Optogenetic Control of Microbial Consortia Populations for Chemical Production

Lalwani, Makoto A.; Kawabe, Hinako; Mays, Rebecca L.; Hoffman, Shannon M.; Avalos, José L.

doi:10.1021/acssynbio.1c00182

Optogenetic Control of Microbial Consortia Populations for Chemical Production

Journal Article · 05 August 2021 · ACS Synthetic Biology

DOI:https://doi.org/10.1021/acssynbio.1c00182· OSTI ID:1853119

^[1]; Kawabe, Hinako ^[1]; Mays, Rebecca L. ^[1]; Hoffman, Shannon M. ^[1]; ^[2]

Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States; The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States; Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States

Not provided.

Research Organization:: Princeton Univ., NJ (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0019363

OSTI ID:: 1853119

Journal Information:: ACS Synthetic Biology, Vol. 10, Issue 8; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

References (75)

Toward a science of metabolic engineering Bailey, J. E. Science, Vol. 252, Issue 5013, p. 1668-1675 https://doi.org/10.1126/science.2047876	journal	June 1991
Current and future modalities of dynamic control in metabolic engineering Lalwani, Makoto A.; Zhao, Evan M.; Avalos, José L. Current Opinion in Biotechnology, Vol. 52 https://doi.org/10.1016/j.copbio.2018.02.007	journal	August 2018
Harnessing yeast organelles for metabolic engineering Hammer, Sarah K.; Avalos, José L. Nature Chemical Biology, Vol. 13, Issue 8 https://doi.org/10.1038/nchembio.2429	journal	July 2017
Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering Portnoy, Vasiliy A.; Bezdan, Daniela; Zengler, Karsten Current Opinion in Biotechnology, Vol. 22, Issue 4 https://doi.org/10.1016/j.copbio.2011.03.007	journal	August 2011
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications Wu, Gang; Yan, Qiang; Jones, J. Andrew Trends in Biotechnology, Vol. 34, Issue 8 https://doi.org/10.1016/j.tibtech.2016.02.010	journal	August 2016
Alleviation of feedback inhibition in Saccharomyces cerevisiae aromatic amino acid biosynthesis: Quantification of metabolic impact Luttik, M. A. H.; Vuralhan, Z.; Suir, E. Metabolic Engineering, Vol. 10, Issue 3-4 https://doi.org/10.1016/j.ymben.2008.02.002	journal	May 2008
Recombinant production of a hard‐to‐express membrane‐bound cytochrome P450 in different yeasts—Comparison of physiology and productivity Hausjell, Johanna; Schendl, Dominik; Weissensteiner, Julia Yeast, Vol. 37, Issue 2 https://doi.org/10.1002/yea.3441	journal	December 2019
Efficient production of 2,3-butanediol in Saccharomyces cerevisiae by eliminating ethanol and glycerol production and redox rebalancing Kim, Sujin; Hahn, Ji-Sook Metabolic Engineering, Vol. 31 https://doi.org/10.1016/j.ymben.2015.07.006	journal	September 2015
An Engineered Aro1 Protein Degradation Approach for Increased cis,cis -Muconic Acid Biosynthesis in Saccharomyces cerevisiae Pyne, Michael E.; Narcross, Lauren; Melgar, Mindy Applied and Environmental Microbiology, Vol. 84, Issue 17 https://doi.org/10.1128/AEM.01095-18	journal	September 2018
Production of active eukaryotic proteins through bacterial expression systems: a review of the existing biotechnology strategies Sahdev, Sudhir; Khattar, Sunil K.; Saini, Kulvinder Singh Molecular and Cellular Biochemistry, Vol. 307, Issue 1-2 https://doi.org/10.1007/s11010-007-9603-6	journal	September 2007
Advances in the development and application of microbial consortia for metabolic engineering Jawed, Kamran; Yazdani, Syed Shams; Koffas, Mattheos AG. Metabolic Engineering Communications, Vol. 9 https://doi.org/10.1016/j.mec.2019.e00095	journal	December 2019
Relevance of microbial coculture fermentations in biotechnology: Coculture fermentations in biotechnology Bader, J.; Mast-Gerlach, E.; Popović, M. K. Journal of Applied Microbiology, Vol. 109, Issue 2 https://doi.org/10.1111/j.1365-2672.2009.04659.x	journal	December 2009
Engineering Escherichia coli coculture systems for the production of biochemical products Zhang, Haoran; Pereira, Brian; Li, Zhengjun Proceedings of the National Academy of Sciences, Vol. 112, Issue 27 https://doi.org/10.1073/pnas.1506781112	journal	June 2015
De novo resveratrol production through modular engineering of an Escherichia coli–Saccharomyces cerevisiae co-culture Yuan, Shuo-Fu; Yi, Xiunan; Johnston, Trevor G. Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01401-5	journal	July 2020
Balancing the non-linear rosmarinic acid biosynthetic pathway by modular co-culture engineering Li, Zhenghong; Wang, Xiaonan; Zhang, Haoran Metabolic Engineering, Vol. 54 https://doi.org/10.1016/j.ymben.2019.03.002	journal	July 2019
Consolidated bioprocessing of lignocellulose by a microbial consortium Brethauer, Simone; Studer, Michael Hanspeter Energy & Environmental Science, Vol. 7, Issue 4 https://doi.org/10.1039/c3ee41753k	journal	January 2014
Developing a mesophilic co-culture for direct conversion of cellulose to butanol in consolidated bioprocess Wang, Zhenyu; Cao, Guangli; Zheng, Ju Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0266-3	journal	June 2015
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 36 https://doi.org/10.1073/pnas.1218447110	journal	August 2013
Heterologous biosynthesis of natural product naringenin by co-culture engineering Ganesan, Vijaydev; Li, Zhenghong; Wang, Xiaonan Synthetic and Systems Biotechnology, Vol. 2, Issue 3 https://doi.org/10.1016/j.synbio.2017.08.003	journal	September 2017
Distributing a metabolic pathway among a microbial consortium enhances production of natural products Zhou, Kang; Qiao, Kangjian; Edgar, Steven Nature Biotechnology, Vol. 33, Issue 4 https://doi.org/10.1038/nbt.3095	journal	January 2015
Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System Dinh, Christina V.; Chen, Xingyu; Prather, Kristala L. J. ACS Synthetic Biology, Vol. 9, Issue 3 https://doi.org/10.1021/acssynbio.9b00451	journal	February 2020
Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway Li, Zhu; Wang, Huiying; Ding, Dongqin Journal of Industrial Microbiology and Biotechnology, Vol. 47, Issue 6-7 https://doi.org/10.1007/s10295-020-02288-2	journal	July 2020
Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering Zhao, Evan M.; Lalwani, Makoto A.; Lovelett, Robert J. ACS Synthetic Biology, Vol. 9, Issue 12 https://doi.org/10.1021/acssynbio.0c00305	journal	November 2020
Engineering an Optogenetic CRISPRi Platform for Improved Chemical Production Wu, Peiling; Chen, Yufen; Liu, Mingyu ACS Synthetic Biology, Vol. 10, Issue 1 https://doi.org/10.1021/acssynbio.0c00488	journal	December 2020
Optogenetic control of the lac operon for bacterial chemical and protein production Lalwani, Makoto A.; Ip, Samantha S.; Carrasco-López, César Nature Chemical Biology, Vol. 17, Issue 1 https://doi.org/10.1038/s41589-020-0639-1	journal	September 2020
Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth Milias-Argeitis, Andreas; Rullan, Marc; Aoki, Stephanie K. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12546	journal	August 2016
Optogenetic regulation of engineered cellular metabolism for microbial chemical production Zhao, Evan M.; Zhang, Yanfei; Mehl, Justin Nature, Vol. 555, Issue 7698 https://doi.org/10.1038/nature26141	journal	March 2018
'Deadman' and 'Passcode' microbial kill switches for bacterial containment Chan, Clement T. Y.; Lee, Jeong Wook; Cameron, D. Ewen Nature Chemical Biology, Vol. 12, Issue 2 https://doi.org/10.1038/nchembio.1979	journal	December 2015
Recoded organisms engineered to depend on synthetic amino acids Rovner, Alexis J.; Haimovich, Adrian D.; Katz, Spencer R. Nature, Vol. 518, Issue 7537 https://doi.org/10.1038/nature14095	journal	January 2015
Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes Cai, Yizhi; Agmon, Neta; Choi, Woo Jin Proceedings of the National Academy of Sciences, Vol. 112, Issue 6 https://doi.org/10.1073/pnas.1424704112	journal	January 2015
An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Aizenman, E.; Engelberg-Kulka, H.; Glaser, G. Proceedings of the National Academy of Sciences, Vol. 93, Issue 12 https://doi.org/10.1073/pnas.93.12.6059	journal	June 1996
Crystal Structure of the MazE/MazF Complex Kamada, Katsuhiko; Hanaoka, Fumio; Burley, Stephen K. Molecular Cell, Vol. 11, Issue 4 https://doi.org/10.1016/S1097-2765(03)00097-2	journal	April 2003
MazF-induced Growth Inhibition and Persister Generation in Escherichia coli Tripathi, Arti; Dewan, Pooja C.; Siddique, Shahbaz A. Journal of Biological Chemistry, Vol. 289, Issue 7 https://doi.org/10.1074/jbc.M113.510511	journal	February 2014
MazF-Mediated Cell Death in Escherichia coli: a Point of No Return Amitai, S.; Yassin, Y.; Engelberg-Kulka, H. Journal of Bacteriology, Vol. 186, Issue 24 https://doi.org/10.1128/JB.186.24.8295-8300.2004	journal	December 2004
RNA Futile Cycling in Model Persisters Derived from MazF Accumulation Mok, Wendy W. K.; Park, Junyoung O.; Rabinowitz, Joshua D. mBio, Vol. 6, Issue 6 https://doi.org/10.1128/mBio.01588-15	journal	November 2015
Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds Rodriguez, Alberto; Martnez, Juan A.; Flores, Noem Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/s12934-014-0126-z	journal	September 2014
From Dusk till Dawn: One-Plasmid Systems for Light-Regulated Gene Expression Ohlendorf, Robert; Vidavski, Roee R.; Eldar, Avigdor Journal of Molecular Biology, Vol. 416, Issue 4 https://doi.org/10.1016/j.jmb.2012.01.001	journal	March 2012
Design and Signaling Mechanism of Light-Regulated Histidine Kinases Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith Journal of Molecular Biology, Vol. 385, Issue 5 https://doi.org/10.1016/j.jmb.2008.12.017	journal	February 2009
Rate of DNA synthesis during the division cycle of Escherichia coli B/r Helmstetter, Charles E. Journal of Molecular Biology, Vol. 24, Issue 3 https://doi.org/10.1016/0022-2836(67)90228-8	journal	March 1967
Saccharomyces cerevisiae Exponential Growth Kinetics in Batch Culture to Analyze Respiratory and Fermentative Metabolism Olivares-Marin, Ivanna Karina; González-Hernández, Juan Carlos; Regalado-Gonzalez, Carlos Journal of Visualized Experiments, Issue 139 https://doi.org/10.3791/58192	journal	January 2018
Production of naringenin from D-xylose with co-culture of E. coli and S. cerevisiae Zhang, Wei; Liu, Hong; Li, Xia Engineering in Life Sciences, Vol. 17, Issue 9 https://doi.org/10.1002/elsc.201700039	journal	June 2017
Two-dimensional isobutyl acetate production pathways to improve carbon yield Tashiro, Yohei; Desai, Shuchi H.; Atsumi, Shota Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8488	journal	June 2015
Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids Shiba, Yoichiro; Paradise, Eric M.; Kirby, James Metabolic Engineering, Vol. 9, Issue 2 https://doi.org/10.1016/j.ymben.2006.10.005	journal	March 2007
De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae Koopman, Frank; Beekwilder, Jules; Crimi, Barbara Microbial Cell Factories, Vol. 11, Issue 1 https://doi.org/10.1186/1475-2859-11-155	journal	January 2012
Modular Engineering of l-Tyrosine Production in Escherichia coli Juminaga, Darmawi; Baidoo, Edward E. K.; Redding-Johanson, Alyssa M. Applied and Environmental Microbiology, Vol. 78, Issue 1, p. 89-98 https://doi.org/10.1128/AEM.06017-11	journal	October 2011
Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains Rodriguez, Angelica; Chen, Yun; Khoomrung, Sakda Metabolic Engineering, Vol. 44 https://doi.org/10.1016/j.ymben.2017.10.013	journal	November 2017
Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast Skjoedt, Mette L.; Snoek, Tim; Kildegaard, Kanchana R. Nature Chemical Biology, Vol. 12, Issue 11 https://doi.org/10.1038/nchembio.2177	journal	September 2016
Improving Production of Malonyl Coenzyme A-Derived Metabolites by Abolishing Snf1-Dependent Regulation of Acc1 Shi, Shuobo; Chen, Yun; Siewers, Verena mBio, Vol. 5, Issue 3 https://doi.org/10.1128/mBio.01130-14	journal	May 2014
Encapsulation of polyphenols – a review Fang, Zhongxiang; Bhandari, Bhesh Trends in Food Science & Technology, Vol. 21, Issue 10 https://doi.org/10.1016/j.tifs.2010.08.003	journal	October 2010
Engineered biosynthesis of medium-chain esters in Escherichia coli Tai, Yi-Shu; Xiong, Mingyong; Zhang, Kechun Metabolic Engineering, Vol. 27 https://doi.org/10.1016/j.ymben.2014.10.004	journal	January 2015
Effects of metabolic pathway gene copy numbers on the biosynthesis of (2S)-naringenin in Saccharomyces cerevisiae Li, Hongbiao; Gao, Song; Zhang, Siqi Journal of Biotechnology, Vol. 325 https://doi.org/10.1016/j.jbiotec.2020.11.009	journal	January 2021
Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis Hammer, Sarah K.; Avalos, José L. Metabolic Engineering, Vol. 44 https://doi.org/10.1016/j.ymben.2017.10.001	journal	November 2017
Enhancement of Naringenin Biosynthesis from Tyrosine by Metabolic Engineering of Saccharomyces cerevisiae Lyu, Xiaomei; Ng, Kuan Rei; Lee, Jie Lin Journal of Agricultural and Food Chemistry, Vol. 65, Issue 31 https://doi.org/10.1021/acs.jafc.7b02507	journal	July 2017
Engineering Saccharomyces cerevisiae Coculture Platform for the Production of Flavonoids Du, Yun; Yang, Binrui; Yi, Zhiqiang Journal of Agricultural and Food Chemistry, Vol. 68, Issue 7 https://doi.org/10.1021/acs.jafc.9b07916	journal	January 2020
YddG from Escherichia coli promotes export of aromatic amino acids Doroshenko, Vera; Airich, Larisa; Vitushkina, Maria FEMS Microbiology Letters, Vol. 275, Issue 2 https://doi.org/10.1111/j.1574-6968.2007.00894.x	journal	October 2007
Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation La, Angéla; Perré, Patrick; Taidi, Behnam Applied Microbiology and Biotechnology, Vol. 103, Issue 2 https://doi.org/10.1007/s00253-018-9506-3	journal	November 2018
Toxin-antitoxin systems in bacterial growth arrest and persistence Page, Rebecca; Peti, Wolfgang Nature Chemical Biology, Vol. 12, Issue 4 https://doi.org/10.1038/nchembio.2044	journal	March 2016
Optogenetic Amplification Circuits for Light-Induced Metabolic Control Zhao, Evan M.; Lalwani, Makoto A.; Chen, Jhong-Min ACS Synthetic Biology, Vol. 10, Issue 5 https://doi.org/10.1021/acssynbio.0c00642	journal	April 2021
Optogenetic Control by Pulsed Illumination Hennemann, Julia; Iwasaki, Roman S.; Grund, Tamara N. ChemBioChem, Vol. 19, Issue 12 https://doi.org/10.1002/cbic.201800030	journal	April 2018
Cyanobacteriochrome CcaS is the green light receptor that induces the expression of phycobilisome linker protein Hirose, Y.; Shimada, T.; Narikawa, R. Proceedings of the National Academy of Sciences, Vol. 105, Issue 28 https://doi.org/10.1073/pnas.0801826105	journal	July 2008
Engineering an E. coli Near-Infrared Light Sensor Ong, Nicholas T.; Olson, Evan J.; Tabor, Jeffrey J. ACS Synthetic Biology, Vol. 7, Issue 1 https://doi.org/10.1021/acssynbio.7b00289	journal	August 2017
Investigating the dynamics of microbial consortia in spatially structured environments Gupta, Sonali; Ross, Tyler D.; Gomez, Marcella M. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16200-0	journal	May 2020
In silico feedback for in vivo regulation of a gene expression circuit Milias-Argeitis, Andreas; Summers, Sean; Stewart-Ornstein, Jacob Nature Biotechnology, Vol. 29, Issue 12 https://doi.org/10.1038/nbt.2018	journal	November 2011
Optogenetics and biosensors set the stage for metabolic cybergenetics Carrasco-López, César; García-Echauri, Sergio A.; Kichuk, Therese Current Opinion in Biotechnology, Vol. 65 https://doi.org/10.1016/j.copbio.2020.07.012	journal	October 2020
Bioremediation of organophosphorus pesticide phorate in soil by microbial consortia Jariyal, Monu; Jindal, Vikas; Mandal, Kousik Ecotoxicology and Environmental Safety, Vol. 159 https://doi.org/10.1016/j.ecoenv.2018.04.063	journal	September 2018
Ecosystem Functions of Microbial Consortia in Sustainable Agriculture Aguilar-Paredes, Ana; Valdés, Gabriela; Nuti, Marco Agronomy, Vol. 10, Issue 12 https://doi.org/10.3390/agronomy10121902	journal	December 2020
Microbe–microbe interactions in mixed culture food fermentations Smid, Eddy J.; Lacroix, Christophe Current Opinion in Biotechnology, Vol. 24, Issue 2 https://doi.org/10.1016/j.copbio.2012.11.007	journal	April 2013
Design of synthetic microbial consortia for gut microbiota modulation Vázquez-Castellanos, Jorge F.; Biclot, Anaïs; Vrancken, Gino Current Opinion in Pharmacology, Vol. 49 https://doi.org/10.1016/j.coph.2019.07.005	journal	December 2019
High efficiency transformation of Escherichia coli with plasmids Inoue, Hiroaki; Nojima, Hiroshi; Okayama, Hiroto Gene, Vol. 96, Issue 1 https://doi.org/10.1016/0378-1119(90)90336-P	journal	January 1990
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
Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols Avalos, José L.; Fink, Gerald R.; Stephanopoulos, Gregory Nature Biotechnology, Vol. 31, Issue 4 https://doi.org/10.1038/nbt.2509	journal	February 2013
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Datsenko, K. A.; Wanner, B. L. Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645 https://doi.org/10.1073/pnas.120163297	journal	May 2000
High efficiency transformation of E.coli by high voltage electroporation Dower, W. J.; Miller, J. F.; Ragsdale, C. W. Nucleic Acids Research, Vol. 16, Issue 13 https://doi.org/10.1093/nar/16.13.6127	journal	July 1988
Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant Cherepanov, Peter P.; Wackernagel, Wilfried Gene, Vol. 158, Issue 1 https://doi.org/10.1016/0378-1119(95)00193-A	journal	January 1995
Dormancy Is Not Necessary or Sufficient for Bacterial Persistence Orman, Mehmet A.; Brynildsen, Mark P. Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 7 https://doi.org/10.1128/AAC.00243-13	journal	April 2013

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