Project description

Viruses can be described as complex three-dimensional structures capable of efficient infection of their target organism. Because of their highly specific infection ability, they can be used as vessels for "smart" therapeutic strategies. Diseases such as cancer, diabetes, or any other autoimmune disease are a potential target for a therapeutic agent that can effectively analyze the cellular environment and compute an appropriate response.

To demonstrate the potential of a "smart" strategy, we are developing a "Trojan Horse" type of approach based on bactriophage lambda; an organism we dubbed "Trojan Phage". Our project uses phage lambda and its target organism, Escherichia coli, as a proof of concept for creating a system with predefined actions that demonstrates the described strategy. The design is based on a high specificity system that combines several different cell elements that will function as a type of logic AND gate. The phage will not harm the bacteria unless three independent conditions are met, activating the phage's lytic cycle and resulting in the bacteria's death; imitating a "Trojan Horse".

The system design uses three logical YES gates followed by the AND gate. The three YES gates will be implemented as three specific protein interactions between the phage and the bacteria. At first, three polymerase enzymes will be produced by the bacteria in response to the presence of specific concentrations of inducers in the medium. The control over the production of the polymerase enzymes will be done by three independent systems, each consisting of a different promoter. The first two will be based on the pTetO (induced by tetracycline) and pLac/Ara (induced by lactose and arabinose) promoters, the third one we intend to create ourselves by combining the pLux promoter (induced by an acyl homoserine lactone) with a theophylline induced riboswitch. Afterwards, the three polymerases will induce transcription from their matching promoters in the phage which will replace normal promoters controlling gene expression necessary for the phage's lytic life cycle. Thus, the phage will not complete its lytic cycle until all three factors in the host cell will activate it, allowing the three dimensional structure of the phage to assemble.

The Trojan Phage is a biological entity that has autonomous computational capabilities based on its ability to analyze its environment. Once the phage infects the host cell, it acts as an independent analyzer of its surrounding. If it doesn't sense the right inputs, the three polymerase proteins are not expressed, which in turn do not allow their cognate promoters to turn on and express three critical phage genes. As a result, the phage will be creating most of its parts needed for the lytic cycle, but not all of them, therefore staying in an OFF state. If the three polymerases are synthesized they translate the phage proteins and the state turns to ON, allowing replication and lysis of the cell, thus achieving an analogue output to digital inputs provided by its surrounding.

The system we describe is a combined analogue - digital computational system. Its digital property emerges from the 3-input AND gate to generate the output, and its analogue property from the creation of the 3D structure that requires the cooperation and coordination of all of the phage's cell components. The interaction between the digital and analogue components is self-determining; our role is only in the first step that "jump-starts" the system.

By creating a functional "Trojan Phage", we will have created a high specificity system composed of two different engineered living elements that interact causing a creation of a living output capable of self replication. This sort of system can be adapted to function as a therapeutic agent for a wide range of conditions.