大肠杆菌一直是研究染色体结构的重要模式生物,谢谢,在某种程度上,其小且环状的基因组(460万个碱基对)和特征明确的生化途径。在过去的几十年里,我们已经取得了相当大的进展,在理解复杂的结构和随后的功能的大肠杆菌。在最小的尺度上,DNA,没有物理限制,呈现出一种让人联想到随机扭曲的电缆的形状,形成大部分随机线圈,但部分受到其刚度的影响。这种类似意大利面球的形状形成了一种结构,这种结构大到无法容纳在细胞中。一旦增加了细胞的生理约束,DNA具有过度扭曲(负超螺旋)结构,它是由许多蛋白质进行基本生物过程的复杂相互作用形成的。在较短的长度尺度(高达约1kb),类核蛋白通过诱导环来组织和凝聚染色体,弯管,形成桥梁。进一步缩小,包括细胞过程,拓扑域形成,两侧是超螺旋屏障。在大型数据库规模上,已经观察到高度自我相互作用的区域(宏结构域)和远处但共同调节的基因之间的强接触。在最大的尺度上,类核子形成螺旋椭圆体。在这次审查中,我们将探索历史和最新进展,为更好地理解大肠杆菌染色体的组织和结构铺平道路,讨论驱动DNA形状变化的细胞过程,以及有助于压实和形成动态结构的因素,以及细菌染色质如何影响转录和复制等关键过程。
Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by
supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.