Transcriptional regulation by the stringent response-associated alarmone (p)ppGpp in Pseudomonas putida

The stringent response is an adaptive physiological response triggered by different conditions of nutritional or environmental stress and aimed at increasing survival under harsh conditions. This response is mediated the signalling nucleotides guanosine tetraphosphate (ppGpp) and pentaphospate (pppGpp), collectively known as (p)ppGpp. In this study we aim to identify genome-wide targets of regulation by the stringent-response associated alarmone (p)ppGpp in Pseudomonas putida by performing RNA-seq experiments using the wild-type KT2440tel strain and a KT2440tel-derivative bearing deletions of the (p)ppGpp synthetase-encoding genes relA and spoT (ppGpp0 mutant). Three biological replicates of wild-type P. putida KT2440tel and the ppGpp0 mutant were grown to stationary phase (OD600=4.0) in lysogeny broth (LB) at 30ºC and 180 rpm shaking.