Shimada Tomohiro, Ishihama Akira, Busby Stephen J W, Grainger David C
Department of Frontier Bioscience and Micro-Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184-8584, Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan.
Nucleic Acids Res. 2008 Jul;36(12):3950-5. doi: 10.1093/nar/gkn339. Epub 2008 May 30.
The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure the binding of RutR across the chromosome of exponentially growing E. coli cells. Twenty RutR-binding targets were identified and analysis of these targets generated a DNA consensus logo for RutR binding. Complementary in vitro binding assays showed high-affinity RutR binding to 16 of the 20 targets, with the four low-affinity RutR targets lacking predicted key binding determinants. Surprisingly, most of the DNA targets for RutR are located within coding segments of the genome and appear to have little or no effect on transcript levels in the conditions tested. This contrasts sharply with other E. coli transcription factors whose binding sites are primarily located in intergenic regions. We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness.
大肠杆菌RutR蛋白是嘧啶分解代谢相关基因的主要调控因子。在此，我们运用染色质免疫沉淀技术结合DNA微阵列，来测定指数生长期大肠杆菌细胞染色体上RutR的结合情况。我们鉴定出了20个RutR结合靶点，并对这些靶点进行分析，生成了RutR结合的DNA共有序列标志。互补的体外结合试验表明，RutR与20个靶点中的16个具有高亲和力结合，而4个低亲和力的RutR靶点缺乏预测的关键结合决定因素。令人惊讶的是，RutR的大多数DNA靶点位于基因组的编码区段内，并且在测试条件下似乎对转录水平几乎没有影响。这与其他大肠杆菌转录因子形成鲜明对比，其他转录因子的结合位点主要位于基因间区域。我们认为，要么RutR具有尚未被发现的功能，要么是进化过程中消除RutR无功能DNA位点的速度较慢，因为它们对细胞适应性没有不利影响。
