Source 1primary paper2014ACS Synthetic Biology
Toolkit/TULIPs
TULIPs
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
TULIPs is an optical dimerizer system benchmarked as a multi-component light-controlled switch for regulating protein interactions in yeast. In the cited comparison, it produced a transcriptional response similar to CRY2/CIB1 and was evaluated in assays relevant to transcription and MAPK signaling control.
Usefulness & Problems
Why this is useful
TULIPs is useful as a light-controlled protein interaction switch for modulating cellular processes such as transcription and signaling in yeast. Its inclusion in a systematic benchmark against CRY2/CIB1, phyB/PIF3, and phyB/PIF6 provides comparative performance context for selecting optical dimerizers.
Source:
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
Problem solved
TULIPs helps address the need for reversible optical control of protein interactions in living cells. The cited work specifically places it in the context of regulating yeast transcriptional outputs and MAPK signaling with light.
Source:
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
Problem links
Need conditional control of signaling activity
DerivedTULIPs is an optical dimerizer system benchmarked as a multi-component light-controlled switch for regulating protein interactions in yeast. In the cited comparison, it produced a transcriptional response similar to CRY2/CIB1 and was evaluated for control of signaling and transcription.
Need tighter control over gene expression timing or amplitude
DerivedTULIPs is an optical dimerizer system benchmarked as a multi-component light-controlled switch for regulating protein interactions in yeast. In the cited comparison, it produced a transcriptional response similar to CRY2/CIB1 and was evaluated for control of signaling and transcription.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Target processes
signalingtranscriptionImplementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: multi component delivery burdenoperating role: regulatorswitch architecture: multi componentswitch architecture: recruitment
The available evidence supports use of TULIPs in yeast and evaluation in transcriptional and MAPK signaling assays. The supplied material does not specify construct architecture, chromophore requirements, wavelengths, or delivery details for this system.
The supplied evidence does not provide molecular composition, illumination parameters, kinetics, or fold-activation values for TULIPs. In regulation of a yeast MAPK signaling pathway, CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system, indicating somewhat higher dark-state activity for TULIPs in that assay.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2review2015Photochemical & Photobiological Sciences
Ranked Claims
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB dimerizers were successfully applied using a membrane-tethered CRY2 configuration, which may allow better local control of protein interactions.
we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
The red-light-regulated systems phyB/PIF3 and phyB/PIF6 showed significant differences in light sensitivity and fold-activation levels in a yeast transcriptional assay.
Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
Approval Evidence
2 sources3 linked approval claimsfirst-pass slug tulips
The supplied web research summary identifies TULIPs as a tunable LOV-based interaction tag system explicitly cited by the review.
Source:
Here, we set about to systematically benchmark the properties of four optical dimerizer systems, CRY2/CIB1, TULIPs, phyB/PIF3, and phyB/PIF6.
Source:
background activity comparisonsupports
CRY2/CIB1 showed slightly less background activity in the dark than the TULIP system during regulation of a yeast MAPK signaling pathway.
with slightly less background activity in the dark observed with CRY2/CIB
Source:
benchmark resultsupports
CRY2/CIB1 and TULIPs showed similar responses in a yeast transcriptional assay.
but similar responses between the CRY2/CIB and TULIP systems
Source:
pathway regulation comparisonsupports
CRY2/CIB1 and TULIP systems showed similar responses when used to regulate a yeast MAPK signaling pathway.
Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses
Source:
Comparisons
Source-backed strengths
In a yeast transcriptional assay, TULIPs showed a response similar to CRY2/CIB1. It was also sufficiently functional to be benchmarked alongside multiple established optical dimerizer systems in a systematic comparison.
Compared with BcLOV4-RhoA optogenetic fusion
TULIPs and BcLOV4-RhoA optogenetic fusion address a similar problem space because they share signaling, transcription.
Shared frame: same top-level item type; shared target processes: signaling, transcription; shared mechanisms: heterodimerization
Strengths here: looks easier to implement in practice.
Compared with Cry2
TULIPs and Cry2 address a similar problem space because they share signaling, transcription.
Shared frame: same top-level item type; shared target processes: signaling, transcription; shared mechanisms: heterodimerization
Strengths here: looks easier to implement in practice; may avoid an exogenous cofactor requirement.
Relative tradeoffs: appears more independently replicated.
Compared with LOVpep/ePDZb
TULIPs and LOVpep/ePDZb address a similar problem space because they share signaling, transcription.
Shared frame: same top-level item type; shared target processes: signaling, transcription; shared mechanisms: heterodimerization
Relative tradeoffs: appears more independently replicated.
Ranked Citations
- 1.
- 2.
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