Pseudomonas putida KT2440 RNA-Seq and Ribo-Seq in M9 medium + glucose

We reconstructed a ME-model for P. putida KT2440, iPpu1676-ME, offering an unprecedented level of detail in the cellular function and proteome allocation of this bacterium. We interrogated the gene expression of P. putida KT2440 using transcriptomics (RNA-Seq) and translatomics (Ribo-Seq) data. We analyzed the translational prioritization of pathways, as well as pathways that were significantly less prioritized for translation. When contrasting the model predictions against these sequencing datasets, we found stronger agreement with the ME-model compared to the M-model. Thus iPpu1676-ME represents a valuable asset for accurate predictive modeling as a tool for bioprocess design and optimization and metabolic engineering in this industrially important strain.