Fig. 3
Characterization of growth of engineered and evolved strains of P. putida on dicarboxylic acids of varying chain lengths. A All strains were cultured in MSM containing the specified carbon source, that are C-mol equivalent to 30 mM adipate. The growth was monitored using a Growth Profiler. Error bars indicate the standard error of the mean (n = 3). B Relative expression levels of gcdH in cells of P. putida with wild type or mutated versions of the regulator GcdR on different C-sources were determined by RT-qPCR. The Ct values were normalized to the Ct of rpoD. Standard errors of the means were calculated using three technical replicates of two biological replicates. Expression levels in cells that did not grow on certain substrates were set equal to unexpressed values and are indicated with “X”. C Three-dimensional structures were predicted with ColabFold and visualized with PyMOL. Docking of glutaric acid in the wild type regulator was calculated using YASARA (orange arrow). The mutated amino acid (D148) is marked in green. The blue surface color indicates the effector binding domain and the red surface color indicates the DNA binding domain. The visualization of the mutant gcdRG154D is shown in Fig. S6