Conserved economics of transcription termination in eubacteria
Conserved economics of transcription termination in eubacteria
复制标题
DOI：
10.1093/nar/30.3.675
复制
发表时间：
2002-02-01
影响因子：
14.9
通讯作者：
Nagaraja, V
中科院分区：
文献类型：
--
作者：
Unniraman, S;Prakash, R;Nagaraja, V
新生的RNA中的二级结构，后面跟着一串U残基，被认为是终止转录所必需的，也是足够的。这种结构代表了一种非常经济的转录终止机制，因为它们在没有任何额外蛋白质因子的情况下发挥作用。我们开发了一种新的算法，Gester，来识别假定的终止子，并分析了所有可用的完整细菌基因组。该算法将结构分为五类。我们发现在大多数细菌基因组中，潜在的二级结构序列集中在编码区的下游。有趣的是，这些结构中的许多都没有明显的U形轨迹。然而，无论TRAIL序列的性质如何，这些结构都显示出相似的分布，表明它们服务于相同的目的。相反，这种分布在古生菌基因组中是不存在的，这表明它们使用了一种独特的转录终止机制。本算法代表了最快和最准确的算法来识别真细菌基因组中的终止子，而不受经典的大肠杆菌范例的限制。
A secondary structure in the nascent RNA followed by a trail of U residues is believed to be necessary and sufficient to terminate transcription. Such structures represent an extremely economical mechanism of transcription termination since they function in the absence of any additional protein factors. We have developed a new algorithm, GeSTer, to identify putative terminators and analysed all available complete bacterial genomes. The algorithm classifies the structures into five classes. We find that potential secondary structure sequences are concentrated downstream of coding regions in most bacterial genomes. Interestingly, many of these structures are not followed by a discernible U-trail. However, irrespective of the nature of the trail sequence, the structures show a similar distribution, indicating that they serve the same purpose. In contrast, such a distribution is absent in archaeal genomes, indicating that they employ a distinct mechanism for transcription termination. The present algorithm represents the fastest and most accurate algorithm for identifying terminators in eubacterial genomes without being restricted by the classical Escherichia coli paradigm.