Optogenetics: Light-control of genes, pathways, and cells

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Introduction: Optogenenetics refers to a family of techniques which allow modulation of biological processes using light. Over the past 12 years, optogenetics has revolutionized neuroscience and is now expanding to impact many fields of biology. There are now genetic tools which can be used for photo-control of signal transduction, gene expression, apoptosis, histone modification, cytoskeletal dynamics, and many more processes.


The incredible power of optogenetics comes from the very high spatial and temporal resolution possible using light, as opposed to chemical or genetic effects. Optogenetics can also be combined with other genetic or chemical approaches to further increase the level of experimental control. For example, optogenetic constructs can be targeted to specific cell types or subcellular locations, or can be engineered to require specific chemical cofactors, further limiting when and where light-induced effects will occur.

The key component of an optogenetics experiment are light-sensitive proteins or protein domains. Membrane-bound rhodopsin family-members were the first proteins to be used as optogenetic actuators in neuroscience. Rhodopsins can be either type I, which are generally channels or pumps, and can be used to modulate voltage and ion gradients across membranes, or type II, which are GPCR family members, and allow broad effects on cellular signaling pathways (1-3). Newer, engineered optogenetic tools consist of diverse photo-sensor domains linked to protein domains which mediate a biological function specified by the researcher. Here are a few examples of how some photo-sensor domains have been used in optogenetic experiments.

The light-oxygen-voltage sensor (LOV) family domains are used to engineer chimeric proteins in which photoexcitation controls dimerization and conformational changes. Some notable examples include using the AsLOV2 domain to optogenetically inhibit REST, a master regulator of neural genes (4), using the VVD domain linked to caspase-9 to optically control apoptosis5, use of the LOV2 domain to introduce allosteric switches into diverse motility signaling proteins (6), and using AsLOV2 to regulate the binding of tetracycline to the Tet repressor (7). Blue-light sensor (BLUF) domains induce more limited structural changes in response to light, and have been used to regulate transcription factor activity (8), and to control nucleotidyl cyclases (9). Cryptochrome (CRY) domains have been used for light-dependent control of the Raf/MEK/ERK pathway (10), have been combined with the transcription activator-like effector (TALE) DNA-binding domains to allow optogenetic control of gene expression and epigenetic modifications (11), and have been combined with the CRISPR/Cas9 system to achieve light-controlled genome editing (12).

References

  1. Fenno L, Yizhar O, Deisseroth K. The development and application of optogenetics. Annu Rev Neurosci. 2011;34:389-412.
  2. Zhang F, Vierock J, Yizhar O, Fenno LE, Tsunoda S, Kianianmomeni A, Prigge M, Berndt A, Cushman J, Polle J, Magnuson J, Hegemann P, Deisseroth K. The microbial opsin family of optogenetic tools. Cell. 2011 Dec 23;147(7):1446-57.
  3. Koyanagi M, Terakita A. Diversity of animal opsin-based pigments and their optogenetic potential. Biochim Biophys Acta. 2014 May;1837(5):710-6.
  4. Paonessa F, Criscuolo S, Sacchetti S, Amoroso D, Scarongella H, Pecoraro Bisogni F, Carminati E, Pruzzo G, Maragliano L, Cesca F, Benfenati F. Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor. Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):E91-100.
  5. Nihongaki Y, Suzuki H, Kawano F, Sato M. Genetically engineered photoinducible homodimerization system with improved dimer-forming efficiency. ACS Chem Biol. 2014 Mar 21;9(3):617-21.
  6. Dagliyan O, Tarnawski M, Chu PH, Shirvanyants D, Schlichting I, Dokholyan NV, Hahn KM. Engineering extrinsic disorder to control protein activity in living cells. Science. 2016 Dec 16;354(6318):1441-1444.
  7. Moon J, Gam J, Lee SG, Suh YG, Lee J. Light-regulated tetracycline binding to the Tet repressor. Chemistry. 2014 Feb 24;20(9):2508-14.
  8. Masuda S, Nakatani Y, Ren S, Tanaka M. Blue light-mediated manipulation of transcription factor activity in vivo. ACS Chem Biol. 2013 Dec 20;8(12):2649-53.
  9. Ryu MH, Moskvin OV, Siltberg-Liberles J, Gomelsky M. Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J Biol Chem. 2010 Dec 31;285(53):41501-8.
  10. Zhang K, Duan L, Ong Q, Lin Z, Varman PM, Sung K, Cui B. Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLoS One. 2014 Mar 25;9(3):e92917.
  11. Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F. Optical control of mammalian endogenous transcription and epigenetic states. Nature. 2013 Aug 22;500(7463):472-6.
  12. Nihongaki Y, Kawano F, Nakajima T, Sato M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat Biotechnol. 2015 Jul;33(7):755-60.

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