Glossary

A list of commonly used terms in optogenetics, together with short definitions.
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.
BeCyclOp
Blastocladiella emersonii cyclase opsin; alternatively named BeGC1 (for Blastocladiella emersonii guanylyl cyclase 1). A green light responsive opsin-coupled guanylyl cyclase.
BeGC1
Blastocladiella emersonii guanylyl cyclase 1; alternatively named BeCyclOp (for Blastocladiella emersonii cyclase opsin). A green light responsive opsin-coupled guanylyl cyclase.
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.