sigma(28) RNA polymerase is an alternative RNA polymerase that has been proposed to have a role in late developmental gene regulation in Chlamydia, but only a single target gene has been identified. To discover additional sigma(28)-dependent genes in the Chlamydia trachomatis genome, we applied bioinformatic methods using a probability weight matrix based on known sigma(28) promoters in other bacteria and a second matrix based on a functional analysis of the sigma(28) promoter. We tested 16 candidate sigma(28) promoters predicted with these algorithms and found that 5 were active in a chlamydial sigma(28) in vitro transcription assay. hctB, the known sigma(28)-regulated gene, is only expressed late in the chlamydial developmental cycle only, and two of the newly identified sigma(28) target genes (tsp and tlyC_1) also have late expression profiles, providing support for sigma(28) as a regulator of late gene expression. One of the other novel sigma(28)-regulated genes is dnaK, a known heat shock-responsive gene, suggesting that sigma(28) RNA polymerase may be involved in the response to cellular stress. Our sigma(28) prediction algorithm can be applied to other bacteria, and by performing a similar analysis on the Escherichia coli genome, we have predicted and functionally identified five previously unknown sigma(28)-regulated genes in E. coli.

译文

sigma(28) RNA聚合酶是一种替代的RNA聚合酶,已被提议在衣原体的晚期发育基因调控中起作用,但仅鉴定出单个靶基因。为了在沙眼衣原体基因组中发现其他依赖sigma(28) 的基因,我们使用生物信息学方法,使用基于其他细菌中已知sigma(28) 启动子的概率权重矩阵和基于sigma(28) 启动子的功能分析的第二个矩阵。28) 启动子。我们测试了用这些算法预测的16个候选sigma(28) 启动子,发现5个在衣原体sigma(28) 体外转录测定中具有活性。已知的sigma(28) 调控基因hctB仅在衣原体发育周期的晚期表达,新鉴定的sigma(28) 靶基因 (tsp和tlyC_1) 中的两个也具有晚期表达谱,为sigma(28) 作为晚期基因表达的调节剂提供支持。另一个新的sigma(28) 调控基因是dnaK,这是一种已知的热休克反应基因,表明sigma(28) RNA聚合酶可能参与了对细胞应激的反应。我们的sigma(28) 预测算法可以应用于其他细菌,并且通过对大肠杆菌基因组进行类似的分析,我们已经预测并在功能上鉴定了大肠杆菌中五个以前未知的sigma(28) 调控基因。

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