Prediction of transcriptional terminators in Bacillus subtilis and related species.
Prediction of transcriptional terminators in Bacillus subtilis and related species.
复制标题
枯草芽孢杆菌和相关物种中转录终止剂的预测。
DOI：
10.1371/journal.pcbi.0010025
复制
发表时间：
2005-08
影响因子：
4.3
通讯作者：
Miyano, Satoru
中科院分区：
文献类型：
--
作者：
de Hoon, Michiel J L;Makita, Yuko;Nakai, Kenta;Miyano, Satoru
在原核生物中，属于同一操纵子的基因转录在单个mRNA分子中。转录从RNA聚合酶与启动子结合开始，一直持续到到达转录终止子。一些终止子依赖于Rho蛋白的存在，而其他终止子则独立于Rho蛋白起作用。这种与rho无关的终止子由一个反向重复组成，然后是一段胸腺嘧啶残基，使我们能够直接从DNA序列中预测它们的存在。与大肠杆菌不同的是，枯草芽孢杆菌中没有Rho蛋白，这表明在这种生物中Rho依赖终止的作用有限，可能在其他厚壁菌门中也是如此。我们分析了463个实验已知的枯草芽孢杆菌终止序列，发现了区分rho独立转录终止序列和非终止序列的决策规则。该决策规则使我们能够以约94%的灵敏度和特异性找到枯草芽孢杆菌的操作子边界。使用相同的决策规则，我们发现57种属于厚壁菌门的细菌的平均灵敏度为94%，而对其他细菌的灵敏度则低得多。我们的分析表明，rho非依赖性终止在厚壁菌门中普遍占主导地位，并且转录终止子的性质是保守的。即使在没有实验已知的操纵子的情况下，终结者预测也可以用来可靠地预测这些生物中的操纵子结构。57种厚壁菌门的rho独立终止子的全基因组预测可在支持信息部分获得。在原核生物中，属于同一操纵子的基因转录在单个mRNA分子中。转录从RNA聚合酶与启动子结合开始，一直持续到到达转录终止子。为了了解细菌转录的基因调控网络，确定操纵子的结构是重要的第一步。在本文中，作者表明（与大肠杆菌不同）枯草芽孢杆菌中的大多数终止子独立于终止蛋白Rho起作用。由于这些与rho无关的终止子由一个反向重复序列和一段胸腺嘧啶残基组成，因此它们的存在可以直接从DNA序列中预测。作者通过分析枯草芽孢杆菌中实验已知的终止序列，得出了一个决策规则，并表明在枯草芽孢杆菌和其他厚壁菌门中，即使在没有实验已知的操纵子的情况下，也能以很高的准确率（约94%）找到操纵子边界。转录终止子的特性在厚壁菌门中被证明是保守的。对于厚壁菌门以外的细菌，预测精度相当低，这表明rho依赖性或可能目前未知的终止机制在这些生物中很重要。
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a transcriptional terminator. Some terminators rely on the presence of the Rho protein, whereas others function independently of Rho. Such Rho-independent terminators consist of an inverted repeat followed by a stretch of thymine residues, allowing us to predict their presence directly from the DNA sequence. Unlike in Escherichia coli, the Rho protein is dispensable in Bacillus subtilis, suggesting a limited role for Rho-dependent termination in this organism and possibly in other Firmicutes. We analyzed 463 experimentally known terminating sequences in B. subtilis and found a decision rule to distinguish Rho-independent transcriptional terminators from non-terminating sequences. The decision rule allowed us to find the boundaries of operons in B. subtilis with a sensitivity and specificity of about 94%. Using the same decision rule, we found an average sensitivity of 94% for 57 bacteria belonging to the Firmicutes phylum, and a considerably lower sensitivity for other bacteria. Our analysis shows that Rho-independent termination is dominant for Firmicutes in general, and that the properties of the transcriptional terminators are conserved. Terminator prediction can be used to reliably predict the operon structure in these organisms, even in the absence of experimentally known operons. Genome-wide predictions of Rho-independent terminators for the 57 Firmicutes are available in the Supporting Information section. In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a transcriptional terminator. To understand the gene regulatory network of transcription in bacteria, it is important as a first step to determine the operon structure. In this paper, the authors show that (unlike in Escherichia coli) most terminators in Bacillus subtilis function independently of the terminator protein Rho. As these Rho-independent terminators consist of an inverted repeat followed by a stretch of thymine residues, their presence can be predicted directly from the DNA sequence. The authors derived a decision rule by analyzing experimentally known terminating sequences in B. subtilis, and show that the operon boundaries can be found with a high accuracy (about 94%) in B. subtilis and other Firmicutes, even in the absence of experimentally known operons in the given organism. The properties of the transcriptional terminators are shown to be conserved within the Firmicutes phylum. For bacteria other than Firmicutes, the prediction accuracy is considerably lower, suggesting that Rho-dependent or possibly currently unknown termination mechanisms are important in these organisms.