Scheler
- Carl Correns Foundation for Mathematical Biology, Mountain View, CA , 94040, USA
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23
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Keskin F, Suhre A, Kose K, Ersahin T, Cetin AE, Cetin-Atalay R. Image classification of human carcinoma cells using complex wavelet-based covariance descriptors. PLoS One 2013; 8:e52807. [PMID: 23341908 PMCID: PMC3547046 DOI: 10.1371/journal.pone.0052807] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 11/21/2012] [Indexed: 01/17/2023] Open
Abstract
Cancer cell lines are widely used for research purposes in laboratories all over the world. Computer-assisted classification of cancer cells can alleviate the burden of manual labeling and help cancer research. In this paper, we present a novel computerized method for cancer cell line image classification. The aim is to automatically classify 14 different classes of cell lines including 7 classes of breast and 7 classes of liver cancer cells. Microscopic images containing irregular carcinoma cell patterns are represented by subwindows which correspond to foreground pixels. For each subwindow, a covariance descriptor utilizing the dual-tree complex wavelet transform (DT-[Formula: see text]WT) coefficients and several morphological attributes are computed. Directionally selective DT-[Formula: see text]WT feature parameters are preferred primarily because of their ability to characterize edges at multiple orientations which is the characteristic feature of carcinoma cell line images. A Support Vector Machine (SVM) classifier with radial basis function (RBF) kernel is employed for final classification. Over a dataset of 840 images, we achieve an accuracy above 98%, which outperforms the classical covariance-based methods. The proposed system can be used as a reliable decision maker for laboratory studies. Our tool provides an automated, time- and cost-efficient analysis of cancer cell morphology to classify different cancer cell lines using image-processing techniques, which can be used as an alternative to the costly short tandem repeat (STR) analysis. The data set used in this manuscript is available as supplementary material through http://signal.ee.bilkent.edu.tr/cancerCellLineClassificationSampleImages.html.
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Affiliation(s)
- Furkan Keskin
- Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey
| | - Alexander Suhre
- Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey
| | - Kivanc Kose
- Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey
| | - Tulin Ersahin
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - A. Enis Cetin
- Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey
| | - Rengul Cetin-Atalay
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
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25
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Tsao CY, Quan DN, Bentley WE. Development of the quorum sensing biotechnological toolbox. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Analyzing and engineering cell signaling modules with synthetic biology. Curr Opin Biotechnol 2012; 23:785-90. [DOI: 10.1016/j.copbio.2012.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 12/20/2022]
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27
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Sourjik V, Wingreen NS. Responding to chemical gradients: bacterial chemotaxis. Curr Opin Cell Biol 2011; 24:262-8. [PMID: 22169400 DOI: 10.1016/j.ceb.2011.11.008] [Citation(s) in RCA: 322] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 11/25/2022]
Abstract
Chemotaxis allows bacteria to follow gradients of nutrients and other environmental stimuli. The bacterium Escherichia coli performs chemotaxis via a run-and-tumble strategy in which sensitive temporal comparisons lead to a biased random walk, with longer runs in the preferred gradient direction. The chemotaxis network of E. coli has developed over the years into one of the most thoroughly studied model systems for signal transduction and behavior, yielding general insights into such properties of cellular networks as signal amplification, signal integration, and robustness. Despite its relative simplicity, the operation of the E. coli chemotaxis network is highly refined and evolutionarily optimized at many levels. For example, recent studies revealed that the network adjusts its signaling properties dependent on the extracellular environment, apparently to optimize chemotaxis under particular conditions. The network can even utilize potentially detrimental stochastic fluctuations in protein levels and reaction rates to maximize the chemotactic performance of the population.
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Affiliation(s)
- Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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