Algorithmic co-optimization of genetic constructs and growth conditions: Application to 6-ACA, a potential nylon-6 precursor

Hui Zhou, Brenda Vonk, J. Roubos, Roel A L Bovenberg, Christopher A. Voigt

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32- member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6- ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to cooptimize genetic and non-genetic factors.

Original languageEnglish
Pages (from-to)10560-10570
Number of pages11
JournalNucleic Acids Research
Volume43
Issue number21
DOIs
Publication statusPublished - 2015

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Aminocaproic Acid
Libraries
Statistical Data Interpretation
Growth
Genotype
Genetic Phenomena
DNA
Enzymes
Genes
Escherichia coli
nylon 6

ASJC Scopus subject areas

  • Genetics

Cite this

Algorithmic co-optimization of genetic constructs and growth conditions : Application to 6-ACA, a potential nylon-6 precursor. / Zhou, Hui; Vonk, Brenda; Roubos, J.; Bovenberg, Roel A L; Voigt, Christopher A.

In: Nucleic Acids Research, Vol. 43, No. 21, 2015, p. 10560-10570.

Research output: Contribution to journalArticle

Zhou, Hui ; Vonk, Brenda ; Roubos, J. ; Bovenberg, Roel A L ; Voigt, Christopher A. / Algorithmic co-optimization of genetic constructs and growth conditions : Application to 6-ACA, a potential nylon-6 precursor. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 21. pp. 10560-10570.
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