Choudhary Kumari Sonal, Kleinmanns Julia A, Decker Katherine, Sastry Anand V, Gao Ye, Szubin Richard, Seif Yara, Palsson Bernhard O
Department of Bioengineering, University of California, San Diego, San Diego, California, USA.
Department of Bioengineering, University of California, San Diego, San Diego, California, USA
mSystems. 2020 Nov 10;5(6):e00980-20. doi: 10.1128/mSystems.00980-20.
uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of 's global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in is thus notably expanded. is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. 's two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.
利用双组分系统（TCSs）来响应环境信号。双组分系统影响基因表达，并且是大肠杆菌全局转录调控网络（TRN）的组成部分。在此，我们鉴定了大肠杆菌MG1655中五个双组分系统的调控子：受乙醇胁迫刺激的BaeSR和CpxAR；分别由钾和磷酸盐限制诱导的KdpDE和PhoRB；以及受锌刺激的ZraSR。我们使用独立成分分析（ICA）分析RNA测序数据。染色质免疫沉淀外切酶测序（ChIP-exo）数据用于验证条件特异性靶基因结合位点。基于这些数据，我们进行了以下操作：（i）确定每个双组分系统的靶基因；（ii）展示靶基因如何响应刺激进行转录；以及（iii）揭示双组分系统之间的新关系，这表明各种响应调节因子存在非同源诱导物，例如BaeR对铁饥饿、CpxR对磷酸盐限制以及PhoB和ZraR对细胞包膜应激。因此，我们对大肠杆菌转录调控网络的理解得到了显著扩展。大肠杆菌是在人类肠道微环境中发现的常见共生微生物；然而，一些菌株会引发腹泻、尿路感染和脑膜炎等疾病。大肠杆菌的双组分系统（TCSs）响应环境刺激调节靶基因表达，特别是与毒力、发病机制和抗菌肽相关的基因表达。因此，了解双组分系统的转录调控对于推断细菌的环境适应性和疾病致病性至关重要。利用整合RNA测序（RNA-seq）、独立成分分析、染色质免疫沉淀结合外切酶处理（ChIP-exo）和数据挖掘的组合方法，我们提出了五种不同的双组分系统转录调控模式。我们的数据进一步突出了双组分系统的非同源诱导物，这强调了大肠杆菌中双组分系统的交叉调控性质，并表明双组分系统可能具有超出其同源功能的作用。总之，这些结果有助于理解细菌的代谢能力，并正确预测不同条件下的复杂表型，特别是当进一步与基因组规模的代谢模型结合时。
