文章基本信息

标题：DNA topology confers sequence specificity to nonspecific architectural proteins
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作者：Juan Wei ; Luke Czapla ; Michael A. Grosner 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2014
卷号：111
期号：47
页码：16742-16747
DOI：10.1073/pnas.1405016111
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceThe organization of long genomes in the confined spaces of a cell requires special facilitating mechanisms. A variety of architectural proteins play key roles in these processes. The bacterial heat-unstable (HU) protein helps to condense DNA by introducing sharp turns along its pathway. The protein binds in a sequence-neutral fashion, randomly distorting linear DNA when introduced in computer-simulated structures at levels comparable to those found in the cell. The natural resistance of DNA to severe deformation, however, restricts the nonspecific protein to specific loci when the molecule is covalently closed or looped by a protein. The interplay of DNA topology and protein-induced bending provides insights into ways in which gene fragments may be organized and linked to biological function. Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequence-recognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability--the stiff, naturally straight double-helical structure--rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressor-operator interactions in the context of the bacterial nucleoid.
关键词：DNA cyclization ; lac operon ; Monte Carlo simulation ; nonspecific binding ; protein-mediated looping