Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

Byrne, David; Dumitriu, Alexandra; Segrè, Daniel

doi:10.1186/1752-0509-6-127

BMC Systems Biology

Table 1 Selected Pareto optimal engineering designs

From: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

Design identifiers		Design criteria		Design annotations			Design metrics
Design Id^a	Cluster Id^b	Design goals^c	Design type^d	Gene deletions	Nutrient sources^e	Organism^f	Acetate production rate (mmol gDW^-1 hr^-1)	Acetate purity	Biomass production rate (hr^-1)	Microarray consistency^g	Succinate production rate (mmol gDW^-1 hr^-1)	Succinate purity	Total economic cost rate ($ hr^-1)
1	8	Succinate production rate (0.99), Succinate purity (0.01)	candidate	edd, gnd	malthx, fum, gam, pi, so4	ec	0	0	1.85	NA	195.34	0.63	19314.4
2	8	Succinate production rate (0.5), Succinate purity (0.5)	candidate	atpH, caiD	malthx, fum, gam, pi, so4	ec	0	0	1.85	NA	181.57	0.71	19305.4
3	3	Succinate purity (1)	candidate	SO4417, SO3136	ac, fum, nh4, pi, so4	so	0	0	0.01	NA	20	1	3.72
4	1	Succinate production rate (0.01), Total economic cost rate (−0.99)	candidate	kgtP, lysP	sucr, o2, gam, ppt, so4	ec	36.17	0.35	1.85	NA	51.45	0.49	4.33
5	30	Succinate purity (0.5), Total economic cost rate (−0.5)	candidate	YBR196C, YMR256C	glc, o2, urea, pi, so4	sc	0	0	0.26	NA	14.77	0.43	0.05
6	1	Succinate production rate (0.33), Succinate purity (0.33), Total economic cost rate (−0.33)	candidate	SO4417, SO3136	glyclt, fum, nh4, pi, so4	so	0	0	0.06	NA	20	1	2.26
7	1	Succinate production rate (1)	validated	ptsG, pykFA, pfl	glc, NA, nh4, pi, so4	ec	4.28	0.24	0.12	NA	9.12	0.5	0.03
8	1	Acetate production rate (1)	microarray	appY	glc, NA, nh4, pi, so4	ec	6.76	0.24	0.17	0.46	0.06	0	0.75
9	1	Acetate purity (1)	microarray	arcA	glc, o2, nh4, pi, so4	ec	1.1	1	0.63	0.02	0	0	2.35
10	1	Microarray consistency (1)	microarray	arcA	glc, NA, nh4, pi, so4	ec	0	0	0.11	0.56	0.04	0	0.02
11	1	Acetate production rate (0.33), Microarray consistency (0.33), Acetate purity (0.33)	microarray	appY	glc, NA, nh4, pi, so4	ec	6.76	0.24	0.17	0.46	0.06	0	0.75

^a Engineering designs are referenced in the text by this identifier. ^b Each engineering design is associated with an engineering phenotype cluster (meta-phenotype) and identified according to the “Clusters” shown in Figure6(A) for E. coli, Additional file1: Figure S13(A) for S. cerevisiae, and Additional file1: Figure S14(A) for S. oneidensis. ^c The specified engineering design goals and weights (shown in parentheses, where positive weights indicate goal maximization and negative weights indicate goal minimization) are used to determine the optimal engineering designs for the corresponding “Design type”. ^d “Validated” designs are designs that were experimentally validated, “microarray” designs are designs that had matching experimental microarray data, and “candidate” designs are simulated designs that are neither “validated” nor “microarray” designs. ^e Nutrients are ordered by nutrient type: carbon, electron acceptor, nitrogen, phosphorous, and sulfur source. “NA” indicates that no nutrient source of that type was provided. Metabolite abbreviations: ac = Acetate, fum = Fumarate, gam = D-Glucosamine, glc = D-Glucose, glu-L = L-Glutamate, glyclt = Glycolate, malthx = Maltohexoase, nh4 = Ammonium, o2 = O2, pi = Phosphate, ppt = Phosphonate, sbt-D = D-Sorbitol, so4 = Sulfate, sucr = Sucrose, urea = Urea. ^f Organism abbreviations: ec = Escherichia coli, sc = Saccharomyces cerevisiae, so = Shewanella oneidensis. ^g Engineering design simulations were compared with microarray data to compute experimental microarray consistency. “NA” indicates that no microarray data was available for the corresponding design.

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ISSN: 1752-0509

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