title: Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.
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 co-optimize genetic and non-genetic factors.
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands.
authors.forename: Brenda
authors.initials: B
authors.lastname: Vonk
authors.affiliation: DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands.
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Roubos
authors.affiliation: DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
authors.forename: Roel A L
authors.initials: RA
authors.lastname: Bovenberg
authors.affiliation: Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA cavoigt@gmail.com.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Voigt
mesh_terms: D000465:Algorithms; D015119:Aminocaproic Acid / Q000378:metabolism*; D003470:Culture Media; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development; D060847:Metabolic Engineering / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics
chemical_list: D003470:Culture Media; D015119:Aminocaproic Acid