Modular and tunable biological feedback control using a de novo protein switch

Ng, Andrew H.; Nguyen, Taylor H.; Gómez-Schiavon, Mariana; Dods, Galen; Langan, Robert A.; Boyken, Scott E.; Samson, Jennifer A.; Waldburger, Lucas; Dueber, John E.; Baker, David; El-Samad, Hana

doi:10.1038/s41586-019-1425-7

Cited by 103 publications

(84 citation statements)

References 24 publications

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“…Light is a powerful actuator as it is inexpensive, easily controlled in time and space, and S. cerevisiae contains no known native photoreceptors (Salinas, Rojas, Delgado, Agosin, & Larrondo, ). The ability to rapidly add and remove light from cell culture or spatially target specific cells makes it particularly advantageous for applications that require spatiotemporal precision such as dynamic stimulation or real‐time feedback control of cellular processes (Benzinger & Khammash, ; Castillo‐Hair, Igoshin, & Tabor, ; Harrigan, Madani, & El‐Samad, ; Lugagne & Dunlop, ; Milias‐Argeitis, Rullan, Aoki, Buchmann, & Khammash, ; Ng et al, ; Rullan, Benzinger, Schmidt, Milias‐Argeitis, & Khammash, ; Toettcher, Gong, Lim, & Weiner, ). To continue expanding the utility of optogenetics in S. cerevisiae , here we report the construction and optimization of a light‐activated transcription factor and associated components for use with an existing toolkit of yeast parts (Lee, Deloache, Cervantes, & Dueber, ).…”

Section: Introductionmentioning

confidence: 99%

“…Optogenetic approaches for controlling natural and synthetic biological networks are garnering attention as the toolkit expands and more powerful applications are demonstrated (Harrigan et al, ; Melendez et al, ; Ng et al, ; Rullan et al, ; Zhao et al, ). Here we report an orthogonal light‐inducible transcriptional activator for gene expression control in S. cerevisiae .…”

Section: Introductionmentioning

confidence: 99%

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A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae

An-Adirekkun

Stewart

Geller

et al. 2019

Biotech & Bioengineering

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Optogenetic tools for controlling gene expression are ideal for tuning synthetic biological networks due to the exquisite spatiotemporal control available with light.Here we develop an optogenetic system for gene expression control integrated with an existing yeast toolkit allowing for rapid, modular assembly of light-controlled circuits in the important chassis organism Saccharomyces cerevisiae. We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1. We optimize function of this split TF and demonstrate the utility of the toolkit workflow by assembling cassettes expressing the TF activation domain and DNA-binding domain at different levels.Utilizing this TF and a synthetic promoter we demonstrate that light intensity and duty cycle can be used to modulate gene expression over the range currently available from natural yeast promoters. This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae. K E Y W O R D Slight-inducible promoter, MoClo, optogenetics, Saccharomyces cerevisiae, yeast Jidapas (My) An-adirekkun, Cameron J. Stewart, and Stephanie H. Geller contributed equally to this study.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae

An-Adirekkun

Stewart

Geller

et al. 2019

Biotech & Bioengineering

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“…Degron-LOCKR technology can be used in in-vivo modification of mammalian cells, which opens the door to a wide range of applications in the design of live cell therapeutics [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16].…”

Section: Resultsmentioning

confidence: 99%

LOCKR - A De Novo Biological Switch for Cellular Feedback Control: A Meta-Analysis Research

Iyengar¹,

Gaurav²,

Shibu³

2020

Act Scie Dental

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The functionality of the human body is the result of the interplay of more than twenty thousand different types of proteins. Our understanding and perception of therapeutic measures for maladies has changed over the past few decades, since the advent of molecular interventions and gene therapy as treatment modalities. Endogenous proteins play a major role in the regulation and maintenance of homeostatic mechanisms. Several attempts have been made over the years, to modify endogenous proteins in order to achieve superior outcomes. Although the results have not been satisfactory due to the wide variety of possible conformational changes in endogenous proteins that enable multiple undesirable interactions and the resultant binding to unintended protein domains (off-target binding). To overcome

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“…Results so far show a high degree of experimental reproducibility. The technologies investigated include using chemical triggers to control how cells migrate 1 ; introducing synthetic circuits that control other cell functions 2 ; intricate protein switches that can be programmed to respond to various cellular conditions 3 ; and timed bacterial expression that works even in the variable environment of the mammalian gut 4 . In the future, we expect replication efforts will be reported as supplemental data submitted with manuscripts.…”

Section: Making It Workmentioning

confidence: 99%