Zhang Jian, Li Enhu, Olsen Gary J
Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA.
Nucleic Acids Res. 2009 Jun;37(11):3588-601. doi: 10.1093/nar/gkp213. Epub 2009 Apr 9.
Although Methanocaldococcus (Methanococcus) jannaschii was the first archaeon to have its genome sequenced, little is known about the promoters of its protein-coding genes. To expand our knowledge, we have experimentally identified 131 promoters for 107 protein-coding genes in this genome by mapping their transcription start sites. Compared to previously identified promoters, more than half of which are from genes for stable RNAs, the protein-coding gene promoters are qualitatively similar in overall sequence pattern, but statistically different at several positions due to greater variation among their sequences. Relative binding affinity for general transcription factors was measured for 12 of these promoters by competition electrophoretic mobility shift assays. These promoters bind the factors less tightly than do most tRNA gene promoters. When a position weight matrix (PWM) was constructed from the protein gene promoters, factor binding affinities correlated with corresponding promoter PWM scores. We show that the PWM based on our data more accurately predicts promoters in the genome and transcription start sites than could be done with the previously available data. We also introduce a PWM logo, which visually displays the implications of observing a given base at a position in a sequence.
尽管詹氏甲烷球菌（Methanocaldococcus (Methanococcus) jannaschii）是首个完成基因组测序的古生菌，但对其蛋白质编码基因的启动子却知之甚少。为了拓展我们的认识，我们通过绘制转录起始位点，实验鉴定了该基因组中107个蛋白质编码基因的131个启动子。与先前鉴定的启动子相比（其中超过一半来自稳定RNA的基因），蛋白质编码基因启动子在总体序列模式上定性相似，但由于序列间差异更大，在几个位置上存在统计学差异。通过竞争电泳迁移率变动分析，对其中12个启动子测定了与一般转录因子的相对结合亲和力。这些启动子与因子的结合不如大多数tRNA基因启动子紧密。当从蛋白质基因启动子构建位置权重矩阵（PWM）时，因子结合亲和力与相应启动子的PWM得分相关。我们表明，基于我们的数据构建的PWM比使用先前可得数据能更准确地预测基因组中的启动子和转录起始位点。我们还引入了一个PWM标识，它直观地展示了在序列中某一位置观察到特定碱基的意义。
