Fig. 3: Growth of three Pseudomonas putida deletion mutants on selected carbon sources and activities of XylA, XylB, and selected EDEMP cycle enzymes in P. putida PD310 cells.

a Scheme of the EDEMP cycle with the incorporated xylose isomerase pathway (abbreviations and color coding are the same as in Figs. 1,2) and highlighted reactions that were eliminated by knocking out the respective genes (red crosses). b Growth of PD505 (Δgcd Δedd, green arrow), PD506 (Δgcd Δgnd, brown arrow), and PD507 (Δgcd Δpgi-I Δpgi-II, red arrow) mutants on solid M9 agar medium with 2 g L⁻¹ citrate, D-glucose, or D-xylose used as the sole carbon and energy source. Ctrl- stands for negative control (P. putida EM42 Δgcd with empty pSEVA2213) and Ctrl+ stands for positive control (PD310). Cells pre-cultured in LB medium were washed with M9 medium and 10 µL of cell suspension of OD 2.0 was dropped on the agar and incubated for 24 h (agar with glucose or citrate) or 48 h (agar with xylose) at 30 °C. c Growth of the three mutants and control PD310 in M9 minimal medium with 2 g L⁻¹ D-xylose in a 48-well microplate. Data points are shown as mean ± standard deviation from three (n = 3) biological replicates. d Specific activities of 10 selected enzymes (activity of Eda and Edd was measured in a combined assay) were determined in cell-free extracts (CFE) prepared from PD310 cells cultured till mid-exponential phase in rich LB medium (LB), in M9 medium with 2 g L⁻¹ glucose (GLU), or in M9 medium with 2 g L⁻¹ xylose (XYL) as detailed in Supplementary Method 1 in Supplementary Information. Data are shown as mean ± standard deviation from three (n = 3) biological replicates. Asterisks (**) denote statistically significant difference between two means at p < 0.01 calculated using two-tailed Student t test (p values = 4.07 × 10⁻² for Zwf and 3.73 × 10⁻⁴ for Edd-Eda). Source data are provided as a Source Data file.