Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis
Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis
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DOI：
10.1016/j.jmb.2006.09.043
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发表时间：
2006-12-08
影响因子：
5.6
通讯作者：
Johnson, Reid C.
中科院分区：
文献类型：
--
作者：
Skoko, Dunja;Yoo, Daniel;Johnson, Reid C.
Fis是大肠杆菌快速生长过程中最丰富的DNA结合蛋白，被认为在确定类核结构中起重要作用。利用体相和单DNA分子实验，我们分析了Fis与DNA非特异性结合的结构后果。Fis在纳摩尔浓度下以基本上序列中性的方式结合DNA，导致在施加的力下由于DNA弯曲而轻微压实。随着浓度的增加，Fis首先包覆DNA以形成每21 bp结合一个Fis二聚体的有序阵列，然后突然转变形成更高阶的Fis-DNA细丝，称为低迁移率复合物（LMC）。LMC最初每21 bp DNA含有两个Fis二聚体，但随着浓度进一步增加，额外的Fis二聚体组装到LMC中。这些复合物，在或高于1 μ M的Fis形成，能够通过稳定DNA环的崩溃大的DNA分子。单个DNA分子上的环的打开和关闭可以在真实的时间内作为DNA延伸的突然跳跃而被跟踪。环稳定复合物的形成对高离子强度敏感，即使在DNA弯曲-压缩不变的条件下也是如此。突变体的分析表明，FIS介导的DNA循环不涉及三级或四级变化的FIS二聚体结构，但一些表面暴露的残基位于内部和外部的螺旋-转角-螺旋DNA结合区域是至关重要的。这些结果表明，Fis可能在体内通过在E. coli染色体。(c)2006爱思唯尔有限公司保留所有权利。
Fis, the most abundant DNA-binding protein in Escherichia coli during rapid growth, has been suspected to play an important role in defining nucleoid structure. Using bulk-phase and single-DNA molecule experiments, we analyze the structural consequences of non-specific binding by Fis to DNA. Fis binds DNA in a largely sequence-neutral fashion at nanomolar concentrations, resulting in mild compaction under applied force due to DNA bending. With increasing concentration, Fis first coats DNA to form an ordered array with one Fis dimer bound per 21 bp and then abruptly shifts to forming a higher-order Fis-DNA filament, referred to as a low-mobility complex (LMC). The LMC initially contains two Fis dimers per 21 bp of DNA, but additional Fis dimers assemble into the LMC as the concentration is increased further. These complexes, formed at or above 1 mu M Fis, are able to collapse large DNA molecules via stabilization of DNA loops. The opening and closing of loops on single DNA molecules can be followed in real time as abrupt jumps in DNA extension. Formation of loop-stabilizing complexes is sensitive to high ionic strength, even under conditions where DNA bending-compaction is unaltered. Analyses of mutants indicate that Fis-mediated DNA looping does not involve tertiary or quaternary changes in the Fis dimer structure but that a number of surface-exposed residues located both within and outside the helix-turn-helix DNA-binding region are critical. These results suggest that Fis may play a role in vivo as a domain barrier element by organizing DNA loops within the E. coli chromosome. (c) 2006 Elsevier Ltd. All rights reserved.