Team:British Columbia


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UBC iGEM 2012 notebook
Synthetic Syntrophy

The field of synthetic biology has seen the development of many biological monocultures capable of performing a wide range of novel functions (Figure 1). In contrast to this current paradigm, microbes have naturally evolved to survive as members of dynamic communities with distributed metabolism. This “divide and conquer” strategy allows the community to perform more complicated metabolic processing than would be possible in single microorganisms while being resilient to environmental changes. Despite very recent proof of concepts in developing model microbial consortia, or synthetic ecology, questions remain as to whether complex metabolic pathways can be engineered in context of microbial populations. The 2012 University of British Columbia iGEM team sets a precedent by engineering a tunable consortium with a distributed 4S desulfurization pathway for increased efficiency in the removal of organosulfurs in heavy oils and bitumen resources.

Figure 1. Synthetic biology has tackled many different kinds of problems

Foundational Advance: BioBricks to BioRooms to BioFactories

BioBrick standard biological parts are DNA sequences of defined structure and function designed to be incorporated into living cells to construct new biological systems. Synthetic biologists have been building BioRooms by engineering single microbes that contain purposeful compositions of BioBricks to perform tasks such as bio-sensing, bio-degradation, bio-transformation or bio-synthesis. However, most of these BioRooms are designed to be self-containing, self-sufficient systems in stark contrast to how microbes normally exist in community in natural environments.

The UBC iGEM 2012 team sets a foundational advance by engineering microbial BioRooms that are compatible with each other and can be regulated based on their interdependencies. In the future, it may be possible to mix and match BioRooms to create BioFactories with novel synergistic metabolisms.

We hypothesize that distributing metabolic pathways in the field of synthetic biology may proffer separate advantages compared to engineering a single microbe containing an entire independent metabolism. For instance, distributing pathways can (i) reduce the metabolic burden on any one microbe and (ii) increase compartmentalization so that there is reduced cross-talk regulation/feedback inhibition and each reaction is sequestered within a more conducive cellular environment. Microbial consortia have also been engineered to be tunable so that addition of certain inducers can easily modulate population dynamics within the community. This is tenable in the context of up- or down-regulating certain steps of the metabolic pathway to optimize efficiency and alleviate bottle-necks.

Our team utilizes three different strains of E. coli with complementary prototrophies and auxotrophies: each strain expresses a specific amino acid synthetase under a particular inducible promoter, which is required for the growth of another strain.