通过DNA酶I足迹技术揭示的大肠杆菌RNA聚合酶开放启动子复合物的结构：汇编分析
Structure of open promoter complexes with Escherichia coli RNA polymerase as revealed by the DNase I footprinting technique: compilation analysis.
作者信息
Ozoline O N, Tsyganov M A
机构信息
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
出版信息
Nucleic Acids Res. 1995 Nov 25;23(22):4533-41. doi: 10.1093/nar/23.22.4533.
Abstract
Footprinting data for 33 open promoter complexes with Escherichia coli RNA polymerase, as well as 17 ternary complexes with different regulators, have been compiled using a computer program FUTPR. The typical and individual properties of their structural organization are analyzed. Promoters are subgrouped according to the extent of the polymerase contact area. A set of alternative sequence elements that could be responsible for RNA polymerase attachment in different promoter groups is suggested on the basis of their sequence homology near the hyperreactive sites. The model of alternative pathways used for promoter activation is discussed.
摘要
利用计算机程序FUTPR汇编了33个大肠杆菌RNA聚合酶开放启动子复合物以及17个与不同调节因子的三元复合物的足迹数据。分析了它们结构组织的典型和个体特性。启动子根据聚合酶接触区域的范围进行分组。基于它们在高反应性位点附近的序列同源性，提出了一组可能负责不同启动子组中RNA聚合酶附着的替代序列元件。讨论了用于启动子激活的替代途径模型。
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本文引用的文献
1
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Mol Microbiol. 1993 Mar;7(6):859-64. doi: 10.1111/j.1365-2958.1993.tb01176.x.
2
Compilation of E. coli mRNA promoter sequences.大肠杆菌信使核糖核酸启动子序列的汇编。
Nucleic Acids Res. 1993 Apr 11;21(7):1507-16. doi: 10.1093/nar/21.7.1507.
3
Effects of a single base-pair deletion in the bacteriophage lambda PRM promoter. Repression of PRM by repressor bound at OR2 and by RNA polymerase bound at PR.噬菌体λ PRM启动子中单碱基对缺失的影响。阻遏蛋白结合在OR2以及RNA聚合酶结合在PR时对PRM的抑制作用。
J Mol Biol. 1993 Jan 5;229(1):37-51. doi: 10.1006/jmbi.1993.1006.
4
E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter.在其α亚基的C末端部分缺失的大肠杆菌RNA聚合酶，在lacP1和galP1启动子处与cAMP-CRP复合物的相互作用不同。
Nucleic Acids Res. 1993 Jan 25;21(2):319-26. doi: 10.1093/nar/21.2.319.
5
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Science. 1993 Nov 26;262(5138):1407-13. doi: 10.1126/science.8248780.
6
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Biochim Biophys Acta. 1993 Mar 20;1172(3):251-61. doi: 10.1016/0167-4781(93)90211-u.
8
Multiple protein-DNA and protein-protein interactions are involved in transcriptional activation by MalT.多种蛋白质-DNA和蛋白质-蛋白质相互作用参与了MalT介导的转录激活过程。
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9
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J Mol Biol. 1994 Aug 19;241(3):341-52. doi: 10.1006/jmbi.1994.1511.
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