Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.
32 items matching 1 filter
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Showing 1-32 of 32
CRY1 is a blue-light-sensing cryptochrome protein from the Arabidopsis cryptochrome family, and the name cry1 is also used for a Drosophila-like insect cryptochrome gene family. The supplied evidence indicates that CRY1 mediates blue light responses, contributes to regulation of early blue light-induced genes, and has functional overlap with CRY2.
Cryptochromes are evolutionarily conserved flavoprotein photoreceptors that sense blue light in multiple organisms. As a protein-domain class, they are used as light-responsive modules in optogenetic systems, while native cryptochromes regulate plant photoresponses and circadian-associated transcriptional programs.
HY5 is an Arabidopsis thaliana basic leucine zipper (bZIP) transcription factor that directly binds light-responsive promoters and functions as a positive regulator of photomorphogenesis. It also mediates crosstalk between light signaling and the unfolded protein response (UPR) by negatively regulating UPR gene expression through promoter competition.
P_GAL1-S is an engineered inducible GAL1 promoter for yeast reported to be stronger than constitutive or inducible promoters commonly used in this host. In the cited study, it was coupled to the OptoINVRT7 light-responsive circuit to drive strong, light-tunable gene expression and metabolic pathway control.
The CpbHLH gene family is the set of basic helix-loop-helix transcription factor genes identified in Chimonanthus praecox. A genome-wide study reported 131 CpbHLH genes distributed across 11 chromosomes and characterized their expression across tissues and flower developmental stages.
BEE2 (brassinosteroid enhanced expression2) is an Arabidopsis HBI1-related basic helix-loop-helix transcription factor considered here as an overexpressed protein domain tool. Source evidence indicates that BEE2 overexpression partially inhibits immunity and that BEE2 may function redundantly with HBI1-related growth–immunity regulatory activities.
Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.
The Escherichia coli-based biosensor harbors a plasmid-based fusion of a gene promoter, acting as the sensing element, to a microbial bioluminescence gene cassette as the reporter.
HBI1 is an Arabidopsis basic helix-loop-helix transcription factor, identified as HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1. Reported evidence indicates that its expression is induced by brassinosteroid treatment and reduced by different pathogen-associated molecular patterns, consistent with a role in antagonistic regulation of growth and immunity.
The PORC promoter is an Arabidopsis promoter element that functions as an in vivo binding target of the scarecrow-like transcription factor SCL27. Available evidence indicates that SCL27 binds GT cis-elements within this promoter and regulates PORC promoter activity, with DELLA proteins reducing SCL27 promoter binding.
It enables a 20-fold increase in sensitivity, reducing the EC50 of PsiR-allulose biosensors (PABs) from 16 mM to 0.8 mM, and delivers a PAB box possessing the detection range from 10 bcM to 100 mM.
Transcription factor-based biosensors (TFBs) are powerful tools in microbial biosensor applications, enabling dynamic control of metabolic pathways, real-time monitoring of intracellular metabolites, and high-throughput screening (HTS) for strain engineering.
VvCEB1 is a Vitis vinifera basic helix-loop-helix transcription factor identified as a controller of cell expansion in grape. It is described as fruit-specific, expressed in berry-expanding tissues with maximal expression around veraison, and implicated in grape berry development.
Here, we present an alternative tool for AC detection using a whole-cell bacterial biosensor, which utilises the YwbIR transcriptional regulator from Bacillus subtilis.
The upstream summary states that the review abstract explicitly covers engineered cells with synthetic DNA circuits.
Automated 96-well microplate illumination and measurement is an assay method for high-throughput optogenetic characterization of cultures under controlled light input. In the cited Saccharomyces cerevisiae workflow, it supported construction and characterization of split transcription factors containing cryptochrome and Enhanced Magnet light-sensitive dimerizers.
DspA, also called Hik33, is a sensor histidine kinase from Synechocystis sp. strain PCC6803. It functions in signal transduction that controls photosynthetic and high-light-responsive gene sets and contributes to adaptation of cellular metabolism and growth to environmental light conditions.
We also discuss biotechnological strategies such as CRISPR/Cas-mediated genome editing, stress-inducible promoter engineering, and synthetic transcriptional circuits that offer promising avenues for fine-tuning HSF expression and enhancing multi-stress resilience in crops.
R2R3 MYB transcription factors are plant transcriptional regulators implicated in light-responsive control of flavonoid biosynthesis. The supplied evidence indicates that their differential expression regulates the biosynthesis of distinct flavonoids in response to specific light wavelengths.
The Rel/NF-κB family is a mammalian set of transcription factors comprising RelA, c-Rel, RelB, NF-κB1 (p50 and precursor p105), and NF-κB2 (p52 and precursor p100). These factors are differentially activated as NF-κB heterodimers by signals from antigen receptors, pattern-recognition receptors, and receptors for TNF and IL-1 family cytokines to regulate transcription.
A NIMPLY B gates are compressed two-input mixed-phenotype transcriptional logic operations reported in a 2023 ACS Synthetic Biology study on performance prediction of fundamental transcriptional programs. The study indicates that their behavior can be modeled and predicted from experimentally characterized single-input logical operations and associated metrology.
Chlorophyll a/b binding protein promoters are Arabidopsis light-regulated promoter elements described as three red-light-regulated promoters. The cited evidence indicates that these promoters drive expression patterns that are altered in det1 mutant roots, consistent with red-light-responsive transcriptional control.
To address current limitations of metabolic engineering, this article gives insights on recent systems metabolic engineering approaches based on functional tools and method such as genome reduction, amino acid sensors based on transcriptional regulators and riboswitches...
HY5ox/pifQein3eil1 is an Arabidopsis multi-component genetic switch-like genotype comprising HY5 overexpression combined with loss of EIN3, EIL1, and four PIF genes. In dark-grown seedlings, this combination drives strong photomorphogenic development and produces phenotypes highly similar to wild-type seedlings grown in continuous light.
Light-inducible transcriptional effectors (LITEs) are an optogenetic two-hybrid system that combines a customizable TALE DNA-binding domain with Arabidopsis thaliana CRY2 and its interacting partner CIB1. The system enables light-triggered, reversible control of endogenous mammalian gene expression and targeted epigenetic chromatin modification.
The PA-Tet-OFF/ON system is a photoactivatable version of the Tet gene expression platform that incorporates the Cry2-CIB1 light-inducible binding switch to control expression of a gene of interest. It enables light- and drug-regulated transcription with precise temporal control and was demonstrated for optogenetic regulation of exogenous gene expression in developing and adult mouse brains.
Here, we find that our previously engineered E. coli green light sensor CcaSR, which functions robustly in exponential phase, fails in stationary phase due to spontaneous loss of an engineered chromophore biosynthetic pathway and accumulation of CcaS and CcaR.
The copper-regulated expression system is described only at the level of a plant chemical-inducible transgene control strategy for regulating transcription. The supplied evidence supports that plant chemically inducible systems usually comprise a chimeric transcription factor and a reporter gene, but it does not define a copper-specific molecular implementation.
The MphR(A)/PmphR photochemical gene switch is an engineered bacterial transcription system in which the MphR(A)/PmphR regulatory module is coupled to a light-activatable erythromycin derivative. In E. coli, photoactivation of the erythromycin derivative enables ligand-dependent activation of transcription from the PmphR-controlled output.
Here, we present an Escherichia coli biosensor for arsenic in which the transcription factor (TF) gene arsR is inducible by naringenin, a plant-derived secondary metabolite.
The steroid-regulated expression system is a plant chemical-inducible transcription control platform. The available evidence only supports that such systems typically include a chimeric transcription factor and a reporter gene, without describing a steroid-specific molecular architecture or performance.
The tetracycline-regulated expression system is a chemical-inducible transcriptional switch used in plants. The available evidence indicates that plant systems of this class usually comprise a chimeric transcription factor and a reporter gene.