Programmable genetic circuits for pathway engineering.

Synthetic biology has the potential to provide decisive advances in genetic control of metabolic pathways. However, there are several challenges that synthetic biologists must overcome before this vision becomes a reality. First, a library of diverse and well-characterized sensors, such as metabolite-sensing or condition-sensing promoters, must be constructed. Second, robust programmable circuits that link input conditions with a specific gene regulation response must be developed. Finally, multi-gene targeting strategies must be integrated with metabolically relevant sensors and complex, robust logic. Achievements in each of these areas, which employ the CRISPR/Cas system, in silico modeling, and dynamic sensor-regulators, among other tools, provide a strong basis for future research. Overall, the future for synthetic biology approaches in metabolic engineering holds immense promise.

[1]  Jameson K. Rogers,et al.  Evolution-guided optimization of biosynthetic pathways , 2014, Proceedings of the National Academy of Sciences.

[2]  Timothy K Lu,et al.  Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.

[3]  Jason T Stevens,et al.  Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways. , 2015, ACS synthetic biology.

[4]  Chase L. Beisel,et al.  Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control , 2014, ACS synthetic biology.

[5]  Wilfred Chen,et al.  Microbial Biosensors: Engineered Microorganisms as the Sensing Machinery , 2013, Sensors.

[6]  Chase L. Beisel,et al.  Understanding and exploiting feedback in synthetic biology , 2013 .

[7]  Adam P Arkin,et al.  Supplementary information for Rationally designed families of orthogonal RNA regulators of translation , 2012 .

[8]  Kevin V Solomon,et al.  Tuning primary metabolism for heterologous pathway productivity. , 2013, ACS synthetic biology.

[9]  Rahul Sarpeshkar,et al.  Synthetic analog computation in living cells , 2013, Nature.

[10]  Adam J. Meyer,et al.  A ‘resource allocator’ for transcription based on a highly fragmented T7 RNA polymerase , 2014, Molecular systems biology.

[11]  Zengyi Shao,et al.  DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways , 2008, Nucleic acids research.

[12]  J. Keasling,et al.  Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids , 2012, Nature Biotechnology.

[13]  Martin Fussenegger,et al.  Engineering synergy in biotechnology. , 2014, Nature chemical biology.

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

[15]  J. Collins,et al.  A brief history of synthetic biology , 2014, Nature Reviews Microbiology.

[16]  Adam P. Arkin,et al.  A versatile framework for microbial engineering using synthetic non-coding RNAs , 2014, Nature Reviews Microbiology.

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

[18]  Tae Seok Moon,et al.  De novo design of heat-repressible RNA thermosensors in E. coli , 2015, Nucleic acids research.

[19]  Christopher A. Voigt,et al.  Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks , 2014, Molecular systems biology.

[20]  Jerome T. Mettetal,et al.  Stochastic switching as a survival strategy in fluctuating environments , 2008, Nature Genetics.

[21]  G. Stephanopoulos,et al.  Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption , 2014, Nature Biotechnology.

[22]  Swapnil Bhatia,et al.  Functional optimization of gene clusters by combinatorial design and assembly , 2014, Nature Biotechnology.

[23]  R. Weiss,et al.  Foundations for the design and implementation of synthetic genetic circuits , 2012, Nature Reviews Genetics.

[24]  U. Alon,et al.  Diverse two-dimensional input functions control bacterial sugar genes. , 2008, Molecular cell.

[25]  Kate Thodey,et al.  Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. , 2012, Metabolic engineering.

[26]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

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

[28]  Herbert M Sauro,et al.  Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. , 2013, ACS synthetic biology.

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

[30]  J. Park,et al.  Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs , 2013, Nature Biotechnology.

[31]  J. Keasling,et al.  Engineering microbial biofuel tolerance and export using efflux pumps , 2011, Molecular systems biology.

[32]  Luke A. Gilbert,et al.  Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds , 2015, Cell.

[33]  G. Stephanopoulos,et al.  Improving fatty acids production by engineering dynamic pathway regulation and metabolic control , 2014, Proceedings of the National Academy of Sciences.

[34]  Christopher A. Voigt,et al.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca , 2012, Proceedings of the National Academy of Sciences.

[35]  Farren J. Isaacs,et al.  Tracking, tuning, and terminating microbial physiology using synthetic riboregulators , 2010, Proceedings of the National Academy of Sciences.

[36]  Christopher A. Voigt,et al.  Principles of genetic circuit design , 2014, Nature Methods.

[37]  Ryan T Gill,et al.  Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.

[38]  Drew Endy,et al.  Amplifying Genetic Logic Gates , 2013, Science.

[39]  Fuzhong Zhang,et al.  Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator. , 2015, ACS synthetic biology.

[40]  Thomas H. Segall-Shapiro,et al.  Modular control of multiple pathways using engineered orthogonal T7 polymerases , 2012, Nucleic acids research.

[41]  Hiroaki Kitano,et al.  Biological robustness , 2008, Nature Reviews Genetics.

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

[43]  G. Stan,et al.  Quantifying cellular capacity identifies gene expression designs with reduced burden , 2015, Nature Methods.

[44]  M. Bennett,et al.  Metabolic gene regulation in a dynamically changing environment , 2008, Nature.

[45]  Christopher A. Voigt,et al.  Genetic programs constructed from layered logic gates in single cells , 2012, Nature.

[46]  L. You,et al.  Emergent bistability by a growth-modulating positive feedback circuit. , 2009, Nature chemical biology.

[47]  Jay D Keasling,et al.  Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression , 2011, Science.

[48]  Pamela A. Silver,et al.  Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly , 2013, Nucleic acids research.

[49]  Ron Weiss,et al.  Design and connection of robust genetic circuits. , 2011, Methods in enzymology.

[50]  James J. Collins,et al.  Genetic switchboard for synthetic biology applications , 2012, Proceedings of the National Academy of Sciences.

[51]  Christopher A. Voigt,et al.  Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. , 2013, Current opinion in chemical biology.

[52]  J. Keasling,et al.  Engineering dynamic pathway regulation using stress-response promoters , 2013, Nature Biotechnology.

[53]  James C Liao,et al.  Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways. , 2014, Metabolic engineering.

[54]  Kevin V. Solomon,et al.  A dynamic metabolite valve for the control of central carbon metabolism. , 2012, Metabolic engineering.

[55]  Benoit Guieysse,et al.  Mechanistic modeling of broth temperature in outdoor photobioreactors. , 2010, Environmental science & technology.

[56]  Gregory Stephanopoulos,et al.  Synthetic biology and metabolic engineering. , 2012, ACS synthetic biology.

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

[58]  Jay D. Keasling,et al.  Engineering Static and Dynamic Control of Synthetic Pathways , 2010, Cell.

[59]  Nikolaos Anesiadis,et al.  Engineering metabolism through dynamic control. , 2015, Current opinion in biotechnology.