Background

DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment.

Methods

We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding.

Results

In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively.

Conclusions

We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG.

General Significance

Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.

中文翻译：

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磁性镊子探测类核蛋白H-NS和拥挤剂PEG对DNA片段致密化的协同作用。

背景

H-NS蛋白促进的DNA桥接结合细胞拥挤诱导的紧缩作用，在大肠杆菌基因组的结构中起着重要作用。但是，只有很少的研究考虑了在受控环境中这两个因素的物理相互作用的影响。

方法

我们应用单分子技术（磁性镊子）来研究由H-NS桥接和/或PEG拥挤诱导的6 kb DNA片段的压缩和折叠动力学的纳米力学。

结果

在单独存在H-NS的情况下，DNA显示出由多个桥的形成驱动的逐步塌陷，并且H-NS浓度依赖性的解折叠力几乎没有变化。相反，用PEG观察到的DNA塌陷力高度取决于拥挤剂的体积分数。分别考虑了在拉动链中形成环和拉动平衡小球的模型来解释这两种极限情况。

结论

我们观察到H-NS活性与PEG诱导的力耗竭之间有明显的协同作用。

一般意义

我们的数据表明H-NS在增强紧实性同时形成特定环的过程中起着双重作用，这可能是体内对于响应环境变化而定义染色体区域中特定中尺度域的关键。