Bayram O, Braus GH, Fischer R, Rodriguez-Romero J
(2010) Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol 47:900–908
Beiert T, Bruegmann T, Sasse P (2014) Optogenetic
activation of Gq signalling modulates pacemaker
activity of cardiomyocytes. Cardiovasc Res
102:507–516
Benner SA, Sismour AM (2005) Synthetic biology. Nat
Rev Genet 6:533–543
Bieszke JA, Braun EL, Bean LE et al (1999a) The nop-1
gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins. Proc Natl Acad Sci U
S A 96:8034–8039
Bieszke JA, Spudich EN, Scott KL et al (1999b) A
eukaryotic protein, NOP-1, binds retinal to form
an archaeal rhodopsin-like photochemically reactive pigment. Biochemistry 38:14138–14145
Blackwell M (2011) The Fungi: 1 2, 3 . . . 5.1 million
species? Am J Bot 98:426–438. https://doi.org/
10.3732/ajb.1000298
Blumenstein A, Vienken K, Tasler R et al (2005) The
Aspergillus nidulans phytochrome FphA represses
sexual development in red light. Curr Biol
15:1833–1838
Boyden ES, Zhang F, Bamberg E et al (2005)
Millisecond-timescale, genetically targeted optical
control of neural activity. Nat Neurosci 8:1263–
1268
Brenker K, Osthof K, Yang J, Reth M (2016) LED
thermo flow—combining optogenetics with flow
cytometry. J Vis Exp. https://doi.org/10.3791/
54707
Briggs WR (2014) Phototropism: some history some
puzzles, and a look ahead. Plant Physiol 164:13–
23. https://doi.org/10.1104/pp.113.230573
Bruegmann T, Malan D, Hesse M et al (2010) Optogenetic control of heart muscle in vitro and in vivo.
Nat Methods 7:897–900
Bugaj LJ, Choksi AT, Mesuda CK et al (2013) Optogenetic protein clustering and signaling activation in
mammalian cells. Nat Methods 10:249–252
Bugaj LJ, Spelke DP, Mesuda CK et al (2015) Regulation
of endogenous transmembrane receptors through
optogenetic Cry2 clustering. Nat Commun 6:6898
Canessa P, Schumacher J, Hevia MA et al (2013) Assessing the effects of light on differentiation and virulence of the plant pathogen Botrytis cinerea:
characterization of the White Collar Complex.
PLoS One 8:e84223
Carafoli E, Krebs J (2016) Why calcium? How calcium
became the best communicator. J Biol Chem
291:20849–20857
Castellanos F, Schmoll M, Martı ´nez P et al (2010) Crucial factors of the light perception machinery and
their impact on growth and cellulase gene transcription in Trichoderma reesei. Fungal Genet Biol
47:468–476
Cesbron F, Brunner M, Diernfellner AC (2013) Lightdependent and circadian transcription dynamics
in vivo recorded with a destabilized luciferase
reporter in Neurospora. PLoS One 8:e83660
Chen CH, Ringelberg CS, Gross RH et al (2009)
Genome-wide analysis of light-inducible responses
reveals hierarchical light signalling in Neurospora.
EMBO J 28:1029–1042
Chen CH, DeMay BS, Gladfelter AS et al (2010) Physical
interaction between VIVID and white collar complex regulates photoadaptation in Neurospora.
Proc Natl Acad Sci U S A 107:16715–16720
Cheng P, Yang Y, Wang L et al (2003) WHITE
COLLAR-1, a multifunctional neurospora protein
involved in the circadian feedback loops, light
sensing, and transcription repression of wc-2.
J Biol Chem 278:3801–3808
Christie JM, Salomon M, Nozue K et al (1999) LOV
(light, oxygen, or voltage) domains of the bluelight photoreceptor phototropin (nph1): binding
sites for the chromophore flavin mononucleotide.
Proc Natl Acad Sci U S A 96:8779–8783
Christie JM, Arvai AS, Baxter KJ et al (2012) Plant
UVR8 photoreceptor senses UV-B by tryptophanmediated disruption of cross-dimer salt bridges.
Science 335:1492–1496
Corrochano LM (2007) Fungal photoreceptors: sensory
molecules for fungal development and behaviour.
Photochem Photobiol Sci 6:725–736
Corrochano LM (2019) Light in the fungal world: from
photoreception to gene transcription and beyond.
Annu Rev Genet 53:149–170
Corrochano LM, Garre V (2010) Photobiology in the
Zygomycota: multiple photoreceptor genes for
complex responses to light. Fungal Genet Biol
47:893–899
Dasgupta A, Chen CH, Lee C et al (2015) Biological
significance of photoreceptor photocycle length:
VIVID photocycle governs the dynamic VIVIDwhite collar complex pool mediating photoadaptation and response to changes in light intensity. PLoS Genet 11:e1005215
Dean R, Van KJA, Pretorius ZA et al (2012) The Top 10
fungal pathogens in molecular plant pathology.
Mol Plant Pathol 13:414–430
Deisseroth K (2011) Optogenetics. Nat Methods 8:26–29
Drepper T, Krauss U, Meyer zu BS et al (2011) Lights on
and action! Controlling microbial gene expression
by light. Appl Microbiol Biotechnol 90:23–40
Essen LO (2006) Photolyases and cryptochromes: common mechanisms of DNA repair and light-driven
signaling? Curr Opin Struct Biol 16:51–59
Fairchild CD, Quail PH (1998) The phytochromes:
photosensory perception and signal transduction.
Symp Soc Exp Biol 51:85–92
Favory JJ, Stec A, Gruber H et al (2009) Interaction of
COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J 28:591–601
12 Exploiting Fungal Photobiology as a Source of Novel Bio-blocks for Optogenetic Systems
315
(2010) Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol 47:900–908
Beiert T, Bruegmann T, Sasse P (2014) Optogenetic
activation of Gq signalling modulates pacemaker
activity of cardiomyocytes. Cardiovasc Res
102:507–516
Benner SA, Sismour AM (2005) Synthetic biology. Nat
Rev Genet 6:533–543
Bieszke JA, Braun EL, Bean LE et al (1999a) The nop-1
gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins. Proc Natl Acad Sci U
S A 96:8034–8039
Bieszke JA, Spudich EN, Scott KL et al (1999b) A
eukaryotic protein, NOP-1, binds retinal to form
an archaeal rhodopsin-like photochemically reactive pigment. Biochemistry 38:14138–14145
Blackwell M (2011) The Fungi: 1 2, 3 . . . 5.1 million
species? Am J Bot 98:426–438. https://doi.org/
10.3732/ajb.1000298
Blumenstein A, Vienken K, Tasler R et al (2005) The
Aspergillus nidulans phytochrome FphA represses
sexual development in red light. Curr Biol
15:1833–1838
Boyden ES, Zhang F, Bamberg E et al (2005)
Millisecond-timescale, genetically targeted optical
control of neural activity. Nat Neurosci 8:1263–
1268
Brenker K, Osthof K, Yang J, Reth M (2016) LED
thermo flow—combining optogenetics with flow
cytometry. J Vis Exp. https://doi.org/10.3791/
54707
Briggs WR (2014) Phototropism: some history some
puzzles, and a look ahead. Plant Physiol 164:13–
23. https://doi.org/10.1104/pp.113.230573
Bruegmann T, Malan D, Hesse M et al (2010) Optogenetic control of heart muscle in vitro and in vivo.
Nat Methods 7:897–900
Bugaj LJ, Choksi AT, Mesuda CK et al (2013) Optogenetic protein clustering and signaling activation in
mammalian cells. Nat Methods 10:249–252
Bugaj LJ, Spelke DP, Mesuda CK et al (2015) Regulation
of endogenous transmembrane receptors through
optogenetic Cry2 clustering. Nat Commun 6:6898
Canessa P, Schumacher J, Hevia MA et al (2013) Assessing the effects of light on differentiation and virulence of the plant pathogen Botrytis cinerea:
characterization of the White Collar Complex.
PLoS One 8:e84223
Carafoli E, Krebs J (2016) Why calcium? How calcium
became the best communicator. J Biol Chem
291:20849–20857
Castellanos F, Schmoll M, Martı ´nez P et al (2010) Crucial factors of the light perception machinery and
their impact on growth and cellulase gene transcription in Trichoderma reesei. Fungal Genet Biol
47:468–476
Cesbron F, Brunner M, Diernfellner AC (2013) Lightdependent and circadian transcription dynamics
in vivo recorded with a destabilized luciferase
reporter in Neurospora. PLoS One 8:e83660
Chen CH, Ringelberg CS, Gross RH et al (2009)
Genome-wide analysis of light-inducible responses
reveals hierarchical light signalling in Neurospora.
EMBO J 28:1029–1042
Chen CH, DeMay BS, Gladfelter AS et al (2010) Physical
interaction between VIVID and white collar complex regulates photoadaptation in Neurospora.
Proc Natl Acad Sci U S A 107:16715–16720
Cheng P, Yang Y, Wang L et al (2003) WHITE
COLLAR-1, a multifunctional neurospora protein
involved in the circadian feedback loops, light
sensing, and transcription repression of wc-2.
J Biol Chem 278:3801–3808
Christie JM, Salomon M, Nozue K et al (1999) LOV
(light, oxygen, or voltage) domains of the bluelight photoreceptor phototropin (nph1): binding
sites for the chromophore flavin mononucleotide.
Proc Natl Acad Sci U S A 96:8779–8783
Christie JM, Arvai AS, Baxter KJ et al (2012) Plant
UVR8 photoreceptor senses UV-B by tryptophanmediated disruption of cross-dimer salt bridges.
Science 335:1492–1496
Corrochano LM (2007) Fungal photoreceptors: sensory
molecules for fungal development and behaviour.
Photochem Photobiol Sci 6:725–736
Corrochano LM (2019) Light in the fungal world: from
photoreception to gene transcription and beyond.
Annu Rev Genet 53:149–170
Corrochano LM, Garre V (2010) Photobiology in the
Zygomycota: multiple photoreceptor genes for
complex responses to light. Fungal Genet Biol
47:893–899
Dasgupta A, Chen CH, Lee C et al (2015) Biological
significance of photoreceptor photocycle length:
VIVID photocycle governs the dynamic VIVIDwhite collar complex pool mediating photoadaptation and response to changes in light intensity. PLoS Genet 11:e1005215
Dean R, Van KJA, Pretorius ZA et al (2012) The Top 10
fungal pathogens in molecular plant pathology.
Mol Plant Pathol 13:414–430
Deisseroth K (2011) Optogenetics. Nat Methods 8:26–29
Drepper T, Krauss U, Meyer zu BS et al (2011) Lights on
and action! Controlling microbial gene expression
by light. Appl Microbiol Biotechnol 90:23–40
Essen LO (2006) Photolyases and cryptochromes: common mechanisms of DNA repair and light-driven
signaling? Curr Opin Struct Biol 16:51–59
Fairchild CD, Quail PH (1998) The phytochromes:
photosensory perception and signal transduction.
Symp Soc Exp Biol 51:85–92
Favory JJ, Stec A, Gruber H et al (2009) Interaction of
COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J 28:591–601
12 Exploiting Fungal Photobiology as a Source of Novel Bio-blocks for Optogenetic Systems
315