Bonocora Richard P, Smith Carol, Lapierre Pascal, Wade Joseph T
Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.
Wadsworth Center, New York State Department of Health, Albany, New York, United States of America; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America.
PLoS Genet. 2015 Oct 1;11(10):e1005552. doi: 10.1371/journal.pgen.1005552. eCollection 2015 Oct.
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.
细菌RNA聚合酶必须与一个σ因子结合才能结合启动子DNA并启动转录。σ因子有两个家族：σ70家族和σ54家族。在RNA聚合酶全酶的背景下，处于转录非活性状态时，σ54家族成员在结合启动子DNA序列的能力上有所不同。在这里，我们绘制了大肠杆菌σ54（σ54家族的原型成员）在全基因组范围内的关联图谱。因此，我们将已知的σ54结合位点列表大幅扩展至135个。此外，我们估计总共有超过250个σ54位点。令人惊讶的是，大多数σ54结合位点位于基因内部。基因内σ54结合位点的位置和方向并非随机，并且许多基因内σ54结合位点是保守的。我们得出结论，许多基因内σ54结合位点可能具有功能。与此断言一致的是，我们鉴定出三个保守的基因内σ54启动子，它们驱动具有异常长5'非翻译区的mRNA的转录。
