A New Noncoding RNA Arranges Bacterial Chromosome Organization.
A New Noncoding RNA Arranges Bacterial Chromosome Organization.
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DOI：
10.1128/mbio.00998-15
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发表时间：
2015-08-25
期刊：
影响因子：
6.4
通讯作者：
Adhya S
中科院分区：
文献类型：
--
作者：
Qian Z;Macvanin M;Dimitriadis EK;He X;Zhurkin V;Adhya S
肠细菌基因组中的重复基因外回文序列（REP）通常由连接序列分隔的单个回文单元组成。总共有355个注释的REP沿着大肠杆菌基因组分布。RNA序列（RNAseq）分析显示，大肠杆菌中几乎80%的REP被转录。REP 325的DNA序列表明，它是一个由六个重复序列组成的簇，每个重复序列有两个回文单元，能够在超螺旋DNA中形成十字形结构。在这里，我们报告的REP 325元件的组件和至少一个其RNA产物在细菌类核DNA凝聚中发挥作用。这些RNA不仅存在于纯化的类核中，而且与细菌类核相关的HU蛋白结合，如通过RNA IP随后通过微阵列分析（RIP-Chip）测定所揭示的。使用透射电子显微镜（TEM）观察到REP 325的缺失导致类核大小的急剧增加，并且从质粒中表达REP 325 RNA之一，核相关非编码RNA 4（naRNA4），恢复了野生型浓缩结构。独立地，染色体构象捕获（3C）分析证明了染色体周围的各种REP元件之间的物理连接。这些连接以某种方式依赖于HU和REP 325元件的存在; HU基因和/或REP 325元件的缺失去除了连接。最后，通过原子力显微镜（AFM）观察，naRNA4与HU一起通过以成对方式连接REP 325或其他含有十字形结构的DNA序列而在体外浓缩DNA。在我们的研究结果的基础上，我们提出了分子模型来解释由HU和naRNA4介导的远程十字形结构的连接。细菌中的类核组织正在被广泛研究，并且已经提出了几种模型。然而，结构组织的分子性质还没有得到很好的理解。在这里，我们的特点是一种新的类核相关的非编码RNA，naRNA4，在体内和体外的类核结构的作用。我们提出的模型来解释如何naRNA4与类核相关蛋白HU连接远程DNA元素的类核凝聚。我们提出的第一个证据，一个非编码RNA连同一个核相关蛋白直接凝聚核DNA。
Repeated extragenic palindromes (REPs) in the enterobacterial genomes are usually composed of individual palindromic units separated by linker sequences. A total of 355 annotated REPs are distributed along the Escherichia coli genome. RNA sequence (RNAseq) analysis showed that almost 80% of the REPs in E. coli are transcribed. The DNA sequence of REP325 showed that it is a cluster of six repeats, each with two palindromic units capable of forming cruciform structures in supercoiled DNA. Here, we report that components of the REP325 element and at least one of its RNA products play a role in bacterial nucleoid DNA condensation. These RNA not only are present in the purified nucleoid but bind to the bacterial nucleoid-associated HU protein as revealed by RNA IP followed by microarray analysis (RIP-Chip) assays. Deletion of REP325 resulted in a dramatic increase of the nucleoid size as observed using transmission electron microscopy (TEM), and expression of one of the REP325 RNAs, nucleoid-associated noncoding RNA 4 (naRNA4), from a plasmid restored the wild-type condensed structure. Independently, chromosome conformation capture (3C) analysis demonstrated physical connections among various REP elements around the chromosome. These connections are dependent in some way upon the presence of HU and the REP325 element; deletion of HU genes and/or the REP325 element removed the connections. Finally, naRNA4 together with HU condensed DNA in vitro by connecting REP325 or other DNA sequences that contain cruciform structures in a pairwise manner as observed by atomic force microscopy (AFM). On the basis of our results, we propose molecular models to explain connections of remote cruciform structures mediated by HU and naRNA4. Nucleoid organization in bacteria is being studied extensively, and several models have been proposed. However, the molecular nature of the structural organization is not well understood. Here we characterized the role of a novel nucleoid-associated noncoding RNA, naRNA4, in nucleoid structures both in vivo and in vitro. We propose models to explain how naRNA4 together with nucleoid-associated protein HU connects remote DNA elements for nucleoid condensation. We present the first evidence of a noncoding RNA together with a nucleoid-associated protein directly condensing nucleoid DNA.