Lesnik E A, Sampath R, Levene H B, Henderson T J, McNeil J A, Ecker D J
IBIS Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA.
Nucleic Acids Res. 2001 Sep 1;29(17):3583-94. doi: 10.1093/nar/29.17.3583.
A new algorithm called RNAMotif containing RNA structure and sequence constraints and a thermodynamic scoring system was used to search for intrinsic rho-independent terminators in the Escherichia coli K-12 genome. We identified all 135 reported terminators and 940 putative terminator sequences beginning no more than 60 nt away from the 3'-end of the annotated transcription units (TU). Putative and reported terminators with the scores above our chosen threshold were found for 37 of the 53 non-coding RNA TU and for almost 50% of the 2592 annotated protein-encoding TU, which correlates well with the number of TU expected to contain rho-independent terminators. We also identified 439 terminators that could function in a bi-directional fashion, servicing one gene on the positive strand and a different gene on the negative strand. Approximately 700 additional termination signals in non-coding regions (NCR) far away from the nearest annotated gene were predicted. This number correlates well with the excess number of predicted 'orphan' promoters in the NCR, and these promoters and terminators may be associated with as yet unidentified TU. The significant number of high scoring hits that occurred within the reading frame of annotated genes suggests that either an additional component of rho-independent terminators exists or that a suppressive mechanism to prevent unwanted termination remains to be discovered.
一种名为RNAMotif的新算法，它包含RNA结构和序列限制以及一个热力学评分系统，被用于在大肠杆菌K-12基因组中搜索内在的不依赖ρ因子的终止子。我们鉴定出了所有135个已报道的终止子以及940个推定的终止子序列，这些序列起始位置距离注释转录单元（TU）的3'端不超过60个核苷酸。在53个非编码RNA TU中的37个以及2592个注释的蛋白质编码TU中的近50%中，发现了得分高于我们所选阈值的推定终止子和已报道终止子，这与预期包含不依赖ρ因子终止子的TU数量高度相关。我们还鉴定出了439个可以双向发挥作用的终止子，它们为正链上的一个基因和负链上的另一个不同基因提供服务。在远离最近注释基因的非编码区域（NCR）中预测到了大约700个额外的终止信号。这个数字与NCR中预测的“孤儿”启动子的多余数量高度相关，并且这些启动子和终止子可能与尚未鉴定的TU相关联。在注释基因的阅读框内出现的大量高分命中结果表明，要么存在不依赖ρ因子终止子的额外组成部分，要么存在一种抑制不必要终止的机制有待发现。
