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Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board: Buchner, Johannes / Lei, Ming / Ludwig, Stephan / Sies, Helmut / Thomas, Douglas D. / Turk, Boris / Wittinghofer, Alfred


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Volume 400, Issue 3

Issues

Characterization and engineering of photoactivated adenylyl cyclases

Birthe Stüven / Robert Stabel / Robert Ohlendorf / Julian Beck / Roman Schubert / Andreas MöglichORCID iD: https://orcid.org/0000-0002-7382-2772
  • Corresponding author
  • Lehrstuhl für Biochemie, Universität Bayreuth, D-95447 Bayreuth, Germany
  • Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
  • Research Center for Bio-Macromolecules, Universität Bayreuth, D-95447 Bayreuth, Germany
  • Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, D-95447 Bayreuth, Germany
  • North-Bavarian NMR Center, Universität Bayreuth, D-95447 Bayreuth, Germany
  • orcid.org/0000-0002-7382-2772
  • Email
  • Other articles by this author:
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Published Online: 2019-01-09 | DOI: https://doi.org/10.1515/hsz-2018-0375

Abstract

Cyclic nucleoside monophosphates (cNMP) serve as universal second messengers in signal transduction across prokaryotes and eukaryotes. As signaling often relies on transiently formed microdomains of elevated second messenger concentration, means to precisely perturb the spatiotemporal dynamics of cNMPs are uniquely poised for the interrogation of the underlying physiological processes. Optogenetics appears particularly suited as it affords light-dependent, accurate control in time and space of diverse cellular processes. Several sensory photoreceptors function as photoactivated adenylyl cyclases (PAC) and hence serve as light-regulated actuators for the control of intracellular levels of 3′, 5′-cyclic adenosine monophosphate. To characterize PACs and to refine their properties, we devised a test bed for the facile analysis of these photoreceptors. Cyclase activity is monitored in bacterial cells via expression of a fluorescent reporter, and programmable illumination allows the rapid exploration of multiple lighting regimes. We thus probed two PACs responding to blue and red light, respectively, and observed significant dark activity for both. We next engineered derivatives of the red-light-sensitive PAC with altered responses to light, with one variant, denoted DdPAC, showing enhanced response to light. These PAC variants stand to enrich the optogenetic toolkit and thus facilitate the detailed analysis of cNMP metabolism and signaling.

Keywords: adenylyl cyclase; BLUF; optogenetics; phytochrome; sensory photoreceptor; synthetic biology

References

  • Andersen, K.R., Leksa, N.C., and Schwartz, T.U. (2013). Optimized E. coli expression strain LOBSTR eliminates common contaminants from His-tag purification. Proteins Struct. Funct. Bioinform. 81, 1857–1861.CrossrefGoogle Scholar

  • Andrée, B., Hillemann, T., Kessler-Icekson, G., Schmitt-John, T., Jockusch, H., Arnold, H.-H., and Brand, T. (2000). Isolation and characterization of the novel Popeye gene family expressed in skeletal muscle and heart. Dev. Biol. 223, 371–382.PubMedCrossrefGoogle Scholar

  • Ashman, D.F., Lipton, R., Melicow, M.M., and Price, T.D. (1963). Isolation of adenosine 3′, 5′-monophosphate and guanosine 3′, 5′-monophosphate from rat urine. Biochem. Biophys. Res. Commun. 11, 330–334.CrossrefPubMedGoogle Scholar

  • Avelar, G.M., Schumacher, R.I., Zaini, P.A., Leonard, G., Richards, T.A., and Gomes, S.L. (2014). A rhodopsin-guanylyl cyclase gene fusion functions in visual perception in a fungus. Curr. Biol. 24, 1234–1240.CrossrefGoogle Scholar

  • Blain-Hartung, M., Rockwell, N.C., Moreno, M.V., Martin, S.S., Gan, F., Bryant, D.A., and Lagarias, J.C. (2018). Cyanobacteriochrome-based photoswitchable adenylyl cyclases (cPACs) for broad spectrum light regulation of cAMP levels in cells. J. Biol. Chem. 293, 8473–8483.CrossrefPubMedGoogle Scholar

  • Datsenko, K.A. and Wanner, B.L. (2000). One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640–6645.CrossrefGoogle Scholar

  • de Rooij, J., Zwartkruis, F.J.T., Verheijen, M.H.G., Cool, R.H., Nijman, S.M.B., Wittinghofer, A., and Bos, J.L. (1998). Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP. Nature 396, 474–477.CrossrefPubMedGoogle Scholar

  • Deisseroth, K., Feng, G., Majewska, A.K., Miesenböck, G., Ting, A., and Schnitzer, M.J. (2006). Next-generation optical technologies for illuminating genetically targeted brain circuits. J. Neurosci. 26, 10380–10386.CrossrefPubMedGoogle Scholar

  • Escobar, F.V., Buhrke, D., Michael, N., Sauthof, L., Wilkening, S., Tavraz, N.N., Salewski, J., Frankenberg-Dinkel, N., Mroginski, M.A., Scheerer, P., et al. (2017). Common structural elements in the chromophore binding pocket of the Pfr state of bathy phytochromes. Photochem. Photobiol. 93, 724–732.PubMedCrossrefGoogle Scholar

  • Etzl, S., Lindner, R., Nelson, M.D., and Winkler, A. (2018). Structure-guided design and functional characterization of an artificial red light–regulated guanylate/adenylate cyclase for optogenetic applications. J. Biol. Chem. 293, 9078–9089.CrossrefPubMedGoogle Scholar

  • Fesenko, E.E., Kolesnikov, S.S., and Lyubarsky, A.L. (1985). Induction by cyclic GMP of cationic conductance in plasma membrane of retinal rod outer segment. Nature 313, 310–313.CrossrefPubMedGoogle Scholar

  • Gao, S., Nagpal, J., Schneider, M.W., Kozjak-Pavlovic, V., Nagel, G., and Gottschalk, A. (2015). Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp. Nat. Commun. 6, 8046.PubMedCrossrefGoogle Scholar

  • Gasser, C., Taiber, S., Yeh, C.-M., Wittig, C.H., Hegemann, P., Ryu, S., Wunder, F., and Möglich, A. (2014). Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. Proc. Natl. Acad. Sci. USA 111, 8803–8808.CrossrefGoogle Scholar

  • Gibson, D.G., Young, L., Chuang, R.-Y., Venter, J.C., Hutchison, C.A., and Smith, H.O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345.CrossrefPubMedGoogle Scholar

  • Gleichmann, T., Diensthuber, R.P., and Möglich, A. (2013). Charting the signal trajectory in a light-oxygen-voltage photoreceptor by random mutagenesis and covariance analysis. J. Biol. Chem. 288, 29345–29355.CrossrefGoogle Scholar

  • Gold, M.G., Gonen, T., and Scott, J.D. (2013). Local cAMP signaling in disease at a glance. J. Cell Sci. 126, 4537–4543.CrossrefGoogle Scholar

  • Gomelsky, M. (2011). cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all! Mol. Microbiol. 79, 562–565.CrossrefPubMedGoogle Scholar

  • Gomelsky, M. and Klug, G. (2002). BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms. Trends Biochem. Sci. 27, 497–500.PubMedCrossrefGoogle Scholar

  • Görke, B. and Stülke, J. (2008). Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat. Rev. Microbiol. 6, 613–624.CrossrefPubMedGoogle Scholar

  • Hennemann, J., Iwasaki, R.S., Grund, T.N., Diensthuber, R.P., Richter, F., and Möglich, A. (2018). Optogenetic control by pulsed illumination. ChemBioChem 19, 1296–1304.CrossrefPubMedGoogle Scholar

  • Iseki, M., Matsunaga, S., Murakami, A., Ohno, K., Shiga, K., Yoshida, K., Sugai, M., Takahashi, T., Hori, T., and Watanabe, M. (2002). A blue-light-activated adenylyl cyclase mediates photoavoidance in Euglena gracilis. Nature 415, 1047–1051.PubMedCrossrefGoogle Scholar

  • Jansen, V., Alvarez, L., Balbach, M., Strünker, T., Hegemann, P., Kaupp, U.B., and Wachten, D. (2015). Controlling fertilization and cAMP signaling in sperm by optogenetics. eLife 4, e05161.CrossrefGoogle Scholar

  • Jansen, V., Jikeli, J.F., and Wachten, D. (2017). How to control cyclic nucleotide signaling by light. Curr. Opin. Biotechnol. 48, 15–20.PubMedCrossrefGoogle Scholar

  • Jenal, U., Reinders, A., and Lori, C. (2017). Cyclic di-GMP: second messenger extraordinaire. Nat. Rev. Microbiol. 15, 271–284.CrossrefPubMedGoogle Scholar

  • Kim, T., Folcher, M., Baba, M.D.-E., and Fussenegger, M. (2015). A synthetic erectile optogenetic stimulator enabling blue-light-inducible penile erection. Angew. Chem. Int. Ed. 54, 5933–5938.CrossrefGoogle Scholar

  • Krauss, G. (2014). Biochemistry of Signal Transduction and Regulation (Weinheim, Germany: Wiley-VCH).Google Scholar

  • Kuo, J.F. and Greengard, P. (1970). Cyclic nucleotide-dependent protein kinases. VI. Isolation and partial purification of a protein kinase activated by guanosine 3′,5′-monophosphate. J. Biol. Chem. 245, 2493–2498.PubMedGoogle Scholar

  • Losi, A., Gardner, K.H., and Möglich, A. (2018). Blue-light receptors for optogenetics. Chem. Rev. 118, 10659–10709.CrossrefPubMedGoogle Scholar

  • Malan, T.P. and McClure, W.R. (1984). Dual promoter control of the Escherichia coli lactose operon. Cell 39, 173–180.CrossrefPubMedGoogle Scholar

  • Marden, J.N., Dong, Q., Roychowdhury, S., Berleman, J.E., and Bauer, C.E. (2011). Cyclic GMP controls Rhodospirillum centenum cyst development. Mol. Microbiol. 79, 600–615.CrossrefPubMedGoogle Scholar

  • Mathes, T., Vogl, C., Stolz, J., and Hegemann, P. (2009). In vivo generation of flavoproteins with modified cofactors. J. Mol. Biol. 385, 1511–1518.PubMedCrossrefGoogle Scholar

  • McDonough, K.A. and Rodriguez, A. (2012). The myriad roles of cyclic AMP in microbial pathogens: from signal to sword. Nat. Rev. Microbiol. 10, 27–38.CrossrefGoogle Scholar

  • Möglich, A. (2018). An open-source, cross-platform resource for nonlinear least-squares curve fitting. J. Chem. Educ. 95, 2273–2278.CrossrefGoogle Scholar

  • Möglich, A., Ayers, R.A., and Moffat, K. (2009). Design and signaling mechanism of light-regulated histidine kinases. J. Mol. Biol. 385, 1433–1444.PubMedCrossrefGoogle Scholar

  • Möglich, A., Yang, X., Ayers, R.A., and Moffat, K. (2010). Structure and function of plant photoreceptors. Annu. Rev. Plant Biol. 61, 21–47.PubMedCrossrefGoogle Scholar

  • Mukougawa, K., Kanamoto, H., Kobayashi, T., Yokota, A., and Kohchi,T. (2006). Metabolic engineering to produce phytochromes with phytochromobilin, phycocyanobilin, or phycoerythrobilin chromophore in Escherichia coli. FEBS Lett. 580, 1333–1338.CrossrefPubMedGoogle Scholar

  • Ohlendorf, R., Vidavski, R.R., Eldar, A., Moffat, K., and Möglich, A. (2012). From dusk till dawn: one-plasmid systems for light-regulated gene expression. J. Mol. Biol. 416, 534–542.PubMedCrossrefGoogle Scholar

  • Ohlendorf, R., Schumacher, C.H., Richter, F., and Möglich, A. (2016). Library-aided probing of linker determinants in hybrid photoreceptors. ACS Synth. Biol. 5, 1117–1126.PubMedCrossrefGoogle Scholar

  • Raffelberg, S., Wang, L., Gao, S., Losi, A., Gärtner, W., and Nagel, G. (2013). A LOV-domain-mediated blue-light-activated adenylate (adenylyl) cyclase from the cyanobacterium Microcoleus chthonoplastes PCC 7420. Biochem. J. 455, 359–365.PubMedCrossrefGoogle Scholar

  • Rall, T.W., Sutherland, E.W., and Berthet, J. (1957). The relationship of epinephrine and glucagon to liver phosphorylase Iv. Effect of epinephrine and glucagon on the reactivation of phosphorylase in liver homogenates. J. Biol. Chem. 224, 463–475.PubMedGoogle Scholar

  • Rauch, A., Leipelt, M., Russwurm, M., and Steegborn, C. (2008). Crystal structure of the guanylyl cyclase Cya2. Proc. Natl. Acad. Sci. USA 105, 15720–15725.CrossrefGoogle Scholar

  • Richter, F., Scheib, U.S., Mehlhorn, J., Schubert, R., Wietek, J., Gernetzki, O., Hegemann, P., Mathes, T., and Möglich, A. (2015). Upgrading a microplate reader for photobiology and all-optical experiments. Photochem. Photobiol. Sci. 14, 270–279.PubMedCrossrefGoogle Scholar

  • Richter, F., Fonfara, I., Bouazza, B., Schumacher, C.H., Bratovič, M., Charpentier, E., and Möglich, A. (2016). Engineering of temperature- and light-switchable Cas9 variants. Nucleic Acids Res. 44, 10003–10014.PubMedGoogle Scholar

  • Rink, T.J., Tsien, R.Y., and Pozzan, T. (1982). Cytoplasmic pH and free Mg2+ in lymphocytes. J. Cell Biol. 95, 189–196.PubMedCrossrefGoogle Scholar

  • Rockwell, N.C. and Lagarias, J.C. (2010). A brief history of phytochromes. Chemphyschem Eur. J. Chem. Phys. Phys. Chem. 11, 1172–1180.CrossrefGoogle Scholar

  • Roychowdhury, S., Dong, Q., and Bauer, C.E. (2015). DNA-binding properties of a cGMP-binding CRP homologue that controls development of metabolically dormant cysts of Rhodospirillum centenum. Microbiology 161, 2256–2264.PubMedCrossrefGoogle Scholar

  • Ryu, M.-H. and Gomelsky, M. (2014). Near-infrared light responsive synthetic c-di-GMP module for optogenetic applications. ACS Synth. Biol. 3, 802–810.PubMedCrossrefGoogle Scholar

  • Ryu, M.-H., Moskvin, O.V., Siltberg-Liberles, J., and Gomelsky, M. (2010). Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J. Biol. Chem. 285, 41501–41508.PubMedCrossrefGoogle Scholar

  • Ryu, M.-H., Kang, I.-H., Nelson, M.D., Jensen, T.M., Lyuksyutova, A.I., Siltberg-Liberles, J., Raizen, D.M., and Gomelsky, M. (2014). Engineering adenylate cyclases regulated by near-infrared window light. Proc. Natl. Acad. Sci. USA 111, 10167–10172.CrossrefGoogle Scholar

  • Ryu, M.-H., Youn, H., Kang, I.-H., and Gomelsky, M. (2015). Identification of bacterial guanylate cyclases. Proteins 83, 799–804.PubMedCrossrefGoogle Scholar

  • Scheib, U., Stehfest, K., Gee, C.E., Körschen, H.G., Fudim, R., Oertner, T.G., and Hegemann, P. (2015). The rhodopsin–guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling. Sci. Signal 8, rs8.Google Scholar

  • Schröder-Lang, S., Schwärzel, M., Seifert, R., Strünker, 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.PubMedCrossrefGoogle Scholar

  • Schumacher, C.H., Körschen, H.G., Nicol, C., Gasser, C., Seifert, R., Schwärzel, M., and Möglich, A. (2016). A fluorometric activity assay for light-regulated cyclic-nucleotide-monophosphate actuators. Methods Mol. Biol. 1408, 93–105.PubMedCrossrefGoogle Scholar

  • Shimada, T., Fujita, N., Yamamoto, K., and Ishihama, A. (2011). Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources. PLoS One 6, e20081.PubMedCrossrefGoogle Scholar

  • Shu, X., Royant, A., Lin, M.Z., Aguilera, T.A., Lev-Ram, V., Steinbach, P.A., and Tsien, R.Y. (2009). Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science 324, 804–807.PubMedCrossrefGoogle Scholar

  • Stierl, M., Stumpf, P., Udwari, D., Gueta, R., Hagedorn, R., Losi, A., Gärtner, 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.CrossrefPubMedGoogle Scholar

  • Strack, R.L., Strongin, D.E., Bhattacharyya, D., Tao, W., Berman, A., Broxmeyer, H.E., Keenan, R.J., and Glick, B.S. (2008). A noncytotoxic DsRed variant for whole-cell labeling. Nat. Methods 5, 955–957.CrossrefPubMedGoogle Scholar

  • Walsh, D.A., Perkins, J.P., and Krebs, E.G. (1968). An adenosine 3′,5′-monophosphate-dependant protein kinase from rabbit skeletal muscle. J. Biol. Chem. 243, 3763–3765.PubMedGoogle Scholar

  • Yang, X., Kuk, J., and Moffat, K. (2008). Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction. Proc. Natl. Acad. Sci. USA 105, 14715–14720.CrossrefGoogle Scholar

  • Ziegler, T. and Möglich, A. (2015). Photoreceptor engineering. Front. Mol. Biosci. 2, 30.PubMedGoogle Scholar

About the article

aBirthe Stüven and Robert Stabel: These authors contributed equally to this work.

bPresent address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.


Received: 2018-09-15

Accepted: 2018-12-07

Published Online: 2019-01-09

Published in Print: 2019-02-25


Citation Information: Biological Chemistry, Volume 400, Issue 3, Pages 429–441, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: https://doi.org/10.1515/hsz-2018-0375.

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