Optogenetic switches for light-controlled gene expression in yeast
- 2k Downloads
Light is increasingly recognized as an efficient means of controlling diverse biological processes with high spatiotemporal resolution. Optogenetic switches are molecular devices for regulating light-controlled gene expression, protein localization, signal transduction and protein-protein interactions. Such molecular components have been mainly developed through the use of photoreceptors, which upon light stimulation undergo conformational changes passing to an active state. The current repertoires of optogenetic switches include red, blue and UV-B light photoreceptors and have been implemented in a broad spectrum of biological platforms. In this review, we revisit different optogenetic switches that have been used in diverse biological platforms, with emphasis on those used for light-controlled gene expression in the budding yeast Saccharomyces cerevisiae. The implementation of these switches overcomes the use of traditional chemical inducers, allowing precise control of gene expression at lower costs, without leaving chemical traces, and positively impacting the production of high-value metabolites and heterologous proteins. Additionally, we highlight the potential of utilizing this technology beyond laboratory strains, by optimizing it for use in yeasts tamed for industrial processes. Finally, we discuss how fungal photoreceptors could serve as a source of biological parts for the development of novel optogenetic switches with improved characteristics. Although optogenetic tools have had a strong impact on basic research, their use in applied sciences is still undervalued. Therefore, the invitation for the future is to utilize this technology in biotechnological and industrial settings.
KeywordsLight Optogenetic switch Yeast Fungal photoreceptors Synthetic biology
We are grateful to all members of Larrondo’s lab for their constructive comments on this review and Michael Handford (Universidad de Chile) for language support. No yeast cells were harmed during the writing of this article. This work was supported by Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB, grant no. NC120043), CONICYT/FONDECYT to L.F.L. (grant no. 1131030) and CONICYT/FONDECYT to E.A. (grant no. 1130822). F.S. was supported by CONICYT/FONDECYT postdoctoral fellowship (grant no. 3150156) and V.D. by CONICYT/PhD Scholarship (grant no. 6313018).
Compliance with ethical standards
This article does not contain any studies with human participants or animals performed by any of the authors.
Conflict of interest
The authors declare that they have no conflict of interest.
- Bergström A, Simpson JT, Salinas F, Barre B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G (2014) A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 31(4):872–888. doi: 10.1093/molbev/msu037 CrossRefPubMedPubMedCentralGoogle Scholar
- Canessa P, Schumacher J, Hevia MA, Tudzynski P, Larrondo LF (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(12):e84223. doi: 10.1371/journal.pone.0084223 CrossRefPubMedPubMedCentralGoogle Scholar
- Christie JM, Arvai AS, Baxter KJ, Heilmann M, Pratt AJ, O’Hara A, Kelly SM, Hothorn M, Smith BO, Hitomi K, Jenkins GI, Getzoff ED (2012) Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335(6075):1492–1496. doi: 10.1126/science.1218091 CrossRefPubMedPubMedCentralGoogle Scholar
- Cloix C, Kaiserli E, Heilmann M, Baxter KJ, Brown BA, O’Hara A, Smith BO, Christie JM, Jenkins GI (2012) C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein. Proc Natl Acad Sci U S A 109(40):16366–16370. doi: 10.1073/pnas.1210898109 CrossRefPubMedPubMedCentralGoogle Scholar
- Favory JJ, Stec A, Gruber H, Rizzini L, Oravecz A, Funk M, Albert A, Cloix C, Jenkins GI, Oakeley EJ, Seidlitz HK, Nagy F, Ulm R (2009) Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J 28(5):591–601. doi: 10.1038/emboj.2009.4 CrossRefPubMedPubMedCentralGoogle Scholar
- Folcher M, Oesterle S, Zwicky K, Thekkottil T, Heymoz J, Hohmann M, Christen M, Daoud El-Baba M, Buchmann P, Fussenegger M (2014) Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant. Nat Commun 5:5392. doi: 10.1038/ncomms6392 CrossRefPubMedPubMedCentralGoogle Scholar
- Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA 3rd (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A 105(51):20404–20409. doi: 10.1073/pnas.0811011106 CrossRefPubMedPubMedCentralGoogle Scholar
- Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B (2015) Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc Natl Acad Sci U S A 112(1):112–117. doi: 10.1073/pnas.1417910112 CrossRefPubMedGoogle Scholar
- Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O’Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ (2009) Population genomics of domestic and wild yeasts. Nature 458(7236):337–341. doi: 10.1038/nature07743 CrossRefPubMedPubMedCentralGoogle Scholar
- Müller K, Engesser R, Metzger S, Schulz S, Kampf MM, Busacker M, Steinberg T, Tomakidi P, Ehrbar M, Nagy F, Timmer J, Zubriggen MD, Weber W (2013a) A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Res 41(7):e77. doi: 10.1093/nar/gkt002 CrossRefPubMedPubMedCentralGoogle Scholar
- Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR, Teoh KH, Reed DW, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens KW, Fickes S, Galazzo J, Gaucher SP, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade LF, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello PS, Keasling JD, Reiling KK, Renninger NS, Newman JD (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496(7446):528–532. doi: 10.1038/nature12051 CrossRefPubMedGoogle Scholar
- Zhu Y, Tepperman JM, Fairchild CD, Quail PH (2000) Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3. Proc Natl Acad Sci U S A 97(24):13419–13424. doi: 10.1073/pnas.230433797 CrossRefPubMedPubMedCentralGoogle Scholar