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DNA环化和易位为III型限制酶提供了一种最佳的切割机制。

DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.

作者信息

Crampton Neal, Roes Stefanie, Dryden David T F, Rao Desirazu N, Edwardson J Michael, Henderson Robert M

机构信息

Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, UK.

出版信息

EMBO J. 2007 Aug 22;26(16):3815-25. doi: 10.1038/sj.emboj.7601807. Epub 2007 Jul 26.

DOI:10.1038/sj.emboj.7601807
PMID:17660745
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1952222/
Abstract

EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site-bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site-bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.

摘要

EcoP15I是一种III型限制酶，它需要两个特定方向的识别位点，两个位点之间的距离可达3.5千碱基对，才能有效切割DNA。位点结合的EcoP15I酶在两个位点之间进行通讯的机制尚不清楚。在这里，我们使用原子力显微镜来研究EcoP15I-DNA预切割复合物。从形成的环的数量和大小分布来看，我们得出结论，观察到的环不是由易位产生的，而是由位点结合的EcoP15I与DNA的非特异性区域之间的接触形成的。这一结论得到了理论聚合物模型的证实。进一步表明易位必定起了一定作用，因为当易位被乳糖阻遏蛋白阻断时，DNA切割同样被阻断。基于这些结果，我们提出了一个III型限制酶限制作用的模型，并强调了它与其他类限制酶之间的相似性。

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DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.DNA环化和易位为III型限制酶提供了一种最佳的切割机制。
EMBO J. 2007 Aug 22;26(16):3815-25. doi: 10.1038/sj.emboj.7601807. Epub 2007 Jul 26.
2
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本文引用的文献

1
When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.当解旋酶并非解旋酶时：马达蛋白EcoR124I对双链DNA的追踪
EMBO J. 2006 May 17;25(10):2230-9. doi: 10.1038/sj.emboj.7601104. Epub 2006 Apr 27.
2
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.多亚基I型C类限制修饰DNA甲基转移酶M.EcoR124I与DNA复合物的结构模型。
Nucleic Acids Res. 2006 Apr 13;34(7):1992-2005. doi: 10.1093/nar/gkl132. Print 2006.
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Protein assembly and DNA looping by the FokI restriction endonuclease.由FokI限制性内切核酸酶介导的蛋白质组装与DNA环化
Nucleic Acids Res. 2006 Mar 23;34(6):1711-20. doi: 10.1093/nar/gkl076. Print 2006.
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Kinetics of interior loop formation in semiflexible chains.半柔性链中内部环形成的动力学。
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Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I.动力蛋白EcoR124I介导的DNA易位起始、终止和重新起始的动力学
EMBO J. 2005 Dec 7;24(23):4188-97. doi: 10.1038/sj.emboj.7600881. Epub 2005 Nov 17.
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The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.I型限制性内切核酸酶EcoR124I将ATP水解与双向DNA易位偶联起来。
J Mol Biol. 2005 Sep 30;352(4):837-59. doi: 10.1016/j.jmb.2005.07.055.
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Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.斯氏普罗威登斯菌III型限制性内切酶PstII的特性分析。
Nucleic Acids Res. 2005 Aug 24;33(15):4775-87. doi: 10.1093/nar/gki787. Print 2005.
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Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases.利用荧光三链体解离进行DNA易位的连续分析：应用于I型限制性内切核酸酶
J Mol Biol. 2005 May 13;348(4):895-915. doi: 10.1016/j.jmb.2005.03.018.
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Formation of loops in DNA under tension.DNA在张力作用下形成环。
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021911. doi: 10.1103/PhysRevE.71.021911. Epub 2005 Feb 24.
10
Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.来自识别位点的单向易位以及与DNA末端的必要相互作用，以便III型限制酶进行切割。
Nucleic Acids Res. 2004 Oct 22;32(19):5703-11. doi: 10.1093/nar/gkh899. Print 2004.