Functional interplay between the jaw domain of bacterial RNA polymerase and allele-specific residues in the product RNA-binding pocket
Functional interplay between the jaw domain of bacterial RNA polymerase and allele-specific residues in the product RNA-binding pocket
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DOI：
10.1016/j.jmb.2005.11.080
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发表时间：
2006-03-10
影响因子：
5.6
通讯作者：
Landick, R
中科院分区：
文献类型：
--
作者：
Ederth, J;Mooney, RA;Landick, R
细菌RNA聚合酶（RNAP）是一种复杂的分子机器，其中相互作用部分的网络及其运动，包括与新生RNA和DNA模板的接触，最多只能部分理解。颚结构域是RNAP的一部分，当它从下游进入酶时，它与双链体DNA进行关键接触，并且还接触RNAP的两个其他部分，触发环，其位于RNAP二级通道中，以及在大肠杆菌RNAP触发环中的序列插入，其形成外部结构域并且还接触下游DNA。缺失颚结构域会导致转录暂停和细菌生长的缺陷。我们在这里报告说，这些缺陷可以部分纠正一组有限的取代在一个遥远的部分RNAP，产品RNA结合口袋。产物RNA结合口袋结合活性位点上游的新生RNA，并且当RNA不存在时是RNAP抑制剂利福平的结合位点。这些取代对转录延长暂停站点之间的影响不大，实际上加剧了颚缺失缺陷的转录起始，这表明暂停缺陷可能是主要负责在体内表型的颚缺失。我们认为，暂停的改变在下巴和产品RNA结合位点的抵消作用，可以介导的易位或通过变构通信的RNAP活性位点的影响。(c)2006爱思唯尔有限公司保留所有权利。
Bacterial RNA polymerase (RNAP) is a complex molecular machine in which the network of interacting parts and their movements, including contacts to nascent RNA and the DNA template, are at best partially understood. The jaw domain is a part of RNAP that makes a key contact to duplex DNA as it enters the enzyme from downstream and also contacts two other parts of RNAP, the trigger loop, which lies in the RNAP secondary channel, and a sequence insertion in the Escherichia coli RNAP trigger loop that forms an external domain and also contacts downstream DNA. Deletion of the jaw domain causes defects in transcriptional pausing and in bacterial growth. We report here that these defects can be partially corrected by a limited set of substitutions in a distant part of RNAP, the product RNA-binding pocket. The product RNA-binding pocket binds nascent RNA upstream of the active site and is the binding site for the RNAP inhibitor rifampicin when RNA is absent. These substitutions have little effect on transcript elongation between pause sites and actually exacerbate jaw-deletion defects in transcription initiation, suggesting that the pausing defects may be principally responsible for the in vivo phenotype of the jaw deletion. We suggest that the counteracting effects on pausing of the alterations in the jaw and the product RNA binding site may be mediated either by effects on translocation or via allosteric communication to the RNAP active site. (c) 2006 Elsevier Ltd. All rights reserved.