CH391L/S13/Genetic Circuits

Introduction

History

The concept of a “genetic circuit” has a long and storied past. When summarizing conclusions made during the 1961 Cold Spring Harbor Symposium, Francois Jacob and Jacques Monod – of Lac operon fame – established the electronic circuit paradigm for gene regulation. Jacob and Monod stated that different regulatory elements (i.e repressors, activators, etc.) could be assembled into a diversity of ‘circuits’ [1]. Here, we see a surprisingly accurate prediction for the developments that form a one of the major thrusts in synthetic biology.

Later, increased computing power was a considerable driving force for modeling gene regulation. Still, a paucity of understood pathways and regulatory elements prevented major gains. This situation changed with the onset of the ‘genomic era’, which was defined by developments like Sanger sequencing and PCR. Armed with new biological ‘parts’, researchers began constructing genetic circuits that experimentally validated mathematical modeling as well as the belief that engineering principles could be applied to biological systems. In the year 2000, a trinity of Nature papers demonstrated synthetic genetic circuitry [2][3][4].

Definitions

The definition of a genetic circuit is one rather important issue that is often overlooked. Also, it should be noted that there is a difference between ‘natural’ and ‘synthetic’ genetic circuits. The Lac operon is one example of a well-characterized natural genetic circuit. By contrast, the repressilator represents a genetic circuit that was synthesized or assembled from different regulatory elements.

Given the established paradigm, it helps to first consider the electronic circuit. A simple explanation defines the electronic circuit as connected elements or components that permit the flow of electrical current. Typically, that electrical current derives from an external source (i.e. another circuit), which represents an input signal. In general, a genetic circuit is a series of interacting biological components that exert regulatory, actuator, and or signaling function(s). The circuit may also have one or more of the following characteristics listed below.

• Signal Processing
• Signal Transduction
• Cell-state
• Genetic Memory

Purpose with Perspective: Rising above the ‘noise’

As with many aspects of synthetic biology, engineering synthetic genetic circuits is a young field. As such, there is both considerable promise and, at times, undue hype. It is wise to consider the utility of increased circuit engineering and its impact upon the two types of genetic circuits: naturally occurring and synthetic. Natural genetic circuits include a vast array of regulatory networks that ranges from the simple, yet sophisticated Lac operon to complex chromatin remodeling. During the study of these and other naturally occurring regulatory networks, synthetic genetic circuits offer a means for examining the operating principles of regulatory elements or modules from a more complex system [Yokobayashi2002]. Conversely, application-driven efforts seek to create new genetic circuits for pharmaceutical

Despite their differences, both research thrusts employ so-called “top-down” – or decomposition – and “bottom-up” – or synthesis – strategies. In the study of complex regulatory systems, a top-down approach is employed to identify key elements of a regulatory pathway. However, this approach may yield an incomplete picture or a general lack of depth. In this scenario, bottom-up engineering of simpler synthetic circuit - representative of a more complex natural system - could facilitate investigations and afford a deeper understanding. This bottom-up approach is typically used when designing synthetic circuits. Still, some synthetic biologists now advocate for the use of top-down design for synthetic circuits[5].

Circuitry Concepts

Digital/Analog Signals

Two recently published articles exemplify the concept of digital/analog signals. In both publications, two orthogonal recombinases - also called an integrases - invert the orientation of DNA segments flanked by their respective recognition sequences. By arranging different flanked components (i.e terminators, promoters, and a GFP reporter gene), the researchers are able to assemble a logic gate that interprets a two-bit digital signal and produces a detectable output signal [6][7]. Here, the digital inputs are small molecules that induce expression of each recombinase and the analog output the presence or lack of constitutive (i.e. continuous) GFP expression.

Natural Genetic Circuits

Tryptophan Operon

The E. coli tryptophan (Trp) operon provides an interesting example of genetic regulation through input signal integration. In brief, the Trp operon regulates expression of tryptophan biosynthesis enzymes. In the presence of high tryptophan, Trp operon gene expression is undesirable. While transcriptional silencing depends upon tryptophan levels, two different detection methods are employed.

When the concentration of free tryptophan is high, a tryptophan–activated repressor (trp repressor) will bind to operator sequences blocking transcription by RNA polymerase. Next, a short leader transcript (trpL) detects tryptophanyl-tRNA levels as the coding sequence has two sequential tryptophan codons. Sufficiently high tryptophan levels permit adequate aminoacylation of the tRNATrp and standard translation. After translation termination, the ribosome will dissociate allowing the mRNA to fold into a terminator, which ends transcription. Should tryptophan and tryptophanyl-tRNA levels be low, the ribosome will pause upon encountering the adjacent tryptophan codons. Ribosome stalling leads to formation of an antiterminator that allows the RNA polymerase resume transcription. [Yanofsky2007]

Salmonella Phase Variation

Salmonella has the adaptive ability to switch or toggle between two flagellin genes thereby avoiding detection by the immune system. This so-called phase variation represents a nature example of bistability; the bacteria can exist in one of two ‘states’ [Yamamoto2006]. Interestingly, phase variation employs an inversion-mediated mechanism similar to recently published synthetic logic circuits [Siuti2013] [Bonnet2013].

Synthetic Genetic Circuits

CRISPRi

[]