Source 1primary paper2019Biotechnology and Bioengineering
Toolkit/yeast optogenetic toolkit
yeast optogenetic toolkit
Also known as: yOTK
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The yeast optogenetic toolkit (yOTK) is a modular construct system for light-controlled gene expression in Saccharomyces cerevisiae. It integrates optogenetic parts into an existing yeast toolkit and supports rapid assembly of light-controlled circuits, including split transcription factors built from cryptochrome and Enhanced Magnet dimerizers.
Usefulness & Problems
Why this is useful
yOTK is useful for building and testing light-regulated transcriptional circuits in S. cerevisiae within a modular cloning framework. The associated automation-enabled workflow supports high-throughput construction and characterization of optogenetic split transcription factors.
Source:
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Source:
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
Problem solved
yOTK addresses the need for a rapid, modular way to assemble optogenetic gene-expression systems in yeast. It also helps solve the throughput bottleneck in constructing and characterizing multiple split transcription factor designs.
Source:
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
Published Workflows
The Yeast Optogenetic Toolkit (yOTK) for Spatiotemporal Control of Gene Expression in Budding Yeast.
2025Objective: Assemble, integrate, and test optogenetic systems in Saccharomyces cerevisiae and select systems with desirable properties.
Why it works: The workflow standardizes construct definition, part identification, rule-based assembly, one-pot multigene construction, yeast transformation, and screening so that candidate optogenetic systems can be built rapidly and then narrowed to those with desirable properties.
light-sensitive protein control of gene expressionlight-sensitive protein control of protein localizationdesign-test-build cyclesModular Cloningone-pot multigene assemblyyeast transformationscreening of transformants
Stages
- 1.Construct definition and part identification(library_design)
This stage establishes the intended construct architecture and the required parts before assembly begins.
Selection: Define the structure of the final construct and identify all basic parts and vectors required for the construction strategy.
- 2.Rule-based assembly definition and one-pot multigene build(library_build)
This stage converts the planned construct design into assembled multigene DNA constructs using the identified parts and vectors.
Selection: Assembly is defined following a set of standard rules and executed through one-pot assembly steps.
- 3.Yeast transformation(recovery)
Transformation places assembled optogenetic constructs into the yeast host for downstream testing.
Selection: Assembled constructs are transformed into yeast.
- 4.Transformant screening and selection(broad_screen)
This stage narrows transformed candidates to systems with preferred performance characteristics.
Selection: Screen transformants to identify optogenetic systems with optimal properties.
Steps
- 1.Define final construct structuretoolkit being configured
Specify the intended architecture of the optogenetic system before build steps begin.
The abstract states this happens first and is required before identifying parts and vectors for the construction strategy.
- 2.Identify required parts and vectors and domesticate light-sensitive proteins if neededtoolkit part set
Determine the basic parts and vectors needed for the construction strategy and prepare light-sensitive proteins for toolkit compatibility when necessary.
Part and vector identification must follow construct definition so the assembly strategy can be specified correctly.
- 3.Define assembly according to standard rulesassembly method
Translate the chosen construct architecture and parts into a standardized assembly plan.
Assembly rules are defined after parts are identified and before one-pot build steps are executed.
- 4.Assemble multigene constructs by one-pot assemblyengineered construct and assembly method
Build multigene optogenetic constructs from the identified parts and vectors.
One-pot assembly is performed after the assembly plan is defined and before transformation into yeast.
- 5.Transform assembled constructs into yeastassembled optogenetic construct
Introduce assembled optogenetic constructs into Saccharomyces cerevisiae for testing.
Transformation follows DNA assembly because the constructs must be present in yeast before screening can occur.
- 6.Screen transformants to select systems with optimal propertiesoptogenetic systems under evaluation
Evaluate transformants and select optogenetic systems with optimal properties.
Screening is performed after transformation because only yeast transformants can be evaluated for system performance.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Mechanisms
light-regulated transcriptional controllight-sensitive heterodimerizationsplit transcription factor reconstitutionTechniques
No technique tags yet.
Target processes
No target processes tagged yet.
Input: Light
Implementation Constraints
The reported implementation is in Saccharomyces cerevisiae and is based on modular assembly within an existing yeast toolkit. Constructs include split transcription factors incorporating cryptochrome and Enhanced Magnet light-sensitive dimerizers, and the 2023 study links the toolkit to laboratory automation for high-throughput build-and-test workflows.
The supplied evidence establishes toolkit integration, component classes, and improved performance for an optimized Enhanced Magnet design, but it does not provide quantitative performance metrics or detailed benchmarking. The evidence also does not specify illumination wavelengths, dynamic range, leakiness, response kinetics, or validation outside S. cerevisiae.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2023
Ranked Claims
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Laboratory automation combined with a modular cloning scheme enables high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae.
We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae .
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
Cryptochrome and Enhanced Magnet light-sensitive dimerizers were incorporated into split transcription factors.
incorporate these light-sensitive dimerizers into split transcription factors
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
An optimized Enhanced Magnet transcription factor showed improved light-sensitive gene expression.
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Activity of a split synthetic zinc-finger transcription factor is reconstituted using CRY2- and CIB1-mediated light-induced dimerization.
We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Using the split transcription factor and a synthetic promoter, light intensity and duty cycle can modulate gene expression over the range currently available from natural yeast promoters.
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.
Approval Evidence
3 sources7 linked approval claimsfirst-pass slug yeast-optogenetic-toolkit
A yeast optogenetic toolkit (yOTK) allows rapid assembly of optogenetic constructs using Modular Cloning, or MoClo.
Source:
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
Source:
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
Source:
protocol scopesupports
The protocol describes how to assemble, integrate, and test optogenetic systems in Saccharomyces cerevisiae.
In this protocol, we describe how to assemble, integrate, and test optogenetic systems in the budding yeast Saccharomyces cerevisiae.
Source:
tool capabilitysupports
The yeast optogenetic toolkit enables rapid assembly of optogenetic constructs using Modular Cloning.
A yeast optogenetic toolkit (yOTK) allows rapid assembly of optogenetic constructs using Modular Cloning, or MoClo.
Source:
workflow outcomesupports
Screening transformants allows selection of optogenetic systems with optimal properties.
Screening of the transformants allows optogenetic systems with optimal properties to be selected.
Source:
workflow requirementsupports
Generation of an optogenetic system requires defining the final construct structure and identifying required parts and vectors, including domestication of light-sensitive proteins into the toolkit when needed.
Generating an optogenetic system requires the user to first define the structure of the final construct and identify all basic parts and vectors required for the construction strategy, including light-sensitive proteins that need to be domesticated into the toolkit.
Source:
toolkit expansionsupports
The yeast optogenetic toolkit was expanded to include variants of cryptochromes and Enhanced Magnets.
We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets
Source:
application scopesupports
The study enables rapid generation and prototyping of optogenetic circuits to control gene expression in Saccharomyces cerevisiae.
This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
Source:
developmentsupports
The study develops an optogenetic system for gene expression control integrated with an existing yeast toolkit for rapid modular assembly of light-controlled circuits in Saccharomyces cerevisiae.
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.
Source:
Comparisons
Source-backed strengths
The toolkit was specifically described as integrated with an existing yeast toolkit, enabling rapid modular assembly of light-controlled circuits. It includes variants of cryptochromes and Enhanced Magnets, and an optimized Enhanced Magnet transcription factor was reported to show improved light-sensitive gene expression.
Source:
We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression.
Ranked Citations
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