Exploring artificial biosynthesis
Metabolic route explorer helps to optimize the pathways for artificial biosynthesis of valuable products.
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Artificial synthesis of natural products for medical and commercial use could be improved with new software developed by KAUST researchers. The system, called metabolic route explorer (MRE), is designed to optimize heterologous biosynthesis pathways by taking into account more information than existing software.
In heterologous biosynthesis, organisms such as yeast and bacteria are genetically engineered to produce high quantities of specific products that are of medical or commercial value.
“The production of antimalarial drugs in baker’s yeast and the production of spider silk in Escherichia coli are examples,” explained Xin Gao from the KAUST Computational Bioscience Research Center, who led the new work.
Software can be used to design the most appropriate synthetic pathways for heterologous biosynthesis, but existing systems do not take into account the possibility of unwanted interactions between the host organism’s own metabolic machinery and the elements introduced by engineering. As a result, the pathways suggested by these systems may be suboptimal or, in some cases, impossible.
Gao and colleagues developed MRE to address this problem. “For a given pair of starting and desired compounds in a given host organism, MRE ranks biosynthesis routes by predicting the effects of integrating new reactions into the endogenous metabolic system of the host,” Gao said.
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