Jaworski Pawel, Donczew Rafal, Mielke Thorsten, Thiel Marcel, Oldziej Stanislaw, Weigel Christoph, Zawilak-Pawlik Anna
Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wrocław, Poland.
Max Planck Institute for Molecular Genetics Berlin, Germany.
Front Microbiol. 2016 Sep 30;7:1555. doi: 10.3389/fmicb.2016.01555. eCollection 2016.
In bacteria, chromosome replication is initiated by the interaction of the initiator protein DnaA with a defined region of a chromosome at which DNA replication starts (). While DnaA proteins share significant homology regardless of phylogeny, regions exhibit more variable structures. The general architecture of s is universal, i.e., they are composed of a cluster of DnaA binding sites, a DNA-unwinding element, and sequences that bind regulatory proteins. However, detailed structures of s are shared by related species while being significantly different in unrelated bacteria. In this work, we characterized Epsilonproteobacterial regions. was the only species of the class for which was characterized. A few unique features were found such as bipartite structure, not encountered in any other Gram-negative species, and topology-sensitive DnaA-DNA interactions, which have not been found in any other bacterium. These unusual features raised questions of whether structure and DnaA-DNA interactions are unique to this bacterium or whether they are common to related species. By and analyses we identified putative s in three Epsilonproteobacterial species: pathogenic , symbiotic , and free-living . We propose that s typically co-localize with in Epsilonproteobacteria, with the exception of Helicobacteriaceae species. The clusters of DnaA boxes localize upstream () and downstream () of , and they likely constitute bipartite origins. In all cases, DNA unwinding was shown to occur in . Unlike the DnaA box pattern, which is not conserved in Epsilonproteobacterial s, the consensus DnaA box sequences and the mode of DnaA-DnaA box interactions are common to the class. We propose that the typical Epsilonproteobacterial DnaA box consists of the core nucleotide sequence 5'-TTCAC-3' (4-8 nt), which, together with the significant changes in the DNA-binding motif of corresponding DnaAs, determines the unique molecular mechanism of DnaA-DNA interaction. Our results will facilitate identification of s and subsequent identification of factors which regulate chromosome replication in other Epsilonproteobacteria. Since replication is controlled at the initiation step, it will help to better characterize life cycles of these species, many of which are considered as emerging pathogens.
在细菌中，染色体复制由起始蛋白DnaA与染色体上特定区域（DNA复制起始处）的相互作用引发。尽管无论系统发育如何，DnaA蛋白都具有显著的同源性，但这些区域呈现出更多可变的结构。复制起点（oriC）的总体结构是通用的，即它们由一组DnaA结合位点、一个DNA解旋元件以及结合调节蛋白的序列组成。然而，相关物种的oriC具有共享的详细结构，而在不相关的细菌中则有显著差异。在这项工作中，我们对ε-变形菌纲的oriC区域进行了表征。弯曲杆菌属是该纲中唯一其oriC被表征的物种。我们发现了一些独特的特征，例如二分oriC结构，这在任何其他革兰氏阴性菌中都未遇到，以及拓扑敏感的DnaA - DNA相互作用，这在任何其他细菌中也未发现。这些不寻常的oriC特征引发了这样的问题：弯曲杆菌属的oriC结构和DnaA - DNA相互作用是该细菌所特有的，还是相关物种所共有的。通过比较基因组学和系统发育分析，我们在三种ε-变形菌纲物种中鉴定出了假定的oriC：致病性的空肠弯曲杆菌、共生的幽门螺杆菌和自由生活的嗜热栖热放线菌。我们提出，除了螺杆菌科物种外，oriC在ε-变形菌纲中通常与rRNA操纵子共定位。DnaA框簇位于rRNA操纵子的上游和下游，它们可能构成二分起源。在所有情况下，DNA解旋都显示发生在oriC中。与在ε-变形菌纲的oriC中不保守的DnaA框模式不同，共有DnaA框序列和DnaA - DnaA框相互作用模式在该纲中是常见的。我们提出，典型的ε-变形菌纲DnaA框由核心核苷酸序列5'-TTCAC-3'（4 - 8个核苷酸）组成，它与相应DnaA的DNA结合基序的显著变化一起，决定了DnaA - DNA相互作用的独特分子机制。我们的结果将有助于鉴定oriC，并随后鉴定调节其他ε-变形菌纲中染色体复制的因子。由于复制在起始步骤受到控制，这将有助于更好地表征这些物种的生命周期，其中许多被认为是新兴病原体。
