Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis

Kurata, Hiroyuki; Inoue, Kentaro; Maeda, Kazuhiro; Masaki, Koichi; Shimokawa, Yuki; Zhao, Quanyu

doi:10.1093/nar/gkm769

Cited by 32 publications

(20 citation statements)

References 17 publications

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“…2, using the CADLIVE notation [32,33]. This map is one of the most sophisticated images of the whole system of an yeast cell cycle, which is consistent with the previous work [34].…”

Section: A Biochemical Network Mapsupporting

confidence: 83%

An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks

Maeda

Fukano

Yamamichi

et al. 2010

Bioprocess Biosyst Eng

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Computer simulation is an important technique to capture the dynamics of biochemical networks. Numerical optimization is the key to estimate the values of kinetic parameters so that the dynamic model reproduces the behaviors of the existing experimental data. It is required to develop general strategies for the optimization of complex biochemical networks with a huge space of search parameters, under the condition that kinetic and quantitative data are hardly available. We propose an integrative and practical strategy for optimizing a complex dynamic model by using qualitative and incomplete experimental data. The key technologies are the divide and conquer method for reducing the search space, handling of multiple objective functions representing different types of biological behaviors, and design of rule-based objective functions that are suitable for qualitative and error-prone experimental data. This strategy is applied to optimizing a dynamic model of the yeast cell cycle to demonstrate the feasibility of it.

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“…2, using the CADLIVE notation [32,33]. This map is one of the most sophisticated images of the whole system of an yeast cell cycle, which is consistent with the previous work [34].…”

Section: A Biochemical Network Mapsupporting

confidence: 83%

An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks

Maeda

Fukano

Yamamichi

et al. 2010

Bioprocess Biosyst Eng

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“…The notation of CADLIVE [46]–[48] is used for simplifying the diagram. The dashed circle represents nucleus.…”

Section: Resultsmentioning

confidence: 99%

A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator

Maeda

Kurata

2012

PLoS ONE

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Many organisms have evolved molecular clocks to anticipate daily changes in their environment. The molecular mechanisms by which the circadian clock network produces sustained cycles have extensively been studied and transcriptional-translational feedback loops are common structures to many organisms. Although a simple or single feedback loop is sufficient for sustained oscillations, circadian clocks implement multiple, complicated feedback loops. In general, different types of feedback loops are suggested to affect the robustness and entrainment of circadian rhythms.To reveal the mechanism by which such a complex feedback system evolves, we quantify the robustness and light entrainment of four competing models: the single, semi-dual, dual, and redundant feedback models. To extract the global properties of those models, all plausible kinetic parameter sets that generate circadian oscillations are searched to characterize their oscillatory features. To efficiently perform such analyses, we used the two-phase search (TPS) method as a fast and non-biased search method and quasi-multiparameter sensitivity (QMPS) as a fast and exact measure of robustness to uncertainty of all kinetic parameters.So far the redundant feedback model has been regarded as the most robust oscillator, but our extensive analysis corrects or overcomes this hypothesis. The dual feedback model, which is employed in biology, provides the most robust oscillator to multiple parameter perturbations within a cell and most readily entrains to a wide range of light-dark cycles. The kinetic symmetry between the dual loops and their coupling via a protein complex are found critically responsible for robust and entrainable oscillations. We first demonstrate how the dual feedback architecture with kinetic symmetry evolves out of many competing feedback systems.

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“…Several differences surfaced between the biological ammonium assimilation model and classical engineering systems. In another application of the method, it was shown that the redundant feedback loops generate robust properties to multiple gene deletions (574). A steady-state analysis of a network consisting of the GS cascade, the NRI/NRII system, and the glnALG operon indicated that the output of the operon should be switch-like, while the activation of the transcription factor NRI should be graded (575).…”

Section: Estimating Fluxes In Vivomentioning

confidence: 99%

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

Heeswijk¹,

Westerhoff

Boogerd³

2013

Microbiol Mol Biol Rev

228

246

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SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli . The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.

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Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis

Cited by 32 publications

References 17 publications

An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks

An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks

A Symmetric Dual Feedback System Provides a Robust and Entrainable Oscillator

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

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