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Title: Biosensor-based engineering of biosynthetic pathways

Abstract

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.

Authors:
 [1];  [1];  [1]
  1. Harvard Univ., Boston, MA (United States). Wyss Inst. For Biologically Inspired Engineering
Publication Date:
Research Org.:
Harvard Univ., Cambridge, MA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1242558
Alternate Identifier(s):
OSTI ID: 1429374
Grant/Contract Number:  
FG02-02ER63445
Resource Type:
Published Article
Journal Name:
Current Opinion in Biotechnology
Additional Journal Information:
Journal Name: Current Opinion in Biotechnology Journal Volume: 42 Journal Issue: C; Journal ID: ISSN 0958-1669
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 36 MATERIALS SCIENCE

Citation Formats

Rogers, Jameson K., Taylor, Noah D., and Church, George M. Biosensor-based engineering of biosynthetic pathways. United Kingdom: N. p., 2016. Web. doi:10.1016/j.copbio.2016.03.005.
Rogers, Jameson K., Taylor, Noah D., & Church, George M. Biosensor-based engineering of biosynthetic pathways. United Kingdom. https://doi.org/10.1016/j.copbio.2016.03.005
Rogers, Jameson K., Taylor, Noah D., and Church, George M. Fri . "Biosensor-based engineering of biosynthetic pathways". United Kingdom. https://doi.org/10.1016/j.copbio.2016.03.005.
@article{osti_1242558,
title = {Biosensor-based engineering of biosynthetic pathways},
author = {Rogers, Jameson K. and Taylor, Noah D. and Church, George M.},
abstractNote = {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.},
doi = {10.1016/j.copbio.2016.03.005},
journal = {Current Opinion in Biotechnology},
number = C,
volume = 42,
place = {United Kingdom},
year = {Fri Mar 18 00:00:00 EDT 2016},
month = {Fri Mar 18 00:00:00 EDT 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.copbio.2016.03.005

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Cited by: 142 works
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Works referenced in this record:

Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae
journal, March 2015


A three-hybrid system for detecting small ligand-protein receptor interactions
journal, November 1996

  • Licitra, E. J.; Liu, J. O.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 23
  • DOI: 10.1073/pnas.93.23.12817

Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways
journal, July 2013

  • Schendzielorz, Georg; Dippong, Martin; Grünberger, Alexander
  • ACS Synthetic Biology, Vol. 3, Issue 1
  • DOI: 10.1021/sb400059y

Toward a Generalized and High-throughput Enzyme Screening System Based on Artificial Genetic Circuits
journal, December 2013

  • Choi, Su-Lim; Rha, Eugene; Lee, Sang Jun
  • ACS Synthetic Biology, Vol. 3, Issue 3
  • DOI: 10.1021/sb400112u

An efficient platform for genetic selection and screening of gene switches in Escherichia coli
journal, February 2009

  • Muranaka, Norihito; Sharma, Vandana; Nomura, Yoko
  • Nucleic Acids Research, Vol. 37, Issue 5
  • DOI: 10.1093/nar/gkp039

Structure and Function of the Macrolide Biosensor Protein, MphR(A), with and without Erythromycin
journal, April 2009

  • Zheng, Jianting; Sagar, Vatsala; Smolinsky, Adam
  • Journal of Molecular Biology, Vol. 387, Issue 5
  • DOI: 10.1016/j.jmb.2009.02.058

The development and application of a single-cell biosensor for the detection of l-methionine and branched-chain amino acids
journal, July 2012

  • Mustafi, Nurije; Grünberger, Alexander; Kohlheyer, Dietrich
  • Metabolic Engineering, Vol. 14, Issue 4
  • DOI: 10.1016/j.ymben.2012.02.002

A Common Regulator for the Operons Encoding the Enzymes Involved in d -Galactarate, d -Glucarate, and d -Glycerate Utilization in Escherichia coli
journal, May 2000


Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation
journal, April 2013

  • Binder, Stephan; Siedler, Solvej; Marienhagen, Jan
  • Nucleic Acids Research, Vol. 41, Issue 12
  • DOI: 10.1093/nar/gkt312

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process
journal, March 2010

  • LeProust, Emily M.; Peck, Bill J.; Spirin, Konstantin
  • Nucleic Acids Research, Vol. 38, Issue 8
  • DOI: 10.1093/nar/gkq163

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

  • Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A.
  • Nature, Vol. 460, Issue 7257, p. 894-898
  • DOI: 10.1038/nature08187

Construction and Characterization of Escherichia coli Whole-Cell Biosensors for Toluene and Related Compounds
journal, September 2010


Programming adaptive control to evolve increased metabolite production
journal, October 2013

  • Chou, Howard H.; Keasling, Jay D.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3595

Genetically encoded sensors enable real-time observation of metabolite production
journal, February 2016

  • Rogers, Jameson K.; Church, George M.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 9
  • DOI: 10.1073/pnas.1600375113

Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis
journal, September 2012

  • Dietrich, Jeffrey A.; Shis, David L.; Alikhani, Azadeh
  • ACS Synthetic Biology, Vol. 2, Issue 1
  • DOI: 10.1021/sb300091d

Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology
journal, May 2013


Computational design of ligand-binding proteins with high affinity and selectivity
journal, September 2013

  • Tinberg, Christine E.; Khare, Sagar D.; Dou, Jiayi
  • Nature, Vol. 501, Issue 7466, p. 212-216
  • DOI: 10.1038/nature12443

Evolution-guided optimization of biosynthetic pathways
journal, December 2014

  • Raman, Srivatsan; Rogers, Jameson K.; Taylor, Noah D.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 50, p. 17803-17808
  • DOI: 10.1073/pnas.1409523111

Engineering an Acinetobacter regulon for biosensing and high-throughput enzyme screening in E. coli via flow cytometry
journal, May 2014

  • Jha, Ramesh K.; Kern, Theresa L.; Fox, David T.
  • Nucleic Acids Research, Vol. 42, Issue 12
  • DOI: 10.1093/nar/gku444

Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor: A Comparative Approach for Protein Design
journal, May 2015

  • Jha, Ramesh K.; Chakraborti, Subhendu; Kern, Theresa L.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 83, Issue 7
  • DOI: 10.1002/prot.24828

Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1
journal, May 2009


Synthetic biosensors for precise gene control and real-time monitoring of metabolites
journal, July 2015

  • Rogers, Jameson K.; Guzman, Christopher D.; Taylor, Noah D.
  • Nucleic Acids Research, Vol. 43, Issue 15
  • DOI: 10.1093/nar/gkv616

Multiplexed Engineering in Biology
journal, March 2016


Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
journal, May 2011

  • Yim, Harry; Haselbeck, Robert; Niu, Wei
  • Nature Chemical Biology, Vol. 7, Issue 7
  • DOI: 10.1038/nchembio.580

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
journal, November 2010

  • Kosuri, Sriram; Eroshenko, Nikolai; LeProust, Emily M.
  • Nature Biotechnology, Vol. 28, Issue 12, p. 1295-1299
  • DOI: 10.1038/nbt.1716

Negative Feedback Regulation of Fatty Acid Production Based on a Malonyl-CoA Sensor–Actuator
journal, January 2014

  • Liu, Di; Xiao, Yi; Evans, Bradley S.
  • ACS Synthetic Biology, Vol. 4, Issue 2
  • DOI: 10.1021/sb400158w

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
journal, May 2010


Fluorescent biosensors — Probing protein kinase function in cancer and drug discovery
journal, July 2013


Biosensor-guided screening for macrolides
journal, May 2007

  • Möhrle, V.; Stadler, M.; Eberz, G.
  • Analytical and Bioanalytical Chemistry, Vol. 388, Issue 5-6
  • DOI: 10.1007/s00216-007-1300-5

Design and Application of a Mevalonate-Responsive Regulatory Protein
journal, December 2010

  • Tang, Shuang-Yan; Cirino, Patrick C.
  • Angewandte Chemie International Edition, Vol. 50, Issue 5
  • DOI: 10.1002/anie.201006083

A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level
journal, January 2012


Antibiotic-Dependent Induction of Pseudomonas putida DOT-T1E TtgABC Efflux Pump Is Mediated by the Drug Binding Repressor TtgR
journal, September 2003


SoxR as a Single-Cell Biosensor for NADPH-Consuming Enzymes in Escherichia coli
journal, December 2013

  • Siedler, Solvej; Schendzielorz, Georg; Binder, Stephan
  • ACS Synthetic Biology, Vol. 3, Issue 1
  • DOI: 10.1021/sb400110j

Advances in de novo strain design using integrated systems and synthetic biology tools
journal, October 2015


Molecular Biology of the LysR Family of Transcriptional Regulators
journal, October 1993


Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
journal, March 2013

  • DiCarlo, James E.; Norville, Julie E.; Mali, Prashant
  • Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343
  • DOI: 10.1093/nar/gkt135

Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR
journal, May 2006

  • Collins, Cynthia H.; Leadbetter, Jared R.; Arnold, Frances H.
  • Nature Biotechnology, Vol. 24, Issue 6
  • DOI: 10.1038/nbt1209

Synthetic RNA devices to expedite the evolution of metabolite-producing microbes
journal, January 2013

  • Yang, Jina; Seo, Sang Woo; Jang, Sungho
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms2404

Genetically encoded FRET sensors to monitor intracellular Zn2+ homeostasis
journal, August 2009

  • Vinkenborg, Jan L.; Nicolson, Tamara J.; Bellomo, Elisa A.
  • Nature Methods, Vol. 6, Issue 10
  • DOI: 10.1038/nmeth.1368

Mechanism-Guided Library Design and Dual Genetic Selection of Synthetic OFF Riboswitches
journal, September 2009

  • Muranaka, Norihito; Abe, Koichi; Yokobayashi, Yohei
  • ChemBioChem, Vol. 10, Issue 14
  • DOI: 10.1002/cbic.200900313

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
journal, July 2011

  • Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H.
  • Science, Vol. 333, Issue 6040, p. 348-353
  • DOI: 10.1126/science.1205822

Using a Riboswitch Sensor to Examine Coenzyme B12 Metabolism and Transport in E. coli
journal, July 2010


Selection of biocatalysts for chemical synthesis
journal, January 2006

  • van Sint Fiet, S.; van Beilen, J. B.; Witholt, B.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 6
  • DOI: 10.1073/pnas.0504733102

Imaging Mitochondrial Flux in Single Cells with a FRET Sensor for Pyruvate
journal, January 2014


A flow cytometry-based screen for synthetic riboswitches
journal, November 2008

  • Lynch, Sean A.; Gallivan, Justin P.
  • Nucleic Acids Research, Vol. 37, Issue 1, p. 184-192
  • DOI: 10.1093/nar/gkn924

A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics
journal, April 2015

  • Peroza, Estevão A.; Ewald, Jennifer C.; Parakkal, Geetha
  • Analytical Biochemistry, Vol. 474
  • DOI: 10.1016/j.ab.2014.12.019

A Decade of Riboswitches
journal, January 2013


Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
journal, March 2012

  • Zhang, Fuzhong; Carothers, James M.; Keasling, Jay D.
  • Nature Biotechnology, Vol. 30, Issue 4
  • DOI: 10.1038/nbt.2149

Role of the Alternative Sigma Factor ς S in Expression of the AlkS Regulator of the Pseudomonas oleovorans Alkane Degradation Pathway
journal, March 1999


Genome-scale promoter engineering by coselection MAGE
journal, April 2012

  • Wang, Harris H.; Kim, Hwangbeom; Cong, Le
  • Nature Methods, Vol. 9, Issue 6, p. 591-593
  • DOI: 10.1038/nmeth.1971

A general strategy to construct small molecule biosensors in eukaryotes
journal, December 2015

  • Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.
  • eLife, Vol. 4
  • DOI: 10.7554/eLife.10606

Riboswitch engineering — making the all-important second and third steps
journal, February 2015


GPCR-Based Chemical Biosensors for Medium-Chain Fatty Acids
journal, May 2015

  • Mukherjee, Kuntal; Bhattacharyya, Souryadeep; Peralta-Yahya, Pamela
  • ACS Synthetic Biology, Vol. 4, Issue 12
  • DOI: 10.1021/sb500365m

High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection
journal, June 2010


RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013

  • Jiang, Wenyan; Bikard, David; Cox, David
  • Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
  • DOI: 10.1038/nbt.2508

Screening for Enhanced Triacetic Acid Lactone Production by Recombinant Escherichia coli Expressing a Designed Triacetic Acid Lactone Reporter
journal, June 2013

  • Tang, Shuang-Yan; Qian, Shuai; Akinterinwa, Olubolaji
  • Journal of the American Chemical Society, Vol. 135, Issue 27, p. 10099-10103
  • DOI: 10.1021/ja402654z

Next-generation genome-scale models for metabolic engineering
journal, December 2015


High-Throughput Bioanalytical LC/MS/MS Determination of Benzodiazepines in Human Urine:  1000 Samples per 12 Hours
journal, July 1999

  • Zweigenbaum, Jerry; Heinig, Katja; Steinborner, Simon
  • Analytical Chemistry, Vol. 71, Issue 13
  • DOI: 10.1021/ac9813540