Morgan W D, Bear D G, Litchman B L, von Hippel P H
Nucleic Acids Res. 1985 May 24;13(10):3739-54. doi: 10.1093/nar/13.10.3739.
The interaction of E. coli termination factor rho with the nascent RNA transcript appears to be a central feature of the rho-dependent transcription termination process. Based on in vitro studies of the rho-dependent termination of the transcript initiated at the PR promoter of bacteriophage lambda, and on earlier studies, Morgan, Bear and von Hippel (J. Biol. Chem. 258, 9565-9574, 1983) proposed a model defining the features of a potential binding site for rho protein on transcripts subject to rho-dependent termination. This model suggested that an effective rho binding site on a nascent RNA transcript should be: (i) greater than 70-80 nucleotide residues in length; (ii) essentially unencumbered with stable secondary structure; (iii) relatively sequence non-specific; and (iv) located within a few hundred nucleotide residues upstream of the potential rho-dependent terminus. In this paper we examine the sequences and secondary structures of several transcripts that exhibit rho-dependent termination to test this hypothesis further. Unstructured regions of approximately the expected size and location were found on all the transcripts examined. Though several short specific sequence elements were found to occur in a very similar arrangement on the lambda PR- and lambda PL-initiated transcripts of lambda phage, no such elements of sequence regularity were found on any of the other rho-dependent transcripts. The results of the sequence comparisons reported here strongly support the generality of the "unstructured binding site" hypothesis for rho-dependent termination.
大肠杆菌终止因子ρ与新生RNA转录本的相互作用似乎是ρ依赖性转录终止过程的核心特征。基于对噬菌体λ PR启动子起始转录本的ρ依赖性终止的体外研究以及早期研究，摩根、贝尔和冯·希佩尔（《生物化学杂志》258, 9565 - 9574, 1983）提出了一个模型，定义了在受ρ依赖性终止的转录本上ρ蛋白潜在结合位点的特征。该模型表明，新生RNA转录本上一个有效的ρ结合位点应该：（i）长度大于70 - 80个核苷酸残基；（ii）基本没有稳定的二级结构；（iii）相对序列非特异性；（iv）位于潜在的ρ依赖性终止位点上游几百个核苷酸残基内。在本文中，我们研究了几个表现出ρ依赖性终止的转录本的序列和二级结构，以进一步检验这一假设。在所有检测的转录本上都发现了预期大小和位置的非结构化区域。尽管在噬菌体λ的λ PR和λ PL起始转录本上发现了几个短的特定序列元件以非常相似的排列出现，但在任何其他ρ依赖性转录本上都没有发现这种序列规律性元件。此处报道的序列比较结果有力地支持了“非结构化结合位点”假说对于ρ依赖性终止的普遍性。
