|
Term
|
Definition |
|---|---|
| A | |
| AdoCbl | Adenosylcobalamin (5'-deoxyadenosine). A cofactor of the cobalamin-binding domain photoreceptors. |
| AsLOV2 | LOV2 domain of Avena sativa Phototropin 1. A blue light responsive photoreceptor. |
| AtLOV2 | LOV2 domain of Arabidopsis thaliana Phototropin 1. A blue light responsive photoreceptor. |
| B | |
| BLUF domain | Blue-light-utilizing flavin adenine dinucleotide (FAD) domain. A class of blue light responsive optogenetic switches, which for their function require FAD. |
| BV | Biliverdin. A cofactor of some of the phytochromes. |
| BcLOV4 | Botrytis cinerea LOV 4; alternatively named BcRGS1 (for Botrytis cinerea regulator of G-protein signaling 1). A blue light responsive LOV domain photoreceptor from Botrytis cinerea. |
| BlaC | Bacterial light-activated adenylyl cyclase; alternatively named bPAC (for Beggiatoa photoactivated adenylyl cyclase). A blue light responsive BLUF domain-coupled adenylyl cyclase. |
| BlgC | Bacterial light-activated guanylyl cyclase. A blue light responsive BLUF domain-coupled guanylyl cyclase, derived from photoactivated adenylyl cyclase bPAC by the introduction of point mutations in its substrate-binding pocket. |
| BlrP1 | Blue light-regulated phosphodiesterase 1. |
| BphG | Bacterial phytochrome G. |
| BphP1 | Bacterial phytochrome P1; also known as RpBphP1. A far-red/red light responsive bathy phytochrome photoreceptor from Rhodopseudomonas palustris. |
| BphS | A BphG-derived optogenetic switch. |
| C | |
| CBD | Cobalamin-binding domain. |
| CIB1 | Cryptochrome-interacting basic helix-loop-helix (bHLH) 1. Blue light dependent interaction partner of the CRY2 photoreceptor. |
| CIBN | N-terminal portion (a truncated version) of CIB1, commonly amino acids 1-170. Blue light dependent interaction partner of the CRY2 photoreceptor. |
| CNCbl | Cyanocobalamin. A cofactor of the cobalamin-binding domain photoreceptors. |
| COP1 | Constitutive photomorphogenic 1. UV light dependent interaction partner of the UVR8 photoreceptor. |
| CRY2 | Cryptochrome 2. A blue light responsive photoreceptor from Arabidopsis thaliana. |
| CRY2clust | CRY2-derived optogenetic switch for enhanced CRY2 homooligomerization. |
| CRY2olig | CRY2-derived optogenetic switch for enhanced CRY2 homooligomerization. |
| CcaR | Chromatic acclimation regulator. |
| CcaS | Chromatic acclimation sensor. A green light responsive photoreceptor from Synechocystis sp. PCC 6803. |
| Cph1 | Cyanobacterial phytochrome 1. A red/far-red light responsive photoreceptor from Synechocystis sp. PCC 6803. |
| Cph8 | A chimeric light receptor, which is a fusion of the photoreceptor Cph1 and the EnvZ histidine kinase from E. coli. |
| CrLOV1 | LOV1 domain from Chlamydomonas reinhardtii Photoropin. A blue light responsive photoreceptor. |
| D | |
| DGC | Diguanylate cyclase. |
| DrBphP | Deinococcus radiodurans bacterial phytochrome. A red/far-red light responsive photoreceptor from Deinococcus radiodurans. |
| Dronpa145K | Wild type Dronpa. In optogenetics, Dronpa145K is commonly used as an alternative label for the wild type photochromic florescent protein Dronpa, to more clearly distinguish between the wild type and the Lys145Asn mutant of the protein. |
| Dronpa145K/N | Wild type Dronpa & Dronpa Lys145Asn. |
| Dronpa145N | Dronpa Lys145Asn. A mutant of the photochromic florescent protein Dronpa. |
| E | |
| EAL | A conserved protein domain with the diguanylate (c-di-GMP) phosphodiesterase activity; named after its conserved residues. |
| EB1 | "EAL-BLUF 1" fragment of Magnetococcus marinus BldP. A blue light-activated c-di-GMP phosphodiesterase. |
| EL222 | Erythrobacter litoralis 222 amino acid protein. A blue light responsive LOV domain photoreceptor, which contains also a HTH motif. |
| F | |
| FAD | Flavin adenine dinucleotide (i.e. riboflavin 5'-adenosine diphosphate). |
| FHL | Far-red elongated hypocotyl 1-like. Red light dependent interaction partner of the PhyA photoreceptor. |
| FHY1 | Far-red elongated hypocotyl 1. Red light dependent interaction partner of the PhyA photoreceptor. |
| FKF1 | Flavin-binding kelch repeat F-box 1. A blue light responsive LOV domain photoreceptor from Arabidopsis thaliana. |
| FMN | Flavin mononucleotide (i.e. riboflavin 5'-monophosphate). |
| G | |
| GGDEF | A conserved protein domain with diguanylate cyclase activity, whereby GTP is consumed as a substrate to synthesize c-di-GMP. |
| GI | GIGANTEA. Blue light dependent interaction partner of the FKF1 photoreceptor. |
| GTP | Guanosine triphosphate. |
| H | |
| HTH motif | Helix-turn-helix motif. A major protein structural motif, composed of two α helices joined by a short strand of amino acids, which is capable of binding DNA. |
| I | |
| IlaC | Infrared light-activated adenylyl cyclase. |
| L | |
| LAPD | Light-activated phosphodiesterase. |
| LOV domain | Light-oxygen-voltage-sensing domain. A class of blue light responsive optogenetic switches. |
| LOVTRAP | AsLOV2-derived optogenetic switch for blue light inducible protein dissociation. |
| M | |
| Magnets | VVD-derived optogenetic switch for blue light inducible heterodimerization, obtained by divergent engineering of VVD. It consists of a pMag and a nMag VVD-derivative. |
| MetCbl | Methylcobalamin. A cofactor of the cobalamin-binding domain photoreceptors. |
| MxCBD | Cobalamin-binding domain from Myxococcus xanthus. A green light responsive photoreceptor. |
| N | |
| NIR light | Near-infrared light. |
| NcWC1-LOV | LOV domain of Neurospora crassa White Collar-1. A blue light responsive photoreceptor. |
| NgPAC | Naegleria gruberi photoactivated adenylyl cyclase. A blue light responsive BLUF domain-coupled adenylyl cyclase. |
| O | |
| OaPAC | Oscillatoria acuminata photoactivated adenylyl cyclase. A blue light responsive BLUF domain-coupled adenylyl cyclase. |
| P | |
| PAC | Photoactivated adenylyl cyclase. |
| PCB | Phycocyanobilin. |
| PDE | Phosphodiesterase. |
| PIF3 | Phytochrome interacting factor 3. Red light dependent interaction partner of the PhyB photoreceptor. |
| PIF6 | Phytochrome interacting factor 6. Red light dependent interaction partner of the PhyB photoreceptor. |
| POI | Protein of interest. |
| PYP | Photoactive yellow protein. A blue light responsive photoreceptor from Halorhodospira halophila. |
| Pfr | Far-red light absorbing form of a phytochrome. |
| PhyA | Phytochrome A. A red/far-red light responsive photoreceptor from Arabidopsis thaliana. |
| PhyB | Phytochrome B. A red/far-red light responsive photoreceptor from Arabidopsis thaliana. |
| PixD | A blue light responsive BLUF domain photoreceptor from Synechocystis sp. PCC 6803. |
| PixE | Blue light dependent interaction partner of the PixD photoreceptor. |
| PpsR2 | Far-red light dependent interaction partner of the BphP1 photoreceptor. |
| Pr | Red light absorbing form of a phytochrome. |
| Q | |
| Q-PAS1 | A truncated (minimal) variant of PpsR2, a far-red light dependent interaction partner of the BphP1 photoreceptor. Q-PAS1 is one third of the size of PpsR2 and is, unlike PpsR2, unable to homooligomerize. |
| R | |
| RF | Riboflavin. |
| ROS | Reactive oxygen species. |
| RsLOV | LOV domain from Rhodobacter sphaeroides. A blue light responsive photoreceptor. |
| S | |
| SspB | Stringent starvation protein B. |
| SsrA | Stringent starvation response A. |
| T | |
| TULIP | Tunable, light-controlled interacting protein tag system. AsLOV2-derived optogenetic switch for blue light inducible heterodimerization. |
| TtCBD | Cobalamin-binding domain from Thermus thermophilus. A green light responsive photoreceptor. |
| U | |
| UV light | Ultraviolet light. |
| UVR8 | UV-B resistance locus 8. An UV light responsive photoreceptor from Arabidopsis thaliana. |
| UirR | UV intensity response regulator. |
| UirS | UV intensity response sensor. A violet light responsive photoreceptor from Synechocystis sp. PCC 6803. |
| V | |
| VVD | Vivid. A blue light responsive LOV domain photoreceptor from Neurospora crassa. |
| VfAU1-LOV | LOV domain of Vaucheria frigida Aureochrome 1. A blue light responsive photoreceptor. |
| Y | |
| YtvA | A blue light responsive LOV domain photoreceptor from Bacillus subtilis. |
| Z | |
| Zdk | Zdark. A small protein, consisting of a tightly folded three helix bundle, that selectively binds to the dark state of the AsLOV2 photoreceptor. It was generated by mRNA display screening of a library based on the Z subunit of immunoglobulin binding staphylococcal protein A. |
| bPAC | Beggiatoa photoactivated adenylyl cyclase; alternatively named BlaC (for bacterial light-activated adenylyl cyclase). A blue light responsive BLUF domain-coupled adenylyl cyclase. |
| bathy phytochrome | A phytochrome that has a Pfr ground state and in the dark undergoes a conversion from Pr to Pfr, as opposed to the "classical" phytochromes, which have Pr as a ground state. |
| c-di-GMP | Cyclic diguanylate monophosphate. A second messenger, synthesized from 2 molecules of GTP by diguanylate cyclase. |
| cAMP | Cyclic adenosine monophosphate. A second messenger, synthesized from ATP by adenylyl cyclase. |
| cGMP | Cyclic guanosine monophosphate. A second messenger, synthesized from GTP by guanylyl cyclase. |
| cPAC | Cyanobacteriochrome-based photoactivated adenylyl cyclase. |
| chromophore | Chemical group in a compound or macromolecule that absorbs visible or ultraviolet light. |
| euPAC | Euglena gracilis photoactivated adenylyl cyclase. A blue light responsive BLUF domain-coupled adenylyl cyclase. |
| iLID | Improved light inducible dimer. AsLOV2-derived optogenetic switch for blue light inducible heterodimerization. |
| mPAC | Microcoleus photoactivated adenylyl cyclase. A blue light responsive BLUF domain-coupled adenylyl cyclase from Microcoleus chthonoplastes. |
| miniSOG | Mini singlet oxygen generator. A protein photosensitizer, engineered from Arabidopsis thaliana phototropin 2, that upon blue light illumination generates reactive oxygen species to trigger irreversible inactivation of nearby proteins or cell ablation. |
| nMag | Negative Magnet. One of the halves of the optogenetic switch Magnets. |
| p-coumaric acid | β-(4-hydroxyphenyl)acrylic acid. A cofactor of the photoreceptor PYP. |
| pGpG | 5'-phosphoguanylyl-(3'-5')- guanosine. The c-di-GMP degradation product, obtained when a c-di-GMP-specific phosphodisterase hydrolizes a single phosphodiester group in c-di-GMP. |
| pMag | Positive Magnet. One of the halves of the optogenetic switch Magnets. |
| pdDronpa1 | Photodissociable dimeric Dronpa 1. |
