Construction and Enhancement of a Minimal Genetic AND Logic Gate

ABSTRACT The ability of genetic networks to integrate multiple inputs in the generation of cellular responses is critical for the adaptation of cellular phenotype to distinct environments and of great interest in the construction of complex artificial circuits. To develop artificial genetic circuits that can integrate intercellular signaling molecules and commonly used inducing agents, we have constructed an artificial genetic AND gate based on the PluxI quorum-sensing promoter and the lac repressor. The hybrid promoter exhibited reduced basal and induced expression levels but increased expression capacity, generating clear logical responses that could be described using a simple mathematical model. The model also predicted that the AND gate's logic could be improved by altering the properties of the LuxR transcriptional activator and, in particular, by increasing its rate of transcriptional activation. Following these predictions, we were able to improve the AND gate's logic by ∼1.5-fold using a LuxR mutant library generated by directed evolution, providing the first example of the use of mutant transcriptional activators to improve the logic of a complex regulatory circuit. In addition, detailed characterizations of the AND gate's responses shed light on how LuxR, LacI, and RNA polymerase interact to activate gene expression.

[1]  Aindrila Mukhopadhyay,et al.  Integrating Input from Multiple Signals: The VirA/VirG Two‐Component System of Agrobacterium tumefaciens , 2004, Chembiochem : a European journal of chemical biology.

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

[3]  P. Kambam,et al.  Engineering and applications of genetic circuits. , 2007, Molecular bioSystems.

[4]  U. Alon,et al.  Plasticity of the cis-Regulatory Input Function of a Gene , 2006, PLoS biology.

[5]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  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.

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

[8]  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.

[9]  B. Bassler,et al.  Quorum sensing: cell-to-cell communication in bacteria. , 2005, Annual review of cell and developmental biology.

[10]  E. P. Greenberg,et al.  Conversion of the Vibrio fischeriTranscriptional Activator, LuxR, to a Repressor , 2000, Journal of bacteriology.

[11]  S. Mangan,et al.  The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. , 2003, Journal of molecular biology.

[12]  W. Lim,et al.  Integration of multiple signals through cooperative regulation of the N-WASP-Arp2/3 complex. , 2000, Science.

[13]  Daniel J. Sayut,et al.  Construction and engineering of positive feedback loops. , 2006, ACS chemical biology.

[14]  M. Thattai,et al.  Attenuation of noise in ultrasensitive signaling cascades. , 2002, Biophysical journal.

[15]  M. Capp,et al.  Inhibition of Transcription Initiation buIacRepressor , 1995 .

[16]  Stephen Busby,et al.  Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. , 2004, Current opinion in microbiology.

[17]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[18]  Pietro Alifano,et al.  Control of mRNA processing and decay in prokaryotes , 2005, Genetica.

[19]  Nicolas E. Buchler,et al.  On schemes of combinatorial transcription logic , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Record,et al.  Inhibition of transcription initiation by lac repressor. , 1995, Journal of molecular biology.

[21]  Virginia W Cornish,et al.  Transcription factor logic using chemical complementation. , 2008, Molecular bioSystems.

[22]  Terence Hwa,et al.  Combinatorial transcriptional control of the lactose operon of Escherichia coli , 2007, Proceedings of the National Academy of Sciences.

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

[24]  James E. Ferrell,et al.  Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. , 2001, Chaos.

[25]  M. Elowitz,et al.  Programming gene expression with combinatorial promoters , 2007, Molecular systems biology.

[26]  Sorin Istrail,et al.  Logic functions of the genomic cis-regulatory code. , 2005 .

[27]  Mat E. Barnet,et al.  A synthetic Escherichia coli predator–prey ecosystem , 2008, Molecular systems biology.

[28]  K. Wassarman Small RNAs in Bacteria Diverse Regulators of Gene Expression in Response to Environmental Changes , 2002, Cell.

[29]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[30]  Vincenzo Crunelli,et al.  Hardwiring goes soft: long-term modulation of electrical synapses in the mammalian brain. , 2006, Cellscience.

[31]  S Falkow,et al.  FACS-optimized mutants of the green fluorescent protein (GFP). , 1996, Gene.

[32]  Ali Kinkhabwala,et al.  Uncovering cis Regulatory Codes Using Synthetic Promoter Shuffling , 2008, PloS one.

[33]  A. Ishihama,et al.  Involvement of region 4 of the sigma70 subunit of RNA polymerase in transcriptional activation of the lux operon during quorum sensing. , 2003, FEMS microbiology letters.

[34]  M. Wall,et al.  Design of gene circuits: lessons from bacteria , 2004, Nature Reviews Genetics.

[35]  Hernan G. Garcia,et al.  Transcriptional Regulation by the Numbers 2: Applications , 2004, q-bio/0412011.

[36]  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.

[37]  Frances H Arnold,et al.  Synthetic gene circuits: design with directed evolution. , 2007, Annual review of biophysics and biomolecular structure.

[38]  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.

[39]  Christopher A. Voigt,et al.  Environmental signal integration by a modular AND gate , 2007, Molecular systems biology.

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

[41]  Pieter Rein ten Wolde,et al.  Transcriptional Regulation by Competing Transcription Factor Modules , 2006, PLoS Comput. Biol..

[42]  M. Barkley,et al.  Repressor Recognition of Operator and Effectors , 1980 .

[43]  Ertugrul M. Ozbudak,et al.  Multistability in the lactose utilization network of Escherichia coli , 2004, Nature.

[44]  E. P. Greenberg,et al.  Reversible Acyl-Homoserine Lactone Binding to Purified Vibrio fischeri LuxR Protein , 2004, Journal of bacteriology.