Synthetic physiology: Strategies for adapting tools from nature for genetically targeted control of fast biological processes

Synthetic Neurobiology Group, The Media Laboratory and McGovern Institute, Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Methods in enzymology (Impact Factor: 2.09). 01/2011; 497:425-43. DOI: 10.1016/B978-0-12-385075-1.00018-4
Source: PubMed


The life and operation of cells involve many physiological processes that take place over fast timescales of milliseconds to minutes. Genetically encoded technologies for driving or suppressing specific fast physiological processes in intact cells, perhaps embedded within intact tissues in living organisms, are critical for the ability to understand how these physiological processes contribute to emergent cellular and organismal functions and behaviors. Such "synthetic physiology" tools are often incredibly complex molecular machines, in part because they must operate at high speeds, without causing side effects. We here explore how synthetic physiology molecules can be identified and deployed in cells, and how the physiology of these molecules in cellular contexts can be assessed and optimized. For concreteness, we discuss these methods in the context of the "optogenetic" light-gated ion channels and pumps that we have developed over the past few years as synthetic physiology tools and widely disseminated for use in neuroscience for probing the role of specific brain cell types in neural computations, behaviors, and pathologies. We anticipate that some of the insights revealed here may be of general value for the field of synthetic physiology, as they raise issues that will be of importance for the development and use of high-performance, high-speed, side-effect free physiological control tools in heterologous expression systems.

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    • "However, at high expression levels, Halo forms intracellular aggregates (Gradinaru et al., 2008; Zhao et al., 2008), an issue that can be ameliorated by the appending of trafficking sequences from the Kir2.1 channel (Gradinaru et al., 2008, 2010; Zhao et al., 2008), which reduces aggregation and increases photocurrent manifold over that of the baseline molecule. Other signal sequences, such as a prolactin localization sequence, also increase halorhodopsin photocurrent (Chow et al., 2011a); it is important to note, however, that different sequences may do different things in different cell types in different species. The H. sodomense archaerhodopsin Arch (Fig. 1b), possesses strong photocurrents that exceed the original N. pharaonis halorhodopsin currents by an order of magnitude, both at low and at high light power (Fig. 1bii, top) (Chow et al., 2010). "
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    • "The diversity and biophysical properties of microbial opsins and their use in neuroscience were reviewed extensively (Boyden, 2011; Fenno et al., 2011; Hegemann and Moglich, 2011; Lin, 2011; Yizhar et al., 2011a,b,c). State-of-the-art methodologies to deploy these tools in mammalian cells were reviewed in detailed by Chow et al. (2011). An overview of available tools for controlling genetically defined neurons is given in Fig. 2. Emerging optogenetic approaches outside neuroscience The origins of optogenetics are deeply rooted in neuroscience. "
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