Pseudomonas bijieensis Raw sequence reads

Bacterial adaptive regulation is pivotal in responding to environmental changes. Pseudomonas, one of the largest groups in the environment, is rich in RsmA family proteins. RsmA protein is the central component of the Rsm system that controls gene expression and physiology on a global scale. Different RsmA homologues often coexist in a strain, and functionally redundancy of these proteins has been known. Here, we used RNA immunoprecipitation and high-throughput sequencing (RIP-seq) to analyse differences in the targets of RsmA and the homologous protein RsmE in P. bijieensis, and also to analyse whether the target profiles of the two proteins were affected by pH. We found that the targeting of RsmA and RsmE increased under acidic conditions compared to neutral conditions. pH had a greater effect on the targeting of RsmA than RsmE. Binding of antibiotic synthesis genes was most abundant for RsmE than RsmA under neutral conditions. Our study reveals functional differences between RsmA and RsmE, which deepens our understanding of the mechanisms by which multiple RsmA family proteins coexist and bacteria adapt to their environment.