Linden H, Macino G (1997) White collar 2, a partner in
blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa.
EMBO J 16:98–109
Liu Q, Tucker CL (2017) Engineering geneticallyencoded tools for optogenetic control of protein
activity. Curr Opin Chem Biol 40:17–23
Liu H, Yu X, Li K et al (2008) Photoexcited CRY2
interacts with CIB1 to regulate transcription and
floral initiation in Arabidopsis. Science 322:1535–
1539
Lorrain S, Genoud T, Fankhauser C (2006) Let there be
light in the nucleus! Curr Opin Plant Biol 9:509–
514
Ma Z, Du Z, Chen X et al (2013) Fine tuning the LightOn
light-switchable transgene expression system. Biochem Biophys Res Commun 440:419–423
Malzahn E, Ciprianidis S, Ka ´ldi K et al (2010) Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains.
Cell 142:762–772
Mao D, Li N, Xiong Z et al (2019) Single-cell optogenetic control of calcium signaling with a highdensity micro-LED array. iScience 21:403–412
Martinez D, Berka RM, Henrissat B et al (2008) Genome
sequencing and analysis of the biomass-degrading
fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26:553–560
McIsaac RS, Oakes BL, Wang X et al (2013) Synthetic
gene expression perturbation systems with rapid,
tunable, single-gene specificity in yeast. Nucleic
Acids Res 41:e57
McLellan MA, Rosenthal NA, Pinto AR (2017) CreloxP-mediated recombination: general principles
and experimental considerations. Curr Protoc
Mouse Biol 7:1–12
Melyan Z, Tarttelin EE, Bellingham J et al (2005) Addition of human melanopsin renders mammalian
cells photoresponsive. Nature 433:741–745
Mo ¨glich A, Moffat K (2010) Engineered photoreceptors
as novel optogenetic tools. Photochem Photobiol
Sci 9:1286–1300
Motta-Mena LB, Reade A, Mallory MJ et al (2014) An
optogenetic gene expression system with rapid
activation and deactivation kinetics. Nat Chem
Biol 10:196–202
Mu ¨hlha ¨user WW, Fischer A, Weber W, Radziwill G
(2017) Optogenetics—bringing light into the darkness of mammalian signal transduction. Biochim
Biophys Acta Mol Cell Res 1864:280–292
Mu ¨ller K, Engesser R, Metzger S et al (2013a) A red/farred light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic
Acids Res 41:e77
Mu ¨ller K, Engesser R, Timmer J et al (2013b) Synthesis
of phycocyanobilin in mammalian cells. Chem
Commun (Camb) 49:8970–8972
Mu ¨ller K, Zurbriggen MD, Weber W (2014) Control of
gene expression using a red- and far-red lightresponsive bi-stable toggle switch. Nat Protoc
9:622–632
Nagel G, Szellas T, Huhn W et al (2003)
Channelrhodopsin-2, a directly light-gated
cation-selective membrane channel. Proc Natl
Acad Sci U S A 100:13940–13945
Navara KJ, Nelson RJ (2007) The dark side of light at
night: physiological epidemiological, and ecological consequences. J Pineal Res 43:215–224. https://
doi.org/10.1111/j.1600-079x.2007.00473.x
Nihongaki Y, Kawano F, Nakajima T, Sato M (2015a)
Photoactivatable CRISPR-Cas9 for optogenetic
genome editing. Nat Biotechnol 33:755–760
Nihongaki Y, Yamamoto S, Kawano F et al (2015b)
CRISPR-Cas9-based photoactivatable transcription system. Chem Biol 22:169–174
Olmedo M, Ruger-Herreros C, Luque EM, Corrochano
LM (2010) A complex photoreceptor system mediates the regulation by light of the conidiation
genes con-10 and con-6 in Neurospora crassa. Fungal Genet Biol 47:352–363
Oravecz A, Baumann A, Ma ´te ´ Z et al (2006) CONSTITUTIVELY PHOTOMORPHOGENIC1 is required
for the UV-B response in Arabidopsis. Plant Cell
18:1975–1990
Pathak GP, Strickland D, Vrana JD, Tucker CL (2014)
Benchmarking of optical dimerizer systems. ACS
Synth Biol 3:832–838
Polstein LR, Gersbach CA (2015) A light-inducible
CRISPR-Cas9 system for control of endogenous
gene activation. Nat Chem Biol 11:198–200
Pudasaini A, El-Arab KK, Zoltowski BD (2015) LOVbased optogenetic devices: light-driven modules to
impart photoregulated control of cellular signaling. Front Mol Biosci 2:18
Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev
Mol Cell Biol 10:410–422
Purschwitz J, Mu ¨ller S, Kastner C et al (2008) Functional and physical interaction of blue- and redlight sensors in Aspergillus nidulans. Curr Biol
18:255–259
Quail PH (2010) Phytochromes. Curr Biol 20:R504–
R507
Renicke C, Schuster D, Usherenko S et al (2013) A
LOV2 domain-based optogenetic tool to control
protein degradation and cellular function. Chem
Biol 20:619–626
Rizzini L, Favory JJ, Cloix C et al (2011) Perception of
UV-B by the Arabidopsis UVR8 protein. Science
332:103–106
Robertson JB, Davis CR, Johnson CH (2013) Visible
light alters yeast metabolic rhythms by inhibiting
respiration. Proc Natl Acad Sci U S A 110:21130–
21135
Rullan M, Benzinger D, Schmidt GW et al (2018) An
optogenetic platform for real-time, single-cell
interrogation of stochastic transcriptional regulation. Mol Cell 70:745–756.e6
12 Exploiting Fungal Photobiology as a Source of Novel Bio-blocks for Optogenetic Systems
317
blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa.
EMBO J 16:98–109
Liu Q, Tucker CL (2017) Engineering geneticallyencoded tools for optogenetic control of protein
activity. Curr Opin Chem Biol 40:17–23
Liu H, Yu X, Li K et al (2008) Photoexcited CRY2
interacts with CIB1 to regulate transcription and
floral initiation in Arabidopsis. Science 322:1535–
1539
Lorrain S, Genoud T, Fankhauser C (2006) Let there be
light in the nucleus! Curr Opin Plant Biol 9:509–
514
Ma Z, Du Z, Chen X et al (2013) Fine tuning the LightOn
light-switchable transgene expression system. Biochem Biophys Res Commun 440:419–423
Malzahn E, Ciprianidis S, Ka ´ldi K et al (2010) Photoadaptation in Neurospora by competitive interaction of activating and inhibitory LOV domains.
Cell 142:762–772
Mao D, Li N, Xiong Z et al (2019) Single-cell optogenetic control of calcium signaling with a highdensity micro-LED array. iScience 21:403–412
Martinez D, Berka RM, Henrissat B et al (2008) Genome
sequencing and analysis of the biomass-degrading
fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26:553–560
McIsaac RS, Oakes BL, Wang X et al (2013) Synthetic
gene expression perturbation systems with rapid,
tunable, single-gene specificity in yeast. Nucleic
Acids Res 41:e57
McLellan MA, Rosenthal NA, Pinto AR (2017) CreloxP-mediated recombination: general principles
and experimental considerations. Curr Protoc
Mouse Biol 7:1–12
Melyan Z, Tarttelin EE, Bellingham J et al (2005) Addition of human melanopsin renders mammalian
cells photoresponsive. Nature 433:741–745
Mo ¨glich A, Moffat K (2010) Engineered photoreceptors
as novel optogenetic tools. Photochem Photobiol
Sci 9:1286–1300
Motta-Mena LB, Reade A, Mallory MJ et al (2014) An
optogenetic gene expression system with rapid
activation and deactivation kinetics. Nat Chem
Biol 10:196–202
Mu ¨hlha ¨user WW, Fischer A, Weber W, Radziwill G
(2017) Optogenetics—bringing light into the darkness of mammalian signal transduction. Biochim
Biophys Acta Mol Cell Res 1864:280–292
Mu ¨ller K, Engesser R, Metzger S et al (2013a) A red/farred light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic
Acids Res 41:e77
Mu ¨ller K, Engesser R, Timmer J et al (2013b) Synthesis
of phycocyanobilin in mammalian cells. Chem
Commun (Camb) 49:8970–8972
Mu ¨ller K, Zurbriggen MD, Weber W (2014) Control of
gene expression using a red- and far-red lightresponsive bi-stable toggle switch. Nat Protoc
9:622–632
Nagel G, Szellas T, Huhn W et al (2003)
Channelrhodopsin-2, a directly light-gated
cation-selective membrane channel. Proc Natl
Acad Sci U S A 100:13940–13945
Navara KJ, Nelson RJ (2007) The dark side of light at
night: physiological epidemiological, and ecological consequences. J Pineal Res 43:215–224. https://
doi.org/10.1111/j.1600-079x.2007.00473.x
Nihongaki Y, Kawano F, Nakajima T, Sato M (2015a)
Photoactivatable CRISPR-Cas9 for optogenetic
genome editing. Nat Biotechnol 33:755–760
Nihongaki Y, Yamamoto S, Kawano F et al (2015b)
CRISPR-Cas9-based photoactivatable transcription system. Chem Biol 22:169–174
Olmedo M, Ruger-Herreros C, Luque EM, Corrochano
LM (2010) A complex photoreceptor system mediates the regulation by light of the conidiation
genes con-10 and con-6 in Neurospora crassa. Fungal Genet Biol 47:352–363
Oravecz A, Baumann A, Ma ´te ´ Z et al (2006) CONSTITUTIVELY PHOTOMORPHOGENIC1 is required
for the UV-B response in Arabidopsis. Plant Cell
18:1975–1990
Pathak GP, Strickland D, Vrana JD, Tucker CL (2014)
Benchmarking of optical dimerizer systems. ACS
Synth Biol 3:832–838
Polstein LR, Gersbach CA (2015) A light-inducible
CRISPR-Cas9 system for control of endogenous
gene activation. Nat Chem Biol 11:198–200
Pudasaini A, El-Arab KK, Zoltowski BD (2015) LOVbased optogenetic devices: light-driven modules to
impart photoregulated control of cellular signaling. Front Mol Biosci 2:18
Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev
Mol Cell Biol 10:410–422
Purschwitz J, Mu ¨ller S, Kastner C et al (2008) Functional and physical interaction of blue- and redlight sensors in Aspergillus nidulans. Curr Biol
18:255–259
Quail PH (2010) Phytochromes. Curr Biol 20:R504–
R507
Renicke C, Schuster D, Usherenko S et al (2013) A
LOV2 domain-based optogenetic tool to control
protein degradation and cellular function. Chem
Biol 20:619–626
Rizzini L, Favory JJ, Cloix C et al (2011) Perception of
UV-B by the Arabidopsis UVR8 protein. Science
332:103–106
Robertson JB, Davis CR, Johnson CH (2013) Visible
light alters yeast metabolic rhythms by inhibiting
respiration. Proc Natl Acad Sci U S A 110:21130–
21135
Rullan M, Benzinger D, Schmidt GW et al (2018) An
optogenetic platform for real-time, single-cell
interrogation of stochastic transcriptional regulation. Mol Cell 70:745–756.e6
12 Exploiting Fungal Photobiology as a Source of Novel Bio-blocks for Optogenetic Systems
317