Programmable genetic circuits for pathway engineering

Hoynes-O’Connor, Allison; Moon, Tae Seok

doi:10.1016/j.copbio.2015.08.007

Title: Programmable genetic circuits for pathway engineering

Journal Article · Tue Dec 01 00:00:00 EST 2015 · Current Opinion in Biotechnology

DOI:https://doi.org/10.1016/j.copbio.2015.08.007· OSTI ID:1250360

Hoynes-O’Connor, Allison;

View Accepted Manuscript (Publisher)

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: CBET-1350498; MCB-1331194; SC0012705

OSTI ID:: 1250360

Journal Information:: Current Opinion in Biotechnology, Journal Name: Current Opinion in Biotechnology Vol. 36 Journal Issue: C; ISSN 0958-1669

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 26 works

Citation information provided by
Web of Science

References (59)

Multi‐input CRISPR / C as genetic circuits that interface host regulatory networks Nielsen, Alec AK; Voigt, Christopher A. Molecular Systems Biology, Vol. 10, Issue 11 https://doi.org/10.15252/msb.20145735	journal	November 2014
Designing RNA-Based Genetic Control Systems for Efficient Production from Engineered Metabolic Pathways Stevens, Jason T.; Carothers, James M. ACS Synthetic Biology, Vol. 4, Issue 2 https://doi.org/10.1021/sb400201u	journal	April 2014
Synthetic Biology and Metabolic Engineering Stephanopoulos, Gregory ACS Synthetic Biology, Vol. 1, Issue 11 https://doi.org/10.1021/sb300094q	journal	November 2012
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control Xu, P.; Li, L.; Zhang, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 31 https://doi.org/10.1073/pnas.1406401111	journal	July 2014
A versatile framework for microbial engineering using synthetic non-coding RNAs Qi, Lei S.; Arkin, Adam P. Nature Reviews Microbiology, Vol. 12, Issue 5 https://doi.org/10.1038/nrmicro3244	journal	April 2014
A ‘resource allocator’ for transcription based on a highly fragmented T7 RNA polymerase Segall‐Shapiro, Thomas H.; Meyer, Adam J.; Ellington, Andrew D. Molecular Systems Biology, Vol. 10, Issue 7 https://doi.org/10.15252/msb.20145299	journal	July 2014
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression Carothers, J. M.; Goler, J. A.; Juminaga, D. Science, Vol. 334, Issue 6063 https://doi.org/10.1126/science.1212209	journal	December 2011
A universal RNAi-based logic evaluator that operates in mammalian cells Rinaudo, Keller; Bleris, Leonidas; Maddamsetti, Rohan Nature Biotechnology, Vol. 25, Issue 7 https://doi.org/10.1038/nbt1307	journal	May 2007
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca Temme, K.; Zhao, D.; Voigt, C. A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 18 https://doi.org/10.1073/pnas.1120788109	journal	April 2012
Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits Sleight, Sean C.; Sauro, Herbert M. ACS Synthetic Biology, Vol. 2, Issue 9 https://doi.org/10.1021/sb400055h	journal	May 2013
Metabolic gene regulation in a dynamically changing environment Bennett, Matthew R.; Pang, Wyming Lee; Ostroff, Natalie A. Nature, Vol. 454, Issue 7208 https://doi.org/10.1038/nature07211	journal	July 2008
Engineering metabolism through dynamic control Venayak, Naveen; Anesiadis, Nikolaos; Cluett, William R. Current Opinion in Biotechnology, Vol. 34 https://doi.org/10.1016/j.copbio.2014.12.022	journal	August 2015
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
Improving lycopene production in Escherichia coli by engineering metabolic control Farmer, William R.; Liao, James C. Nature Biotechnology, Vol. 18, Issue 5 https://doi.org/10.1038/75398	journal	May 2000
Higher-Order Cellular Information Processing with Synthetic RNA Devices Win, M. N.; Smolke, C. D. Science, Vol. 322, Issue 5900 https://doi.org/10.1126/science.1160311	journal	October 2008
Emergent bistability by a growth-modulating positive feedback circuit Tan, Cheemeng; Marguet, Philippe; You, Lingchong Nature Chemical Biology, Vol. 5, Issue 11 https://doi.org/10.1038/nchembio.218	journal	October 2009
Functional optimization of gene clusters by combinatorial design and assembly Smanski, Michael J.; Bhatia, Swapnil; Zhao, Dehua Nature Biotechnology, Vol. 32, Issue 12, p. 1241-1249 https://doi.org/10.1038/nbt.3063	journal	November 2014
Genetic programs constructed from layered logic gates in single cells Moon, Tae Seok; Lou, Chunbo; Tamsir, Alvin Nature, Vol. 491, Issue 7423 https://doi.org/10.1038/nature11516	journal	October 2012
A dynamic metabolite valve for the control of central carbon metabolism Solomon, Kevin V.; Sanders, Tarielle M.; Prather, Kristala L. J. Metabolic Engineering, Vol. 14, Issue 6 https://doi.org/10.1016/j.ymben.2012.08.006	journal	November 2012
Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes Kaplan, Shai; Bren, Anat; Zaslaver, Alon Molecular Cell, Vol. 29, Issue 6 https://doi.org/10.1016/j.molcel.2008.01.021	journal	March 2008
De novo design of heat-repressible RNA thermosensors in E. coli Hoynes-O'Connor, Allison; Hinman, Kristina; Kirchner, Lukas Nucleic Acids Research, Vol. 43, Issue 12 https://doi.org/10.1093/nar/gkv499	journal	May 2015
Versatile RNA-sensing transcriptional regulators for engineering genetic networks Lucks, J. B.; Qi, L.; Mutalik, V. K. Proceedings of the National Academy of Sciences, Vol. 108, Issue 21, p. 8617-8622 https://doi.org/10.1073/pnas.1015741108	journal	May 2011
Evolution-guided optimization of biosynthetic pathways Raman, Srivatsan; Rogers, Jameson K.; Taylor, Noah D. Proceedings of the National Academy of Sciences, Vol. 111, Issue 50, p. 17803-17808 https://doi.org/10.1073/pnas.1409523111	journal	December 2014
Modular control of multiple pathways using engineered orthogonal T7 polymerases Temme, Karsten; Hill, Rena; Segall-Shapiro, Thomas H. Nucleic Acids Research, Vol. 40, Issue 17 https://doi.org/10.1093/nar/gks597	journal	June 2012
Engineering dynamic pathway regulation using stress-response promoters Dahl, Robert H.; Zhang, Fuzhong; Alonso-Gutierrez, Jorge Nature Biotechnology, Vol. 31, Issue 11 https://doi.org/10.1038/nbt.2689	journal	October 2013
Understanding and exploiting feedback in synthetic biology Afroz, Taliman; Beisel, Chase L. Chemical Engineering Science, Vol. 103 https://doi.org/10.1016/j.ces.2013.02.017	journal	November 2013
Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control Afroz, Taliman; Biliouris, Konstantinos; Boykin, Kelsey E. ACS Synthetic Biology, Vol. 4, Issue 2 https://doi.org/10.1021/sb400162z	journal	April 2014
Tuning Primary Metabolism for Heterologous Pathway Productivity Solomon, Kevin V.; Moon, Tae Seok; Ma, Brian ACS Synthetic Biology, Vol. 2, Issue 3 https://doi.org/10.1021/sb300055e	journal	August 2012
Principles of genetic circuit design Brophy, Jennifer A. N.; Voigt, Christopher A. Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2926	journal	April 2014
Quantifying cellular capacity identifies gene expression designs with reduced burden Ceroni, Francesca; Algar, Rhys; Stan, Guy-Bart Nature Methods, Vol. 12, Issue 5 https://doi.org/10.1038/nmeth.3339	journal	April 2015
Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways Lee, Yun; Lafontaine Rivera, Jimmy G.; Liao, James C. Metabolic Engineering, Vol. 25 https://doi.org/10.1016/j.ymben.2014.06.006	journal	September 2014
Negative Feedback Regulation of Fatty Acid Production Based on a Malonyl-CoA Sensor–Actuator Liu, Di; Xiao, Yi; Evans, Bradley S. ACS Synthetic Biology, Vol. 4, Issue 2 https://doi.org/10.1021/sb400158w	journal	January 2014
Engineering microbial biofuel tolerance and export using efflux pumps Dunlop, Mary J.; Dossani, Zain Y.; Szmidt, Heather L. Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.21	journal	January 2011
Mechanistic Modeling of Broth Temperature in Outdoor Photobioreactors Béchet, Quentin; Shilton, Andy; Fringer, Oliver B. Environmental Science & Technology, Vol. 44, Issue 6 https://doi.org/10.1021/es903214u	journal	March 2010
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators Callura, J. M.; Dwyer, D. J.; Isaacs, F. J. Proceedings of the National Academy of Sciences, Vol. 107, Issue 36 https://doi.org/10.1073/pnas.1009747107	journal	August 2010
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na, Dokyun; Yoo, Seung Min; Chung, Hannah Nature Biotechnology, Vol. 31, Issue 2 https://doi.org/10.1038/nbt.2461	journal	January 2013
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Shao, Zengyi; Zhao, Hua; Zhao, Huimin Nucleic Acids Research, Vol. 37, Issue 2 https://doi.org/10.1093/nar/gkn991	journal	December 2008
Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption Wang, Benjamin L.; Ghaderi, Adel; Zhou, Hang Nature Biotechnology, Vol. 32, Issue 5 https://doi.org/10.1038/nbt.2857	journal	April 2014
A synthetic oscillatory network of transcriptional regulators Elowitz, Michael B.; Leibler, Stanislas Nature, Vol. 403, Issue 6767 https://doi.org/10.1038/35002125	journal	January 2000
Amplifying Genetic Logic Gates Bonnet, J.; Yin, P.; Ortiz, M. E. Science, Vol. 340, Issue 6132 https://doi.org/10.1126/science.1232758	journal	March 2013
Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds Zalatan, Jesse G.; Lee, Michael E.; Almeida, Ricardo Cell, Vol. 160, Issue 1-2 https://doi.org/10.1016/j.cell.2014.11.052	journal	January 2015
Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression Nielsen, Alec AK; Segall-Shapiro, Thomas H.; Voigt, Christopher A. Current Opinion in Chemical Biology, Vol. 17, Issue 6 https://doi.org/10.1016/j.cbpa.2013.10.003	journal	December 2013
Biological robustness Kitano, Hiroaki Nature Reviews Genetics, Vol. 5, Issue 11 https://doi.org/10.1038/nrg1471	journal	November 2004
A brief history of synthetic biology Cameron, D. Ewen; Bashor, Caleb J.; Collins, James J. Nature Reviews Microbiology, Vol. 12, Issue 5 https://doi.org/10.1038/nrmicro3239	journal	April 2014
Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways Michener, Joshua K.; Thodey, Kate; Liang, Joe C. Metabolic Engineering, Vol. 14, Issue 3 https://doi.org/10.1016/j.ymben.2011.09.004	journal	May 2012
Construction of a genetic toggle switch in Escherichia coli Gardner, Timothy S.; Cantor, Charles R.; Collins, James J. Nature, Vol. 403, Issue 6767 https://doi.org/10.1038/35002131	journal	January 2000
Synthetic analog computation in living cells Daniel, Ramiz; Rubens, Jacob R.; Sarpeshkar, Rahul Nature, Vol. 497, Issue 7451 https://doi.org/10.1038/nature12148	journal	May 2013
Rationally designed families of orthogonal RNA regulators of translation Mutalik, Vivek K.; Qi, Lei; Guimaraes, Joao C. Nature Chemical Biology, Vol. 8, Issue 5, p. 447-454 https://doi.org/10.1038/nchembio.919	journal	March 2012
Engineering Static and Dynamic Control of Synthetic Pathways Holtz, William J.; Keasling, Jay D. Cell, Vol. 140, Issue 1 https://doi.org/10.1016/j.cell.2009.12.029	journal	January 2010
Synthetic circuits integrating logic and memory in living cells Siuti, Piro; Yazbek, John; Lu, Timothy K. Nature Biotechnology, Vol. 31, Issue 5 https://doi.org/10.1038/nbt.2510	journal	February 2013
Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Zhang, Fuzhong; Carothers, James M.; Keasling, Jay D. Nature Biotechnology, Vol. 30, Issue 4 https://doi.org/10.1038/nbt.2149	journal	March 2012
Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides Warner, Joseph R.; Reeder, Philippa J.; Karimpour-Fard, Anis Nature Biotechnology, Vol. 28, Issue 8, p. 856-862 https://doi.org/10.1038/nbt.1653	journal	July 2010
Engineering synergy in biotechnology Nielsen, Jens; Fussenegger, Martin; Keasling, Jay Nature Chemical Biology, Vol. 10, Issue 5 https://doi.org/10.1038/nchembio.1519	journal	April 2014
Stochastic switching as a survival strategy in fluctuating environments Acar, Murat; Mettetal, Jerome T.; van Oudenaarden, Alexander Nature Genetics, Vol. 40, Issue 4 https://doi.org/10.1038/ng.110	journal	March 2008
Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly Torella, Joseph P.; Boehm, Christian R.; Lienert, Florian Nucleic Acids Research, Vol. 42, Issue 1 https://doi.org/10.1093/nar/gkt860	journal	September 2013
Foundations for the design and implementation of synthetic genetic circuits Slusarczyk, Adrian L.; Lin, Allen; Weiss, Ron Nature Reviews Genetics, Vol. 13, Issue 6 https://doi.org/10.1038/nrg3227	journal	May 2012
Design and Connection of Robust Genetic Circuits Randall, Adrian; Guye, Patrick; Gupta, Saurabh Methods in Enzymology https://doi.org/10.1016/B978-0-12-385075-1.00007-X	book	January 2011
Microbial Biosensors: Engineered Microorganisms as the Sensing Machinery Park, Miso; Tsai, Shen-Long; Chen, Wilfred Sensors, Vol. 13, Issue 5 https://doi.org/10.3390/s130505777	journal	May 2013
Genetic switchboard for synthetic biology applications Callura, J. M.; Cantor, C. R.; Collins, J. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 15 https://doi.org/10.1073/pnas.1203808109	journal	March 2012

Similar Records

Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana

Journal Article · Thu Feb 04 00:00:00 EST 2016 · New Phytologist · OSTI ID:1250360

Smith, Sarah R.; Gle, Corine; Abbriano, Raffaela M.; +6 more

The renaissance of life near the boiling point – at last, genetics and metabolic engineering

Journal Article · Thu Dec 08 00:00:00 EST 2016 · Microbial Biotechnology (Online) · OSTI ID:1250360

Adams, Michael W. W.; Kelly, Robert M.

Engineered polyketides: Synergy between protein and host level engineering

Journal Article · Fri Sep 01 00:00:00 EDT 2017 · Synthetic and Systems Biotechnology · OSTI ID:1250360

Barajas, Jesus F.; Blake-Hedges, Jacquelyn M.; Bailey, Constance B.; +2 more

Title: Programmable genetic circuits for pathway engineering

Citation Formats

References (59)

Similar Records

Related Subjects