Additional file 1 of Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes
Creators: name: Gotsmy, Mathias
name: Strobl, Florian
name: Weiß, Florian
name: Gruber, Petra
name: Kraus, Barbara
name: Mairhofer, Juergen
name: Zanghellini, Jürgen
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Physical Sciences not elsewhere classified
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Additional file 1: Table S1. Parameters for dFBA simulations. Cells marked with "–" are not applicable and cells marked with "var" are not constant in the respective process. Table S2. Growth media components of the experiments. Growth media were sterilized by filtration. The trace element solution was prepared in 5 M HCl and contained (g/L): 4.41 CaCl2 ⋅ 2H2O, 3.34 FeSO4 ⋅ 7H2O, 1.43 CoCl2 ⋅ 6H2O, 1.03MnSO4 ⋅H2O, 0.15 CuSO4 ⋅ 5H2O, 0.17 ZnSO4 ⋅ 7H2O. † In total, 9.6 mL of a 200 g/L MgSO4 ⋅ 7 H2O stock solution were pulsed into the bioreactor (3.2 mL at feed start, 3.2 mL at 7 h after feed start and 3.2 mL at 15 h after feed start). ‡ According to our stoichiometric model [29], the amount of MgSO4 ⋅ 7 H2O in the batch medium alone can support more than 50 g of biomass. However, to ensure that Mg2+ is present in excess throughout the sulfate limited process we further added Mg2+ in the form of MgCl2 ⋅ 6 H2O. Table S3. Average values of several process variables of interest and their p-values compared to the control at 31 h (one-sided t-test). ccc pDNA corresponds to the supercoiled fraction of plasmid DNA measured.Table S4. List of potential targets for process optimization with sulfate limitation. We used lexicographic FBA (Table 1) to calculate maximal theoretical production rates during sulfate starvation (max. q∗) and sulfate excess (max. qμ) in mmol g−1 h−1. Compounds marked with † are displayed with their BiGG ID [75] to shorten the name. Previously described sulfate limitation target mevalonate is not naturally synthesized in E. coli [43] and, thus, not present in the list. Figure S1. Predicted optimal timing in a $${\text {SO}_4^{2-}}$$ SO 4 2 - limited linear fed-batch (A, B, C) and batch (D, E, F) process. Figure S2. Predicted optimal timing in a $${\text {SO}_4^{2-}}$$ SO 4 2 - limited linear (A, B, C) and exponential (D, E, F) fed-batch process. Figure S3. Predicted optimal timing in a $${\text {SO}_4^{2-}}$$ SO 4 2 - limited linear fed-batch process with different maximum starvation lengths. Figure S4. Visualization explanation of $$t^*_\text {breakthrough}$$ t breakthrough ∗ . Figure S5. Acetate accumulation during control and $${\text {SO}_4^{2-}}$$ SO 4 2 - limited processes. Figure S6. Control and sulfate limited process with time-dependent qpDNA. Figure S7. Predicted optimal timing in a $${\text {SO}_4^{2-}}$$ SO 4 2 - limited linear fed-batch process with variable qpDNA.