大肠杆菌启动子组成与DNA链相互作用及启动子活性的规律。

Regularities in the E. coli promoters composition in connection with the DNA strands interaction and promoter activity.

作者信息

Berezhnoy Andrey Yu, Shckorbatov Yuriy G, Hisanori Kiryu

机构信息

National Scientific Center, Kharkov Physical-Technical Institute, Kharkov 61108, Ukraine.

出版信息

J Zhejiang Univ Sci B. 2006 Dec;7(12):969-73. doi: 10.1631/jzus.2006.B0969.

DOI:10.1631/jzus.2006.B0969

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1661676/

Abstract

The energy of interaction between DNA strands in promoters is of great functional importance. Visualization of the energy of DNA strands distribution in promoter sequences was achieved. The separation of promoters in groups by their energetic properties enables evaluation of the dependence of promoter strength on the energetic properties. The analysis of groups (clusters) of promoters distributed by the energy of DNA strands interaction in -55, -35, -10 and +6 sequences indicates their connection with the transcriptional activity.

摘要

启动子中DNA链之间的相互作用能量具有重要的功能意义。实现了启动子序列中DNA链能量分布的可视化。根据启动子的能量特性对其进行分组，能够评估启动子强度对能量特性的依赖性。对在-55、-35、-10和+6序列中按DNA链相互作用能量分布的启动子组（簇）进行分析，表明它们与转录活性有关。

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本文引用的文献

1

Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence.

J Zhejiang Univ Sci B. 2005 Nov;6(11):1063-8. doi: 10.1631/jzus.2005.B1063.

2

The KEGG resource for deciphering the genome.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80. doi: 10.1093/nar/gkh063.

3

Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates.

J Mol Biol. 2002 Jun 7;319(3):649-71. doi: 10.1016/S0022-2836(02)00293-0.

4

Functional genomics of Escherichia coli in Japan.

Res Microbiol. 2000 Mar;151(2):121-8. doi: 10.1016/s0923-2508(00)00119-4.

5

DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA.

J Mol Biol. 1998 Nov 6;283(4):741-56. doi: 10.1006/jmbi.1998.2129.

6

sigma factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA.

Nucleic Acids Res. 1997 Jul 1;25(13):2603-9. doi: 10.1093/nar/25.13.2603.

7

Recognition of the -10 promoter sequence by a partial polypeptide of sigma70 in vitro.

J Biol Chem. 1997 Feb 7;272(6):3487-94.

8

Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase.

Cell. 1996 Aug 9;86(3):495-501. doi: 10.1016/s0092-8674(00)80122-1.

9

Compilation and analysis of Escherichia coli promoter DNA sequences.

Nucleic Acids Res. 1983 Apr 25;11(8):2237-55. doi: 10.1093/nar/11.8.2237.

10

Analysis of E. coli promoter sequences.

Nucleic Acids Res. 1987 Mar 11;15(5):2343-61. doi: 10.1093/nar/15.5.2343.

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