A general strategy to construct small molecule biosensors in eukaryotes

Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.; Mandell, Daniel J.; Antunes, Mauricio S.; Chari, Raj; Morey, Kevin J.; Rios, Xavier; Medford, June I.; Church, George M.; Fields, Stanley; Baker, David

doi:10.7554/eLife.10606

Title: A general strategy to construct small molecule biosensors in eukaryotes

Journal Article · Tue Dec 29 00:00:00 EST 2015 · eLife

DOI:https://doi.org/10.7554/eLife.10606· OSTI ID:1235744

Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.; Mandell, Daniel J.; Antunes, Mauricio S.; Chari, Raj; Morey, Kevin J.; Rios, Xavier; Medford, June I.; Church, George M.; Fields, Stanley; Baker, David

Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. As a result, this work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.

View Journal Article

Cite

Export

Save

Research Organization:: Harvard Univ., Cambridge, MA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: FG02- 02ER63445; FG02-02ER63445

OSTI ID:: 1235744

Alternate ID(s):: OSTI ID: 1235745; OSTI ID: 1258761

Journal Information:: eLife, Journal Name: eLife Vol. 4; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 112 works

Citation information provided by
Web of Science

References (60)

A comparative study examining the cytotoxicity of inducible gene expression system ligands in different cell types Xie, Jinger; Nair, Ayyappan; Hermiston, Terry W. Toxicology in Vitro, Vol. 22, Issue 1 https://doi.org/10.1016/j.tiv.2007.08.019	journal	February 2008
Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease Gratz, Scott J.; Cummings, Alexander M.; Nguyen, Jennifer N. Genetics, Vol. 194, Issue 4 https://doi.org/10.1534/genetics.113.152710	journal	May 2013
Broadly Applicable Methodology for the Rapid and Dosable Small Molecule-Mediated Regulation of Transcription Factors in Human Cells Shoulders, Matthew D.; Ryno, Lisa M.; Cooley, Christina B. Journal of the American Chemical Society, Vol. 135, Issue 22 https://doi.org/10.1021/ja402756p	journal	May 2013
Failure to launch Nature Biotechnology, Vol. 31, Issue 1, p. 1-1 https://doi.org/10.1038/nbt.2482	journal	January 2013
Fusion of GAL4-VP16 to a steroid-binding domain provides a tool for gratuitous induction of galactose-responsive genes in yeast Louvion, Jean-François; Havaux-Copf, Biserka; Picard, Didier Gene, Vol. 131, Issue 1 https://doi.org/10.1016/0378-1119(93)90681-R	journal	September 1993
One-step measurement of firefly luciferase activity in yeast Leskinen, P.; Virta, M.; Karp, M. Yeast, Vol. 20, Issue 13 https://doi.org/10.1002/yea.1024	journal	January 2003
The 50:50 method for PCR-based seamless genome editing in yeast: The 50:50 method for seamless genome editing Horecka, Joe; Davis, Ronald W. Yeast, Vol. 31, Issue 3 https://doi.org/10.1002/yea.2992	journal	December 2013
Total biosynthesis of hydrocortisone from a simple carbon source in yeast Szczebara, Florence Ménard; Chandelier, Cathy; Villeret, Coralie Nature Biotechnology, Vol. 21, Issue 2 https://doi.org/10.1038/nbt775	journal	January 2003
Self-sufficient biosynthesis of pregnenolone and progesterone in engineered yeast Duport, Catherine; Spagnoli, Roberto; Degryse, Eric Nature Biotechnology, Vol. 16, Issue 2 https://doi.org/10.1038/nbt0298-186	journal	February 1998
Programming adaptive control to evolve increased metabolite production Chou, Howard H.; Keasling, Jay D. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3595	journal	October 2013
Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis Dietrich, Jeffrey A.; Shis, David L.; Alikhani, Azadeh ACS Synthetic Biology, Vol. 2, Issue 1 https://doi.org/10.1021/sb300091d	journal	September 2012
A yeast sensor of ligand binding Tucker, Chandra L.; Fields, Stanley Nature Biotechnology, Vol. 19, Issue 11 https://doi.org/10.1038/nbt1101-1042	journal	November 2001
Ligand-switchable Substrates for a Ubiquitin-Proteasome System Egeler, Emily L.; Urner, Lorenz M.; Rakhit, Rishi Journal of Biological Chemistry, Vol. 286, Issue 36 https://doi.org/10.1074/jbc.M111.264101	journal	July 2011
Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity Ran, F. Ann; Hsu, Patrick D.; Lin, Chie-Yu Cell, Vol. 154, Issue 6, p. 1380-1389 https://doi.org/10.1016/j.cell.2013.08.021	journal	September 2013
Computational design of ligand-binding proteins with high affinity and selectivity Tinberg, Christine E.; Khare, Sagar D.; Dou, Jiayi Nature, Vol. 501, Issue 7466, p. 212-216 https://doi.org/10.1038/nature12443	journal	September 2013
Pharmaceutically controlled designer circuit for the treatment of the metabolic syndrome Ye, H.; Charpin-El Hamri, G.; Zwicky, K. Proceedings of the National Academy of Sciences, Vol. 110, Issue 1 https://doi.org/10.1073/pnas.1216801110	journal	December 2012
Ultrahigh-throughput screening in drop-based microfluidics for directed evolution Agresti, J. J.; Antipov, E.; Abate, A. R. Proceedings of the National Academy of Sciences, Vol. 107, Issue 9, p. 4004-4009 https://doi.org/10.1073/pnas.0910781107	journal	February 2010
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
Chemically Regulated Zinc Finger Transcription Factors Beerli, Roger R.; Schopfer, Ulrich; Dreier, Birgit Journal of Biological Chemistry, Vol. 275, Issue 42 https://doi.org/10.1074/jbc.M005108200	journal	August 2000
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases Cho, S. W.; Kim, S.; Kim, Y. Genome Research, Vol. 24, Issue 1 https://doi.org/10.1101/gr.162339.113	journal	November 2013
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0024109	journal	August 2011
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs Fu, Yanfang; Sander, Jeffry D.; Reyon, Deepak Nature Biotechnology, Vol. 32, Issue 3 https://doi.org/10.1038/nbt.2808	journal	January 2014
High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method Gietz, R. Daniel; Schiestl, Robert H. Nature Protocols, Vol. 2, Issue 1 https://doi.org/10.1038/nprot.2007.13	journal	January 2007
A Rapid, Reversible, and Tunable Method to Regulate Protein Function in Living Cells Using Synthetic Small Molecules Banaszynski, Laura A.; Chen, Ling-chun; Maynard-Smith, Lystranne A. Cell, Vol. 126, Issue 5 https://doi.org/10.1016/j.cell.2006.07.025	journal	September 2006
Fluorescence Imaging of Cellular Metabolites with RNA Paige, Jeremy S.; Nguyen-Duc, Thinh; Song, Wenjiao Science, Vol. 335, Issue 6073 https://doi.org/10.1126/science.1218298	journal	March 2012
Efficient Ablation of Genes in Human Hematopoietic Stem and Effector Cells using CRISPR/Cas9 Mandal, Pankaj K.; Ferreira, Leonardo M. R.; Collins, Ryan Cell Stem Cell, Vol. 15, Issue 5 https://doi.org/10.1016/j.stem.2014.10.004	journal	November 2014
Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression Sakuma, Y.; Maruyama, K.; Qin, F. Proceedings of the National Academy of Sciences, Vol. 103, Issue 49 https://doi.org/10.1073/pnas.0605639103	journal	October 2006
Design and Application of a Mevalonate-Responsive Regulatory Protein Tang, Shuang-Yan; Cirino, Patrick C. Angewandte Chemie International Edition, Vol. 50, Issue 5 https://doi.org/10.1002/anie.201006083	journal	December 2010
Destabilizing Domains Derived from the Human Estrogen Receptor Miyazaki, Yusuke; Imoto, Hiroshi; Chen, Ling-chun Journal of the American Chemical Society, Vol. 134, Issue 9, p. 3942-3945 https://doi.org/10.1021/ja209933r	journal	February 2012
Inducible in vivo genome editing with CRISPR-Cas9 Dow, Lukas E.; Fisher, Jonathan; O'Rourke, Kevin P. Nature Biotechnology, Vol. 33, Issue 4 https://doi.org/10.1038/nbt.3155	journal	February 2015
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation Polstein, Lauren R.; Gersbach, Charles A. Nature Chemical Biology, Vol. 11, Issue 3 https://doi.org/10.1038/nchembio.1753	journal	February 2015
Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis Yoo, Sang-Dong; Cho, Young-Hee; Sheen, Jen Nature Protocols, Vol. 2, Issue 7 https://doi.org/10.1038/nprot.2007.199	journal	June 2007
Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients Schwank, Gerald; Koo, Bon-Kyoung; Sasselli, Valentina Cell Stem Cell, Vol. 13, Issue 6 https://doi.org/10.1016/j.stem.2013.11.002	journal	December 2013
A split-Cas9 architecture for inducible genome editing and transcription modulation Zetsche, Bernd; Volz, Sara E.; Zhang, Feng Nature Biotechnology, Vol. 33, Issue 2 https://doi.org/10.1038/nbt.3149	journal	February 2015
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems DiCarlo, James E.; Norville, Julie E.; Mali, Prashant Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343 https://doi.org/10.1093/nar/gkt135	journal	March 2013
Synthetic RNA devices to expedite the evolution of metabolite-producing microbes Yang, Jina; Seo, Sang Woo; Jang, Sungho Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2404	journal	January 2013
Chemical control of protein stability and function in living mice Banaszynski, Laura A.; Sellmyer, Mark A.; Contag, Christopher H. Nature Medicine, Vol. 14, Issue 10 https://doi.org/10.1038/nm.1754	journal	September 2008
Yeast ATP‐Binding Cassette Transporters: Cellular Cleaning Pumps Ernst, Robert; Klemm, Robin; Schmitt, Lutz Methods in Enzymology https://doi.org/10.1016/S0076-6879(05)00026-1	book	January 2005
A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures Murashige, Toshio; Skoog, Folke Physiologia Plantarum, Vol. 15, Issue 3, p. 473-497 https://doi.org/10.1111/j.1399-3054.1962.tb08052.x	journal	July 1962
An improved yeast transformation method for the generation of very large human antibody libraries Benatuil, Lorenzo; Perez, Jennifer M.; Belk, Jonathan Protein Engineering, Design and Selection, Vol. 23, Issue 4 https://doi.org/10.1093/protein/gzq002	journal	February 2010
A biosensor for the detection of gas toxicity using a recombinant bioluminescent bacterium Cheol Gil, Geun; Mitchell, Robert J.; Tai Chang, Suk Biosensors and Bioelectronics, Vol. 15, Issue 1-2 https://doi.org/10.1016/S0956-5663(99)00074-3	journal	March 2000
A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly Lee, Michael E.; DeLoache, William C.; Cervantes, Bernardo ACS Synthetic Biology, Vol. 4, Issue 9 https://doi.org/10.1021/sb500366v	journal	April 2015
Correction of a Genetic Disease in Mouse via Use of CRISPR-Cas9 Wu, Yuxuan; Liang, Dan; Wang, Yinghua Cell Stem Cell, Vol. 13, Issue 6 https://doi.org/10.1016/j.stem.2013.10.016	journal	December 2013
Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets Alper, Hal; Miyaoku, Kohei; Stephanopoulos, Gregory Nature Biotechnology, Vol. 23, Issue 5 https://doi.org/10.1038/nbt1083	journal	April 2005
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana Clough, Steven J.; Bent, Andrew F. The Plant Journal, Vol. 16, Issue 6, p. 735-743 https://doi.org/10.1046/j.1365-313x.1998.00343.x	journal	December 1998
Evaluation of FKBP and DHFR based destabilizing domains in Saccharomyces cerevisiae Rakhit, Rishi; Edwards, Sarah R.; Iwamoto, Mari Bioorganic & Medicinal Chemistry Letters, Vol. 21, Issue 17 https://doi.org/10.1016/j.bmcl.2011.06.006	journal	September 2011
RNA-Guided Human Genome Engineering via Cas9 Mali, P.; Yang, L.; Esvelt, K. M. Science, Vol. 339, Issue 6121, p. 823-826 https://doi.org/10.1126/science.1232033	journal	January 2013
High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity Pattanayak, Vikram; Lin, Steven; Guilinger, John P. Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2673	journal	August 2013
Biosensors and their applications in microbial metabolic engineering Zhang, Fuzhong; Keasling, Jay Trends in Microbiology, Vol. 19, Issue 7 https://doi.org/10.1016/j.tim.2011.05.003	journal	July 2011
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Mali, Prashant; Aach, John; Stranges, P. Benjamin Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2675	journal	August 2013
A General Chemical Method to Regulate Protein Stability in the Mammalian Central Nervous System Iwamoto, Mari; Björklund, Tomas; Lundberg, Cecilia Chemistry & Biology, Vol. 17, Issue 9 https://doi.org/10.1016/j.chembiol.2010.07.009	journal	September 2010
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
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells Fu, Yanfang; Foden, Jennifer A.; Khayter, Cyd Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2623	journal	June 2013
High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection Dietrich, Jeffrey A.; McKee, Adrienne E.; Keasling, Jay D. Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev-biochem-062608-095938	journal	June 2010
A One Pot, One Step, Precision Cloning Method with High Throughput Capability Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre PLoS ONE, Vol. 3, Issue 11, Article No. e3647 https://doi.org/10.1371/journal.pone.0003647	journal	November 2008
Screening for Enhanced Triacetic Acid Lactone Production by Recombinant Escherichia coli Expressing a Designed Triacetic Acid Lactone Reporter Tang, Shuang-Yan; Qian, Shuai; Akinterinwa, Olubolaji Journal of the American Chemical Society, Vol. 135, Issue 27, p. 10099-10103 https://doi.org/10.1021/ja402654z	journal	June 2013
Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification Guilinger, John P.; Thompson, David B.; Liu, David R. Nature Biotechnology, Vol. 32, Issue 6 https://doi.org/10.1038/nbt.2909	journal	April 2014
Rapid and efficient site-specific mutagenesis without phenotypic selection. Kunkel, T. A. Proceedings of the National Academy of Sciences, Vol. 82, Issue 2, p. 488-492 https://doi.org/10.1073/pnas.82.2.488	journal	January 1985
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing Tsai, Shengdar Q.; Wyvekens, Nicolas; Khayter, Cyd Nature Biotechnology, Vol. 32, Issue 6 https://doi.org/10.1038/nbt.2908	journal	April 2014

Similar Records

Small molecule biosensors

Patent · Tue Jul 04 00:00:00 EDT 2023 · OSTI ID:1235744

Mandell, Daniel J.; Feng, Justin; Rios Villanueva, Xavier; +1 more

Evolution-guided engineering of small-molecule biosensors

Journal Article · Thu Nov 28 00:00:00 EST 2019 · Nucleic Acids Research · OSTI ID:1235744

Snoek, Tim; Chaberski, Evan K.; Ambri, Francesca; +7 more

Biosensors engineered from conditionally stable ligand-binding domains

Patent · Tue Sep 19 00:00:00 EDT 2017 · OSTI ID:1235744

Church, George M.; Feng, Justin; Mandell, Daniel J.; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: A general strategy to construct small molecule biosensors in eukaryotes

Citation Formats

References (60)

Similar Records

Related Subjects