Foley BJ, Stutts H, Schmitt SL et al (2018) Characterization of a vivid homolog in Botrytis cinerea. Photochem Photobiol 94:985–993
Froehlich AC, Liu Y, Loros JJ, Dunlap JC (2002) White
Collar-1, a circadian blue light photoreceptor,
binding to the frequency promoter. Science
297:815–819
Froehlich AC, Chen CH, Belden WJ et al (2010) Genetic
and molecular characterization of a cryptochrome
from the filamentous fungus Neurospora crassa.
Eukaryot Cell 9:738–750
Fuller KK, Dunlap JC, Loros JJ (2016) Fungal light sensing at the bench and beyond. Adv Genet 96:1–51
Fuller KK, Dunlap JC, Loros JJ (2018) Light-regulated
promoters for tunable, temporal, and affordable
control of fungal gene expression. Appl Microbiol
Biotechnol 102:3849–3863
Galagan JE, Calvo SE, Borkovich KA et al (2003) The
genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868
Gautier A, Gauron C, Volovitch M et al (2014) How to
control proteins with light in living systems. Nat
Chem Biol 10:533–541
Gerhardt KP, Olson EJ, Castillo-Hair SM et al (2016) An
open-hardware platform for optogenetics and
photobiology. Sci Rep 6:35363
Gin E, Diernfellner AC, Brunner M, Ho ¨fer T (2013) The
Neurospora photoreceptor VIVID exerts negative
and positive control on light sensing to achieve
adaptation. Mol Syst Biol 9:667
Glantz ST, Carpenter EJ, Melkonian M et al (2016)
Functional and topological diversity of LOV
domain photoreceptors. Proc Natl Acad Sci U S
A 113:E1442–E1451
Glantz ST, Berlew EE, Jaber Z et al (2018) Directly lightregulated binding of RGS-LOV photoreceptors to
anionic membrane phospholipids. Proc Natl Acad
Sci U S A 115:E7720–E7727
Goffeau A, Barrell BG, Bussey H et al (1996) Life with
6000 genes. Science 274(546):563–567
Guinn MT, Bala ´zsi G (2019) Noise-reducing optogenetic negative-feedback gene circuits in human
cells. Nucleic Acids Res 47:7703–7714
Gyalai-Korpos M, Nagy G, Mareczky Z et al (2010)
Relevance of the light signaling machinery for
cellulase expression in Trichoderma reesei (Hypocrea jecorina). BMC Res Notes 3:330
Han X, Boyden ES (2007) Multiple-color optical activation, silencing, and desynchronization of neural
activity, with single-spike temporal resolution.
PLoS One 2:e299
Harper SM, Neil LC, Gardner KH (2003) Structural
basis of a phototropin light switch. Science
301:1541–1544
He Q, Liu Y (2005) Molecular mechanism of light
responses in Neurospora: from light-induced
transcription to photoadaptation. Genes Dev
19:2888–2899
He Q, Cheng P, Yang Y et al (2002) White collar-1, a
DNA binding transcription factor and a light sensor. Science 297:840–843
Herrera-Estrella A, Horwitz BA (2007) Looking through
the eyes of fungi: molecular genetics of photoreception. Mol Microbiol 64:5–15
Hevia MA, Canessa P, Mu ¨ller-Esparza H, Larrondo LF
(2015) A circadian oscillator in the fungus Botrytis
cinerea regulates virulence when infecting Arabidopsis thaliana. Proc Natl Acad Sci U S A
112:8744–8749
Hughes J, Lamparter T, Mittmann F et al (1997) A
prokaryotic phytochrome. Nature 386:663
Hughes RM, Bolger S, Tapadia H, Tucker CL (2012)
Light-mediated control of DNA transcription in
yeast. Methods 58:385–391
Hunt SM, Thompson S, Elvin M, Heintzen C (2010)
VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase
to alter light and clock responses in Neurospora.
Proc Natl Acad Sci U S A 107:16709–16714
Hurley JM, Chen CH, Loros JJ, Dunlap JC (2012) Lightinducible system for tunable protein expression in
Neurospora crassa. G3 (Bethesda) 2:1207–1212
Idnurm A, Heitman J (2005) Photosensing fungi: phytochrome in the spotlight. Curr Biol 15:R829–R832
Idnurm A, Verma S, Corrochano LM (2010) A glimpse
into the basis of vision in the kingdom Mycota.
Fungal Genet Biol 47:881–892
Jenkins GI (2017) Photomorphogenic responses to
ultraviolet-B light. Plant Cell Environ 40:2544–
2557
Kaberniuk AA, Shemetov AA, Verkhusha VV (2016) A
bacterial phytochrome-based optogenetic system
controllable with near-infrared light. Nat Methods
13:591–597
Kawano F, Suzuki H, Furuya A, Sato M (2015) Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins. Nat Commun
6:6256
Kawano F, Okazaki R, Yazawa M, Sato M (2016) A
photoactivatable Cre-loxP recombination system
for optogenetic genome engineering. Nat Chem
Biol 12:1059–1064
Kennedy MJ, Hughes RM, Peteya LA et al (2010) Rapid
blue-light-mediated induction of protein interactions in living cells. Nat Methods 7:973–975
Kojadinovic M, Laugraud A, Vuillet L et al (2008) Dual
role for a bacteriophytochrome in the bioenergetic
control of Rhodopseudomonas palustris: enhancement of photosystem synthesis and limitation of
respiration. Biochim Biophys Acta 1777:163–172
Kolar K, Knobloch C, Stork H et al (2018) OptoBase: a
web platform for molecular optogenetics. ACS
Synth Biol 7:1825–1828
Lee S, Park H, Kyung T et al (2014) Reversible protein
inactivation by optogenetic trapping in cells. Nat
Methods 11:633–636
316
V. Rojas et al.
Froehlich AC, Liu Y, Loros JJ, Dunlap JC (2002) White
Collar-1, a circadian blue light photoreceptor,
binding to the frequency promoter. Science
297:815–819
Froehlich AC, Chen CH, Belden WJ et al (2010) Genetic
and molecular characterization of a cryptochrome
from the filamentous fungus Neurospora crassa.
Eukaryot Cell 9:738–750
Fuller KK, Dunlap JC, Loros JJ (2016) Fungal light sensing at the bench and beyond. Adv Genet 96:1–51
Fuller KK, Dunlap JC, Loros JJ (2018) Light-regulated
promoters for tunable, temporal, and affordable
control of fungal gene expression. Appl Microbiol
Biotechnol 102:3849–3863
Galagan JE, Calvo SE, Borkovich KA et al (2003) The
genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859–868
Gautier A, Gauron C, Volovitch M et al (2014) How to
control proteins with light in living systems. Nat
Chem Biol 10:533–541
Gerhardt KP, Olson EJ, Castillo-Hair SM et al (2016) An
open-hardware platform for optogenetics and
photobiology. Sci Rep 6:35363
Gin E, Diernfellner AC, Brunner M, Ho ¨fer T (2013) The
Neurospora photoreceptor VIVID exerts negative
and positive control on light sensing to achieve
adaptation. Mol Syst Biol 9:667
Glantz ST, Carpenter EJ, Melkonian M et al (2016)
Functional and topological diversity of LOV
domain photoreceptors. Proc Natl Acad Sci U S
A 113:E1442–E1451
Glantz ST, Berlew EE, Jaber Z et al (2018) Directly lightregulated binding of RGS-LOV photoreceptors to
anionic membrane phospholipids. Proc Natl Acad
Sci U S A 115:E7720–E7727
Goffeau A, Barrell BG, Bussey H et al (1996) Life with
6000 genes. Science 274(546):563–567
Guinn MT, Bala ´zsi G (2019) Noise-reducing optogenetic negative-feedback gene circuits in human
cells. Nucleic Acids Res 47:7703–7714
Gyalai-Korpos M, Nagy G, Mareczky Z et al (2010)
Relevance of the light signaling machinery for
cellulase expression in Trichoderma reesei (Hypocrea jecorina). BMC Res Notes 3:330
Han X, Boyden ES (2007) Multiple-color optical activation, silencing, and desynchronization of neural
activity, with single-spike temporal resolution.
PLoS One 2:e299
Harper SM, Neil LC, Gardner KH (2003) Structural
basis of a phototropin light switch. Science
301:1541–1544
He Q, Liu Y (2005) Molecular mechanism of light
responses in Neurospora: from light-induced
transcription to photoadaptation. Genes Dev
19:2888–2899
He Q, Cheng P, Yang Y et al (2002) White collar-1, a
DNA binding transcription factor and a light sensor. Science 297:840–843
Herrera-Estrella A, Horwitz BA (2007) Looking through
the eyes of fungi: molecular genetics of photoreception. Mol Microbiol 64:5–15
Hevia MA, Canessa P, Mu ¨ller-Esparza H, Larrondo LF
(2015) A circadian oscillator in the fungus Botrytis
cinerea regulates virulence when infecting Arabidopsis thaliana. Proc Natl Acad Sci U S A
112:8744–8749
Hughes J, Lamparter T, Mittmann F et al (1997) A
prokaryotic phytochrome. Nature 386:663
Hughes RM, Bolger S, Tapadia H, Tucker CL (2012)
Light-mediated control of DNA transcription in
yeast. Methods 58:385–391
Hunt SM, Thompson S, Elvin M, Heintzen C (2010)
VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase
to alter light and clock responses in Neurospora.
Proc Natl Acad Sci U S A 107:16709–16714
Hurley JM, Chen CH, Loros JJ, Dunlap JC (2012) Lightinducible system for tunable protein expression in
Neurospora crassa. G3 (Bethesda) 2:1207–1212
Idnurm A, Heitman J (2005) Photosensing fungi: phytochrome in the spotlight. Curr Biol 15:R829–R832
Idnurm A, Verma S, Corrochano LM (2010) A glimpse
into the basis of vision in the kingdom Mycota.
Fungal Genet Biol 47:881–892
Jenkins GI (2017) Photomorphogenic responses to
ultraviolet-B light. Plant Cell Environ 40:2544–
2557
Kaberniuk AA, Shemetov AA, Verkhusha VV (2016) A
bacterial phytochrome-based optogenetic system
controllable with near-infrared light. Nat Methods
13:591–597
Kawano F, Suzuki H, Furuya A, Sato M (2015) Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins. Nat Commun
6:6256
Kawano F, Okazaki R, Yazawa M, Sato M (2016) A
photoactivatable Cre-loxP recombination system
for optogenetic genome engineering. Nat Chem
Biol 12:1059–1064
Kennedy MJ, Hughes RM, Peteya LA et al (2010) Rapid
blue-light-mediated induction of protein interactions in living cells. Nat Methods 7:973–975
Kojadinovic M, Laugraud A, Vuillet L et al (2008) Dual
role for a bacteriophytochrome in the bioenergetic
control of Rhodopseudomonas palustris: enhancement of photosystem synthesis and limitation of
respiration. Biochim Biophys Acta 1777:163–172
Kolar K, Knobloch C, Stork H et al (2018) OptoBase: a
web platform for molecular optogenetics. ACS
Synth Biol 7:1825–1828
Lee S, Park H, Kyung T et al (2014) Reversible protein
inactivation by optogenetic trapping in cells. Nat
Methods 11:633–636
316
V. Rojas et al.