# IGEM:Caltech/2007

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Our Project
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Our Project
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iGEM is an international synthetic biology competition between teams at various universities.  Each team designs and implements a genetic system which performs a task.  This system should use parts taken from the Registry of Standardized Biological Parts ("Biobricks") whenever possible, to prove that devices and system in bioengineering, much like those in other engineering fields, can be made from standardized parts.  Parts standardization improves the predictability of engineered systems and reduces or eliminates the need for the bioengineer to construct his/her own parts, leaving him/her free to focus on overall system design.  If a part used during the competition is newly designed due to a lack of an equivalent RSBP part, then the part will be entered into the registry.

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Enterobacteriophage $\lambda$ is a temperate virus that infects Escherichia Coli cells.  Once inside the cell, $\lambda$ chooses between two pathways.  It can enter the lytic pathway, in which it uses host cell machinery to manufacture copies of itself and eventually releases them by lysing the cell. It can also enter the lysogenic pathway, in which it inserts its genome into that of the host where it is replicated along with the host genome.  We want to manipulate $\lambda$'s decision in response to molecular signals inside the host cell, so that it only lyses a specific subpopulation of cells. If successful, this will give us more insight on how life cycle decisions are made in the $\lambda$ bacteriophage.

+ [[Image:Caltech_igem_2007.jpg|right|250px]]The Caltech iGEM 2007 team is composed of four undergraduates from Caltech and one undergraduate from MIT. Team members are current juniors and seniors in biology, chemistry, chemical engineering, and biological engineering. The team was advised by three graduate students and three faculty mentors. -

There are three control points in the [itex]\lambda genome we want to regulate: cro, N, and Q. Using three control points gives us more control over \lambda's life cycle, as well as providing us with redundancy in case one of the regulatory systems don't work.

+ Our project attacks the following problem: can one engineer viruses to selectively kill or modify specific subpopulations of target cells, based on their RNA or protein expression profiles? This addresses an important issue in gene therapy, where viruses engineered for fine target discrimination would selectively kill only those cells over- or under-expressing specific disease or cancer associated genes. An even more ambitious goal would be to rewire target cells, by integrating a small gene cassette which would modify the target cell's expression profile, possibly fixing a disease state. - [[Image:Lambda life cycle.jpg|center|A schematic of lambda's life cycle.]] + This is clearly an ambitious goal, so we brainstormed a simple model of this problem suitable for undergraduates working over a summer. The bacteriophage λ is a classic, well studied virus capable of infecting E. coli, another classic model genetic sytem. We therefore seek to engineer a λ strain targeted to lyse specific subpopulations of ''E. coli'' based on their transcriptional profiles. Together, λ and E. coli provide a tractable genetic model for this larger problem, while hopefully providing lessons applicable to more ambitious, future projects. -

Riboregulators a form of post-transcriptional gene expression control. A riboregulator consists of a cis-repressor, which acts as a lock, preventing translation, and a trans-activator, the "key" that allows translation. The cis-repressor consists of a region complementary to an mRNA transcript's ribosome binding site (RBS) and a short loop, both upstream of the RBS. When transcribed, the complementary region binds to the RBS, preventing ribosomal access. The trans-activator, also an mRNA, contains a stem-loop structure as well as a region complementary to the cis-repressor. When introduced, the trans-activator binds to the cis-repressor, allowing ribosomal access to the RBS of the riboregulated gene. + Briefly, our project relies on controlling key viral developmental processes in a target-cell specific manner. In our design, the engineered viruses are capable of entering all cells. The viruses are engineered to lack the native copy of a key developmental gene, while containing a second, regulated, copy which is only expressed when the virus infects specific target cells. Thus, viruses infecting non-target cells stall early in their development and are quickly destroyed by the host. Viruses infecting target cells, however, manage to express these essential genes and successfully complete their infection cycle. + + As an initial mechanism to target viruses to specific cell types, we will place the viral developmental genes under riboregulator control. Viral mRNAs for the regulated developmental genes will express with a stem loop sequestering ribosome binding sites, preventing translation. Specific mRNA in target E. coli will invade the stem loop, freeing the ribosome binding site and allowing proper translation. We believe this approach is more general than methods which might target specific cell-surface markers. Furthermore, if this method works, it would be possible in principle to extend viral mRNA regulation using aptamers capable of recognizing subtle signals such as post-translational modification. + + We selected the viral developmental genes N, Q, and cro as promising targets for regulation. N and Q are antiterminators required for λ to transcribe its full set of genes. Viruses lacking these genes stall at extremely early developmental stages and are completely inviable, barely producing any viral mRNA. cro biases bias the virus' decision to either + lyse a target cell or integrate into its DNA. This makes it an attractive candidate to investigate the rewiring goals explored above. + + Choosing an appropriate λ strain poses a challenge. Existing strains with defective N, Q, and cro genes lack unique restriction sites to clone our constructs into. Therefore, we will utilize recombineering to introduce introduce these mutations into phages specifically designed to accept cloning inserts. + + [[Image:Caltech_2007_overview.gif|center]] + + ==

== + + Synthetic biology implies the modification of existing biological pathways or construction of new systems to perform useful tasks, as well as the development of foundational technologies to allow for the more reliable design of biological systems. Many major problems in the field stem from the perceived unreliable and variable nature of complex biological systems. Most biological systems exhibit inherent variations in system behavior. These variations, along with the current lack of understanding around organizing principles in biological systems, limit the ability to engineer reliable biological systems. If foundational technologies can be developed that allow for standardization, decoupling, and abstraction, synthetic biology will expand to an engineering discipline that will advance applications in many fields. If successful, engineers could design and construct new systems in relatively short periods of time using well-characterized parts (Endy 2005). + + The International Genetically Engineered Machine (iGEM) competition involves the design and implementation of a synthetic biological system. Construction requires modifying existing components and combining a library of known parts in new ways to construct a novel system. The project has two goals: firstly to create an interesting device for iGEM, and secondly to determine the viability of using standardized parts. The Caltech iGEM project focuses on using the viral lysis/lysogeny switch to have viruses kill selective host cells, with the viral decision resting on whether the host produces a correct riboregulator key. |} |} -

## Current revision

iGEM 2007

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## Our Project

The Caltech iGEM 2007 team is composed of four undergraduates from Caltech and one undergraduate from MIT. Team members are current juniors and seniors in biology, chemistry, chemical engineering, and biological engineering. The team was advised by three graduate students and three faculty mentors.

Our project attacks the following problem: can one engineer viruses to selectively kill or modify specific subpopulations of target cells, based on their RNA or protein expression profiles? This addresses an important issue in gene therapy, where viruses engineered for fine target discrimination would selectively kill only those cells over- or under-expressing specific disease or cancer associated genes. An even more ambitious goal would be to rewire target cells, by integrating a small gene cassette which would modify the target cell's expression profile, possibly fixing a disease state.

This is clearly an ambitious goal, so we brainstormed a simple model of this problem suitable for undergraduates working over a summer. The bacteriophage λ is a classic, well studied virus capable of infecting E. coli, another classic model genetic sytem. We therefore seek to engineer a λ strain targeted to lyse specific subpopulations of E. coli based on their transcriptional profiles. Together, λ and E. coli provide a tractable genetic model for this larger problem, while hopefully providing lessons applicable to more ambitious, future projects.

Briefly, our project relies on controlling key viral developmental processes in a target-cell specific manner. In our design, the engineered viruses are capable of entering all cells. The viruses are engineered to lack the native copy of a key developmental gene, while containing a second, regulated, copy which is only expressed when the virus infects specific target cells. Thus, viruses infecting non-target cells stall early in their development and are quickly destroyed by the host. Viruses infecting target cells, however, manage to express these essential genes and successfully complete their infection cycle.

As an initial mechanism to target viruses to specific cell types, we will place the viral developmental genes under riboregulator control. Viral mRNAs for the regulated developmental genes will express with a stem loop sequestering ribosome binding sites, preventing translation. Specific mRNA in target E. coli will invade the stem loop, freeing the ribosome binding site and allowing proper translation. We believe this approach is more general than methods which might target specific cell-surface markers. Furthermore, if this method works, it would be possible in principle to extend viral mRNA regulation using aptamers capable of recognizing subtle signals such as post-translational modification.

We selected the viral developmental genes N, Q, and cro as promising targets for regulation. N and Q are antiterminators required for λ to transcribe its full set of genes. Viruses lacking these genes stall at extremely early developmental stages and are completely inviable, barely producing any viral mRNA. cro biases bias the virus' decision to either lyse a target cell or integrate into its DNA. This makes it an attractive candidate to investigate the rewiring goals explored above.

Choosing an appropriate λ strain poses a challenge. Existing strains with defective N, Q, and cro genes lack unique restriction sites to clone our constructs into. Therefore, we will utilize recombineering to introduce introduce these mutations into phages specifically designed to accept cloning inserts.