Hengen P N, Bartram S L, Stewart L E, Schneider T D
Laboratory of Mathematical Biology, National Cancer Institute, Frederick Cancer Research and Development Center, PO Box B, Building 469, Room 144, Frederick, MD 21702-1201, USA.
Nucleic Acids Res. 1997 Dec 15;25(24):4994-5002. doi: 10.1093/nar/25.24.4994.
Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Inversion Stimulation) regulates many genetic systems. To determine the base frequency conservation required for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA binding sequences. The sequence logo for Fis binding sites showed the significance and likely kinds of base contacts, and these are consistent with available experimental data. Scanning with an information theory based weight matrix within fis, nrd, tgt/sec and gin revealed Fis sites not previously identified, but for which there are published footprinting and biochemical data. DNA mobility shift experiments showed that a site predicted to be 11 bases from the proximal Salmonella typhimurium hin site and a site predicted to be 7 bases from the proximal P1 cin site are bound by Fis in vitro. Two predicted sites separated by 11 bp found within the nrd promoter region, and one in the tgt/sec promoter, were also confirmed by gel shift analysis. A sequence in aldB previously reported to be a Fis site, for which information theory predicts no site, did not shift. These results demonstrate that information analysis is useful for predicting Fis DNA binding.
Fis（反转刺激因子）最初是在噬菌体Mu DNA反转系统gin中发现的，它调控着许多遗传系统。为了确定Fis定位其结合位点所需的碱基频率保守性，我们收集了一组60个经实验确定的野生型Fis DNA结合序列。Fis结合位点的序列图谱显示了碱基接触的重要性和可能类型，并且这些与现有的实验数据一致。在fis、nrd、tgt/sec和gin中使用基于信息论的权重矩阵进行扫描，发现了以前未鉴定出的Fis位点，但有已发表的足迹和生化数据。DNA迁移率变动实验表明，预测距离近端鼠伤寒沙门氏菌hin位点11个碱基的一个位点和预测距离近端P1 cin位点7个碱基的一个位点在体外被Fis结合。凝胶迁移分析也证实了在nrd启动子区域内发现的两个相隔11 bp的预测位点以及tgt/sec启动子中的一个预测位点。aldB中一个先前报道为Fis位点的序列，信息论预测该位点不存在，该序列未发生迁移。这些结果表明，信息分析对于预测Fis DNA结合是有用的。
