Book contents
- OptogeneticsFrom Neuronal Function to Mapping and Disease Biology
- Optogenetics
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Optogenetics in Model Organisms
- Part II Opsin Biology, Tools, and Technology Platform
- 6 Sodium and Engineered Potassium Light-Driven Pumps
- 7 Methods for Simultaneous Electrophysiology and Optogenetics In Vivo
- 8 Application of an Optogenetic Technique to a Study of Activity-dependent Axon Growth in the Developing Cortex
- 9 Development of an Optogenetic Tool to Regulate Protein Stability In Vivo
- 10 Photoactivatable Nucleotide Cyclases for Synthetic Photobiology Applications
- 11 Bioluminescence Activation of Light-sensing Molecules
- Part III Optogenetics in Neurobiology, Brain Circuits, and Plasticity
- Part IV Optogenetics in Learning, Neuropsychiatric Diseases, and Behavior
- Part V Optogenetics in Vision Restoration and Memory
- Part VI Optogenetics in Sleep, Prosthetics, and Epigenetics of Neurodegenerative Diseases
- Index
- Plate Section (PDF Only)
- References
9 - Development of an Optogenetic Tool to Regulate Protein Stability In Vivo
from Part II - Opsin Biology, Tools, and Technology Platform
Published online by Cambridge University Press: 28 April 2017
Edited by
Book contents
- OptogeneticsFrom Neuronal Function to Mapping and Disease Biology
- Optogenetics
- Copyright page
- Dedication
- Contents
- Contributors
- Foreword
- Preface
- Part I Optogenetics in Model Organisms
- Part II Opsin Biology, Tools, and Technology Platform
- 6 Sodium and Engineered Potassium Light-Driven Pumps
- 7 Methods for Simultaneous Electrophysiology and Optogenetics In Vivo
- 8 Application of an Optogenetic Technique to a Study of Activity-dependent Axon Growth in the Developing Cortex
- 9 Development of an Optogenetic Tool to Regulate Protein Stability In Vivo
- 10 Photoactivatable Nucleotide Cyclases for Synthetic Photobiology Applications
- 11 Bioluminescence Activation of Light-sensing Molecules
- Part III Optogenetics in Neurobiology, Brain Circuits, and Plasticity
- Part IV Optogenetics in Learning, Neuropsychiatric Diseases, and Behavior
- Part V Optogenetics in Vision Restoration and Memory
- Part VI Optogenetics in Sleep, Prosthetics, and Epigenetics of Neurodegenerative Diseases
- Index
- Plate Section (PDF Only)
- References
- Type
- Chapter
- Information
- OptogeneticsFrom Neuronal Function to Mapping and Disease Biology, pp. 118 - 131Publisher: Cambridge University PressPrint publication year: 2017
References
Ausubel, F.M., Kingston, R.E., Seidman, F.G., et al. (ed.) (1995). Current Protocols in Molecular Biology, New York, NY: John Wiley and Sons.Google Scholar
Baarlink, C., Wang, H. and Grosse, R. (2013). Nuclear actin network assembly by formins regulates the SRF coactivator MAL. Science, 340, 864–867.CrossRefGoogle Scholar
Belle, A., Tanay, A., Bitincka, L., et al. (2006). Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A, 103, 13004–13009.CrossRefGoogle ScholarPubMed
Bonger, K.M., Rakhit, R., Payumo, A.Y., et al. (2014). General method for regulating protein stability with light. ACS Chem Biol, 9, 111–115.CrossRefGoogle ScholarPubMed
Chong, Y.T., Koh, J.L., Friesen, H., et al. (2015). Yeast proteome dynamics from single cell imaging and automated analysis. Cell, 161, 1413–1424.CrossRefGoogle ScholarPubMed
Chudakov, D.M., Matz, M.V., Lukyanov, S., et al. (2010). Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev, 90, 1103–1163.CrossRefGoogle ScholarPubMed
Deisseroth, K., Feng, G., Majewska, A.K., et al. (2006). Next-generation optical technologies for illuminating genetically targeted brain circuits. J Neurosci, 26, 10380–10386.CrossRefGoogle ScholarPubMed
Delacour, Q., Li, C., Plamont, M.A., et al. (2015). Light-activated proteolysis for the spatiotemporal control of proteins. ACS Chem Biol, 10, 1643–1647.CrossRefGoogle ScholarPubMed
Descenzo, R.A. and Minocha, S.C. (1993). Modulation of cellular polyamines in tobacco by transfer and expression of mouse ornithine decarboxylase cDNA. Plant Mol Biol, 22, 113–127.CrossRefGoogle ScholarPubMed
Gautier, A., Gauron, C., Volovitch, M., et al. (2014). How to control proteins with light in living systems. Nat Chem Biol, 10, 533–541.CrossRefGoogle ScholarPubMed
Ghaemmaghami, S., Huh, W.K., Bower, K., et al. (2003). Global analysis of protein expression in yeast. Nature, 425, 737–741.CrossRefGoogle ScholarPubMed
Ghoda, L., Van Daalen Wetters, T., Macrae, M., et al. (1989). Prevention of rapid intracellular degradation of ODC by a carboxyl-terminal truncation. Science, 243, 1493–1495.CrossRefGoogle ScholarPubMed
Goldberg, A.L. (2007). Functions of the proteasome: from protein degradation and immune surveillance to cancer therapy. Biochem Soc Trans, 35, 12–17.CrossRefGoogle ScholarPubMed
Guthrie, C., Fink, G., Abelson, J., et al. (1991). Guide to yeast genetics and molecular biology. Methods Enzymol, 194, 1–863.Google Scholar
Harper, S.M., Christie, J.M. and Gardner, K.H. (2004). Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity. Biochemistry, 43, 16184–16192.CrossRefGoogle Scholar
Hausser, M. (2014). Optogenetics: the age of light. Nat Methods, 11, 1012–1014.CrossRefGoogle ScholarPubMed
Hermann, A., Liewald, J.F. and Gottschalk, A. (2015). A photosensitive degron enables acute light-induced protein degradation in the nervous system. Curr Biol, 25, R749–R750.CrossRefGoogle ScholarPubMed
Hoyt, M.A., Zhang, M. and Coffino, P. (2003). Ubiquitin-independent mechanisms of mouse ornithine decarboxylase degradation are conserved between mammalian and fungal cells. J Biol Chem, 278, 12135–12143.CrossRefGoogle ScholarPubMed
Janke, C., Magiera, M.M., Rathfelder, N., et al. (2004). A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast, 21, 947–962.CrossRefGoogle ScholarPubMed
Jungbluth, M., Renicke, C. and Taxis, C. (2010). Targeted protein depletion in Saccharomyces cerevisiae by activation of a bidirectional degron. BMC Syst Biol, 4, 176.CrossRefGoogle Scholar
Kim, B. and Lin, M.Z. (2013). Optobiology: optical control of biological processes via protein engineering. Biochem Soc Trans, 41, 1183–1188.CrossRefGoogle Scholar
Konermann, S., Brigham, M.D., Trevino, A.E., et al. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature, 500, 472–476.CrossRefGoogle ScholarPubMed
Kulak, N.A., Pichler, G., Paron, I., et al. (2014). Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods, 11, 319–324.CrossRefGoogle ScholarPubMed
Laemmli, U.K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680–685.CrossRefGoogle ScholarPubMed
Levskaya, A., Chevalier, A.A., Tabor, J.J., et al. (2005). Synthetic biology: engineering Escherichia coli to see light. Nature, 438, 441–442.CrossRefGoogle ScholarPubMed
Lin, J.Y. (2011). A user’s guide to channelrhodopsin variants: features, limitations and future developments. Exp Physiol, 96, 19–25.CrossRefGoogle ScholarPubMed
Loetscher, P., Pratt, G. and Rechsteiner, M. (1991). The C terminus of mouse ornithine decarboxylase confers rapid degradation on dihydrofolate reductase. Support for the pest hypothesis. J Biol Chem, 266, 11213–11220.CrossRefGoogle Scholar
Matsuzawa, S., Cuddy, M., Fukushima, T., et al. (2005). Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway. Proc Natl Acad Sci U S A, 102, 14982–14987.CrossRefGoogle Scholar
Miesenbock, G. (2009). The optogenetic catechism. Science, 326, 395–399.CrossRefGoogle ScholarPubMed
Neiman, A.M. (2005). Ascospore formation in the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev, 69, 565–584.CrossRefGoogle ScholarPubMed
Newman, J.R., Ghaemmaghami, S., Ihmels, J., et al. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441, 840–846.CrossRefGoogle ScholarPubMed
Ohlendorf, R., Vidavski, R.R., Eldar, A., et al. (2012). From dusk till dawn: one-plasmid systems for light-regulated gene expression. J Mol Biol, 416, 534–542.CrossRefGoogle ScholarPubMed
Pathak, G.P., Strickland, D., Vrana, J.D., et al. (2014). Benchmarking of optical dimerizer systems. ACS Synth Biol, 3, 832–838.CrossRefGoogle ScholarPubMed
Paul, V.D., Muhlenhoff, U., Stumpfig, M., et al. (2015). The deca-GX3 proteins Yae1-Lto1 function as adaptors recruiting the ABC protein Rli1 for iron–sulfur cluster insertion. Elife, 4, e08231.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Pudasaini, A., El-Arab, K.K. and Zoltowski, B.D. (2015). LOV-based optogenetic devices: light-driven modules to impart photoregulated control of cellular signaling. Front Mol Biosci, 2, 18.CrossRefGoogle Scholar
Ravid, T. and Hochstrasser, M. (2008). Diversity of degradation signals in the ubiquitin-proteasome system. Nat Rev Mol Cell Biol, 9, 679–690.CrossRefGoogle ScholarPubMed
Renicke, C., Schuster, D., Usherenko, S., et al. (2013). A LOV2 domain-based optogenetic tool to control protein degradation and cellular function. Chem Biol, 20, 619–626.CrossRefGoogle ScholarPubMed
Selevsek, N., Chang, C.Y., Gillet, L.C., et al. (2015). Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Mol Cell Proteomics, 14, 739–749.CrossRefGoogle ScholarPubMed
Shimizu-Sato, S., Huq, E., Tepperman, J.M., et al. (2002). A light-switchable gene promoter system. Nat Biotechnol, 20, 1041–1044.CrossRefGoogle Scholar
Sorokina, O., Kapus, A., Terecskei, K., et al. (2009). A switchable light-input, light-output system modelled and constructed in yeast. J Biol Eng, 3, 15.CrossRefGoogle ScholarPubMed
Takeuchi, J., Chen, H. and Coffino, P. (2007). Proteasome substrate degradation requires association plus extended peptide. EMBO J, 26, 123–131.CrossRefGoogle ScholarPubMed
Takeuchi, J., Chen, H., Hoyt, M.A., et al. (2008). Structural elements of the ubiquitin-independent proteasome degron of ornithine decarboxylase. Biochem J, 410, 401–407.CrossRefGoogle ScholarPubMed
Towbin, H., Staehelin, T. and Gordon, J. (1979). Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A, 76, 4350–4354.CrossRefGoogle ScholarPubMed
Tsien, R.Y. (1998). The green fluorescent protein. Annu Rev Biochem, 67, 509–544.CrossRefGoogle ScholarPubMed
Usherenko, S., Stibbe, H., Musco, M., et al. (2014). Photo-sensitive degron variants for tuning protein stability by light. BMC Syst Biol, 8, 128.CrossRefGoogle ScholarPubMed
Wang, X., Chen, X. and Yang, Y. (2012). Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods, 9, 266–269.CrossRefGoogle ScholarPubMed
Wu, Y.I., Frey, D., Lungu, O.I., et al. (2009). A genetically encoded photoactivatable Rac controls the motility of living cells. Nature, 461, 104–108.CrossRefGoogle ScholarPubMed
Yaffe, M.P. and Schatz, G. (1984). Two nuclear mutations that block mitochondrial protein import in yeast. Proc Natl Acad Sci U S A, 81, 4819–4823.CrossRefGoogle ScholarPubMed
Zhang, K. and Cui, B. (2015). Optogenetic control of intracellular signaling pathways. Trends Biotechnol, 33, 92–100.CrossRefGoogle ScholarPubMed
Ziegler, T. and Moglich, A. (2015). Photoreceptor engineering. Front Mol Biosci, 2, 30.CrossRefGoogle ScholarPubMed