Biology Reference
In-Depth Information
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FIGURE 8.2
Overall scheme of systems metabolic engineering from (i) the genetic level to (ii) the pathway level and then to (iii) the level of the metabolic network. At the
genetic level, synthetic biology tools are employed to create modifications in the cell, in this case a regulatory NOT and NOR system for the expressionofa
gene. This modification is geared towards the design and engineering of metabolic pathways such that the metabolic flux funnels towards the production of
a target metabolite. From the list of possible pathways that can be used to produce the target compound, a systems level analysis is performed to determine
the optimal route that would not be detrimental to the overall system (e.g. retarded cellular growth or generation of toxic byproducts).
This compound is not synthesized by any known organism and thus, a complete
biosynthetic pathway has not been characterized. The in-house pathway prediction tool Sim
Pheny Biopathway Predictor was used to identify all potential pathways for 14BDO
synthesis based on known chemistry and not enzymatic reactions. More than 10 000
potential pathways were identified and then ranked based on thermodynamics, theoretical
yields, number of steps that are characterized, number of uncharacterized steps, and total
number of steps required for 14BDO synthesis. Ultimately, pathways starting from
tricarboxylic acid cycle intermediates and passing through the intermediate
4-hydroxybutyrate were selected for producing 14BDO.
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CONCLUDING REMARKS
Synthetic biology tools have come a long way since their inception, and consequently
computational methods and tools have been developed to facilitate the design of synthetic
biology components and the development of new synthetic biology tools. However, the
complexity of biological systems and the large gaps in our knowledge of these systems show
that there is still much more we need to do before achieving a true synthetic cell. An
understanding of the mechanisms of the various complex cellular components and how
they are all interconnected to manifest into a fully dynamic and robust living organism is
