Biosensor-based engineering of biosynthetic pathways

Rogers, Jameson K.; Taylor, Noah D.; Church, George M.

doi:10.1016/j.copbio.2016.03.005

Title: Biosensor-based engineering of biosynthetic pathways

Journal Article · Fri Mar 18 00:00:00 EDT 2016 · Current Opinion in Biotechnology

DOI:https://doi.org/10.1016/j.copbio.2016.03.005· OSTI ID:1242558

Rogers, Jameson K. ^[1]; Taylor, Noah D. ^[1]; Church, George M. ^[1]

Harvard Univ., Boston, MA (United States). Wyss Inst. For Biologically Inspired Engineering

Biosynthetic pathways provide an enzymatic route from inexpensive renewable resources to valuable metabolic products such as pharmaceuticals and plastics. However, designing these pathways is challenging due to the complexities of biology. Advances in the design and construction of genetic variants has enabled billions of cells, each possessing a slightly different metabolic design, to be rapidly generated. However, our ability to measure the quality of these designs lags by several orders of magnitude. Recent research has enabled cells to report their own success in chemical production through the use of genetically encoded biosensors. A new engineering discipline is emerging around the creation and application of biosensors. Biosensors, implemented in selections and screens to identify productive cells, are paving the way for a new era of biotechnological progress.

View Journal Article

Cite

Export

Save

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

Sponsoring Organization:: USDOE

Grant/Contract Number:: FG02-02ER63445

OSTI ID:: 1242558

Alternate ID(s):: OSTI ID: 1429374

Journal Information:: Current Opinion in Biotechnology, Journal Name: Current Opinion in Biotechnology Vol. 42 Journal Issue: C; ISSN 0958-1669

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 142 works

Citation information provided by
Web of Science

References (60)

Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae Jakočiūnas, Tadas; Bonde, Ida; Herrgård, Markus Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2015.01.008	journal	March 2015
A three-hybrid system for detecting small ligand-protein receptor interactions Licitra, E. J.; Liu, J. O. Proceedings of the National Academy of Sciences, Vol. 93, Issue 23 https://doi.org/10.1073/pnas.93.23.12817	journal	November 1996
Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways Schendzielorz, Georg; Dippong, Martin; Grünberger, Alexander ACS Synthetic Biology, Vol. 3, Issue 1 https://doi.org/10.1021/sb400059y	journal	July 2013
Toward a Generalized and High-throughput Enzyme Screening System Based on Artificial Genetic Circuits Choi, Su-Lim; Rha, Eugene; Lee, Sang Jun ACS Synthetic Biology, Vol. 3, Issue 3 https://doi.org/10.1021/sb400112u	journal	December 2013
An efficient platform for genetic selection and screening of gene switches in Escherichia coli Muranaka, Norihito; Sharma, Vandana; Nomura, Yoko Nucleic Acids Research, Vol. 37, Issue 5 https://doi.org/10.1093/nar/gkp039	journal	February 2009
Structure and Function of the Macrolide Biosensor Protein, MphR(A), with and without Erythromycin Zheng, Jianting; Sagar, Vatsala; Smolinsky, Adam Journal of Molecular Biology, Vol. 387, Issue 5 https://doi.org/10.1016/j.jmb.2009.02.058	journal	April 2009
The development and application of a single-cell biosensor for the detection of l-methionine and branched-chain amino acids Mustafi, Nurije; Grünberger, Alexander; Kohlheyer, Dietrich Metabolic Engineering, Vol. 14, Issue 4 https://doi.org/10.1016/j.ymben.2012.02.002	journal	July 2012
A Common Regulator for the Operons Encoding the Enzymes Involved in d -Galactarate, d -Glucarate, and d -Glycerate Utilization in Escherichia coli Monterrubio, Rafael; Baldoma, Laura; Obradors, Nuria Journal of Bacteriology, Vol. 182, Issue 9 https://doi.org/10.1128/JB.182.9.2672-2674.2000	journal	May 2000
Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation Binder, Stephan; Siedler, Solvej; Marienhagen, Jan Nucleic Acids Research, Vol. 41, Issue 12 https://doi.org/10.1093/nar/gkt312	journal	April 2013
Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process LeProust, Emily M.; Peck, Bill J.; Spirin, Konstantin Nucleic Acids Research, Vol. 38, Issue 8 https://doi.org/10.1093/nar/gkq163	journal	March 2010
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
Construction and Characterization of Escherichia coli Whole-Cell Biosensors for Toluene and Related Compounds Behzadian, F.; Barjeste, H.; Hosseinkhani, S. Current Microbiology, Vol. 62, Issue 2 https://doi.org/10.1007/s00284-010-9764-5	journal	September 2010
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
A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae Lee, Sang-Woo; Oh, Min-Kyu Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2015.01.004	journal	March 2015
Genetically encoded sensors enable real-time observation of metabolite production Rogers, Jameson K.; Church, George M. Proceedings of the National Academy of Sciences, Vol. 113, Issue 9 https://doi.org/10.1073/pnas.1600375113	journal	February 2016
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
Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology Wilson, Micheal C.; Piel, Jörn Chemistry & Biology, Vol. 20, Issue 5 https://doi.org/10.1016/j.chembiol.2013.04.011	journal	May 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
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
Engineering an Acinetobacter regulon for biosensing and high-throughput enzyme screening in E. coli via flow cytometry Jha, Ramesh K.; Kern, Theresa L.; Fox, David T. Nucleic Acids Research, Vol. 42, Issue 12 https://doi.org/10.1093/nar/gku444	journal	May 2014
Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor: A Comparative Approach for Protein Design Jha, Ramesh K.; Chakraborti, Subhendu; Kern, Theresa L. Proteins: Structure, Function, and Bioinformatics, Vol. 83, Issue 7 https://doi.org/10.1002/prot.24828	journal	May 2015
Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1 Craven, Sarah H.; Ezezika, Obidimma C.; Haddad, Sandra Molecular Microbiology, Vol. 72, Issue 4 https://doi.org/10.1111/j.1365-2958.2009.06686.x	journal	May 2009
Synthetic biosensors for precise gene control and real-time monitoring of metabolites Rogers, Jameson K.; Guzman, Christopher D.; Taylor, Noah D. Nucleic Acids Research, Vol. 43, Issue 15 https://doi.org/10.1093/nar/gkv616	journal	July 2015
Multiplexed Engineering in Biology Rogers, Jameson K.; Church, George M. Trends in Biotechnology, Vol. 34, Issue 3 https://doi.org/10.1016/j.tibtech.2015.12.004	journal	March 2016
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol Yim, Harry; Haselbeck, Robert; Niu, Wei Nature Chemical Biology, Vol. 7, Issue 7 https://doi.org/10.1038/nchembio.580	journal	May 2011
Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips Kosuri, Sriram; Eroshenko, Nikolai; LeProust, Emily M. Nature Biotechnology, Vol. 28, Issue 12, p. 1295-1299 https://doi.org/10.1038/nbt.1716	journal	November 2010
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
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Gibson, D. G.; Glass, J. I.; Lartigue, C. Science, Vol. 329, Issue 5987, p. 52-56 https://doi.org/10.1126/science.1190719	journal	May 2010
Fluorescent biosensors — Probing protein kinase function in cancer and drug discovery Morris, May C. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 7 https://doi.org/10.1016/j.bbapap.2013.01.025	journal	July 2013
Biosensor-guided screening for macrolides Möhrle, V.; Stadler, M.; Eberz, G. Analytical and Bioanalytical Chemistry, Vol. 388, Issue 5-6 https://doi.org/10.1007/s00216-007-1300-5	journal	May 2007
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
A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level Binder, Stephan; Schendzielorz, Georg; Stäbler, Norma Genome Biology, Vol. 13, Issue 5 https://doi.org/10.1186/gb-2012-13-5-r40	journal	January 2012
Antibiotic-Dependent Induction of Pseudomonas putida DOT-T1E TtgABC Efflux Pump Is Mediated by the Drug Binding Repressor TtgR Teran, W.; Felipe, A.; Segura, A. Antimicrobial Agents and Chemotherapy, Vol. 47, Issue 10 https://doi.org/10.1128/AAC.47.10.3067-3072.2003	journal	September 2003
SoxR as a Single-Cell Biosensor for NADPH-Consuming Enzymes in Escherichia coli Siedler, Solvej; Schendzielorz, Georg; Binder, Stephan ACS Synthetic Biology, Vol. 3, Issue 1 https://doi.org/10.1021/sb400110j	journal	December 2013
Advances in de novo strain design using integrated systems and synthetic biology tools Ng, Chiam Yu; Khodayari, Ali; Chowdhury, Anupam Current Opinion in Chemical Biology, Vol. 28 https://doi.org/10.1016/j.cbpa.2015.06.026	journal	October 2015
Molecular Biology of the LysR Family of Transcriptional Regulators Schell, M. A. Annual Review of Microbiology, Vol. 47, Issue 1 https://doi.org/10.1146/annurev.mi.47.100193.003121	journal	October 1993
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
Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR Collins, Cynthia H.; Leadbetter, Jared R.; Arnold, Frances H. Nature Biotechnology, Vol. 24, Issue 6 https://doi.org/10.1038/nbt1209	journal	May 2006
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
Genetically encoded FRET sensors to monitor intracellular Zn2+ homeostasis Vinkenborg, Jan L.; Nicolson, Tamara J.; Bellomo, Elisa A. Nature Methods, Vol. 6, Issue 10 https://doi.org/10.1038/nmeth.1368	journal	August 2009
Mechanism-Guided Library Design and Dual Genetic Selection of Synthetic OFF Riboswitches Muranaka, Norihito; Abe, Koichi; Yokobayashi, Yohei ChemBioChem, Vol. 10, Issue 14 https://doi.org/10.1002/cbic.200900313	journal	September 2009
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H. Science, Vol. 333, Issue 6040, p. 348-353 https://doi.org/10.1126/science.1205822	journal	July 2011
Using a Riboswitch Sensor to Examine Coenzyme B12 Metabolism and Transport in E. coli Fowler, Casey C.; Brown, Eric D.; Li, Yingfu Chemistry & Biology, Vol. 17, Issue 7 https://doi.org/10.1016/j.chembiol.2010.05.025	journal	July 2010
Selection of biocatalysts for chemical synthesis van Sint Fiet, S.; van Beilen, J. B.; Witholt, B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 6 https://doi.org/10.1073/pnas.0504733102	journal	January 2006
Imaging Mitochondrial Flux in Single Cells with a FRET Sensor for Pyruvate San Martín, Alejandro; Ceballo, Sebastián; Baeza-Lehnert, Felipe PLoS ONE, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pone.0085780	journal	January 2014
A flow cytometry-based screen for synthetic riboswitches Lynch, Sean A.; Gallivan, Justin P. Nucleic Acids Research, Vol. 37, Issue 1, p. 184-192 https://doi.org/10.1093/nar/gkn924	journal	November 2008
A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics Peroza, Estevão A.; Ewald, Jennifer C.; Parakkal, Geetha Analytical Biochemistry, Vol. 474 https://doi.org/10.1016/j.ab.2014.12.019	journal	April 2015
A Decade of Riboswitches Serganov, Alexander; Nudler, Evgeny Cell, Vol. 152, Issue 1-2 https://doi.org/10.1016/j.cell.2012.12.024	journal	January 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
Role of the Alternative Sigma Factor ς ^S in Expression of the AlkS Regulator of the Pseudomonas oleovorans Alkane Degradation Pathway Canosa, Inés; Yuste, Luis; Rojo, Fernando Journal of Bacteriology, Vol. 181, Issue 6 https://doi.org/10.1128/JB.181.6.1748-1754.1999	journal	March 1999
Genome-scale promoter engineering by coselection MAGE Wang, Harris H.; Kim, Hwangbeom; Cong, Le Nature Methods, Vol. 9, Issue 6, p. 591-593 https://doi.org/10.1038/nmeth.1971	journal	April 2012
A general strategy to construct small molecule biosensors in eukaryotes Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E. eLife, Vol. 4 https://doi.org/10.7554/eLife.10606	journal	December 2015
Riboswitch engineering — making the all-important second and third steps Berens, Christian; Suess, Beatrix Current Opinion in Biotechnology, Vol. 31 https://doi.org/10.1016/j.copbio.2014.07.014	journal	February 2015
GPCR-Based Chemical Biosensors for Medium-Chain Fatty Acids Mukherjee, Kuntal; Bhattacharyya, Souryadeep; Peralta-Yahya, Pamela ACS Synthetic Biology, Vol. 4, Issue 12 https://doi.org/10.1021/sb500365m	journal	May 2015
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
RNA-guided editing of bacterial genomes using CRISPR-Cas systems Jiang, Wenyan; Bikard, David; Cox, David Nature Biotechnology, Vol. 31, Issue 3, p. 233-239 https://doi.org/10.1038/nbt.2508	journal	January 2013
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
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Lutz, R. Nucleic Acids Research, Vol. 25, Issue 6, p. 1203-1210 https://doi.org/10.1093/nar/25.6.1203	journal	March 1997
Next-generation genome-scale models for metabolic engineering King, Zachary A.; Lloyd, Colton J.; Feist, Adam M. Current Opinion in Biotechnology, Vol. 35 https://doi.org/10.1016/j.copbio.2014.12.016	journal	December 2015
High-Throughput Bioanalytical LC/MS/MS Determination of Benzodiazepines in Human Urine: 1000 Samples per 12 Hours Zweigenbaum, Jerry; Heinig, Katja; Steinborner, Simon Analytical Chemistry, Vol. 71, Issue 13 https://doi.org/10.1021/ac9813540	journal	July 1999

Similar Records

In vivo biosensors: mechanisms, development, and applications

Journal Article · Sun Jul 01 00:00:00 EDT 2018 · Journal of Industrial Microbiology and Biotechnology · OSTI ID:1242558

Shi, Shuobo; Ang, Ee Lui; Zhao, Huimin

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Journal Article · Mon Mar 01 00:00:00 EST 2021 · Metabolic Engineering · OSTI ID:1242558

Ni, Zhuofu; Stine, Andrew E.; Tyo, Keith E. J.; +1 more

In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design

Journal Article · Mon Jun 15 00:00:00 EDT 2020 · Nature Chemical Biology · OSTI ID:1242558

Karim, Ashty S.; Dudley, Quentin M.; Juminaga, Alex; +17 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
36 MATERIALS SCIENCE

Title: Biosensor-based engineering of biosynthetic pathways

Citation Formats

References (60)

Similar Records

Related Subjects