Design of gene circuits: lessons from bacteria

Researchers are now building synthetic circuits for controlling gene expression and considering practical applications for engineered gene circuits. What can we learn from nature about design principles for gene circuits? A large body of experimental data is now available to test some important theoretical predictions about how gene circuits could be organized, but the data also raise some intriguing new questions.

[1]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[2]  Jacques Monod,et al.  On the Regulation of Gene Activity , 1961 .

[3]  J. Power,et al.  Positive Control of Enzyme Synthesis by Gene C in the l-Arabinose System , 1965, Journal of bacteriology.

[4]  A. Novick,et al.  THE PROPERTIES OF REPRESSOR AND THE KINETICS OF ITS ACTION. , 1965, Journal of molecular biology.

[5]  M. Savageau,et al.  Parameter Sensitivity as a Criterion for Evaluating and Comparing the Performance of Biochemical Systems , 1971, Nature.

[6]  W. Reznikoff,et al.  The operon revisited. , 1972, Annual review of genetics.

[7]  R. Helling,et al.  Induction of the ara Operon of Escherichia coli B/r , 1972, Journal of bacteriology.

[8]  M A Savageau,et al.  Genetic regulatory mechanisms and the ecological niche of Escherichia coli. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[9]  M. Savageau.  Comparison of classical and autogenous systems of regulation in inducible operons , 1974, Nature.

[10]  Michael A. Savageau,et al.  Significance of autogenously regulated and constitutive synthesis of regulatory proteins in repressible biosynthetic systems , 1975, Nature.

[11]  M. Casadaban,et al.  Regulation of the regulatory gene for the arabinose pathway, araC. , 1976, Journal of molecular biology.

[12]  M. Savageau.  Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology , 1976 .

[13]  M A Savageau,et al.  Design of molecular control mechanisms and the demand for gene expression. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M. C. Heincz,et al.  Role of small molecules in regulation of D-serine deaminase synthesis , 1978, Journal of bacteriology.

[15]  Michael A. Savageau,et al.  Autogenous and Classical Regulation of Gene Expression: A General Theory and Experimental Evidence , 1979 .

[16]  R. Schimke,et al.  Biological Regulation and Development , 1980, Biological Regulation and Development.

[17]  J. Pittard,et al.  Autoregulation of the tyrR gene , 1982, Journal of bacteriology.

[18]  Keith R. Yamamoto,et al.  Biological Regulation and Development , 1982, Springer US.

[19]  M. C. Heincz,et al.  Identification and control of synthesis of the dsdC activator protein , 1983, Journal of bacteriology.

[20]  S. Hahn,et al.  In vivo regulation of the Escherichia coli araC promoter , 1983, Journal of bacteriology.

[21]  Savageau Ma,et al.  A theory of alternative designs for biochemical control systems. , 1985 .

[22]  M A Savageau,et al.  A theory of alternative designs for biochemical control systems. , 1985, Biomedica biochimica acta.

[23]  F. Neidhardt,et al.  Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology , 1987 .

[24]  M. Urbanowski,et al.  Regulation of the metR gene of Salmonella typhimurium , 1987, Journal of bacteriology.

[25]  C. Yanofsky,et al.  trp repressor interactions with the trp aroH and trpR operators. Comparison of repressor binding in vitro and repression in vivo. , 1988, Journal of molecular biology.

[26]  M. Urbanowski,et al.  Role of homocysteine in metR-mediated activation of the metE and metH genes in Salmonella typhimurium and Escherichia coli , 1989, Journal of bacteriology.

[27]  R. M. Jeter.  Cobalamin-dependent 1,2-propanediol utilization by Salmonella typhimurium. , 1990, Journal of general microbiology.

[28]  Brian C. Goodwin,et al.  Theoretical Biology: Epigenetic and Evolutionary Order from Complex Systems , 1990 .

[29]  J. Roth,et al.  Autogenous regulation of ethanolamine utilization by a transcriptional activator of the eut operon in Salmonella typhimurium , 1992, Journal of bacteriology.

[30]  Y. Sung,et al.  The Escherichia coli K-12 cyn operon is positively regulated by a member of the lysR family , 1992, Journal of bacteriology.

[31]  T. Bobik,et al.  A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation , 1992, Journal of bacteriology.

[32]  R. Somerville.  The Trp repressor, a ligand-activated regulatory protein. , 1992, Progress in nucleic acid research and molecular biology.

[33]  R. Schleif,et al.  A regulatory cascade in the induction of rhaBAD. , 1993, Journal of molecular biology.

[34]  T. Bobik,et al.  Two global regulatory systems (Crp and Arc) control the cobalamin/propanediol regulon of Salmonella typhimurium , 1993, Journal of bacteriology.

[35]  D. Silverman,et al.  A physiological role for cyanate-induced carbonic anhydrase in Escherichia coli , 1993, Journal of bacteriology.

[36]  H. Azakami,et al.  moaR, a gene that encodes a positive regulator of the monoamine regulon in Klebsiella aerogenes , 1993, Journal of bacteriology.

[37]  J. Fuchs,et al.  Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation , 1994, Journal of bacteriology.

[38]  P. Valentin‐Hansen,et al.  Organization and transcriptional regulation of the Escherichia coli K-12 D-serine tolerance locus , 1995, Journal of bacteriology.

[39]  M A Savageau,et al.  Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. , 1995, Journal of molecular biology.

[40]  N. Obradors,et al.  Transcriptional regulation of the Escherichia coli rhaT gene. , 1996, Microbiology.

[41]  K. Jair,et al.  Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli , 1996, Journal of bacteriology.

[42]  K. Shanmugam,et al.  Repression of the Escherichia coli modABCD (molybdate transport) operon by ModE , 1996, Journal of bacteriology.

[43]  W. S. Hlavacek,et al.  Rules for coupled expression of regulator and effector genes in inducible circuits. , 1996, Journal of molecular biology.

[44]  Chankyu Park,et al.  Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator , 1997, Journal of bacteriology.

[45]  W. S. Hlavacek,et al.  Completely uncoupled and perfectly coupled gene expression in repressible systems. , 1997, Journal of molecular biology.

[46]  William S. Hlavacek,et al.  Method for determining natural design principles of biological control circuits , 1998, J. Intell. Fuzzy Syst..

[47]  M A Savageau,et al.  Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. , 1998, Genetics.

[48]  Araceli M. Huerta,et al.  From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[49]  M A Savageau,et al.  Demand theory of gene regulation. I. Quantitative development of the theory. , 1998, Genetics.

[50]  T. Conway,et al.  Sequence Analysis of the GntII (Subsidiary) System for Gluconate Metabolism Reveals a Novel Pathway for l-Idonic Acid Catabolism in Escherichia coli , 1998, Journal of bacteriology.

[51]  J. W. Little,et al.  Robustness of a gene regulatory circuit , 1999, The EMBO journal.

[52]  U. Alon,et al.  Robustness in bacterial chemotaxis , 2022 .

[53]  A. Løbner-Olesen,et al.  Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control , 1999, The EMBO journal.

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

[55]  Rui Alves,et al.  Extending the method of mathematically controlled comparison to include numerical comparisons , 2000, Bioinform..

[56]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

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

[58]  W. R. Farmer,et al.  Improving lycopene production in Escherichia coli by engineering metabolic control , 2000, Nature Biotechnology.

[59]  D. Botstein,et al.  DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[60]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[61]  Juan L. Ramos,et al.  Dual System To Reinforce Biological Containment of Recombinant Bacteria Designed for Rhizoremediation , 2001, Applied and Environmental Microbiology.

[62]  J. Elf,et al.  Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons. , 2001, Journal of molecular biology.

[63]  M. Thattai,et al.  Intrinsic noise in gene regulatory networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[64]  M. Ehrenberg,et al.  Noise in a minimal regulatory network: plasmid copy number control , 2001, Quarterly Reviews of Biophysics.

[65]  Julio Collado-Vides,et al.  RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 , 2001, Nucleic Acids Res..

[66]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[67]  G. Demers,et al.  Re-engineering adenovirus regulatory pathways to enhance oncolytic specificity and efficacy , 2001, Nature Biotechnology.

[68]  U. Alon,et al.  Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria , 2001, Science.

[69]  U. Alon,et al.  Negative autoregulation speeds the response times of transcription networks. , 2002, Journal of molecular biology.

[70]  Jeff Hasty,et al.  Engineered gene circuits , 2002, Nature.

[71]  C. Rao,et al.  Control, exploitation and tolerance of intracellular noise , 2002, Nature.

[72]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[73]  U. Alon,et al.  Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[74]  P. Swain,et al.  Intrinsic and extrinsic contributions to stochasticity in gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[76]  Adam P Arkin,et al.  Fifteen minutes of fim: control of type 1 pili expression in E. coli. , 2002, Omics : a journal of integrative biology.

[77]  S. Leibler,et al.  Mechanisms of noise-resistance in genetic oscillators , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[78]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[79]  J. Rosner,et al.  Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data , 2002, Molecular microbiology.

[80]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[81]  Michael A Savageau,et al.  Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. , 2002, Mathematical biosciences.

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

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

[84]  N. Barkai,et al.  Robustness of the BMP morphogen gradient in Drosophila embryonic patterning , 2022 .

[85]  J. Collins,et al.  Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling , 2003, Science.

[86]  Farren J. Isaacs,et al.  Prediction and measurement of an autoregulatory genetic module , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[87]  A. Yamaguchi,et al.  Comprehensive Studies of Drug Resistance Mediated by Overexpression of Response Regulators of Two-Component Signal Transduction Systems in Escherichia coli , 2003, Journal of bacteriology.

[88]  William S Hlavacek,et al.  Design principles for regulator gene expression in a repressible gene circuit. , 2003, Journal of molecular biology.

[89]  Uri Alon,et al.  Response delays and the structure of transcription networks. , 2003, Journal of molecular biology.

[90]  Naama Barkai,et al.  Self-enhanced ligand degradation underlies robustness of morphogen gradients. , 2003, Developmental cell.

[91]  U. Alon,et al.  Detailed map of a cis-regulatory input function , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Mads Kærn,et al.  Noise in eukaryotic gene expression , 2003, Nature.

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

[94]  K. Hossner,et al.  Cellular and molecular biology. , 2005 .

[95]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .