A red light–responsive photoswitch for deep tissue optogenetics

Kuwasaki, Yuto; Suzuki, Kazushi; Yu, Gaigai; Yamamoto, Shota; Otabe, Takahiro; Kakihara, Yuki; Nishiwaki, Michiru; Miyake, Kunihito; Fushimi, Keiji; Bekdash, Ramsey; Shimizu, Yoshihiro; Narikawa, Rei; Nakajima, Takahiro; Yazawa, Masayuki; Sato, Moritoshi

doi:10.1038/s41587-022-01351-w

Cited by 32 publications

(28 citation statements)

References 59 publications

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“…This is equally true for light-responsive TCSs e.g., (Levskaya et al, 2005;Möglich et al, 2009;Multamäki et al, 2022), and oligomerization-based setups e.g., (Chen et al, 2016;Li et al, 2020;Dietler et al, 2021;Kaberniuk et al, 2021;Romano et al, 2021), either of which can be altered by substituting one photosensor module for another. The latter category stands to benefit from years of basic research and genome mining that provided diverse photoreceptor pairs that associate or dissociate upon light exposure (Strauss et al, 2005;Guntas et al, 2015;Wang et al, 2016;Redchuk et al, 2017;Kuwasaki et al, 2022). Promisingly, recent reports demonstrated the functional expression of plant phytochromes (Raghavan et al, 2020) and cryptochromes (McQuillen et al, 2022) in E. coli, thus raising the prospect of bacterial use of these photoreceptors which underpin manifold and highly stringent optogenetic systems in mammalian cells.…”

Section: Perspectivesmentioning

confidence: 99%

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Ohlendorf

Möglich²

2022

Front. Bioeng. Biotechnol.

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Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.

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Section: Perspectivesmentioning

confidence: 99%

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Ohlendorf

Möglich²

2022

Front. Bioeng. Biotechnol.

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“…Green light activates bacterial transcription factor CarH (~525 nm), requiring cyanocobalamin (vitamin B12) [ 16 ] and the dissociation of PCB-dependent cyanobacteriochrome Am1_c0023g2 (~525 nm) and its partner BAm green [ 17 ]. Far-red (650–750) light activates the binding of PCB-dependent phytochrome B (PhyB) to PIF3 [ 18 ] or PIF6 [ 19 ]; biliverdin-dependent photosensors include c-di-GMP-producing BphS (~730 nm) [ 20 ], MagRed pair [ 21 ] (~660 nm) and oligomerizing iLight [ 22 ] (~660 nm). Near-infrared (NIR) light (750–900 nm) activates biliverdin-dependent bacteriophytochrome-based Rp BphP1-PpsR2 [ 23 ] and Rp BphP1-QPAS1 [ 2 ] (~780 nm) pairs.…”

Section: Introductionmentioning

confidence: 99%

Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore

Chernov

Manoilov

Oliinyk

et al. 2023

IJMS

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Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.

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“…Gene expression during development, homeostatic maintenance and environmental responses in living cells is highly dynamic. To understand the functional significance of dynamic gene expression changes, light-controllable gene expression systems have been developed and are being continuously updated (Crefcoeur et al, 2013;Hallett et al, 2016;Hörner et al, 2017;Konermann et al, 2013;Motta-Mena et al, 2014;Pathak et al, 2017;Polstein and Gersbach, 2012;Shimizu-Sato et al, 2002;Wang et al, 2012;Yazawa et al, 2009;Quejada et al, 2017;Yamada et al, 2018;Liu et al, 2012;Müller et al, 2013b;Zhou et al, 2022;Yamada et al, 2020;Kasatkina et al, 2022;Kuwasaki et al, 2022). Light-controlled gene expression systems are versatile tools to manipulate cellular functions at fine spatiotemporal resolution (Imayoshi et al, 2013;Chan et al, 2015;Nihongaki et al, 2017;Isomura et al, 2017;Shao et al, 2018;Yoshioka-Kobayashi et al, 2020;Zhou et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, various types of photo-activatable (PA) molecules such as Cry2-CIB1 (Kennedy et al, 2010;Aoki et al, 2017;Taslimi et al, 2016;Quejada et al, 2017), Vivid (VVD) (Wang et al, 2012), Magnet (Kawano et al, 2015;di Pietro et al, 2021), tunable light-controlled interacting protein tags (TULIPs) (Strickland et al, 2012), and original light-inducible dimer/improved light-inducible dimer (oLID/iLID) (Guntas et al, 2015;Hallett et al, 2016) have been incorporated to the Gal4/UAS system to develop blue-light inducible PA-gene expression systems. In addition, optical switches responsive to other wavelengths of light such as ultraviolet (Müller et al, 2013a) or near-infrared (Kaberniuk et al, 2016;Redchuk et al, 2017;Kasatkina et al, 2022;Kuwasaki et al, 2022) light, have been integrated for multi-wavelength controls of gene expression systems including the Gal4/UAS system.…”

Section: Introductionmentioning

confidence: 99%

Enhancement of Vivid-based photo-activatable Gal4 transcription factor in mammalian cells

Nagasaki

Fukuda

Yamada

et al. 2023

Cell Struct. Funct.

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The Gal4/UAS system is a versatile tool to manipulate exogenous gene expression of cells spatially and temporally in many model organisms. Many variations of light-controllable Gal4/UAS system are now available, following the development of photo-activatable (PA) molecular switches and integration of these tools. However, many PA-Gal4 transcription factors have undesired background transcription activities even in dark conditions, and this severely attenuates reliable light-controlled gene expression. Therefore, it is important to develop reliable PA-Gal4 transcription factors with robust light-induced gene expression and limited background activity. By optimization of synthetic PA-Gal4 transcription factors, we have validated configurations of Gal4 DNA biding domain, transcription activation domain and blue light-dependent dimer formation molecule Vivid (VVD), and applied types of transcription activation domains to develop a new PA-Gal4 transcription factor we have named eGAV (enhanced Gal4-VVD transcription factor). Background activity of eGAV in dark conditions was significantly lower than that of hGAVPO, a commonly used PA-Gal4 transcription factor, and maximum light-induced gene expression levels were also improved. Light-controlled gene expression was verified in cultured HEK293T cells with plasmid-transient transfections, and in mouse EpH4 cells with lentivirus vectormediated transduction. Furthermore, light-controlled eGAV-mediated transcription was confirmed in transfected neural stem cells and progenitors in developing and adult mouse brain and chick spinal cord, and in adult mouse hepatocytes, demonstrating that eGAV can be applied to a wide range of experimental systems and model organisms.

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A red light–responsive photoswitch for deep tissue optogenetics

Cited by 32 publications

References 59 publications

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore

Enhancement of Vivid-based photo-activatable Gal4 transcription factor in mammalian cells

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