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Revision as of 03:45, 24 September 2008
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Synthetic biological systems are useful both to empirically study fundamental biological behavior and to solve applied biological problems. One of the main challenges in constructing synthetic biological systems is the inability to precisely regulate gene expression using artificial means. It is likely that only a combination of powerful strategies will result in tightly-regulated control of any given set of related transcriptional, translational and posttranslational events, which is crucial to advancing the field of synthetic biology. Therefore, the 2008 VGEM Team is developing a new tool for biological engineering, transcriptional terminators intentionally redesigned to be functionally inefficient. A well-characterized library of standardized transcriptional terminators of various efficiencies should allow finely-tuned transcriptional attenuation by controlling termination efficiency and represents yet another step toward global biological control. This work represents a complimentary approach to other gene expression control methods that focus on initiation of transcription. The desired result is precise, quantitative control of transcript levels, which is often necessary to balance flux through a synthetic metabolic pathway. To demonstrate its potential for real-world application, the team is planning to employ this approach to control the expression of a heterologous pathway in E. coli for the synthesis of polyhydroxybutyrate (PHB), a biodegradable polyester plastic derived from renewable biomass, not from petroleum sources.
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Prokaryotic transcription attenutation by intrinsic terminator engineering
Translating or otherwise implementing a metabolic pathway poses many problems. A major one is the need to tune the relative expression levels of the genes involved in the pathway. The goal is usually to optimize the flux of the intermediates involved. There are many levels at which regulation of expression can occur. Transcriptional, translational and post-translational regulation all exist in natural biological systems. Synthetic biologists have been working on gaining control of these mechanisms at each level to have better control of the novel systems they are designing. In transcriptional regulation a major approach for synthetic biology has been promoter engineering. Modifying natural promoters has yielded a library of promoters of varying strengths which can be used to tweak the transcription rate of genes of interest. However this approach is limited in that each gene that one hopes to affect needs to be placed under the control of its own promoter.
The 2008 team at the University of Virginia will be pursuing another approach to the problem of transcriptional regulation by trying to create a Genetic Attenuator. Terminators are not 100% efficient. When a polymerase working its way down a DNA strand runs into a terminator not all of them are kicked off the strand, some of them keep going. By changing the structure of the terminator we hope to create Genetic Attenuators of varying strengths which could be placed between genes to achieve any desired ratio of transcription.
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Controlled polyhydroxybutyrate (PHB) bioplastic synthesis in E. coli
As the world’s fossil fuel supply starts to decline, new methods of producing fossil-fuel derived products need to be established. Plastics are a major category of fossil-fuel derivatives that make modern life possible. Looking for a solution in the biological realm is an obvious start to this problem as “plastic” is a general term that encompasses “a wide range of synthetic or semisynthetic polymerization products.” Many examples of polymerization products can be found in nature. Among the pathways producing these products is the PHA synthesis pathway found in R. eutropha. This pathway has recently been sequenced allowing the tools of synthetic biology to be applied to translating and optimizing it in E. coli. This is a crucial step towards making this pathway industrially useful as E. coli are a standard chassis used to harness nature’s synthesis capabilities.
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The Registry of Standard Biological Parts is only as good as its contents. Therefore the VGEM Team identified areas where we felt we could make valuable additions to the Registry.
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- Team Members: (left to right)
- Patrick Gildea
- Eyad Lababidi
- Dan Tarjan
- George Washington
- Brandon Freshcorn
»Contact: VGEM Team
