Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling
Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling
复制标题
DOI：
10.1074/jbc.m313454200
复制
发表时间：
2004-03-26
影响因子：
4.8
通讯作者：
De Wulf, P
中科院分区：
文献类型：
--
作者：
Liu, XQ;De Wulf, P
大肠杆菌的 ArcB/ArcA 双组分信号转导系统响应生长的氧化还原条件调节基因表达。多年来，遗传筛选已鉴定出约 30 个参与氧化还原代谢的 ArcA-P 控制操纵子。然而，与呼吸代谢无关的 3 个靶标（用于质粒接合的 tra 操纵子、用于基于 Xer 的重组的 psi 位点和用于染色体复制的 oriC 位点）的发现表明，Arc 模块可能包含参与多种功能的其他操纵子。为了识别这些操纵子，我们使用基于寡核苷酸的微阵列分析得出了大肠杆菌的 ArcA-P 依赖性转录谱。研究结果表明，大肠杆菌中 9% 的开放阅读框直接或间接受到 ArcA-P 的影响。为了确定哪些操纵子受到 ArcA-P 的直接控制，我们根据足迹数据开发了 ArcA-P 识别权重矩阵，并用它来扫描基因组，产生 ArcA-P 序列亲和力图。通过叠加这两种方法，我们鉴定了 55 个新的 Arc 调节操纵子，它们与能量代谢、运输、生存、分解代谢和转录调节有关。数据还表明，Arc 反应途径（转化为基因表达的整体净缩减）与 FNR 调控网络部分重叠。保守但合理的评估是，Arc 途径招募 100 150 个操纵子来介导细胞适应中的作用，其范围比迄今为止预期的更广泛。
The ArcB/ArcA two-component signal transduction system of Escherichia coli regulates gene expression in response to the redox conditions of growth. Over the years, genetic screens have lead to the identification of about 30 ArcA-P-controlled operons that are involved in redox metabolism. However, the discovery of 3 targets that are not implicated in respiratory metabolism ( the tra operon for plasmid conjugation, psi site for Xer-based recombination, and oriC site for chromosome replication) suggests that the Arc modulon may comprise additional operons that are involved in a myriad of functions. To identify these operons, we derived the ArcA-P-dependent transcription profile of E. coli using oligonucleotide-based microarray analysis. The findings indicated that 9% of all open reading frames in E. coli are affected either directly or indirectly by ArcA-P. To identify which operons are under the direct control of ArcA-P, we developed the ArcA-P recognition weight matrix from footprinting data and used it to scan the genome, yielding an ArcA-P sequence affinity map. By overlaying both methods, we identified 55 new Arc-regulated operons that are implicated in energy metabolism, transport, survival, catabolism, and transcriptional regulation. The data also suggest that the Arc response pathway, which translates into a net global downscaling of gene expression, overlaps partly with the FNR regulatory network. A conservative but reasonable assessment is that the Arc pathway recruits 100 150 operons to mediate a role in cellular adaptation that is more extensive than hitherto anticipated.