Abstract
Systems biologists aim to understand how organism-level processes, such as differentiation and multicellular development, are encoded in DNA. Conversely, synthetic biologists aim to program systems-level biological processes, such as engineered tissue growth, by writing artificial DNA sequences. To achieve their goals, these groups have adapted a hierarchical electrical engineering framework that can be applied in the forward direction to design complex biological systems or in the reverse direction to analyze evolved networks. Despite much progress, this framework has been limited by an inability to directly and dynamically characterize biological components in the varied contexts of living cells. Recently, two optogenetic methods for programming custom gene expression and protein localization signals have been developed and used to reveal fundamentally new information about biological components that respond to those signals. This basic dynamic characterization approach will be a major enabling technology in synthetic and systems biology.
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References
Horowitz, P. & Hill, W. The Art of Electronics 2nd edn. (Cambridge University Press, 1989).
Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
Elowitz, M.B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).
Weiss, R. & Subhyu, B. The device physics of cellular logic gates. in NSC-1: The First Workshop of Non-Silicon Computing 54–61 (2002).
Alon, U., Surette, M.G., Barkai, N. & Leibler, S. Robustness in bacterial chemotaxis. Nature 397, 168–171 (1999).
Hartwell, L.H., Hopfield, J.J., Leibler, S. & Murray, A.W. From molecular to modular cell biology. Nature 402, C47–C52 (1999).
Win, M.N. & Smolke, C.D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456–460 (2008).
Friedland, A.E. et al. Synthetic gene networks that count. Science 324, 1199–1202 (2009).
Nevozhay, D., Adams, R.M., Murphy, K.F., Josic, K. & Balázsi, G. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc. Natl. Acad. Sci. USA 106, 5123–5128 (2009).
Culler, S.J., Hoff, K.G. & Smolke, C.D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330, 1251–1255 (2010).
Lou, C. et al. Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol. Syst. Biol. 6, 350 (2010).
Xie, Z., Liu, S.J., Bleris, L. & Benenson, Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 38, 2692–2701 (2010).
Bleris, L. et al. Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Mol. Syst. Biol. 7, 519 (2011).
Lucks, J.B., Qi, L., Mutalik, V.K., Wang, D. & Arkin, A.P. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl. Acad. Sci. USA 108, 8617–8622 (2011).
Regot, S. et al. Distributed biological computation with multicellular engineered networks. Nature 469, 207–211 (2011).
Tamsir, A., Tabor, J.J. & Voigt, C.A. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469, 212–215 (2011).
Wang, B., Kitney, R.I., Joly, N. & Buck, M. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2, 508 (2011).
Ausländer, S., Ausländer, D., Müller, M., Wieland, M. & Fussenegger, M. Programmable single-cell mammalian biocomputers. Nature 487, 123–127 (2012).
Burrill, D.R., Inniss, M.C., Boyle, P.M. & Silver, P.A. Synthetic memory circuits for tracking human cell fate. Genes Dev. 26, 1486–1497 (2012).
Moon, T.S., Lou, C., Tamsir, A., Stanton, B.C. & Voigt, C.A. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249–253 (2012).
Bonnet, J., Yin, P., Ortiz, M.E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599–603 (2013).
Daniel, R., Rubens, J.R., Sarpeshkar, R. & Lu, T.K. Synthetic analog computation in living cells. Nature 497, 619–623 (2013).
Siuti, P., Yazbek, J. & Lu, T.K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).
Stanton, B.C. et al. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol. 10, 99–105 (2014).
Kiani, S. et al. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat. Methods doi:10.1038/nmeth.2969 (5 May 2014).
Zhang, H. et al. Programming a Pavlovian-like conditioning circuit in Escherichia coli. Nat. Commun. 5, 3102 (2014).
Atkinson, M.R., Savageau, M.A., Myers, J.T. & Ninfa, A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113, 597–607 (2003).
Bashor, C.J., Helman, N.C., Yan, S. & Lim, W.A. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319, 1539–1543 (2008).
Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008).
Cağatay, T., Turcotte, M., Elowitz, M.B., Garcia-Ojalvo, J. & Süel, G.M. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512–522 (2009).
Klumpp, S., Zhang, Z. & Hwa, T. Growth rate-dependent global effects on gene expression in bacteria. Cell 139, 1366–1375 (2009).
Scott, M., Gunderson, C.W., Mateescu, E.M., Zhang, Z. & Hwa, T. Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099–1102 (2010).
Balázsi, G., van Oudenaarden, A. & Collins, J.J. Cellular decision making and biological noise: from microbes to mammals. Cell 144, 910–925 (2011).
Locke, J.C.W., Young, J.W., Fontes, M., Hernández Jiménez, M.J. & Elowitz, M.B. Stochastic pulse regulation in bacterial stress response. Science 334, 366–369 (2011).
Nandagopal, N. & Elowitz, M.B. Synthetic biology: integrated gene circuits. Science 333, 1244–1248 (2011).
Chau, A.H., Walter, J.M., Gerardin, J., Tang, C. & Lim, W.A. Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151, 320–332 (2012).
Pai, A., Tanouchi, Y. & You, L. Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme. Proc. Natl. Acad. Sci. USA 109, 19810–19815 (2012).
Sasson, V., Shachrai, I., Bren, A., Dekel, E. & Alon, U. Mode of regulation and the insulation of bacterial gene expression. Mol. Cell 46, 399–407 (2012).
Smith, R. et al. Programmed Allee effect in bacteria causes a tradeoff between population spread and survival. Proc. Natl. Acad. Sci. USA 111, 1969–1974 (2014).
Youk, H. & Lim, W.A. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science 343, 1242782 (2014).
Kobayashi, H. et al. Programmable cells: Interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. USA 101, 8414–8419 (2004).
Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R. & Benenson, Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333, 1307–1311 (2011).
Prindle, A. et al. A sensing array of radically coupled genetic 'biopixels'. Nature 481, 39–44 (2012).
Kotula, J.W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl. Acad. Sci. USA 111, 4838–4843 (2014).
Anderson, J.C., Clarke, E.J., Arkin, A.P. & Voigt, C.A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619–627 (2006).
Huh, J.H., Kittleson, J.T., Arkin, A.P. & Anderson, J.C. Modular design of a synthetic payload delivery device. ACS Synth. Biol. 2, 418–424 (2013).
Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
Liu, C. et al. Sequential establishment of stripe patterns in an expanding cell population. Science 334, 238–241 (2011).
Payne, S. et al. Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Mol. Syst. Biol. 9, 697 (2013).
Tabor, J.J. et al. A synthetic genetic edge detection program. Cell 137, 1272–1281 (2009).
Brenner, K., Karig, D.K., Weiss, R. & Arnold, F.H. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. Proc. Natl. Acad. Sci. USA 104, 17300–17304 (2007).
Balagaddé, F.K. et al. A synthetic Escherichia coli predator-prey ecosystem. Mol. Syst. Biol. 4, 187 (2008).
Purnick, P.E.M. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).
Cardinale, S. & Arkin, A.P. Contextualizing context for synthetic biology— identifying causes of failure of synthetic biological systems. Biotechnol. J. 7, 856–866 (2012).
Kittleson, J.T., Wu, G.C. & Anderson, J.C. Successes and failures in modular genetic engineering. Curr. Opin. Chem. Biol. 16, 329–336 (2012).
Moser, F. et al. Genetic circuit performance under conditions relevant for industrial bioreactors. ACS Synth. Biol. 1, 555–564 (2012).
Mutalik, V.K. et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 10, 354–360 (2013).
Takyar, S., Hickerson, R.P. & Noller, H.F. mRNA helicase activity of the ribosome. Cell 120, 49–58 (2005).
Lou, C., Stanton, B., Chen, Y.-J., Munsky, B. & Voigt, C.A. Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat. Biotechnol. 30, 1137–1142 (2012).
Qi, L., Haurwitz, R.E., Shao, W., Doudna, J.A. & Arkin, A.P. RNA processing enables predictable programming of gene expression. Nat. Biotechnol. 30, 1002–1006 (2012).
Guye, P., Li, Y., Wroblewska, L., Duportet, X. & Weiss, R. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res. 41, e156 (2013).
Torella, J.P. et al. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Res. 42, 681–689 (2014).
Pantazes, R.J., Grisewood, M.J. & Maranas, C.D. Recent advances in computational protein design. Curr. Opin. Struct. Biol. 21, 467–472 (2011).
Dill, K.A., Ozkan, S.B., Weikl, T.R., Chodera, J.D. & Voelz, V.A. The protein folding problem: when will it be solved? Curr. Opin. Struct. Biol. 17, 342–346 (2007).
Jayanthi, S., Nilgiriwala, K.S. & Del Vecchio, D. Retroactivity controls the temporal dynamics of gene transcription. ACS Synth. Biol. 2, 431–441 (2013).
Tabor, J.J., Bayer, T.S., Simpson, Z.B., Levy, M. & Ellington, A.D. Engineering stochasticity in gene expression. Mol. Biosyst. 4, 754–761 (2008).
Cookson, N.A. et al. Queueing up for enzymatic processing: correlated signaling through coupled degradation. Mol. Syst. Biol. 7, 561 (2011).
Prindle, A. et al. Rapid and tunable post-translational coupling of genetic circuits. Nature 508, 387–391 (2014).
Cardinale, S., Joachimiak, M.P. & Arkin, A.P. Effects of Genetic Variation on the E. coli Host-Circuit Interface. Cell Reports 4, 231–237 (2013).
Gefen, O., Fridman, O., Ronin, I. & Balaban, N.Q. Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity. Proc. Natl. Acad. Sci. USA 111, 556–561 (2014).
Hussain, F. et al. Engineered temperature compensation in a synthetic genetic clock. Proc. Natl. Acad. Sci. USA 111, 972–977 (2014).
Brophy, J.A.N. & Voigt, C.A. Principles of genetic circuit design. Nat. Methods 11, 508–520 (2014).
Milias-Argeitis, A. et al. In silico feedback for in vivo regulation of a gene expression circuit. Nat. Biotechnol. 29, 1114–1116 (2011).
Toettcher, J.E., Gong, D., Lim, W.A. & Weiner, O.D. Light-based feedback for controlling intracellular signaling dynamics. Nat. Methods 8, 837–839 (2011).
Uhlendorf, J. et al. Long-term model predictive control of gene expression at the population and single-cell levels. Proc. Natl. Acad. Sci. USA 109, 14271–14276 (2012).
Toettcher, J.E., Weiner, O.D. & Lim, W.A. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell 155, 1422–1434 (2013).
Olson, E.J., Hartsough, L.A., Landry, B.P., Shroff, R. & Tabor, J.J. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat. Methods 11, 449–455 (2014).
Deisseroth, K. Optogenetics. Nat. Methods 8, 26–29 (2011).
Boyden, E.S., Zhang, F., Bamberg, E., Nagel, G. & Deisseroth, K. Millisecond-timescale, genetically targeted optical control of neural activity. Nat. Neurosci. 8, 1263–1268 (2005).
Bacchus, W. & Fussenegger, M. The use of light for engineered control and reprogramming of cellular functions. Curr. Opin. Biotechnol. 23, 695–702 (2012).
Pathak, G.P., Vrana, J.D. & Tucker, C.L. Optogenetic control of cell function using engineered photoreceptors. Biol. Cell 105, 59–72 (2013).
Levskaya, A., Weiner, O.D., Lim, W.A. & Voigt, C.A. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997–1001 (2009).
Levskaya, A. et al. Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441–442 (2005).
Tabor, J.J., Levskaya, A. & Voigt, C.A. Multichromatic control of gene expression in Escherichia coli. J. Mol. Biol. 405, 315–324 (2011).
Meloche, S. & Pouysségur, J. The ERK1/2 mitogen-activated protein kinase pathway as a master regulator of the G1- to S-phase transition. Oncogene 26, 3227–3239 (2007).
Ang, J., Ingalls, B. & McMillen, D. Probing the input-output behavior of biochemical and genetic systems system identification methods from control theory. Methods Enzymol. 487, 279–317 (2011).
Kosuri, S. et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl. Acad. Sci. USA 110, 14024–14029 (2013).
Alon, U. Introduction to Systems Biology: Design Principles of Biological Networks. (CRC Press, 2007).
Qi, L.S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).
Gilbert, L.A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).
Lahav, G. et al. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36, 147–150 (2004).
Hersen, P., McClean, M.N., Mahadevan, L. & Ramanathan, S. Signal processing by the HOG MAP kinase pathway. Proc. Natl. Acad. Sci. USA 105, 7165–7170 (2008).
Süel, G.M., Garcia-Ojalvo, J., Liberman, L.M. & Elowitz, M.B. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440, 545–550 (2006).
Little, J.W. & Mount, D.W. The SOS regulatory system of Escherichia coli. Cell 29, 11–22 (1982).
Dunlop, M.J., Cox, R.S. III, Levine, J.H., Murray, R.M. & Elowitz, M.B. Regulatory activity revealed by dynamic correlations in gene expression noise. Nat. Genet. 40, 1493–1498 (2008).
Acknowledgements
We thank L.A. Hartsough for his comments on the manuscript. E.J.O. and J.J.T. are supported by the US National Science Foundation Biotechnology, Biochemical and Biomass Engineering (BBBE) program (EFRI–1137266) and the Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI) program (N000141310074). J.J.T. is supported by the Defense Advanced Research Projects Agency Living Foundries Advanced Tools and Capabilities for Generalizable Platforms (ATCG) and ONR Young Investigator Programs.
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Olson, E., Tabor, J. Optogenetic characterization methods overcome key challenges in synthetic and systems biology. Nat Chem Biol 10, 502–511 (2014). https://doi.org/10.1038/nchembio.1559
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DOI: https://doi.org/10.1038/nchembio.1559
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