State Key Laboratory of Microbial Technology, Shandong Universitygrid.27255.37, Qingdao, China.
CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
mSystems. 2022 Oct 26;7(5):e0041922. doi: 10.1128/msystems.00419-22. Epub 2022 Sep 7.
The two-component system CpxRA can sense environmental stresses and regulate transcription of a wide range of genes for the purpose of adaptation. Despite extensive research on this system, the identification of the CpxR regulon is not systematic or comprehensive. Herein, genome-wide screening was performed using a position-specific scoring matrix, resulting in the discovery of more than 10,000 putative CpxR binding sites, which provides an extensive and selective set of targets based on sequence. More than half of the candidate genes ultimately selected (73/97) were experimentally confirmed to be CpxR-regulated genes through experimental analysis. These genes are involved in various physiological functions, indicating that the CpxRA system regulates complex cellular processes. The study also found for the first time that the CpxR-regulated genes , , , and contribute to Escherichia coli resistance to acid stress, whereas , , , , , , and contribute to E. coli resistance to cationic antimicrobial peptide stress. Among these CpxR-regulated genes, and responded to both stressors. In a similar way, a cationic antimicrobial peptide is capable of directly activating the periplasmic domain of CpxA kinase , which is consistent with the CpxA response to acid stress. These results greatly expand our understanding of the CpxRA-dependent stress response network in E. coli. CpxRA system is found in many pathogens and plays an essential role in sensing environmental signals and transducing information inside cells for adaptation. It usually regulates expression of specific genes in response to different environmental stresses and is important for bacterial pathogenesis. However, systematically identifying CpxRA-regulated genes and elucidating the regulative role of CpxRA in bacteria responding to environmental stress remains challenging. This study discovered more than 10,000 putative CpxR binding sites based on sequence. This bioinformatics approach, combined with experimental assays, allowed the identification of many previously unknown CpxR-regulated genes. Among the novel 73 CpxRA-regulated genes identified in this study, the role of nine of them in contributing to E. coli resistance to acid or cationic antimicrobial peptide stress was studied. The potential correlation between these two environmental stress responses provides insight into the CpxRA-dependent stress response network. This also improves our understanding of environment-bacterium interaction and Gram-negative pathogenesis.
该双组分系统 CpxRA 可以感知环境压力，并调节广泛的基因转录，以实现适应。尽管对该系统进行了广泛的研究，但 CpxR 调节子的鉴定不是系统或全面的。在此，使用位置特异性评分矩阵进行了全基因组筛选，发现了超过 10000 个假定的 CpxR 结合位点，这提供了基于序列的广泛而有选择性的靶标。最终通过实验分析，有超过一半的候选基因（73/97）被证实是 CpxR 调节的基因。这些基因涉及各种生理功能，表明 CpxRA 系统调节复杂的细胞过程。该研究还首次发现，CpxR 调节的基因 、 、 、 和 有助于大肠杆菌抵抗酸应激，而 、 、 、 、 、 和 有助于大肠杆菌抵抗阳离子抗菌肽应激。在这些 CpxR 调节的基因中， 和 对两种应激源都有反应。同样，阳离子抗菌肽能够直接激活 CpxA 激酶的周质域 ，这与 CpxA 对酸应激的反应一致。这些结果极大地扩展了我们对大肠杆菌中 CpxRA 依赖的应激反应网络的理解。CpxRA 系统存在于许多病原体中，在感知环境信号和传递细胞内信息以适应方面发挥着重要作用。它通常会根据不同的环境压力调节特定基因的表达，对于细菌的发病机制很重要。然而，系统地鉴定 CpxRA 调节的基因并阐明 CpxRA 在细菌应对环境压力方面的调节作用仍然具有挑战性。本研究基于序列发现了超过 10000 个假定的 CpxR 结合位点。这种基于生物信息学的方法，结合实验检测，鉴定了许多以前未知的 CpxR 调节基因。在本研究中鉴定的 73 个新的 CpxRA 调节基因中，研究了其中 9 个基因在大肠杆菌抵抗酸或阳离子抗菌肽应激中的作用。这两种环境应激反应之间的潜在相关性提供了对 CpxRA 依赖的应激反应网络的深入了解。这也提高了我们对环境-细菌相互作用和革兰氏阴性菌发病机制的理解。
