Optogenetics Illuminates Applications in Microbial Engineering

Hoffman, Shannon M.; Tang, Allison Y.; Avalos, José L.

doi:10.1146/annurev-chembioeng-092120-092340

Optogenetics Illuminates Applications in Microbial Engineering

Journal Article · Wed Mar 23 00:00:00 EDT 2022 · Annual Review of Chemical and Biomolecular Engineering

DOI:https://doi.org/10.1146/annurev-chembioeng-092120-092340· OSTI ID:1900143

Hoffman, Shannon M. ^[1]; Tang, Allison Y. ^[2]; Avalos, José L. ^[2]

Princeton Univ., NJ (United States); Princeton University
Princeton Univ., NJ (United States)

Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe–host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Lastly, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0019363

OSTI ID:: 1900143

Journal Information:: Annual Review of Chemical and Biomolecular Engineering, Journal Name: Annual Review of Chemical and Biomolecular Engineering Journal Issue: 1 Vol. 13; ISSN 1947-5438

Publisher:: Annual ReviewsCopyright Statement

Country of Publication:: United States

Language:: English

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Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins Yu, Daseuli; Lee, Hansol; Hong, Jongryul Nature Methods, Vol. 16, Issue 11 https://doi.org/10.1038/s41592-019-0592-7	journal	October 2019
A guide to the optogenetic regulation of endogenous molecules Manoilov, Kyrylo Yu.; Verkhusha, Vladislav V.; Shcherbakova, Daria M. Nature Methods, Vol. 18, Issue 9 https://doi.org/10.1038/s41592-021-01240-1	journal	August 2021
An optogenetic system to control membrane phospholipid asymmetry through flippase activation in budding yeast Suzuki, Tomomi; Mioka, Tetsuo; Tanaka, Kazuma Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-69459-0	journal	July 2020
Upconversion optogenetic micro-nanosystem optically controls the secretion of light-responsive bacteria for systemic immunity regulation Yang, Chun; Cui, Meihui; Zhang, Yingying Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-01287-4	journal	October 2020
Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG Binder, Dennis; Grünberger, Alexander; Loeschcke, Anita Integr. Biol., Vol. 6, Issue 8 https://doi.org/10.1039/C4IB00027G	journal	January 2014
Real-time optogenetic control of intracellular protein concentration in microbial cell cultures Melendez, Justin; Patel, Michael; Oakes, Benjamin L. Integrative Biology, Vol. 6, Issue 3 https://doi.org/10.1039/c3ib40102b	journal	January 2014
Long-term model predictive control of gene expression at the population and single-cell levels Uhlendorf, J.; Miermont, A.; Delaveau, T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 35 https://doi.org/10.1073/pnas.1206810109	journal	August 2012
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
Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins Guntas, Gurkan; Hallett, Ryan A.; Zimmerman, Seth P. Proceedings of the National Academy of Sciences, Vol. 112, Issue 1 https://doi.org/10.1073/pnas.1417910112	journal	December 2014
Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression Jin, Xiaofan; Riedel-Kruse, Ingmar H. Proceedings of the National Academy of Sciences, Vol. 115, Issue 14 https://doi.org/10.1073/pnas.1720676115	journal	March 2018
Synthetic gene-regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae Sorg, Robin A.; Gallay, Clement; Van Maele, Laurye Proceedings of the National Academy of Sciences, Vol. 117, Issue 44 https://doi.org/10.1073/pnas.1920015117	journal	October 2020
Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP Hee, Chee-Seng; Habazettl, Judith; Schmutz, Christoph Proceedings of the National Academy of Sciences, Vol. 117, Issue 29 https://doi.org/10.1073/pnas.2001232117	journal	July 2020
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Natural and Engineered Photoactivated Nucleotidyl Cyclases for Optogenetic Applications Ryu, Min-Hyung; Moskvin, Oleg V.; Siltberg-Liberles, Jessica Journal of Biological Chemistry, Vol. 285, Issue 53 https://doi.org/10.1074/jbc.M110.177600	journal	October 2010
Light Modulation of Cellular cAMP by a Small Bacterial Photoactivated Adenylyl Cyclase, bPAC, of the Soil Bacterium Beggiatoa Stierl, Manuela; Stumpf, Patrick; Udwari, Daniel Journal of Biological Chemistry, Vol. 286, Issue 2 https://doi.org/10.1074/jbc.M110.185496	journal	October 2010
Optogenetic Modulation of an Adenylate Cyclase in Toxoplasma gondii Demonstrates a Requirement of the Parasite cAMP for Host-Cell Invasion and Stage Differentiation Hartmann, Anne; Arroyo-Olarte, Ruben Dario; Imkeller, Katharina Journal of Biological Chemistry, Vol. 288, Issue 19 https://doi.org/10.1074/jbc.M113.465583	journal	May 2013
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CRISPR-Cas Activators for Engineering Gene Expression in Higher Eukaryotes Casas-Mollano, J. Armando; Zinselmeier, Matthew H.; Erickson, Samuel E. The CRISPR Journal, Vol. 3, Issue 5 https://doi.org/10.1089/crispr.2020.0064	journal	October 2020
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Model-guided optogenetic study of PKA signaling in budding yeast Stewart-Ornstein, Jacob; Chen, Susan; Bhatnagar, Rajat Molecular Biology of the Cell, Vol. 28, Issue 1 https://doi.org/10.1091/mbc.e16-06-0354	journal	January 2017
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At Light Speed: Advances in Optogenetic Systems for Regulating Cell Signaling and Behavior Repina, Nicole A.; Rosenbloom, Alyssa; Mukherjee, Abhirup Annual Review of Chemical and Biomolecular Engineering, Vol. 8, Issue 1 https://doi.org/10.1146/annurev-chembioeng-060816-101254	journal	June 2017
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Establishment of Optogenetic Modulation of cAMP for Analyzing Growth, Biofilm Formation, and Virulence Pathways of Bacteria Using a Light-Gated Cyclase Kaushik, Manish Singh; Pati, Swaroop Ranjan; Soni, Shivanika Applied Sciences, Vol. 10, Issue 16 https://doi.org/10.3390/app10165535	journal	August 2020
Modular and Molecular Optimization of a LOV (Light–Oxygen–Voltage)-Based Optogenetic Switch in Yeast Romero, Andrés; Rojas, Vicente; Delgado, Verónica International Journal of Molecular Sciences, Vol. 22, Issue 16 https://doi.org/10.3390/ijms22168538	journal	August 2021
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Dynamic density shaping of photokinetic E. coli Frangipane, Giacomo; Dell'Arciprete, Dario; Petracchini, Serena eLife, Vol. 7 https://doi.org/10.7554/eLife.36608	journal	August 2018
Optogenetic control of gut bacterial metabolism to promote longevity Hartsough, Lucas A.; Park, Mooncheol; Kotlajich, Matthew V. eLife, Vol. 9 https://doi.org/10.7554/eLife.56849	journal	December 2020
A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch Duplus-Bottin, Hélène; Spichty, Martin; Triqueneaux, Gérard eLife, Vol. 10 https://doi.org/10.7554/eLife.61268	journal	February 2021

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