Additional file 2 of Systems biology of electrogenic Pseudomonas putida - multi-omics insights and metabolic engineering for enhanced 2-ketogluconate production
Creators: name: Weimer, Anna
name: Pause, Laura
name: Ries, Fabian
name: Kohlstedt, Michael
name: Adrian, Lorenz
name: Krömer, Jens
name: Lai, Bin
name: Wittmann, Christoph
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Supplementary Material 2: Additional file 2: Table S1-List of primers used for genetic engineering. The overhangs for Gibson assembly are underscored. Table S2: Fatty acid composition of P. putida KT2440 at the start of the process (0 h) and after 100 h incubation in the bio-electrochemical system. The data are given in % of total fatty acids. Table S3: Impact of anoxic-electrochemical conditions on the expression of genes related to central carbon metabolism in P. putida KT2440. The data reflect significant differences between process start (0 h) and 24 h incubation in the bio-electrochemical system. n = 3. Table S4: Impact of anoxic-electrochemical conditions on the expression of genes related to assembly of the flagellum in P. putida KT2440. The data reflect differences between process start (0 h) and 24 h incubation in the bio-electrochemical system. Non-significant differences are shown in red (Benjamini-Hochberg FDR &gt; 0.05). n = 3. Table S5: Impact of anoxic-electrochemical conditions on the expression of genes and protein abundance, related to fatty acid metabolism in P. putida KT2440. The data reflect differences between process start (0 h) and 24 h incubation in the bio-electrochemical system. Non-significant differences are shown in red (Benjamini-Hochberg FDR &gt; 0.05). n = 3. Figure S1: Summed fraction labelling (SFL) of amino acids derived from hydrolyzed P. putida KT2440 cells after 100 h incubation on [13C6] glucose in the bio-electrochemical system. Share of protein-bound (98.4%) and free intracellular amino acids (1.6%) (A). The calculation was based on a cellular protein content of 0.553 g g− 1 [92] and intracellular amino acid levels in P. putida [93]. The SFL data of selected proteinogenic amino acids are given below (B). Figure S2: Principal component analysis of the transcriptome data. 0 h (T0, circle), 24 h (BES T1, down-pointing triangle), 100 h (BES T2, up-pointing triangle). Figure S3: Venn diagram of proteome and transcriptome data at different time points. Significantly down- (blue) and upregulated (yellow) genes at 24 h (T1) and 100 h (T2) compared to the process start (T0) (A). Significantly lower (blue) and higher (yellow) abundant proteins at 24 h (T1), 100 h (T2), and 380 h (Tend) compared to the process start (T0). Figure S4: Volcano plot depicting the differences between process start (0 h) and 100 h incubation in bio-electrochemical system. Significantly down- (Log2(FC) &lt; -2, padj &lt; 0.05; blue) and upregulated (Log2(FC) &gt; 2, padj &lt; 0.05; yellow) genes. Non-significant differences are shown in grey (Benjamini-Hochberg FDR &gt; 0.05). Figure S5: Regression analysis for the determination of acetate/glucose yield coefficients for the wild type P. putida KT2440 (WT) as well as the mutants ΔacsA-I ΔacsA II, ∆PP_5266, ΔaldB-I ΔaldB-II, and ΔscpC. Figure S6: Additional data related to the BES processes of different acetate mutants shown in Fig. 8. The data shown comprise the profiles of lactate, succinate, and pyruvate over time (mM), as well as the cell concentration (OD600) over time. Figure S7: Additional data related to the BES process of P. putida ∆ aldBI ∆aldBII. The data comprise the current density j [mA/cm2], and the concentration of [Fe(CN)6]3− over time.