Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression.

Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria.

[1]  J. Cronan,et al.  Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Kang Wu,et al.  A modular positive feedback-based gene amplifier , 2010, Journal of biological engineering.

[3]  T. Hwa,et al.  Identification of direct residue contacts in protein–protein interaction by message passing , 2009, Proceedings of the National Academy of Sciences.

[4]  E. Brown,et al.  Substituting an α-helix switches the sequence-specific DNA interactions of a repressor , 1984, Cell.

[5]  Jared R. Leadbetter,et al.  Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR , 2006, Nature Biotechnology.

[6]  P. Kambam,et al.  Altering the Substrate Specificity of RhlI by Directed Evolution , 2009, Chembiochem : a European journal of chemical biology.

[7]  S. K. Desai,et al.  Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. , 2004, Journal of the American Chemical Society.

[8]  W. Hillen,et al.  Teaching TetR to recognize a new inducer. , 2003, Journal of molecular biology.

[9]  Albert Siryaporn,et al.  Evolving a robust signal transduction pathway from weak cross-talk , 2010, Molecular systems biology.

[10]  Ann M Stock,et al.  Two-component signal transduction. , 2000, Annual review of biochemistry.

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

[12]  P. Cunningham,et al.  Genetic analysis of the Shine-Dalgarno interaction: selection of alternative functional mRNA-rRNA combinations. , 1996, RNA.

[13]  Farren J. Isaacs,et al.  Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.

[14]  G L Hazelbauer,et al.  Transmembrane signalling by a hybrid protein: communication from the domain of chemoreceptor Trg that recognizes sugar-binding proteins to the kinase/phosphatase domain of osmosensor EnvZ , 1994, Journal of bacteriology.

[15]  S. Pongor,et al.  Rationally designed helix‐turn‐helix proteins and their conformational changes upon DNA binding. , 1995, The EMBO journal.

[16]  Farren J. Isaacs,et al.  RNA synthetic biology , 2006, Nature Biotechnology.

[17]  R. Beerli,et al.  Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.

[18]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[19]  Jun Hyoung Lee,et al.  Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli , 2008, Nucleic acids research.

[20]  H. D. de Boer,et al.  Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Chin,et al.  A network of orthogonal ribosome·mRNA pairs , 2005, Nature chemical biology.

[22]  V. de Lorenzo,et al.  Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. , 2006, Current opinion in biotechnology.

[23]  Christopher V. Rao,et al.  Computational design of orthogonal ribosomes , 2008, Nucleic acids research.

[24]  Francisco M. Camas,et al.  Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family , 2010, PLoS Comput. Biol..

[25]  E. Cox,et al.  Population Fitness and the Regulation of Escherichia coli Genes by Bacterial Viruses , 2005, PLoS biology.

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

[27]  Joe C. Liang,et al.  Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.

[28]  F. Bushman,et al.  Turning λ Cro into a transcriptional activator , 1988, Cell.

[29]  Mikhail S. Gelfand,et al.  Engineering transcription factors with novel DNA-binding specificity using comparative genomics , 2009, Nucleic acids research.

[30]  J. Collado-Vides,et al.  The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. , 2000, Nucleic acids research.

[31]  Robert G. Martin,et al.  A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[32]  M. Laub,et al.  Specificity in two-component signal transduction pathways. , 2007, Annual review of genetics.

[33]  A. Ninfa,et al.  Use of two-component signal transduction systems in the construction of synthetic genetic networks. , 2010, Current opinion in microbiology.

[34]  J. Chin,et al.  Synthesis of orthogonal transcription-translation networks , 2009, Proceedings of the National Academy of Sciences.

[35]  Weston R. Whitaker,et al.  Toward scalable parts families for predictable design of biological circuits. , 2008, Current opinion in microbiology.

[36]  Chuan He,et al.  Engineering a uranyl-specific binding protein from NikR. , 2009, Angewandte Chemie.

[37]  E. Brown,et al.  Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor. , 1984, Cell.

[38]  Andrew D Ellington,et al.  A combined in vitro / in vivo selection for polymerases with novel promoter specificities , 2001, BMC biotechnology.

[39]  W. J. Brammar,et al.  Efficient repression by a heterodimeric repressor in Escherichia coli , 1992, Molecular microbiology.

[40]  G. Friedlander,et al.  Regulation of gene expression by small non-coding RNAs: a quantitative view , 2007, Molecular systems biology.

[41]  Adam P Arkin,et al.  Versatile RNA-sensing transcriptional regulators for engineering genetic networks , 2011, Proceedings of the National Academy of Sciences.

[42]  E. van Nimwegen,et al.  Accurate Prediction of Protein–protein Interactions from Sequence Alignments Using a Bayesian Method , 2022 .

[43]  Christopher A. Voigt,et al.  Synthetic biology: Engineering Escherichia coli to see light , 2005, Nature.

[44]  Plasticity in amino acid sensing of the chimeric receptor Taz , 2005, Molecular microbiology.

[45]  Javier Macía,et al.  Distributed biological computation with multicellular engineered networks , 2011, Nature.

[46]  Jay D. Keasling,et al.  Directed Evolution of AraC for Improved Compatibility of Arabinose- and Lactose-Inducible Promoters , 2007, Applied and Environmental Microbiology.

[47]  Independent Regulation of Two Genes in Escherichia coli by Tetracyclines and Tet Repressor Variants , 2004, Journal of bacteriology.

[48]  Hossein Fazelinia,et al.  AraC regulatory protein mutants with altered effector specificity. , 2008, Journal of the American Chemical Society.

[49]  Christopher A. Voigt,et al.  Genetic parts to program bacteria. , 2006, Current opinion in biotechnology.

[50]  T. Wood,et al.  Construction of a specialized‐ribosome vector or cloned‐gene expression in E. coli , 1991, Biotechnology and bioengineering.

[51]  M. Inouye,et al.  Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. , 1989, Science.

[52]  Luke E. Ulrich,et al.  One-component systems dominate signal transduction in prokaryotes. , 2005, Trends in microbiology.

[53]  N. Wingreen,et al.  A quantitative comparison of sRNA-based and protein-based gene regulation , 2008, Molecular systems biology.

[54]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[55]  M. Elowitz,et al.  Synthetic Biology: Integrated Gene Circuits , 2011, Science.

[56]  F. Arnold,et al.  Directed evolution: new parts and optimized function. , 2009, Current opinion in biotechnology.

[57]  Michael T. Laub,et al.  Rewiring the Specificity of Two-Component Signal Transduction Systems , 2008, Cell.

[58]  Travis S. Bayer,et al.  Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.

[59]  G. Church,et al.  Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. , 2011, Nature biotechnology.

[60]  Andrew D Ellington,et al.  Synthetic RNA circuits. , 2007, Nature chemical biology.

[61]  Christopher A. Voigt,et al.  Multichromatic control of gene expression in Escherichia coli. , 2011, Journal of molecular biology.

[62]  Christopher A. Voigt,et al.  Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.

[63]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[64]  Judith P. Armitage,et al.  Using Structural Information to Change the Phosphotransfer Specificity of a Two-Component Chemotaxis Signalling Complex , 2010, PLoS biology.