UC San Diego

Synthetic biology has enabled the engineering of biological networks capable of producing quantitatively predictable, dynamic function in a host organism. Advanced synthetic toolkits have been developed and applied within model bacterial systems to construct functional assemblies of biological parts that toggle (Gardner et al., 2000), oscillate (Elowitz and Leibler, 2000; Stricker et al., 2008; Danino et al., 2010), control cellular populations (You et al., 2004) and trigger host responses (Lu and Collins, 2007), form logical gates (Tamsir et al., 2010; Moon et al., 2012), perform arithmetic operations (Friedland et al., 2009), filter signals (Sohka et al., 2009) and sense complex environmental cues (Tabor et al., 2009; Kobayashi et al., 2004). This diverse set of genetic circuit designs, varying in complexity and host, have further been applied to systematically engineer biological systems towards applications in biosynthesis, environmental remediation, intracellular diagnostics, and therapeutics. Amidst this rapid expansion of tools and extensive demonstration of complex functional capabilities, the lack of commercially translatable technologies thus far reflects a looming challenge for the field. Specifically, an integrated synthetic design must go beyond matching signal levels between interacting circuits in model organisms. It must also function effectively across relevant spatial scales and among industrial hosts, for which the genetic circuit must predictably integrate with the host's regulatory and metabolic biology. In this thesis, we focus on constructing scalable synthetic circuits that are inspired by the natural functionality of bacteria and translatable into commercially relevant hosts. Here we discuss host selection, modeling, design, construction, and characterization of gene circuits towards applications in biosensing and protein production. In Chapter One, we give an introduction to the field of synthetic biology and how our research area fits into this discipline. In Chapter Two, I describe a circuit design that leverages native regulatory components of bacteria to produce a scalable frequency modulated biosensor. In Chapter Three, I demonstrate further functionalities of quorum sensing signaling in bacteria. In Chapter Four, we discuss the translation of synthetic circuits to a therapeutically relevant host. In Chapter Five, I present an integrated approach to engineer industrially relevant cyanobacteria for efficient protein production. These sections combine to expand our approach in engineering natural biological systems towards directed, translatable applications