Peter Brian J, Arsuaga Javier, Breier Adam M, Khodursky Arkady B, Brown Patrick O, Cozzarelli Nicholas R
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.
Genome Biol. 2004;5(11):R87. doi: 10.1186/gb-2004-5-11-r87. Epub 2004 Nov 1.
The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure.
We measured the transcriptional response to a loss of supercoiling caused either by genetic impairment of a topoisomerase or addition of specific topoisomerase inhibitors during log-phase growth and identified genes whose changes are statistically significant. Transcription of 7% of the genome (306 genes) was rapidly and reproducibly affected by changes in the level of supercoiling; the expression of 106 genes increased upon chromosome relaxation and the expression of 200 decreased. These changes are most likely to be direct effects, as the kinetics of their induction or repression closely follow the kinetics of DNA relaxation in the cells. Unexpectedly, the genes induced by relaxation have a significantly enriched AT content in both upstream and coding regions.
The 306 supercoiling-sensitive genes are functionally diverse and widely dispersed throughout the chromosome. We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell.
大肠杆菌的染色体维持在负超螺旋状态，超螺旋水平受生长阶段和多种环境刺激的影响。反过来，超螺旋影响局部DNA结构并可影响基因表达。我们使用代表大肠杆菌MG1655几乎整个基因组的微阵列来研究染色体结构的动态变化。
我们测量了在对数期生长期间因拓扑异构酶的遗传损伤或添加特定拓扑异构酶抑制剂导致超螺旋丧失后的转录反应，并鉴定了其变化具有统计学意义的基因。基因组中7%（306个基因）的转录受到超螺旋水平变化的快速且可重复的影响；106个基因的表达在染色体松弛时增加，200个基因的表达减少。这些变化很可能是直接效应，因为它们诱导或抑制的动力学与细胞中DNA松弛的动力学密切相关。出乎意料的是，松弛诱导的基因在上游和编码区域的AT含量均显著富集。
306个超螺旋敏感基因功能多样，广泛分布于整个染色体。我们提出超螺旋作为第二信使，将有关环境的信息传递给细胞中的许多调节网络。
