Robust synthetic gene network design via library-based search method

MOTIVATION Synthetic biology aims to develop the artificial gene networks with desirable behaviors using systematic method. These networks with desired behaviors could be constructed using diverse biological parts, which may limit the development to complex synthetic gene networks. Fortunately, some well-characterized promoter libraries for engineering gene networks are widely available. Thus, a synthetic gene network can be constructed by selecting adequate promoters from promoter libraries to achieve the desired behaviors. However, the present promoter libraries cannot be directly applied to engineer a synthetic gene network. In order to efficiently select adequate promoters from promoter libraries for a synthetic gene network, promoter libraries are needed to be redefined based on the dynamic gene regulation. RESULTS Based on four design specifications, a library-based search method is proposed to efficiently select the most adequate promoter set from the redefined promoter libraries by a genetic algorithm (GA) to achieve optimal reference tracking design. As the number and size of promoter libraries increase, the proposed method can play an important role in the systematic design of synthetic biology. CONTACT g883743@alumni.nthu.edu.tw; bschen@ee.nthu.edu.tw SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  B. Martin.  PARAMETER ESTIMATION , 2012, Statistical Methods for Biomedical Research.

[2]  Bor-Sen Chen,et al.  Multiobjective H2/H∞ synthetic gene network design based on promoter libraries. , 2011, Mathematical biosciences.

[3]  Bor-Sen Chen,et al.  Robust Optimal Reference-Tracking Design Method for Stochastic Synthetic Biology Systems: T–S Fuzzy Approach , 2010, IEEE Transactions on Fuzzy Systems.

[4]  Bor-Sen Chen,et al.  GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase , 2010, Gene regulation and systems biology.

[5]  James J. Collins,et al.  Next-Generation Synthetic Gene Networks , 2009, Nature Biotechnology.

[6]  Correction for Win and Smolke, A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2009, Proceedings of the National Academy of Sciences.

[7]  C. Collins,et al.  Engineering multicellular systems by cell-cell communication. , 2009, Current opinion in biotechnology.

[8]  Marc Ostermeier,et al.  Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter , 2009, Journal of biological engineering.

[9]  C. Townsend,et al.  An externally tunable bacterial band-pass filter , 2009, Proceedings of the National Academy of Sciences.

[10]  G. Church,et al.  Synthetic Gene Networks That Count , 2009, Science.

[11]  Kim Sneppen,et al.  Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks , 2009, Journal of bacteriology.

[12]  J. Collins,et al.  DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS , 2009, Nature Biotechnology.

[13]  Drew Endy,et al.  Measuring the activity of BioBrick promoters using an in vivo reference standard , 2009, Journal of biological engineering.

[14]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[15]  Bor-Sen Chen,et al.  A systematic design method for robust synthetic biology to satisfy design specifications , 2009, BMC Systems Biology.

[16]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[17]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[18]  Kim Sneppen,et al.  Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. , 2008, Biophysical journal.

[19]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[20]  Kwang-Hyun Cho,et al.  Sustained oscillations in extended genetic oscillatory systems. , 2008, Biophysical journal.

[21]  M. Win,et al.  A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2007, Proceedings of the National Academy of Sciences.

[22]  J. Collins,et al.  Combinatorial promoter design for engineering noisy gene expression , 2007, Proceedings of the National Academy of Sciences.

[23]  Nigel D Goldenfeld,et al.  An Introduction to Systems Biology: Design Principles of Biological Circuits; Systems Biology: Properties of Reconstructed Networks , 2007 .

[24]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

[25]  N. Mantzaris,et al.  Genetic network driven control of PHBV copolymer composition. , 2006, Journal of biotechnology.

[26]  Ranjini Chatterjee,et al.  Directed evolution of metabolic pathways. , 2006, Trends in biotechnology.

[27]  Yiannis N Kaznessis,et al.  Model-driven designs of an oscillating gene network. , 2005, Biophysical journal.

[28]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[29]  Ron Weiss,et al.  Parameter estimation for two synthetic gene networks: a case study , 2005, Proceedings. (ICASSP '05). IEEE International Conference on Acoustics, Speech, and Signal Processing, 2005..

[30]  R. Weiss,et al.  Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[31]  M. Fussenegger,et al.  An engineered epigenetic transgene switch in mammalian cells , 2004, Nature Biotechnology.

[32]  J. Collins,et al.  Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  S. Basu,et al.  Spatiotemporal control of gene expression with pulse-generating networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[35]  Kazuyuki Aihara,et al.  Modeling genetic switches with positive feedback loops. , 2003, Journal of theoretical biology.

[36]  R. Weiss,et al.  Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[37]  M. Elowitz,et al.  Combinatorial Synthesis of Genetic Networks , 2002, Science.

[38]  Goldberg,et al.  Genetic algorithms , 1993, Robust Control Systems with Genetic Algorithms.

[39]  Steven E. Lindow,et al.  Predictive and Interpretive Simulation of Green Fluorescent Protein Expression in Reporter Bacteria , 2001, Journal of bacteriology.

[40]  Kengo Katayama,et al.  An efficient hybrid genetic algorithm for the traveling salesman problem , 2001 .

[41]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[42]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[43]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[44]  Jean-Michel Renders,et al.  Hybrid methods using genetic algorithms for global optimization , 1996, IEEE Trans. Syst. Man Cybern. Part B.

[45]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[46]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[47]  John J. Grefenstette,et al.  Optimization of Control Parameters for Genetic Algorithms , 1986, IEEE Transactions on Systems, Man, and Cybernetics.