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Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
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DOI：10.1038/ncomms11163.png)
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Abstract
En 中文
Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.
Keywords:
RIBOSOME BINDING-SITES
GENE-EXPRESSION
ESCHERICHIA-COLI
CRUDE VIOLACEIN
DRUGS VIOLACEIN
PROTEIN
DESIGN
INITIATION
TRYPTOPHAN
VECTORS
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