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). Overall design: 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.

严谨应答（stringent response）是一类适应性生理应答，由营养或环境胁迫的不同条件触发，旨在提升极端条件下的存活率。该应答由信号核苷酸四磷酸鸟苷（guanosine tetraphosphate，ppGpp）与五磷酸鸟苷（guanosine pentaphosphate，pppGpp）介导，二者统称为(p)ppGpp。本研究以恶臭假单胞菌（Pseudomonas putida）为研究对象，旨在鉴定严谨应答相关警报素(p)ppGpp的全基因组调控靶标，将通过使用野生型KT2440tel菌株与携带(p)ppGpp合成酶编码基因relA和spoT缺失的KT2440tel衍生菌株（ppGpp0突变株）开展RNA测序（RNA-seq）实验完成相关研究。实验设计概况：将野生型恶臭假单胞菌KT2440tel与ppGpp0突变株各设置3个生物学重复，于30℃、180 rpm振荡培养条件下在LB培养基（lysogeny broth，LB）中培养至稳定生长期（OD600=4.0）。