OPTOGENETIC CHARACTERIZATION METHODS OVERCOME KEY CHALLENGES IN SYNTHETIC BIOLOGY

Jeffrey J. Tabor

Rice University, 6100 Main Street, Houston, TX, USA, 77019; E-mail: jeff.tabor@rice.edu
The goal of synthetic biology is to understand how to program systems-level biological processes, such as the growth of an artificial tissue, by writing unnatural DNA sequences. In order to gain better understanding of, and control over, the path from DNA to cell- and organism-level processes, synthetic biologists have adapted a modular design framework from electrical and systems engineering. In the â??biological systems engineeringâ?? framework, the manner in which individual genetic components, such as signaling proteins or transcription factors, transduce, transform, and transmit biological signals is first understood through rigorous characterization. The goal is then that components can be assembled into higher-order devices, and eventually systems, whose performance can be predicted from the properties of the components. Though researchers have made notable progress, the actual utility of the biological systems engineering framework has been limited by an inability to directly characterize the dynamical performance features of biological components, and thus predict how they will behave when composed and deployed in different contexts. The result is that synthetic biology is not yet a mature engineering discipline. To address this limitation, we have recently developed an all-optical biological â??function generator and oscilloscopeâ?? framework that allows us to directly characterize the dynamical signal processing properties of genetic components in the native cellular environment. In particular, we have created sine waves and linear ramps of a transcriptional repressor in E. coli and shown that the promoter that it regulates transforms the repressor signal linearly with a seven-minute time delay. Our method is based upon our previously engineered light-switchable bacterial two component systems, mathematical models of their input/output dynamics, computational algorithms to design light inputs to program custom gene expression dynamics, and custom-built optical hardware for growing cells in well defined light conditions and making precise fluorescent protein measurements. Ours, and related methods, can help overcome the major characterization bottlenecks that have limited synthetic biology, and along with future advances, enable a complete adaptation of the systems engineering framework to biology.