Core and auxiliary functions of one-carbon metabolism in Pseudomonas putida exposed by a systems-level analysis of transcriptional and physiological responses

P. putida is equipped with functions related to one-carbon (C1) compounds (e.g. methanol, formaldehyde and formate) oxidation—yet pathways to assimilate these carbon sources are largely absent. In this work, we adopted a systems-level approach to study the genetic and molecular basis of C1 metabolism in P. putida (both in EM42 and a double mutant of the characterized formate dehydrogenases in this organism. We incubated P. putida in different C1 compounds (namely methanol and formate) in three biological replicates until expontential phase (OD ca.0.5). For formate, we also tested the double formate dehydrogenase mutant. They were compared to the minimal media with glucose solely. We then performed RNA seq data and gene expression profiling analysis.