NtrC, The Master Regulator Controls the Utilization of Alternative Nitrogen Sources in Pseudomonas Stutzeri A1501

Abstract Pseudomonas stutzeri A1501 is the model strain for studying associative nitrogen fixation and possesses the nitrogen regulatory NtrC protein in the core genome. Nitrogen source is one of the important factors affecting the efficiency of biological nitrogen fixation in the natural environment. However, the regulation of NtrC in nitrogen metabolism of P. stutzeri A1501 is not clear. In this work, phenotypic analysis of the ntrC mutant characterized the roles of NtrC for the nitrogen metabolism and oxidative stress response of P. stutzeri A1501. To systematically identify NtrC-controlled gene expression, RNA-seq was performed to further analyze the gene expression differences between the wild type strain and the ∆ntrC mutant under nitrogen fixation conditions. A total of 1431 genes were found to be significantly altered by the ntrC deletion, among which 147 associative genes had NtrC-binding sites, and pathways for nitrogen fixation regulation, the acquisition and catabolism of nitrogenous compounds and nitrate assimilation were particularly discussed. Furthermore, the oxidative stress-related gene (katB), upregulated by the ntrC deletion, was suggested to be the potential target gene of NtrC, underlining the importance of NtrC to nitrogenase protection against oxygen damage. Based on these findings, we propose that NtrC is a high-ranked element in the regulatory network of P. stutzeri A1501 that controls a variety of nitrogen metabolic and oxidative stress responsive traits required for adaptation to complex rhizosphere environment.