Biol. Chem. 2015; 396(2): 145–152

Minireview Konrad Müller, Sebastian Naumann, Wilfried Weber and Matias D. Zurbriggen*

Optogenetics for gene expression in mammalian cells Abstract: Molecular switches that are controlled by chemicals have evolved as central research instruments in mammalian cell biology. However, these tools are limited in terms of their spatiotemporal resolution due to freely diffusing inducers. These limitations have recently been addressed by the development of optogenetic, genetically encoded, and light-responsive tools that can be controlled with the unprecedented spatiotemporal precision of light. In this article, we first provide a brief overview of currently available optogenetic tools that have been designed to control diverse cellular processes. Then, we focus on recent developments in light-controlled gene expression technologies and provide the reader with a guideline for choosing the most suitable gene expression system. Keywords: gene expression; mammalian cell; optogenetics; photoreceptor; synthetic biology. DOI 10.1515/hsz-2014-0199 Received May 18, 2014; accepted July 29, 2014; previously published online August 2, 2014

Introduction Chemically controlled molecular switches have played a central role in the emergence of synthetic biology (Khalil and Collins, 2010) and have become routine tools in mammalian cell biology research. However, molecule-inherent *Corresponding author: Matias D. Zurbriggen, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, D-79104 Freiburg, Germany, e-mail: [email protected]; and Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 7D-9104 Freiburg, Germany Konrad Müller and Sebastian Naumann: Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 7D-9104 Freiburg, Germany Wilfried Weber: Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 7D-9104 Freiburg, Germany; and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, D-79104 Freiburg, Germany

drawbacks such as difficulties in removing the inducer and diffusion-based transport have prevented rapid reversibility and space-resolved activation. On the other hand, light offers unprecedented spatiotemporal resolution. Consequently, the development of light-controlled devices is highly desirable and has recently received much attention (Muller and Weber, 2013; Pathak et al., 2013; Williams and Deisseroth, 2013), resulting in the development of light-controlled tools in bacteria (Levskaya et al., 2005; Ohlendorf et al., 2012) and yeast (Shimizu-Sato et al., 2002; Yang et al., 2013) as well as in mammalian (Muller and Weber, 2013; Pathak et al., 2013) and in plant (Muller et al., 2014a) cells. The first light-controlled molecular tools were constructed by introducing photo-cleavable inhibiting chemical groups into inducers, nucleic acids, and transactivators that could be cleaved off in response to UVB light (Gardner and Deiters, 2012). However, a significant disadvantage of this method is the need to exogenously apply the caged molecules or to reprogram the translation machinery for the incorporation of non-natural amino acids. This disadvantage has been overcome by the optogenetic approach that combines optical and genetic methods to develop light-responsive tools. The first breakthrough in mammalian optogenetics was the discovery of microbial opsins (Nagel et  al., 2002, 2003) and their subsequent introduction in neuroscience that revolutionized the study of neuronal networks (Boyden et  al., 2005; Li et  al., 2005). Channelrhodopsin, the first opsin that was applied in mammalian neurons, becomes permeable to cations upon blue light illumination (Nagel et al., 2003), thus, triggering neuronal activation. Later, channelrhodopsin was joined by other ionotropic receptors, including the orange light-responsive, chloride pump halorhodopsin that made it possible to use dual-wavelength control to excite or inhibit neurons with subcellular resolution (Han and Boyden, 2007), even in intact brain tissue (Zhang et  al., 2007) and in moving animals (Nagel et al., 2005). Moving beyond neuroscience, more recent optogenetic tools have been developed to control diverse signaling processes in mammalian cells (Pathak et  al., 2013). To this end, photoreceptors from all kingdoms of life that provide

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146      K. Müller et al.: Optogenetics for gene expression in mammalian cells organisms with crucial environmental cues ­(Purschwitz et al., 2006; Purcell and Crosson, 2008; Sand et al., 2012) and that respond to light of distinct regions of the light spectrum have been employed as building blocks (Table 1). In this article, we focus on the latest developments in the optogenetic control of mammalian gene expression.

Light-inducible mammalian gene expression Optogenetic gene switches have been developed that either follow the two-hybrid principle and employ the light-regulated recruitment of a transcriptional activation domain to a DNA-bound protein or use the light-triggered homo-dimerization of a photoreceptor for the reconstitution of a DNA-binding domain to guide an activation domain to the target gene. The first optogenetic gene switch for mammalian cells was based on the blue light-inducible interaction between the Arabidopsis thaliana proteins flavin-binding kelch repeat F-box1 (FKF1) that contains a LOV domain and GIGANTEA (GI) (Yazawa et  al., 2009). GI was tethered to a response construct upstream of a minimal promoter by fusion to the Gal4 DNA-binding domain, while the N-terminal nuclear-localized part of FKF1 was fused to the VP16 transactivation domain (Figure 1A). Blue lightinduced recruitment of the FKF1-VP16 fusion protein to the response construct triggered a five-fold increase in reporter levels in HEK-293T cells. This system has recently been modified by replacing the Gal4 DNA-binding domain with a zinc finger protein and by multimerization of VP16 to three copies (Polstein and Gersbach, 2012). This setup did not permit control of endogenous genes but yielded reporter levels 53-fold above the unilluminated control from a reporter construct. A similar design has recently been applied to target endogenous genes using the blue light-regulated cryptochrome 2 (CRY2)-CIB1 interaction in A. thaliana ­(Konermann et  al., 2013). Following rigorous systematic optimization of the system’s components, the authors obtained a blue light-inducible gene switch that triggered up to 20-fold induction of endogenous gene expression in blue light compared to non-illuminated samples. The gene switch consists, on the one hand, of a transcription activator-like effector (TALE) domain, a novel class of DNA-binding domains that can be engineered to bind various target sequences (Moscou and Bogdanove, 2009), fused to truncated CRY2. On the other hand, the nuclearlocalized N-terminal part of CIB1 is linked to the VP64

transactivation domain and is recruited to DNA-bound CRY2 in response to blue light to initiate gene expression (Figure 1B). In another approach, Wang et  al. capitalized on the VVD protein from the mold Neurospora crassa to engineer an optogenetic gene switch based on light-inducible homodimerization (Wang et  al., 2012). A single fusion protein comprising a monomeric Gal4 DNA-binding domain, the LOV domain from VVD and the p65 transactivation domain (Figure 1C) allowed over 200-fold induction in blue light-illuminated HEK-293 cells compared to the dark-incubated control. Furthermore, the authors demonstrated dose-dependent tuning of expression levels as well as spatially controlled gene expression and applied the system in a mouse model of diabetes for the light-triggered production of therapeutic insulin. An alternative design for blue light-inducible gene expression used the human photopigment melanopsin to induce calcium influx and finally tapped into the endogenous factor of activated T cell (NFAT) pathway to activate expression from a NFAT-specific reporter construct (Ye et al., 2011a). This setup yielded a 20-fold induction of gene expression in HEK-293 cells, and the authors applied the system in a pilot bioproduction process and to treat diabetic mice by the light-induced production of the glucagon-like protein 1 from implanted cells. The blue light-inducible gene switches discussed above have provided an answer to the poor spatiotemporal control of chemically based systems. However, gene expression cannot be actively terminated because the systems return to the OFF state passively in the dark with half-life times ranging from minutes (CRY2-CIB1) to hours (FKF1-GI, VVD, melanopsin). This problem has now been alleviated by a gene switch that is based on the blue light-induced DNA binding of the bacterial LOV domaincontaining protein EL222 (Motta-Mena et al., 2014). EL222 contains a helix-turn-helix DNA-binding domain that is caged in the dark by interaction with the LOV domain. Blue light illumination releases this inhibition, triggering EL222 dimerization and binding to its cognate operator site. This binding is terminated in the dark within 50 s. A fusion of nuclear-targeted EL222 and the VP16 transactivation domain allowed over 100-fold induction of gene expression from a reporter construct harboring five repeats of the EL222 operator site upstream of a minimal promoter and the reporter gene in HEK-293T cells. Most importantly, gene expression was rapidly reversible upon illumination shut-off (Figure 1D). This newest addition to the toolbox of blue lightregulated gene switches has addressed the problem of slow reversibility. Still, this system cannot be actively

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UVB

Violet/ blue Blue

   

VVD PhyB

       

    LOV2 (from   phototropin 1)       CRY2             CRY2     EL222   FKF1     Melanopsin   PAC  

Dronpa

UVR8 UVR8

Photoreceptor  

– PIF6

– –

– GI



CIB1





– COP1

       

                                     

   

Interaction   partner

                                     

   



FMN   Phyco-cyanobilin     

11-cis-retinal FAD

FMN FMN

FAD

FMN





Co-factor



Homo-dimerization   Hetero-dimerization     

Homo-dimerization     Uncaging of   C-terminal fusions       Hetero-dimerization            Oligo-merization     Homo-dimerization   Hetero-dimerization    Ca 2+ influx   cAMP synthesis  

Homo-dimerization   Hetero-dimerization 

Mechanism

Applications



Gene expression Membrane recruitment/cell shape Signaling modulation Gene expression

       

Protein secretion   Nuclear import   Gene expression Chromatin targeting Membrane recruitment/cell shape   Proteolytic cleavage   Membrane recruitment/ Cell shape  Tunable protein dimerization   Nuclear import   Protein degradation   Membrane recruitment   Gene expression   Histone modification   Kinase activation   Phosphoinositide metabolism   Reversible protein inactivation   Signaling modulation   Kinase activation   Gene expression   Membrane recruitment/cell shape   Gene expression   Gene expression   Signaling modulation  

UVB, ∼280 nm–315 nm; violet, ∼380 nm–450 nm; blue, ∼450 nm–495 nm; red/far-red, ∼620 nm–750 nm.

  Red/far red     



Light

(Bugaj et al., 2013; Chang et al., 2014; Kim et al., 2014; Wend et al., 2014) (Motta-Mena et al., 2014) (Yazawa et al., 2009; Polstein and Gersbach, 2012) (Ye et al., 2011a) (Schroder-Lang et al., 2007; Stierl et al., 2011) (Wang et al., 2012) (Levskaya et al., 2009; Muller et al., 2013a; Toettcher et al., 2013)

(Kennedy et al., 2010; Idevall-Hagren et al., 2012; Konermann et al., 2013; Lee et al., 2014; Zhang et al., 2014)

(Wu et al., 2009; Strickland et al., 2012; Bonger et al., 2014; Niopek et al., 2014)

(Zhou et al., 2012)

(Chen et al., 2013) (Crefcoeur et al., 2013; Muller et al., 2013b)

References

Table 1 Overview of currently available optogenetic tools for mammalian systems (excluding ionotropic transmembrane receptors for studying neuronal processes).

K. Müller et al.: Optogenetics for gene expression in mammalian cells      147

148      K. Müller et al.: Optogenetics for gene expression in mammalian cells

A

FKF1

VP16

B

C VP64

Gl

CIB1

TALE (UASG)5

Pmin

goi

TALE binding site

450 nm

P

p65

Gal4(65)

goi

(UASG)5

CRY2 CIB1

VP16

goi

Pmin

D VP16 HTH (C120)5

TALE binding site

P

goi

VP16

VP16

PIF6 TetR

Pmin

660 nm

EL222 EL222 HTH

HTH

Pmin

(tetO)13

PIF6

UVR8

goi

E (etr)8

Pmin

goi

(tetO)13

Pmin

COP1

UVR8

VP16

VP16

Pmin

goi

311 nm

E

E (C120)5

COP1

UVR8

740 nm

PhyB

TetR

goi

Pmin

VP16

E

goi

VP16

(UASG)5

F

450 nm

VP16

p65

PhyB HTH

VVD

Gal4(65)

E EL222 EL222

VVD

VP64

TALE (UASG)5

goi

Pmin

460 nm p65

Gal4

Gal4(65)

466 nm

FKF1

Gl

VVD

p65

CRY2

Gal4

VVD

goi

(etr)8

Pmin

goi

Figure 1 Optogenetic gene switches for mammalian systems. (A) Blue light-inducible gene expression based on the FKF1-GI interaction. (B) Control of endogenous gene expression by combining TALEs with the blue light-responsive recruitment of CIB1 to CRY2. (C) Blue light-dependent transgene control based on homo-dimerization of VVD. (D) Optogenetic gene expression with rapid OFF kinetics using blue light-induced homo-dimerization the EL222 transcription factor. (E) Red/far-red light-switchable gene expression based on the PhyB-PIF6 interaction. (F) UVR8-COP1-dependent, UVB-inducible transgene expression.

switched between the ON and the OFF state, and the use of high-energy blue light raises concerns with regard to the stability of culture medium components (Wang, 1976), cytotoxicity (Cadet et al., 2012; Pattison et al., 2012; Crefcoeur et al., 2013), and tissue penetration that may limit the applicability of blue light-activated tools in certain scenarios. These drawbacks have been overcome by a phytochrome B-based gene switch that capitalizes on the red/far-red light-reversible interaction of PhyB and the phytochrome-interacting factor 6 (PIF6) from A. thaliana and can be toggled between stable ON and OFF states by illumination with low-energy red and far-red light, respectively (Muller et al., 2013a). Tethering PIF6 to a response construct via the TetR DNA-binding domain and fusing nuclear-targeted PhyB to the VP16 transactivation domain yielded a rapidly reversible gene switch with 60-fold induction levels in red light-, compared to far-red lightilluminated CHO-K1 cells (Muller et al., 2014b) (Figure 1E). This system has already been applied in vivo in an animal model of angiogenesis. Still, a major obstacle for many in vivo applications is the need to add the PhyB chromophore

phycocyanoblin (PCB). This limitation has been overcome by the engineering of mammalian cells to endogenously produce the chromophore from heme via the expression of two cyanobacterial enzymes (Muller et al., 2013c). This metabolic engineering approach opened the possibility to operate the red/far-red light switchable expression system in an entirely genetically encoded manner. When operated in isolation, light-responsive gene switches permit the expression of a single transgene with high spatiotemporal precision. However, most biological processes are not controlled by the expression of a single gene but require the concerted action of multiple genes (Davidson, 2010). To enable the control of these processes with the spatiotemporal resolution of light, it is necessary to combine and interconnect multiple orthogonal optogenetic gene switches. Such multi-chromatic control of gene expression has recently been demonstrated by combining red/far-red and blue light-responsive gene switches with a novel UVBcontrolled expression system (Muller et al., 2013b). This gene switch employs the UVB-triggered interaction between the UVR8 photoreceptor from A. thaliana and CONSTITUTIVELY

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K. Müller et al.: Optogenetics for gene expression in mammalian cells      149

PHOTOMORPHOGENIC 1 (COP1). Monomerization of UVR8, which is homodimeric in the absence of UVB illumination, is initiated upon absorption of UVB light by tryptophan clusters at the interaction interface, thus, triggering the recruitment of COP1. By tethering either the WD40 domain of COP1 (Crefcoeur et  al., 2013) or UVR8 (Muller et  al., 2013b) to a response construct upstream of a minimal promoter, it was possible to activate gene expression by recruiting p65-fused UVR8 or a fusion of the WD40 domain of COP1 and the VP16 transactivation domain, respectively, in response to UVB illumination (Figure 1F). The second setup resulted in an induction of gene expression of over 800-fold in UVB-illuminated CHO-K1 cells. To minimize UVB-induced toxicity, a detailed, mathematical model-assisted analysis of the kinetic properties of the system was performed, revealing a 2-h half-life time of the active state. Consequently, it was shown that UVB-related toxicity could be minimized by applying pulsed illumination, while retaining an excellent dynamic range of gene expression. The combination of this UVB-controlled gene switch with red/far-red and blue light-responsive gene expression technology allowed the consecutive activation of three genes in a single cell culture as well as the emulation of blood vessel formation in an in vitro model by the light-triggered sequential expression of growth factors (Muller et al., 2013b). Still, the overlapping absorbance spectra of the photoreceptors (Figure 2A) make their orthogonal operation within a single cell challenging (Figure 2B). It has been shown that the unique, toggle switch-like characteristics of the PhyB-PIF6-based system can be employed to establish orthogonality between the red/far-red light-responsive expression system and the blue light- or the UVB light-controlled gene switch (Muller et al., 2013b). To this end, the red/far-red light-controlled gene switch was co-transfected either with the VVD-based blue light-responsive system or with the UVB light-responsive UVR8-COP1 gene switch. Blue or UVB-dependent gene expression was then activated by pulses of blue or UVB light. At the same time, continuous far-red light illumination was applied to keep the red/ far-red light-responsive system in the OFF state (Figure 2C). Instead of using pulsed blue and UVB light illumination, it is also possible to keep the red/far-red light-responsive system in the OFF state under continuous blue/UVB light, by titrating the intensities of the activating blue/UVB light alongside the intensity of inactivating far-red light.

Conclusion The optogenetic gene switches outlined above constitute molecular tools with minimal technical requirements

Figure 2 Multichromatic control of gene expression. (A) Qualitative representation of the absorbance spectra of the photoreceptors. UVR8 exclusively absorbs UVB light, but the flavin-dependent blue light receptor VVD is activated by UV and by blue light and the inactive PhyBR form of phytochrome B absorbs UV, blue, and red light. PhBFR, active form of phytochrome B. The absorbance spectra are redrawn from (Pratt and Butler, 1970; ­Zoltowski et al., 2007; Christie et al., 2012), and the figure is adapted from Muller and Zubriggen (2013). (B) Lack of orthogonality with continuous illumination. The UVR8-COP1, VVD, and PhyB-PIF6based gene switches are not orthogonal under continuous illumination with UVB, blue, or red light. (C) Partial orthogonality with pulsed blue and UVB light illumination. The combination of pulsed blue and UVB light illumination with constant far-red light illumination results in orthogonality between the PhyB-PIF6 and the VVD or UVR8-COP1 system, but the VVD and UVR8-COP1 system cannot be operated in an orthogonal manner. In (B) and (C), a hyphen indicates no effect, while ‘OFF’ indicates active switching off.

(besides illumination devices such as light-emitting diodes, no elaborate equipment is needed) (Muller et al., 2014b) that permit the spatiotemporal control of gene expression in response to light and simple tuning of expression levels by adjusting the illumination conditions. However, the systems differ with regard to other important characteristics. These include the wavelength of activating light and the chromophore used for its perception, the light intensity required for activation as well as the system’s reversibility and the dynamic range of gene expression (Table 2). Other important features are the ease of handling, the ability to control genes in their native chromosomal context, and the potential for biomedical applications. To assist users in choosing the best-suited optogenetic gene expression system for their particular application, we have summarized important considerations in Table 3.

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150      K. Müller et al.: Optogenetics for gene expression in mammalian cells Table 2 Overview of key characteristics of light-inducible gene expression systems. Light



System

UVB



UVR8-COP1  





     

CRY2-CIB1     EL222  



GI-FKF1

Blue









   

Melanopsin  VVD  

Red/far-red 

PhyB-PIF6  

References



Intensity for maximal  activation [μmol/m2/s] a

Deactivation  kinetics

Expression   levels

Induction

(Muller et al.,   2013b) (Crefcoeur et al.,   2013) (Konermann   et al., 2013)   (Motta-Mena   et al., 2014) (Yazawa et al.,   2009) (Polstein and   Gersbach, 2012) (Ye et al., 2011a)  (Wang et al.,   2012) (Muller et al.,   2013a)

2.5 

T1/2–2 h 

N.A.



N.A. 

N.A.



 > 800-fold in CHO-K1  > 25-fold in U2OS

65 μmol/m2, then 4 h  without illumination 195  (1 s ON every 15 s)  31 

OFF in 15 min    OFF in   100-fold in HEK293T ∼5-fold in HEK-293T

N.D. (several hours) 

N.A.



53-fold in Hela

2.5 (5 s ON every 15 s)  3.2 

N.D. (several hours)  T1/2–2 h 

0.2 (1 h ON then 23 h  without illumination)

Instantaneous upon  740-nm illumination

N.A.   Comparable  to PhCMV ∼20% of Tet   system

∼20-fold in HEK-293  > 200-fold in HEK-293 60-fold in CHO-K1

N.A. not available. When available, the intensity for continuous illumination is provided, and the intensity of illumination is given in μmol/m2/s. For most systems, it is also possible to reach high induction levels with pulsed illumination. a

Table 3 Important factors to consider when choosing a gene expression system. Factor



Decision guidance

Wavelength



Deactivation kinetics



Dynamic range



Chromophore



Handling



If high tissue penetration is required, the red/far-red light-controlled gene switch (Muller et al., 2013a) may be the system of choice. This system is also suited for applications that require minimal toxicity. Alternatively, blue light-responsive systems that respond to low-intensity light [including the FKF1-GI (Yazawa et al., 2009), the VVD (Wang et al., 2012), and the melanopsin-based (Ye et al., 2011b) systems] may be used. If fast reversibility is important, the rapidly reversible blue light-responsive EL222-based tool (Motta-Mena et al., 2014) or the actively switchable red/far-red light-switchable expression system (Muller et al., 2013a) are most suited. The other systems have half-life times of minutes (CRY2-CIB1) or hours (FKF1-GI, VVD, melanopsin, UVR8-COP1). The FKF1-GI (Yazawa et al., 2009), CRY2-CIB1 (Konermann et al., 2013) and melanopsin-based (Ye et al., 2011b) systems are characterized by comparably low (less than 25-fold) induction of gene expression in the illuminated state. On the other hand, the modified FKF1-GI system (Polstein and Gersbach, 2012) and the PhyB-PIF6 (Muller et al., 2013a), EL222 (Motta-Mena et al., 2014), UVR8-COP1 (Crefcoeur et al., 2013; Muller et al., 2013b), and VVD-based (Wang et al., 2012) systems can be induced over 50-fold by illumination. The blue light-responsive expression systems use flavin chromophores that are present in mammalian cells, and UVB-inducible gene switches use tryptophan residues to sense activating light. Therefore, these systems do not require the exogenous addition of a chromophore. The same is true for the red/far-red lightresponsive gene switch, when combined with the chromophore biosynthesis in the cells. Blue light-responsive systems have to be protected from ambient light to prevent unintentional activation. On the other hand, UVB-responsive tools (Crefcoeur et al., 2013; Muller et al., 2013b) are not activated by room light and the red/far-red light-responsive gene switch (Muller et al., 2013a) is only rendered light sensitive upon addition of the chromophore. Only the CRY2-based expression system (Konermann et al., 2013) permits targeting of endogenous genes.

Activation of   endogenous genes Biomedical   application

If the immunogenicity of system components is an issue, the melanopsin-based expression system (Ye et al., 2011a) may be most suited. Although interference with cellular pathways is significant, its components are exclusively of human origin.

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K. Müller et al.: Optogenetics for gene expression in mammalian cells      151

There is a growing number of optogenetic tools that offer unprecedented spatiotemporal control and that can be combined for orthogonal multichromatic multi-gene control. These can be expected to influence experimental approaches in basic research and, thus, contribute to our understanding of biological processes. Moving beyond basic science, it will be exciting to witness the implementation of light-inducible chemical inducer-free bioproduction processes and the development of biomedical interventions with the precision of light. Indeed, while the functionality of most optogenetic gene switches has been demonstrated on a proof-of-concept level, first applications in fields of biomedicine (Ye et al., 2011a; Wang et al., 2012) and bioproduction (Ye et  al., 2011a) are starting to emerge. Acknowledgments: This work was supported by the Initiating and Networking Fund (IVF) of the Helmholtz Association within the Helmholtz Initiative on Synthetic Biology [SO-078], the Baden-Württemberg Stiftung, under the programme ‘Internationale Spitzenforschung II’ [P-LS-SPII/2]; the European Research Council under the European Community’s Seventh Framework Programme [FP7/2007-2013]/ERC [259043]-CompBioMat, the excellence initiative of the German Federal and State Governments [EXC 294-BIOSS, GSC 4-SGBM], and the Interreg IV Upper Rhine program project number A20.

References Bonger, K.M., Rakhit, R., Payumo, A.Y., Chen, J.K., and Wandless, T.J. (2014). General method for regulating protein stability with light. ACS Chem. Biol. 9, 111–115. Boyden, E.S., Zhang, F., Bamberg, E., Nagel, G., and Deisseroth, K. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nat. Neurosci. 8, 1263–1268. Bugaj, L.J., Choksi, A.T., Mesuda, C.K., Kane, R.S., and Schaffer, D.V. (2013). Optogenetic protein clustering and signaling activation in mammalian cells. Nat. Methods 10, 249–252. Cadet, J., Mouret, S., Ravanat, J.L., and Douki, T. (2012). ­Photoinduced damage to cellular DNA: direct and photosensitized reactions. Photochem. Photobiol. 88, 1048–1065. Chang, K.Y., Woo, D., Jung, H., Lee, S., Kim, S., Won, J., Kyung, T., Park, H., Kim, N., Yang, H.W., et al. (2014). Light-inducible receptor tyrosine kinases that regulate neurotrophin signalling. Nat. Commun. 5, 4057. Chen, D., Gibson, E.S., and Kennedy, M.J. (2013). A light-triggered protein secretion system. J. Cell Biol. 201, 631–640. Christie, J.M., Arvai, A.S., Baxter, K.J., Heilmann, M., Pratt, A.J., O’Hara, A., Kelly, S.M., Hothorn, M., Smith, B.O., Hitomi, K., et al. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335, 1492–1496.

Crefcoeur, R.P., Yin, R., Ulm, R., and Halazonetis, T.D. (2013). Ultraviolet-B-mediated induction of protein-protein i­ nteractions in mammalian cells. Nat. Commun. 4, 1779. Davidson, E.H. (2010). Emerging properties of animal gene regulatory networks. Nature 468, 911–920. Gardner, L. and Deiters, A. (2012). Light-controlled synthetic gene circuits. Curr. Opin. Chem. Biol. 16, 292–299. Han, X. and Boyden, E.S. (2007). Multiple-color optical activation, silencing, and desynchronization of neural activity, with singlespike temporal resolution. PLoS One 2, e299. Idevall-Hagren, O., Dickson, E.J., Hille, B., Toomre, D.K., and De Camilli, P. (2012). Optogenetic control of phosphoinositide metabolism. Proc. Natl. Acad. Sci. USA 109, E2316–2323. Kennedy, M.J., Hughes, R.M., Peteya, L.A., Schwartz, J.W., Ehlers, M.D., and Tucker, C.L. (2010). Rapid blue-lightmediated induction of protein interactions in living cells. Nat. Methods 7, 973–975. Khalil, A.S. and Collins, J.J. (2010). Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367–379. Kim, N., Kim, J.M., Lee, M., Kim, C.Y., Chang, K.Y., and Heo, W.D. (2014). Spatiotemporal control of fibroblast growth factor receptor signals by blue light. Chem. Biol. 21, 903–912. Konermann, S., Brigham, M.D., Trevino, A.E., Hsu, P.D., ­Heidenreich, M., Cong, L., Platt, R.J., Scott, D.A., Church, G.M., and Zhang, F. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472–476. Lee, S., Park, H., Kyung, T., Kim, N.Y., Kim, S., Kim, J., and Heo, W.D. (2014). Reversible protein inactivation by optogenetic trapping in cells. Nat. Methods 11, 633–636. Levskaya, A., Chevalier, A.A., Tabor, J.J., Simpson, Z.B., Lavery, L.A., Levy, M., Davidson, E.A., Scouras, A., Ellington, A.D., Marcotte, E.M., et al. (2005). Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441–442. Levskaya, A., Weiner, O.D., Lim, W.A., and Voigt, C.A. (2009). ­Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997–1001. Li, X., Gutierrez, D.V., Hanson, M.G., Han, J., Mark, M.D., Chiel, H., Hegemann, P., Landmesser, L.T., and Herlitze, S. (2005). Fast noninvasive activation and inhibition of neural and network activity by vertebrate rhodopsin and green algae channelrhodopsin. Proc. Natl. Acad. Sci. USA 102, 17816–17821. Moscou, M.J. and Bogdanove, A.J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501. Motta-Mena, L.B., Reade, A., Mallory, M.J., Glantz, S., Weiner, O.D., Lynch, K.W., and Gardner, K.H. (2014). An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat. Chem. Biol. 10, 196–202. Muller, K. and Weber, W. (2013). Optogenetic tools for mammalian systems. Mol. Biosyst. 9, 596–608. Muller, K. and Zubriggen, M.D. (2013). Licht-gesteuerte Kontrolle der Genexpression in Säugerzellen. BIOspektrum 19, 628–630. Muller, K., Engesser, R., Metzger, S., Schulz, S., Kampf, M.M., Busacker, M., Steinberg, T., Tomakidi, P., Ehrbar, M., Nagy, F., et al. (2013a). A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Res. 41, e77. Muller, K., Engesser, R., Schulz, S., Steinberg, T., Tomakidi, P., Weber, C.C., Ulm, R., Timmer, J., Zurbriggen, M.D., and Weber, W. (2013b). Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Res. 41, e124.

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152      K. Müller et al.: Optogenetics for gene expression in mammalian cells Muller, K., Engesser, R., Timmer, J., Nagy, F., Zurbriggen, M.D., and Weber, W. (2013c). Synthesis of phycocyanobilin in mammalian cells. Chem. Commun. (Camb) 49, 8970–8972. Muller, K., Siegel, D., Rodriguez Jahnke, F., Gerrer, K., Wend, S., Decker, E.L., Reski, R., Weber, W., and Zurbriggen, M.D. (2014a). A red light-controlled synthetic gene expression switch for plant systems. Mol. Biosyst. 10, 1679–1688. Muller, K., Zurbriggen, M.D., and Weber, W. (2014b). Control of gene expression using a red- and far-red light-responsive bi-stable toggle switch. Nat. Protoc. 9, 622–632. Nagel, G., Ollig, D., Fuhrmann, M., Kateriya, S., Musti, A.M., Bamberg, E., and Hegemann, P. (2002). Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296, 2395–2398. Nagel, G., Szellas, T., Huhn, W., Kateriya, S., Adeishvili, N., Berthold, P., Ollig, D., Hegemann, P., and Bamberg, E. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc. Natl. Acad. Sci. USA 100, 13940–13945. Nagel, G., Brauner, M., Liewald, J.F., Adeishvili, N., Bamberg, E., and Gottschalk, A. (2005). Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr. Biol. 15, 2279–2284. Niopek, D., Benzinger, D., Roensch, J., Draebing, T., Wehler, P., Eils, R., and Di Ventura, B. (2014). Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells. Nat. Commun. 5, 4404. Ohlendorf, R., Vidavski, R.R., Eldar, A., Moffat, K., and Moglich, A. (2012). From dusk till dawn: one-plasmid systems for lightregulated gene expression. J. Mol. Biol. 416, 534–542. Pathak, G.P., Vrana, J.D., and Tucker, C.L. (2013). Optogenetic control of cell function using engineered photoreceptors. Biol. Cell 105, 59–72. Pattison, D.I., Rahmanto, A.S., and Davies, M.J. (2012). Photo-oxidation of proteins. Photochem. Photobiol. Sci. 11, 38–53. Polstein, L.R. and Gersbach, C.A. (2012). Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors. J. Am. Chem. Soc. 134, 16480–16483. Pratt, L.H. and Butler, W.L. (1970). Phytochrome conversion by ultraviolet light. Photochem. Photobiol. 11, 503–509. Purcell, E.B. and Crosson, S. (2008). Photoregulation in prokaryotes. Curr. Opin. Microbiol. 11, 168–178. Purschwitz, J., Muller, S., Kastner, C., and Fischer, R. (2006). Seeing the rainbow: light sensing in fungi. Curr. Opin. Microbiol. 9, 566–571. Sand, A., Schmidt, T.M., and Kofuji, P. (2012). Diverse types of ­ganglion cell photoreceptors in the mammalian retina. Prog. Retin. Eye Res. 31, 287–302. Schroder-Lang, S., Schwarzel, M., Seifert, R., Strunker, T., Kateriya, S., Looser, J., Watanabe, M., Kaupp, U.B., Hegemann, P., and Nagel, G. (2007). Fast manipulation of cellular cAMP level by light in vivo. Nat. Methods 4, 39–42. Shimizu-Sato, S., Huq, E., Tepperman, J.M., and Quail, P.H. (2002). A light-switchable gene promoter system. Nat. Biotechnol. 20, 1041–1044.

Stierl, M., Stumpf, P., Udwari, D., Gueta, R., Hagedorn, R., Losi, A., Gartner, W., Petereit, L., Efetova, M., Schwarzel, M., et al. (2011). Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J. Biol. Chem. 286, 1181–1188. Strickland, D., Lin, Y., Wagner, E., Hope, C.M., Zayner, J., ­Antoniou, C., Sosnick, T.R., Weiss, E.L., and Glotzer, M. (2012). TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nat. Methods 9, 379–384. Toettcher, J.E., Weiner, O.D., and Lim, W.A. (2013). Using optogenetics to interrogate the dynamic control of signal transmission by the ras/erk module. Cell 155, 1422–1434. Wang, R.J. (1976). Effect of room fluorescent light on the deterioration of tissue culture medium. In Vitro 12, 19–22. Wang, X., Chen, X., and Yang, Y. (2012). Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 9, 266–269. Wend, S., Wagner, H.J., Muller, K., Zurbriggen, M.D., Weber, W., and Radziwill, G. (2014). Optogenetic control of protein kinase activity in mammalian cells. ACS Synth. Biol. 3, 280–285. Williams, S.C. and Deisseroth, K. (2013). Optogenetics. Proc. Natl. Acad. Sci. USA 110, 16287. Wu, Y.I., Frey, D., Lungu, O.I., Jaehrig, A., Schlichting, I., ­Kuhlman, B., and Hahn, K.M. (2009). A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461, 104–108. Yang, X., Jost, A.P., Weiner, O.D., and Tang, C. (2013). A lightinducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol. Biol. Cell 24, 2419–2430. Yazawa, M., Sadaghiani, A.M., Hsueh, B., and Dolmetsch, R.E. (2009). Induction of protein-protein interactions in live cells using light. Nat. Biotechnol. 27, 941–945. Ye, H., Daoud-El Baba, M., Peng, R.W., and Fussenegger, M. (2011a). A synthetic optogenetic transcription device enhances bloodglucose homeostasis in mice. Science 332, 1565–1568. Ye, H.F., Daoud-El Baba, M., Peng, R.W., and Fussenegger, M. (2011b). A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332, 1565–1568. Zhang, F., Wang, L.P., Brauner, M., Liewald, J.F., Kay, K., Watzke, N., Wood, P.G., Bamberg, E., Nagel, G., Gottschalk, A., et al. (2007). Multimodal fast optical interrogation of neural circuitry. Nature 446, 633–639. Zhang, K., Duan, L., Ong, Q., Lin, Z., Varman, P.M., Sung, K., and Cui, B. (2014). Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLoS One 9, e92917. Zhou, X.X., Chung, H.K., Lam, A.J., and Lin, M.Z. (2012). Optical control of protein activity by fluorescent protein domains. Science 338, 810–814. Zoltowski, B.D., Schwerdtfeger, C., Widom, J., Loros, J.J., ­Bilwes, A.M., Dunlap, J.C., and Crane, B.R. (2007). Conformational switching in the fungal light sensor Vivid. Science 316, 1054–1057.

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Optogenetics for gene expression in mammalian cells.

Molecular switches that are controlled by chemicals have evolved as central research instruments in mammalian cell biology. However, these tools are l...
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