A Brownian ratchet model for DNA loop extrusion by the cohesin complex.
A Brownian ratchet model for DNA loop extrusion by the cohesin complex.
复制标题
DOI：
10.7554/elife.67530
复制
发表时间：
2021-07-26
期刊：
影响因子：
7.7
通讯作者：
Uhlmann F
中科院分区：
文献类型：
--
作者：
Higashi TL;Pobegalov G;Tang M;Molodtsov MI;Uhlmann F
粘着蛋白复合物拓扑地包围DNA以促进姐妹染色单体的粘着。或者，粘着蛋白挤出DNA环，被认为反映了染色质结构域的形成。在这里，我们提出了一个基于结构的模型来解释这两种活动。ATP和DNA结合促进了粘附素构象变化，其引导DNA通过Kleisin N-门进入DNA夹持状态。两个热重复DNA结合模块，与凝聚素的头部和铰链，现在并列。ATP水解后的抓握状态分解触发单向铰链模块运动，其通过引导DNA通过ATP酶头门来完成拓扑DNA进入。如果头部浇口通道失效，则铰链模块运动产生布朗棘轮，其反而驱动环挤出。抓持状态形成和分辨率周期的分子力学模拟概括了实验观察到的DNA环挤出特性。我们的模型扩展到不对称和对称的循环挤出，以及Z-环的形成。有偏布朗运动的环挤出对染色体的粘附功能有重要意义。当一个细胞分裂时，它必须确保它的每个子细胞继承它的遗传信息的一个副本。它通过复制其染色体（编码基因组的DNA分子）并将每个染色体的一个拷贝分配给其子细胞来做到这一点。一旦细胞复制了一条染色体，两条相同的染色体必须保持在一起，直到细胞准备好分裂成两个。一种叫做黏连蛋白的环状蛋白复合物通过环绕两条染色体来实现这一点。粘着蛋白包含两个染色体拷贝，因为它们来自DNA复制机器。这种复合物由几种蛋白质组成，它们与一种叫做ATP的小分子结合，ATP的到来和随后的分解释放能量。黏连蛋白还以不同的方式与DNA相互作用：它可以产生染色质环（由DNA及其包装蛋白形成的复合物），帮助调节基因的活性。在实验室分离的单分子上进行的实验表明，粘附素可以形成一个小的DNA环，然后通过一个称为DNA环挤出的过程扩大。但是，不知道单元中是否发生回路挤出。虽然这两种粘附素的作用都与DNA在细胞中的组织方式有关，但目前还不清楚一种蛋白质复合物如何参与两种不同的活动。为了回答这个问题，Higashi等人使用酵母细胞粘附DNA的粘着蛋白结构来建立一个模型，模拟该复合物如何与染色体和染色质相互作用。该模型表明，当ATP被分解时，粘附素结构发生变化，DNA进入环，使DNA被捕获，染色体结合在一起。然而，DNA最初被抓住的方式的一个小变化可能会阻止它进入环，创造一个形成和扩大DNA环的棘轮机制。这个分子模型有助于解释粘附素如何环绕DNA或创建环。然而，Higashi et al.的发现也提出了一个问题，即在细胞内是否有可能产生环挤出，在细胞内DNA是密集的，并与蛋白质结合，这可能是环挤出的障碍。进一步的研究工程cohesin只能执行这些角色之一，将有助于澄清他们在细胞中的个人贡献。
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin’s heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function. When a cell divides, it has to ensure that each of its daughter cells inherits one copy of its genetic information. It does this by duplicating its chromosomes (the DNA molecules that encode the genome) and distributing one copy of each to its daughter cells. Once a cell duplicates a chromosome, the two identical chromosomes must be held together until the cell is ready to divide in two. A ring-shaped protein complex called cohesin does this by encircling the two chromosomes. Cohesin embraces both chromosome copies, as they emerge from the DNA replicating machinery. The complex is formed of several proteins that bind to a small molecule called ATP, whose arrival and subsequent breakdown release energy. Cohesin also interacts with DNA in a different way: it can create loops of chromatin (the complex formed by DNA and its packaging proteins) that help regulate the activity of genes. Experiments performed on single molecules isolated in the laboratory show that cohesin can form a small loop of DNA that is then enlarged through a process called DNA loop extrusion. However, it is not known whether loop extrusion occurs in the cell. Although both of cohesin’s roles have to do with how DNA is organised in the cell, it remains unclear how a single protein complex can engage in two such different activities. To answer this question, Higashi et al. used a structure of cohesin from yeast cells gripping onto DNA to build a model that simulates how the complex interacts with chromosomes and chromatin. This model suggested that when ATP is broken down, the cohesin structure shifts and DNA enters the ring, allowing DNA to be entrapped and chromosomes to be bound together. However, a small change in how DNA is gripped initially could prevent it from entering the ring, creating a ratchet mechanism that forms and enlarges a DNA loop. This molecular model helps explain how cohesin can either encircle DNA or create loops. However, Higashi et al.’s findings also raise the question of whether loop extrusion is possible inside cells, where DNA is densely packed and bound to proteins which could be obstacles to loop extrusion. Further research to engineer cohesin that can only perform one of these roles would help to clarify their individual contributions in the cell.