Toolkit Items

Beggiatoa photoactivated adenylyl cyclase (bPAC) is a blue light-activated optogenetic adenylyl cyclase used to generate cyclic AMP in cells. The cited studies used it to drive cAMP-dependent signaling, including PKA activation, to increase endogenous cortisol in a blue light-dependent manner, and to localize cAMP production to defined subcellular compartments such as the cilium.

As a tool component, CIB1 is most directly supported as the cryptochrome-interacting bHLH partner used with CRY2 to create blue-light-controlled protein association systems. In these systems, CIB1 is typically fused to localization, transcriptional, or enzymatic modules so that blue light drives CRY2–CIB1 binding and light withdrawal reverses the interaction.

AsLOV2 is the light-oxygen-voltage 2 photosensory domain from Avena sativa phototropin 1 used as a blue-light-responsive actuator in engineered fusion proteins. Blue-light activation drives allosteric conformational extension involving sequential unfolding of the N-terminal A'α helix and the C-terminal Jα helix, enabling conformational uncaging and related optogenetic control.

The LOV2 domain of Avena sativa phototropin 1 is a blue-light-responsive protein domain that uses an FMN-dependent photocycle to reversibly switch between dark and lit states through formation and decay of a flavin-cysteinyl adduct. It has been repurposed as a modular photoswitch to control nuclear import/export motif exposure and to generate light-dependent inhibitory peptides.

SOUL is an engineered step-function opsin with ultra-high light sensitivity for optogenetic control of neuronal activity. It was reported to enable activation and modulation of neurons with external light delivery, including use in mice and macaque cortex.

Cryptochrome 1 (CRY1) is an Arabidopsis UV-A/blue-light photoreceptor protein implicated in regulation of chalcone synthase (CHS) gene expression. The supplied evidence supports a role for CRY1 in a distinct cry-mediated light signaling pathway that interacts with UV-B and phytochrome signaling networks.

SspB is the binding partner used in the iLID blue-light-inducible dimerization system. Upon blue-light activation of iLID, the exposed SsrA peptide binds SspB, enabling light-controlled recruitment and localization of SspB-fused cargo proteins.

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.

Arabidopsis cryptochrome 2 (AtCRY2) is a blue-light-responsive plant photoreceptor domain that has been heterologously expressed in mammalian cells. In that context, blue light induces AtCRY2 photobody formation and also triggers AtCRY2 degradation, providing a light-controlled module linked to protein clustering and turnover.

Avena sativa LOV2 domain variants are engineered insertion modules used to build thermosensitive allosteric chimeric proteins. In Escherichia coli, insertion of optimized LOV2 variants into diverse, structurally and functionally unrelated proteins produced potent thermoswitchable variants operating within a narrow 37-41 °C range.

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.

The light-activated nuclear shuttle (LANS) domain is a protein domain used as a fusion module to confer light-controlled subcellular localization. In the cited 2020 yeast study, fusion of LANS to the Set2 methyltransferase enabled rapid and reversible optogenetic control of Set2 function.

Light-harvesting complex II (LHCII) is the major chlorophyll a/b-binding photosynthetic antenna complex of plants that has been studied in isolated native and recombinant forms. The cited literature indicates that light induces reversible conformational changes in LHCII that expose its N-terminal phosphorylation site and can also promote formation of dimeric LHCII states with distinct chlorophyll excitation-quenching properties.

The Light-Oxygen-Voltage (LOV) domain is a small blue-light-sensing protein domain used as an optogenetic input module. It binds flavin nucleotides and undergoes blue-light-induced structural rearrangements that can regulate linked effector domains, including in phototropins where LOV1 and LOV2 are coupled to a C-terminal serine/threonine kinase.

The LOV2 domain of Avena sativa phototropin is a PAS-family blue-light-sensing protein domain that binds flavin mononucleotide (FMN) and undergoes a self-contained photocycle. Illumination causes loss of blue-light absorbance consistent with formation of a flavin-cysteinyl adduct, followed by spontaneous dark recovery.

nano is the wild-type SspB protein used as the binding partner for iLID in a blue-light-responsive dimerization system. In the cited work, the iLID–nano pair is used to control protein interactions and localization with light.

PpSB1-LOV is a bacterial short LOV photosensory domain from Pseudomonas putida KT2440 with a light-induced flavin-cysteinyl photo-adduct and exceptionally slow dark recovery. It has been characterized as a compact LOV building block whose photocycle kinetics can be tuned by conserved hydrophobic-pocket mutation, including the I48T variant that accelerates adduct rupture while remaining structurally and mechanistically benign.

YtvA is a blue-light-sensing LOV-STAS photoreceptor from Bacillus subtilis whose LOV domain has been structurally analyzed for LOV-LOV dimerization and interdomain interactions. Homologous mutations in a conserved LOV hydrophobic pocket alter activation-state kinetics, supporting YtvA as a tunable LOV sensor domain relevant to optogenetic design.

dCas9* is a Streptococcus pyogenes dCas9 variant carrying the PAM-binding mutation R1335K, engineered to eliminate PAM recognition and reduce toxicity in bacteria. In the cited study, dCas9* was also fused to the PhlF repressor to recover targetable transcriptional repression through a combined sgRNA target site and PhlF operator requirement.

SpCas9 is the Streptococcus pyogenes Cas9 CRISPR effector protein used for programmable genome editing and gene regulation. In the cited study, its activity was controlled indirectly by microRNA-dependent expression of the anti-CRISPR protein AcrIIA4, enabling cell-type-restricted activation of full-length Cas9, split-Cas9, and dCas9-VP64 variants.

The ubiquitin-interacting motif (UIM) is a protein domain present in Eps15. In the cited Eps15 knockout-rescue live-cell imaging studies, deletion of the UIM abolished rescue of endocytic initiation defects, indicating that this motif is functionally required for Eps15 activity during clathrin-mediated endocytosis.

α-integrin cytoplasmic tails are short intracellular integrin tail domains that bind calcium and integrin binding protein 1 (CIB1). Evidence indicates that multiple α-integrin cytoplasmic tails engage a shared hydrophobic pocket on CIB1 through a consensus binding site and can compete for CIB1 binding in vitro.

Melanopsin (Opn4) is a light-responsive opsin used as an optogenetic protein domain to activate Gq-linked signaling. Supplied evidence indicates that melanopsin can be functionally linked to an NFAT control circuit and that light-driven activation in cardiomyocytes modulates beating rate and local pacemaker activity.

The LOV2 domain from Avena sativa phototropin-1 is a photosensitive protein domain used as a light-responsive module in optogenetic engineering. It has been fused to other functional elements, including a Keratin 8 2B2-derived peptide in PA-dIF, to confer photoactivatable regulation.

N282 is the N-terminal 282-amino-acid fragment of Arabidopsis COP1, derived from mutant cDNAs and expressed in transgenic plants as a dominant-negative protein domain. Its overexpression induces phenotypes and dark-grown genome expression patterns resembling cop1 loss-of-function and white-light responses, consistent with interference with endogenous COP1 repression of photomorphogenesis.

split-TurboID is a split proximity-labeling enzyme used in the Light Activated BioID (LAB) system, where its two halves are fused to the photodimeric proteins CRY2 and CIB1. Blue light induces CRY2–CIB1 association, reconstitutes split-TurboID, and triggers proximity-dependent biotinylation.

BcLOVclust is a cytoplasmic BcLOV4-derived protein domain engineered for light-controlled intracellular clustering. It enables optogenetic clustering in mammalian cells and has been applied to control signaling proteins and stress granules.

Beggiatoa sp. IS2 PAC (biPAC) is a blue light-responsive photoactivated adenylyl cyclase protein domain used in transfected macrophages. In the cited study, light activation of biPAC suppressed macrophage expression and production of the pro-inflammatory cytokines IL-1 and TNF-β1.

AcrIIC3 is an anti-CRISPR protein that inhibits Neisseria meningitidis Cas9 (NmeCas9). Engineered AcrIIC3-Avena sativa LOV2 hybrids function as blue-light-switchable NmeCas9 inhibitors, blocking genome editing in the dark and permitting robust editing under blue light.

Archaerhodopsin-3 (Arch) is a light-sensitive microbial rhodopsin proton pump used as an optogenetic inhibitory tool. The supplied evidence identifies Arch as a previously available optogenetic tool and specifically as an ion-pumping rhodopsin.

AsLOV2-Jα is the light-oxygen-voltage-2/Jα photoswitch domain from Avena sativa phototropin1. In the reported LOV-TAP fusion, ligation of AsLOV2-Jα to TrpR enables light-dependent control of DNA binding through photoinduced structural and electrostatic changes.

Aureochrome-1 (AUREO1) is a blue-light receptor from Vaucheria frigida with an N-terminal bZIP DNA-binding domain and a C-terminal LOV photosensory domain. Full-length AUREO1 binds DNA in a sequence-specific manner, and light signaling is transmitted from the LOV core via the hydrophobic region of the LOV β-sheet surface.

ChR2(C128A) is a C128A step-function mutant of channelrhodopsin-2 used as a light-responsive protein domain for prolonged optogenetic activation. The supplied evidence indicates that it is unsuitable for chronic neuronal stimulation but is useful for light-controlled induction of immediate early genes, including c-fos promoter-driven protein expression with precise timing and single-cell specificity.

Chrimson is a red light-activated channelrhodopsin with a reported crystal structure. It provides red-shifted optogenetic excitation and has been used with Chronos to support two-color activation of independent neural populations in mouse brain slice without detectable cross-talk.

CrLOV2 is the LOV2 photosensory domain from Chlamydomonas reinhardtii phototropin that has been mechanistically mapped for FMN photoadduct formation. It supports both the canonical triplet-state LOV photoreaction and a direct adduct-forming pathway from the initially excited S1 singlet state, with proton or hydrogen transfer coupling implicated in the direct channel.

Enhanced Magnets (eMags) are Vivid-derived light-sensitive protein dimerization domains used in optogenetic split transcription factors and subcellular recruitment systems. In Saccharomyces cerevisiae, optimized eMag-based transcription factor designs improved light-sensitive gene expression, and eMags were also validated for rapid, reversible protein recruitment to subcellular organelles.

Halorhodopsin (NpHR) is a microbial rhodopsin optogenetic tool described as a hyperpolarizing light-driven chloride ion pump. It is used for optical silencing and artificial modulation of neuronal activity, and has been combined with channelrhodopsin-2 (ChR2) for multimodal remote control of neurons in culture, tissue, and living animals.

Human inward rectifier K+ channel Kir2.1 was used as a protein scaffold to identify engineerable allosteric sites through domain insertion permissibility mapping. Insertion of light-switchable domains into existing or latent allosteric sites, but not other positions, rendered Kir2.1 activity sensitive to light.

The Avena sativa LOV2 domain is a blue-light-sensing photosensory domain used as a photoswitchable scaffold for engineered control of protein interactions. In the iLID design, the bacterial SsrA peptide is embedded in the LOV2 C-terminal helix so that blue light triggers helix undocking and enables binding to SspB.

LOVdeg is an engineered protein tag that is appended to a protein of interest to enable blue-light-inducible degradation in Escherichia coli. It provides optically controlled post-translational regulation by coupling light exposure to loss of the tagged protein.

OptoSTIM1 is an optogenetic protein tool engineered by combining the STIM1 SOAR region with a plant photoreceptor LOV2 domain. It manipulates intracellular Ca2+ levels by light-dependent activation of endogenous Ca2+-selective CRAC channels.

Phototropin is a plant blue-light receptor protein, exemplified by Avena sativa PHOT1/NPH1, that contains two FMN-binding LOV domains and a C-terminal serine/threonine kinase domain. It acts as a light-activated kinase in which LOV2-mediated conformational changes are coupled to kinase activation and signaling.

The Arabidopsis thaliana phototropin 1 LOV2 domain is a blue-light-sensing protein domain from phototropin 1 whose dark-adapted crystal structure has been determined. In this state, the domain is dimeric and contains an N-terminal A'α helix and a C-terminal Jα helix that contribute to coiled-coil-mediated dimerization.

Phytochromes are red/far-red light-sensing photoreceptor protein domains that serve as source scaffolds for engineered fluorescent proteins, biosensors, and optogenetic tools. In native signaling, photoactive phytochromes regulate transcription through direct interaction with PHYTOCHROME INTERACTING FACTOR proteins and through light-dependent inactivation of the COP1/SPA E3 ligase complex.

PpSB2-LOV is a compact "short" light, oxygen, voltage (LOV) photosensory protein from Pseudomonas putida KT2440. It forms a light-induced LOV photoadduct and exhibits rapid dark-state thermal recovery, with a reported recovery time of 3.5 min at 20 °C, making it a candidate building block for genetically encoded photoswitches.

The Avena sativa phototropin-1 LOV2 domain is a blue-light-sensing flavin-binding photosensory domain used as a module for light-controlled conformational uncaging. Available evidence shows that its dark-state recovery follows a base-catalyzed mechanism and that its light responsiveness is influenced by the flavin redox state.

CRYPTOCHROME-INTERACTING BASIC HELIX-LOOP-HELIX 1 (CIB1) is an Arabidopsis thaliana basic helix-loop-helix transcription factor that binds DNA and regulates transcriptional programs linked to cell elongation. It also physically interacts with the blue-light receptor CRYPTOCHROME 2 (CRY2) and has been described as promoting flowering.

Am1_c0023g2 is a cyanobacteriochrome photosensory domain from Acaryochloris marina that covalently binds either phycocyanobilin or biliverdin with high binding efficiency. It has been used as the light-responsive target for engineered, state-selective binders that enable green-, orange-, red-, and far-red-controlled protein-protein interactions and transcriptional regulation in yeast.

Photoactivated adenylyl cyclases are light-responsive adenylyl cyclase protein domains used as optogenetic tools to modulate intracellular cAMP levels. Reported effects include light-induced CREB signaling and Cox-2/prostaglandin E2 upregulation in HEK-293T cells, and altered starvation-induced development in Dictyostelium discoideum.